diff options
Diffstat (limited to 'science')
319 files changed, 6956 insertions, 10167 deletions
diff --git a/science/ALPSCore/Makefile b/science/ALPSCore/Makefile index cf74402f2eed..b2dcc2d64830 100644 --- a/science/ALPSCore/Makefile +++ b/science/ALPSCore/Makefile @@ -3,7 +3,7 @@ DISTVERSIONPREFIX= v DISTVERSION= 2.3.2 CATEGORIES= science -MAINTAINER= alster@vinterdalen.se +MAINTAINER= alven@FreeBSD.org COMMENT= Generic algorithms and utilities for condensed matter physics WWW= https://alpscore.org/ \ https://github.com/ALPSCore/ALPSCore/ diff --git a/science/InsightToolkit/Makefile b/science/InsightToolkit/Makefile index 75f332286234..f11586616811 100644 --- a/science/InsightToolkit/Makefile +++ b/science/InsightToolkit/Makefile @@ -1,7 +1,7 @@ PORTNAME= InsightToolkit DISTVERSIONPREFIX= v DISTVERSION= 5.3.0 -PORTREVISION= 7 +PORTREVISION= 8 CATEGORIES= science biology MASTER_SITES= https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${DISTVERSION}/:data DISTFILES= InsightData-${DISTVERSION}.tar.gz:data diff --git a/science/InsightToolkit/Makefile.remote_modules b/science/InsightToolkit/Makefile.remote_modules index ed3659eabd22..ac598e13d5cf 100644 --- a/science/InsightToolkit/Makefile.remote_modules +++ b/science/InsightToolkit/Makefile.remote_modules @@ -79,7 +79,7 @@ CMAKE_ON+=Module_IOScanco CMAKE_ON+=Module_IOTransformDCMTK CMAKE_OFF+=Module_IsotropicWavelets # cmake fails: No such module: "ITKImageIO" CMAKE_ON+=Module_LabelErodeDilate -CMAKE_ON+=Module_LesionSizingToolkit +#CMAKE_ON+=Module_LesionSizingToolkit CMAKE_ON+=Module_itkMGHImageIO CMAKE_ON+=Module_MeshNoise CMAKE_ON+=Module_MeshToPolyData diff --git a/science/InsightToolkit/pkg-plist b/science/InsightToolkit/pkg-plist index b2301e5560a8..8f1a4fb86c8f 100644 --- a/science/InsightToolkit/pkg-plist +++ b/science/InsightToolkit/pkg-plist @@ -148,12 +148,10 @@ include/ITK-%%ITK_VER%%/ITKTransformExport.h include/ITK-%%ITK_VER%%/ITKVTKExport.h include/ITK-%%ITK_VER%%/ITKVideoCoreExport.h include/ITK-%%ITK_VER%%/ITKVideoIOExport.h -include/ITK-%%ITK_VER%%/ITKVtkGlueExport.h include/ITK-%%ITK_VER%%/ITKWatershedsExport.h include/ITK-%%ITK_VER%%/MinimalPathExtractionExport.h include/ITK-%%ITK_VER%%/MontageExport.h include/ITK-%%ITK_VER%%/NrrdIO.h -include/ITK-%%ITK_VER%%/QuickView.h include/ITK-%%ITK_VER%%/RTKExport.h include/ITK-%%ITK_VER%%/SimpleITKFiltersExport.h include/ITK-%%ITK_VER%%/VNLIterativeSparseSolverTraits.h @@ -413,8 +411,6 @@ include/ITK-%%ITK_VER%%/itkBinaryThinningImageFilter.h include/ITK-%%ITK_VER%%/itkBinaryThinningImageFilter.hxx include/ITK-%%ITK_VER%%/itkBinaryThinningImageFilter3D.h include/ITK-%%ITK_VER%%/itkBinaryThinningImageFilter3D.hxx -include/ITK-%%ITK_VER%%/itkBinaryThresholdFeatureGenerator.h -include/ITK-%%ITK_VER%%/itkBinaryThresholdFeatureGenerator.hxx include/ITK-%%ITK_VER%%/itkBinaryThresholdImageFilter.h include/ITK-%%ITK_VER%%/itkBinaryThresholdImageFilter.hxx include/ITK-%%ITK_VER%%/itkBinaryThresholdImageFunction.h @@ -477,14 +473,6 @@ include/ITK-%%ITK_VER%%/itkCSVNumericObjectFileWriter.hxx include/ITK-%%ITK_VER%%/itkCacheableScalarFunction.h include/ITK-%%ITK_VER%%/itkCannyEdgeDetectionImageFilter.h include/ITK-%%ITK_VER%%/itkCannyEdgeDetectionImageFilter.hxx -include/ITK-%%ITK_VER%%/itkCannyEdgeDetectionRecursiveGaussianImageFilter.h -include/ITK-%%ITK_VER%%/itkCannyEdgeDetectionRecursiveGaussianImageFilter.hxx -include/ITK-%%ITK_VER%%/itkCannyEdgesDistanceAdvectionFieldFeatureGenerator.h -include/ITK-%%ITK_VER%%/itkCannyEdgesDistanceAdvectionFieldFeatureGenerator.hxx -include/ITK-%%ITK_VER%%/itkCannyEdgesDistanceFeatureGenerator.h -include/ITK-%%ITK_VER%%/itkCannyEdgesDistanceFeatureGenerator.hxx -include/ITK-%%ITK_VER%%/itkCannyEdgesFeatureGenerator.h -include/ITK-%%ITK_VER%%/itkCannyEdgesFeatureGenerator.hxx include/ITK-%%ITK_VER%%/itkCannySegmentationLevelSetFunction.h include/ITK-%%ITK_VER%%/itkCannySegmentationLevelSetFunction.hxx include/ITK-%%ITK_VER%%/itkCannySegmentationLevelSetImageFilter.h @@ -579,8 +567,6 @@ include/ITK-%%ITK_VER%%/itkConceptChecking.h include/ITK-%%ITK_VER%%/itkConditionalConstIterator.h include/ITK-%%ITK_VER%%/itkConfidenceConnectedImageFilter.h include/ITK-%%ITK_VER%%/itkConfidenceConnectedImageFilter.hxx -include/ITK-%%ITK_VER%%/itkConfidenceConnectedSegmentationModule.h -include/ITK-%%ITK_VER%%/itkConfidenceConnectedSegmentationModule.hxx include/ITK-%%ITK_VER%%/itkConfigure.h include/ITK-%%ITK_VER%%/itkConformalFlatteningMeshFilter.h include/ITK-%%ITK_VER%%/itkConformalFlatteningMeshFilter.hxx @@ -599,8 +585,6 @@ include/ITK-%%ITK_VER%%/itkConnectedRegionsMeshFilter.h include/ITK-%%ITK_VER%%/itkConnectedRegionsMeshFilter.hxx include/ITK-%%ITK_VER%%/itkConnectedThresholdImageFilter.h include/ITK-%%ITK_VER%%/itkConnectedThresholdImageFilter.hxx -include/ITK-%%ITK_VER%%/itkConnectedThresholdSegmentationModule.h -include/ITK-%%ITK_VER%%/itkConnectedThresholdSegmentationModule.hxx include/ITK-%%ITK_VER%%/itkConstNeighborhoodIterator.h include/ITK-%%ITK_VER%%/itkConstNeighborhoodIterator.hxx include/ITK-%%ITK_VER%%/itkConstNeighborhoodIteratorWithOnlyIndex.h @@ -765,9 +749,6 @@ include/ITK-%%ITK_VER%%/itkDescoteauxEigenToMeasureImageFilter.h include/ITK-%%ITK_VER%%/itkDescoteauxEigenToMeasureImageFilter.hxx include/ITK-%%ITK_VER%%/itkDescoteauxEigenToMeasureParameterEstimationFilter.h include/ITK-%%ITK_VER%%/itkDescoteauxEigenToMeasureParameterEstimationFilter.hxx -include/ITK-%%ITK_VER%%/itkDescoteauxSheetnessFeatureGenerator.h -include/ITK-%%ITK_VER%%/itkDescoteauxSheetnessFeatureGenerator.hxx -include/ITK-%%ITK_VER%%/itkDescoteauxSheetnessImageFilter.h include/ITK-%%ITK_VER%%/itkDiffeomorphicDemonsRegistrationFilter.h include/ITK-%%ITK_VER%%/itkDiffeomorphicDemonsRegistrationFilter.hxx include/ITK-%%ITK_VER%%/itkDifferenceOfGaussiansGradientImageFilter.h @@ -927,10 +908,6 @@ include/ITK-%%ITK_VER%%/itkFastChamferDistanceImageFilter.hxx include/ITK-%%ITK_VER%%/itkFastGrowCut.h include/ITK-%%ITK_VER%%/itkFastGrowCut.hxx include/ITK-%%ITK_VER%%/itkFastIncrementalBinaryDilateImageFilter.h -include/ITK-%%ITK_VER%%/itkFastMarchingAndGeodesicActiveContourLevelSetSegmentationModule.h -include/ITK-%%ITK_VER%%/itkFastMarchingAndGeodesicActiveContourLevelSetSegmentationModule.hxx -include/ITK-%%ITK_VER%%/itkFastMarchingAndShapeDetectionLevelSetSegmentationModule.h -include/ITK-%%ITK_VER%%/itkFastMarchingAndShapeDetectionLevelSetSegmentationModule.hxx include/ITK-%%ITK_VER%%/itkFastMarchingBase.h include/ITK-%%ITK_VER%%/itkFastMarchingBase.hxx include/ITK-%%ITK_VER%%/itkFastMarchingExtensionImageFilter.h @@ -947,8 +924,6 @@ include/ITK-%%ITK_VER%%/itkFastMarchingNumberOfElementsStoppingCriterion.h include/ITK-%%ITK_VER%%/itkFastMarchingQuadEdgeMeshFilterBase.h include/ITK-%%ITK_VER%%/itkFastMarchingQuadEdgeMeshFilterBase.hxx include/ITK-%%ITK_VER%%/itkFastMarchingReachedTargetNodesStoppingCriterion.h -include/ITK-%%ITK_VER%%/itkFastMarchingSegmentationModule.h -include/ITK-%%ITK_VER%%/itkFastMarchingSegmentationModule.hxx include/ITK-%%ITK_VER%%/itkFastMarchingStoppingCriterionBase.h include/ITK-%%ITK_VER%%/itkFastMarchingThresholdStoppingCriterion.h include/ITK-%%ITK_VER%%/itkFastMarchingTraits.h @@ -960,10 +935,6 @@ include/ITK-%%ITK_VER%%/itkFastSymmetricForcesDemonsRegistrationFilter.h include/ITK-%%ITK_VER%%/itkFastSymmetricForcesDemonsRegistrationFilter.hxx include/ITK-%%ITK_VER%%/itkFastSymmetricForcesDemonsRegistrationFunction.h include/ITK-%%ITK_VER%%/itkFastSymmetricForcesDemonsRegistrationFunction.hxx -include/ITK-%%ITK_VER%%/itkFeatureAggregator.h -include/ITK-%%ITK_VER%%/itkFeatureAggregator.hxx -include/ITK-%%ITK_VER%%/itkFeatureGenerator.h -include/ITK-%%ITK_VER%%/itkFeatureGenerator.hxx include/ITK-%%ITK_VER%%/itkFileListVideoIO.h include/ITK-%%ITK_VER%%/itkFileListVideoIOFactory.h include/ITK-%%ITK_VER%%/itkFileOutputWindow.h @@ -1012,9 +983,6 @@ include/ITK-%%ITK_VER%%/itkFrameAverageVideoFilter.h include/ITK-%%ITK_VER%%/itkFrameAverageVideoFilter.hxx include/ITK-%%ITK_VER%%/itkFrameDifferenceVideoFilter.h include/ITK-%%ITK_VER%%/itkFrameDifferenceVideoFilter.hxx -include/ITK-%%ITK_VER%%/itkFrangiTubularnessFeatureGenerator.h -include/ITK-%%ITK_VER%%/itkFrangiTubularnessFeatureGenerator.hxx -include/ITK-%%ITK_VER%%/itkFrangiTubularnessImageFilter.h include/ITK-%%ITK_VER%%/itkFreeSurferAsciiMeshIO.h include/ITK-%%ITK_VER%%/itkFreeSurferAsciiMeshIOFactory.h include/ITK-%%ITK_VER%%/itkFreeSurferBinaryMeshIO.h @@ -1144,8 +1112,6 @@ include/ITK-%%ITK_VER%%/itkGeodesicActiveContourLevelSetFunction.h include/ITK-%%ITK_VER%%/itkGeodesicActiveContourLevelSetFunction.hxx include/ITK-%%ITK_VER%%/itkGeodesicActiveContourLevelSetImageFilter.h include/ITK-%%ITK_VER%%/itkGeodesicActiveContourLevelSetImageFilter.hxx -include/ITK-%%ITK_VER%%/itkGeodesicActiveContourLevelSetSegmentationModule.h -include/ITK-%%ITK_VER%%/itkGeodesicActiveContourLevelSetSegmentationModule.hxx include/ITK-%%ITK_VER%%/itkGeodesicActiveContourShapePriorLevelSetFunction.h include/ITK-%%ITK_VER%%/itkGeodesicActiveContourShapePriorLevelSetFunction.hxx include/ITK-%%ITK_VER%%/itkGeodesicActiveContourShapePriorLevelSetImageFilter.h @@ -1179,8 +1145,6 @@ include/ITK-%%ITK_VER%%/itkGradientMagnitudeImageFilter.h include/ITK-%%ITK_VER%%/itkGradientMagnitudeImageFilter.hxx include/ITK-%%ITK_VER%%/itkGradientMagnitudeRecursiveGaussianImageFilter.h include/ITK-%%ITK_VER%%/itkGradientMagnitudeRecursiveGaussianImageFilter.hxx -include/ITK-%%ITK_VER%%/itkGradientMagnitudeSigmoidFeatureGenerator.h -include/ITK-%%ITK_VER%%/itkGradientMagnitudeSigmoidFeatureGenerator.hxx include/ITK-%%ITK_VER%%/itkGradientNDAnisotropicDiffusionFunction.h include/ITK-%%ITK_VER%%/itkGradientNDAnisotropicDiffusionFunction.hxx include/ITK-%%ITK_VER%%/itkGradientRecursiveGaussianImageFilter.h @@ -1207,8 +1171,6 @@ include/ITK-%%ITK_VER%%/itkGrayscaleGeodesicErodeImageFilter.h include/ITK-%%ITK_VER%%/itkGrayscaleGeodesicErodeImageFilter.hxx include/ITK-%%ITK_VER%%/itkGrayscaleGrindPeakImageFilter.h include/ITK-%%ITK_VER%%/itkGrayscaleGrindPeakImageFilter.hxx -include/ITK-%%ITK_VER%%/itkGrayscaleImageSegmentationVolumeEstimator.h -include/ITK-%%ITK_VER%%/itkGrayscaleImageSegmentationVolumeEstimator.hxx include/ITK-%%ITK_VER%%/itkGrayscaleMorphologicalClosingImageFilter.h include/ITK-%%ITK_VER%%/itkGrayscaleMorphologicalClosingImageFilter.hxx include/ITK-%%ITK_VER%%/itkGrayscaleMorphologicalOpeningImageFilter.h @@ -1466,8 +1428,6 @@ include/ITK-%%ITK_VER%%/itkImageToSpatialObjectMetric.h include/ITK-%%ITK_VER%%/itkImageToSpatialObjectMetric.hxx include/ITK-%%ITK_VER%%/itkImageToSpatialObjectRegistrationMethod.h include/ITK-%%ITK_VER%%/itkImageToSpatialObjectRegistrationMethod.hxx -include/ITK-%%ITK_VER%%/itkImageToVTKImageFilter.h -include/ITK-%%ITK_VER%%/itkImageToVTKImageFilter.hxx include/ITK-%%ITK_VER%%/itkImageToVideoFilter.h include/ITK-%%ITK_VER%%/itkImageToVideoFilter.hxx include/ITK-%%ITK_VER%%/itkImageVectorOptimizerParametersHelper.h @@ -1532,10 +1492,6 @@ include/ITK-%%ITK_VER%%/itkIsolatedWatershedImageFilter.h include/ITK-%%ITK_VER%%/itkIsolatedWatershedImageFilter.hxx include/ITK-%%ITK_VER%%/itkIsotropicFourthOrderLevelSetImageFilter.h include/ITK-%%ITK_VER%%/itkIsotropicFourthOrderLevelSetImageFilter.hxx -include/ITK-%%ITK_VER%%/itkIsotropicResampler.h -include/ITK-%%ITK_VER%%/itkIsotropicResampler.hxx -include/ITK-%%ITK_VER%%/itkIsotropicResamplerImageFilter.h -include/ITK-%%ITK_VER%%/itkIsotropicResamplerImageFilter.hxx include/ITK-%%ITK_VER%%/itkIterateNeighborhoodOptimizer.h include/ITK-%%ITK_VER%%/itkIterationReporter.h include/ITK-%%ITK_VER%%/itkIterativeDeconvolutionImageFilter.h @@ -1686,8 +1642,6 @@ include/ITK-%%ITK_VER%%/itkLandmarkDisplacementFieldSource.h include/ITK-%%ITK_VER%%/itkLandmarkDisplacementFieldSource.hxx include/ITK-%%ITK_VER%%/itkLandmarkSpatialObject.h include/ITK-%%ITK_VER%%/itkLandmarkSpatialObject.hxx -include/ITK-%%ITK_VER%%/itkLandmarksReader.h -include/ITK-%%ITK_VER%%/itkLandmarksReader.hxx include/ITK-%%ITK_VER%%/itkLandweberDeconvolutionImageFilter.h include/ITK-%%ITK_VER%%/itkLandweberDeconvolutionImageFilter.hxx include/ITK-%%ITK_VER%%/itkLaplacianDeformationQuadEdgeMeshFilter.h @@ -1708,10 +1662,6 @@ include/ITK-%%ITK_VER%%/itkLaplacianSegmentationLevelSetImageFilter.h include/ITK-%%ITK_VER%%/itkLaplacianSegmentationLevelSetImageFilter.hxx include/ITK-%%ITK_VER%%/itkLaplacianSharpeningImageFilter.h include/ITK-%%ITK_VER%%/itkLaplacianSharpeningImageFilter.hxx -include/ITK-%%ITK_VER%%/itkLesionSegmentationImageFilter8.h -include/ITK-%%ITK_VER%%/itkLesionSegmentationImageFilter8.hxx -include/ITK-%%ITK_VER%%/itkLesionSegmentationMethod.h -include/ITK-%%ITK_VER%%/itkLesionSegmentationMethod.hxx include/ITK-%%ITK_VER%%/itkLevelSet.h include/ITK-%%ITK_VER%%/itkLevelSetBase.h include/ITK-%%ITK_VER%%/itkLevelSetBase.hxx @@ -1807,7 +1757,6 @@ include/ITK-%%ITK_VER%%/itkLinearInterpolateImageFunction.h include/ITK-%%ITK_VER%%/itkLinearInterpolateImageFunction.hxx include/ITK-%%ITK_VER%%/itkListSample.h include/ITK-%%ITK_VER%%/itkListSample.hxx -include/ITK-%%ITK_VER%%/itkLocalStructureImageFilter.h include/ITK-%%ITK_VER%%/itkLog10ImageAdaptor.h include/ITK-%%ITK_VER%%/itkLog10ImageFilter.h include/ITK-%%ITK_VER%%/itkLogGaborFreqImageSource.h @@ -1822,8 +1771,6 @@ include/ITK-%%ITK_VER%%/itkLoggerOutput.h include/ITK-%%ITK_VER%%/itkLoggerThreadWrapper.h include/ITK-%%ITK_VER%%/itkLoggerThreadWrapper.hxx include/ITK-%%ITK_VER%%/itkLogicOpsFunctors.h -include/ITK-%%ITK_VER%%/itkLungWallFeatureGenerator.h -include/ITK-%%ITK_VER%%/itkLungWallFeatureGenerator.hxx include/ITK-%%ITK_VER%%/itkMINCImageIO.h include/ITK-%%ITK_VER%%/itkMINCImageIOFactory.h include/ITK-%%ITK_VER%%/itkMINCTransformAdapter.h @@ -1896,8 +1843,6 @@ include/ITK-%%ITK_VER%%/itkMaximumDecisionRule.h include/ITK-%%ITK_VER%%/itkMaximumEntropyThresholdCalculator.h include/ITK-%%ITK_VER%%/itkMaximumEntropyThresholdCalculator.hxx include/ITK-%%ITK_VER%%/itkMaximumEntropyThresholdImageFilter.h -include/ITK-%%ITK_VER%%/itkMaximumFeatureAggregator.h -include/ITK-%%ITK_VER%%/itkMaximumFeatureAggregator.hxx include/ITK-%%ITK_VER%%/itkMaximumImageFilter.h include/ITK-%%ITK_VER%%/itkMaximumProjectionImageFilter.h include/ITK-%%ITK_VER%%/itkMaximumRatioDecisionRule.h @@ -2015,8 +1960,6 @@ include/ITK-%%ITK_VER%%/itkMinMaxCurvatureFlowImageFilter.hxx include/ITK-%%ITK_VER%%/itkMiniPipelineSeparableImageFilter.h include/ITK-%%ITK_VER%%/itkMiniPipelineSeparableImageFilter.hxx include/ITK-%%ITK_VER%%/itkMinimumDecisionRule.h -include/ITK-%%ITK_VER%%/itkMinimumFeatureAggregator.h -include/ITK-%%ITK_VER%%/itkMinimumFeatureAggregator.hxx include/ITK-%%ITK_VER%%/itkMinimumImageFilter.h include/ITK-%%ITK_VER%%/itkMinimumMaximumImageCalculator.h include/ITK-%%ITK_VER%%/itkMinimumMaximumImageCalculator.hxx @@ -2039,10 +1982,6 @@ include/ITK-%%ITK_VER%%/itkMorphologicalDistanceTransformImageFilter.h include/ITK-%%ITK_VER%%/itkMorphologicalDistanceTransformImageFilter.hxx include/ITK-%%ITK_VER%%/itkMorphologicalGradientImageFilter.h include/ITK-%%ITK_VER%%/itkMorphologicalGradientImageFilter.hxx -include/ITK-%%ITK_VER%%/itkMorphologicalOpeningFeatureGenerator.h -include/ITK-%%ITK_VER%%/itkMorphologicalOpeningFeatureGenerator.hxx -include/ITK-%%ITK_VER%%/itkMorphologicalOpenningFeatureGenerator.h -include/ITK-%%ITK_VER%%/itkMorphologicalOpenningFeatureGenerator.hxx include/ITK-%%ITK_VER%%/itkMorphologicalSharpeningImageFilter.h include/ITK-%%ITK_VER%%/itkMorphologicalSharpeningImageFilter.hxx include/ITK-%%ITK_VER%%/itkMorphologicalSignedDistanceTransformImageFilter.h @@ -2529,16 +2468,12 @@ include/ITK-%%ITK_VER%%/itkRegionBasedLevelSetFunction.hxx include/ITK-%%ITK_VER%%/itkRegionBasedLevelSetFunctionData.h include/ITK-%%ITK_VER%%/itkRegionBasedLevelSetFunctionData.hxx include/ITK-%%ITK_VER%%/itkRegionBasedLevelSetFunctionSharedData.h -include/ITK-%%ITK_VER%%/itkRegionCompetitionImageFilter.h -include/ITK-%%ITK_VER%%/itkRegionCompetitionImageFilter.hxx include/ITK-%%ITK_VER%%/itkRegionConstrainedSubsampler.h include/ITK-%%ITK_VER%%/itkRegionConstrainedSubsampler.hxx include/ITK-%%ITK_VER%%/itkRegionFromReferenceLabelMapFilter.h include/ITK-%%ITK_VER%%/itkRegionFromReferenceLabelMapFilter.hxx include/ITK-%%ITK_VER%%/itkRegionGrowImageFilter.h include/ITK-%%ITK_VER%%/itkRegionGrowImageFilter.hxx -include/ITK-%%ITK_VER%%/itkRegionGrowingSegmentationModule.h -include/ITK-%%ITK_VER%%/itkRegionGrowingSegmentationModule.hxx include/ITK-%%ITK_VER%%/itkRegionOfInterestImageFilter.h include/ITK-%%ITK_VER%%/itkRegionOfInterestImageFilter.hxx include/ITK-%%ITK_VER%%/itkRegionalMaximaImageFilter.h @@ -2619,12 +2554,6 @@ include/ITK-%%ITK_VER%%/itkSampleToHistogramFilter.h include/ITK-%%ITK_VER%%/itkSampleToHistogramFilter.hxx include/ITK-%%ITK_VER%%/itkSampleToSubsampleFilter.h include/ITK-%%ITK_VER%%/itkSampleToSubsampleFilter.hxx -include/ITK-%%ITK_VER%%/itkSatoLocalStructureFeatureGenerator.h -include/ITK-%%ITK_VER%%/itkSatoLocalStructureFeatureGenerator.hxx -include/ITK-%%ITK_VER%%/itkSatoVesselnessFeatureGenerator.h -include/ITK-%%ITK_VER%%/itkSatoVesselnessFeatureGenerator.hxx -include/ITK-%%ITK_VER%%/itkSatoVesselnessSigmoidFeatureGenerator.h -include/ITK-%%ITK_VER%%/itkSatoVesselnessSigmoidFeatureGenerator.hxx include/ITK-%%ITK_VER%%/itkScalableAffineTransform.h include/ITK-%%ITK_VER%%/itkScalableAffineTransform.hxx include/ITK-%%ITK_VER%%/itkScalarAnisotropicDiffusionFunction.h @@ -2677,11 +2606,7 @@ include/ITK-%%ITK_VER%%/itkSegmentationLevelSetFunction.h include/ITK-%%ITK_VER%%/itkSegmentationLevelSetFunction.hxx include/ITK-%%ITK_VER%%/itkSegmentationLevelSetImageFilter.h include/ITK-%%ITK_VER%%/itkSegmentationLevelSetImageFilter.hxx -include/ITK-%%ITK_VER%%/itkSegmentationModule.h -include/ITK-%%ITK_VER%%/itkSegmentationModule.hxx include/ITK-%%ITK_VER%%/itkSegmentationRegion.h -include/ITK-%%ITK_VER%%/itkSegmentationVolumeEstimator.h -include/ITK-%%ITK_VER%%/itkSegmentationVolumeEstimator.hxx include/ITK-%%ITK_VER%%/itkShanbhagThresholdCalculator.h include/ITK-%%ITK_VER%%/itkShanbhagThresholdCalculator.hxx include/ITK-%%ITK_VER%%/itkShanbhagThresholdImageFilter.h @@ -2689,8 +2614,6 @@ include/ITK-%%ITK_VER%%/itkShapeDetectionLevelSetFunction.h include/ITK-%%ITK_VER%%/itkShapeDetectionLevelSetFunction.hxx include/ITK-%%ITK_VER%%/itkShapeDetectionLevelSetImageFilter.h include/ITK-%%ITK_VER%%/itkShapeDetectionLevelSetImageFilter.hxx -include/ITK-%%ITK_VER%%/itkShapeDetectionLevelSetSegmentationModule.h -include/ITK-%%ITK_VER%%/itkShapeDetectionLevelSetSegmentationModule.hxx include/ITK-%%ITK_VER%%/itkShapeKeepNObjectsLabelMapFilter.h include/ITK-%%ITK_VER%%/itkShapeKeepNObjectsLabelMapFilter.hxx include/ITK-%%ITK_VER%%/itkShapeLabelMapFilter.h @@ -2741,8 +2664,6 @@ include/ITK-%%ITK_VER%%/itkSiddonJacobsRayCastInterpolateImageFunction.h include/ITK-%%ITK_VER%%/itkSiddonJacobsRayCastInterpolateImageFunction.hxx include/ITK-%%ITK_VER%%/itkSiemensVisionImageIO.h include/ITK-%%ITK_VER%%/itkSiemensVisionImageIOFactory.h -include/ITK-%%ITK_VER%%/itkSigmoidFeatureGenerator.h -include/ITK-%%ITK_VER%%/itkSigmoidFeatureGenerator.hxx include/ITK-%%ITK_VER%%/itkSigmoidImageFilter.h include/ITK-%%ITK_VER%%/itkSignedDanielssonDistanceMapImageFilter.h include/ITK-%%ITK_VER%%/itkSignedDanielssonDistanceMapImageFilter.hxx @@ -2775,8 +2696,6 @@ include/ITK-%%ITK_VER%%/itkSinRegularizedHeavisideStepFunction.h include/ITK-%%ITK_VER%%/itkSinRegularizedHeavisideStepFunction.hxx include/ITK-%%ITK_VER%%/itkSingleImageCostFunction.h include/ITK-%%ITK_VER%%/itkSingleImageCostFunction.hxx -include/ITK-%%ITK_VER%%/itkSinglePhaseLevelSetSegmentationModule.h -include/ITK-%%ITK_VER%%/itkSinglePhaseLevelSetSegmentationModule.hxx include/ITK-%%ITK_VER%%/itkSingleValuedCostFunction.h include/ITK-%%ITK_VER%%/itkSingleValuedCostFunctionv4.h include/ITK-%%ITK_VER%%/itkSingleValuedNonLinearOptimizer.h @@ -3105,8 +3024,6 @@ include/ITK-%%ITK_VER%%/itkVTKImageIO.h include/ITK-%%ITK_VER%%/itkVTKImageIOFactory.h include/ITK-%%ITK_VER%%/itkVTKImageImport.h include/ITK-%%ITK_VER%%/itkVTKImageImport.hxx -include/ITK-%%ITK_VER%%/itkVTKImageToImageFilter.h -include/ITK-%%ITK_VER%%/itkVTKImageToImageFilter.hxx include/ITK-%%ITK_VER%%/itkVTKPolyDataMeshIO.h include/ITK-%%ITK_VER%%/itkVTKPolyDataMeshIOFactory.h include/ITK-%%ITK_VER%%/itkVTKPolyDataReader.h @@ -3227,8 +3144,6 @@ include/ITK-%%ITK_VER%%/itkVersorTransform.hxx include/ITK-%%ITK_VER%%/itkVersorTransformOptimizer.h include/ITK-%%ITK_VER%%/itkVertexCell.h include/ITK-%%ITK_VER%%/itkVertexCell.hxx -include/ITK-%%ITK_VER%%/itkVesselEnhancingDiffusion3DImageFilter.h -include/ITK-%%ITK_VER%%/itkVesselEnhancingDiffusion3DImageFilter.hxx include/ITK-%%ITK_VER%%/itkVideoFileReader.h include/ITK-%%ITK_VER%%/itkVideoFileReader.hxx include/ITK-%%ITK_VER%%/itkVideoFileWriter.h @@ -3241,8 +3156,6 @@ include/ITK-%%ITK_VER%%/itkVideoStream.h include/ITK-%%ITK_VER%%/itkVideoStream.hxx include/ITK-%%ITK_VER%%/itkVideoToVideoFilter.h include/ITK-%%ITK_VER%%/itkVideoToVideoFilter.hxx -include/ITK-%%ITK_VER%%/itkViewImage.h -include/ITK-%%ITK_VER%%/itkViewImage.hxx include/ITK-%%ITK_VER%%/itkVnlComplexToComplex1DFFTImageFilter.h include/ITK-%%ITK_VER%%/itkVnlComplexToComplex1DFFTImageFilter.hxx include/ITK-%%ITK_VER%%/itkVnlComplexToComplexFFTImageFilter.h @@ -3276,8 +3189,6 @@ include/ITK-%%ITK_VER%%/itkVoronoiSegmentationImageFilterBase.h include/ITK-%%ITK_VER%%/itkVoronoiSegmentationImageFilterBase.hxx include/ITK-%%ITK_VER%%/itkVoronoiSegmentationRGBImageFilter.h include/ITK-%%ITK_VER%%/itkVoronoiSegmentationRGBImageFilter.hxx -include/ITK-%%ITK_VER%%/itkVotingBinaryHoleFillFloodingImageFilter.h -include/ITK-%%ITK_VER%%/itkVotingBinaryHoleFillFloodingImageFilter.hxx include/ITK-%%ITK_VER%%/itkVotingBinaryHoleFillingImageFilter.h include/ITK-%%ITK_VER%%/itkVotingBinaryHoleFillingImageFilter.hxx include/ITK-%%ITK_VER%%/itkVotingBinaryImageFilter.h @@ -3321,8 +3232,6 @@ include/ITK-%%ITK_VER%%/itkWeightedCovarianceSampleFilter.h include/ITK-%%ITK_VER%%/itkWeightedCovarianceSampleFilter.hxx include/ITK-%%ITK_VER%%/itkWeightedMeanSampleFilter.h include/ITK-%%ITK_VER%%/itkWeightedMeanSampleFilter.hxx -include/ITK-%%ITK_VER%%/itkWeightedSumFeatureAggregator.h -include/ITK-%%ITK_VER%%/itkWeightedSumFeatureAggregator.hxx include/ITK-%%ITK_VER%%/itkWhitakerSparseLevelSetImage.h include/ITK-%%ITK_VER%%/itkWhitakerSparseLevelSetImage.hxx include/ITK-%%ITK_VER%%/itkWhiteTopHatImageFilter.h @@ -3855,7 +3764,6 @@ include/ITK-%%ITK_VER%%/rtkZengBackProjectionImageFilter.hxx include/ITK-%%ITK_VER%%/rtkZengForwardProjectionImageFilter.h include/ITK-%%ITK_VER%%/rtkZengForwardProjectionImageFilter.hxx include/ITK-%%ITK_VER%%/stub.h -include/ITK-%%ITK_VER%%/vtkCaptureScreen.h include/ITK-%%ITK_VER%%/znzlib.h include/RTK/lpsolve/lp_Hash.h include/RTK/lpsolve/lp_MDO.h @@ -4045,11 +3953,9 @@ lib/cmake/ITK-%%ITK_VER%%/Modules/ITKVideoCore.cmake lib/cmake/ITK-%%ITK_VER%%/Modules/ITKVideoFiltering.cmake lib/cmake/ITK-%%ITK_VER%%/Modules/ITKVideoIO.cmake lib/cmake/ITK-%%ITK_VER%%/Modules/ITKVoronoi.cmake -lib/cmake/ITK-%%ITK_VER%%/Modules/ITKVtkGlue.cmake lib/cmake/ITK-%%ITK_VER%%/Modules/ITKWatersheds.cmake lib/cmake/ITK-%%ITK_VER%%/Modules/ITKZLIB.cmake lib/cmake/ITK-%%ITK_VER%%/Modules/LabelErodeDilate.cmake -lib/cmake/ITK-%%ITK_VER%%/Modules/LesionSizingToolkit.cmake lib/cmake/ITK-%%ITK_VER%%/Modules/MeshNoise.cmake lib/cmake/ITK-%%ITK_VER%%/Modules/MeshToPolyData.cmake lib/cmake/ITK-%%ITK_VER%%/Modules/MinimalPathExtraction.cmake @@ -4231,8 +4137,6 @@ lib/libITKVideoCore-%%ITK_VER%%.so lib/libITKVideoCore-%%ITK_VER%%.so.1 lib/libITKVideoIO-%%ITK_VER%%.so lib/libITKVideoIO-%%ITK_VER%%.so.1 -lib/libITKVtkGlue-%%ITK_VER%%.so -lib/libITKVtkGlue-%%ITK_VER%%.so.1 lib/libITKWatersheds-%%ITK_VER%%.so lib/libITKWatersheds-%%ITK_VER%%.so.1 lib/libITKgiftiio-%%ITK_VER%%.so diff --git a/science/Makefile b/science/Makefile index 72853a4fae99..0fd8eb49e6d3 100644 --- a/science/Makefile +++ b/science/Makefile @@ -12,7 +12,6 @@ SUBDIR += R-cran-bayesm SUBDIR += R-cran-cmprsk SUBDIR += R-cran-e1071 - SUBDIR += R-cran-eco SUBDIR += R-cran-epicalc SUBDIR += R-cran-etm SUBDIR += R-cran-fastICA @@ -79,7 +78,6 @@ SUBDIR += dlib-cpp SUBDIR += drawxtl SUBDIR += dssp - SUBDIR += dvc SUBDIR += dwave-preprocessing SUBDIR += dynare SUBDIR += eccodes @@ -278,7 +276,6 @@ SUBDIR += precice SUBDIR += psi4 SUBDIR += pulseview - SUBDIR += py-DendroPy SUBDIR += py-GPy SUBDIR += py-GPyOpt SUBDIR += py-HepMC3 @@ -414,7 +411,6 @@ SUBDIR += py-pyphot SUBDIR += py-pyprecice SUBDIR += py-pyqubo - SUBDIR += py-pysal SUBDIR += py-pyscf SUBDIR += py-pyteomics SUBDIR += py-qcelemental diff --git a/science/PETSc/Makefile b/science/PETSc/Makefile index 4684b21a9b24..b7ab3e403b9f 100644 --- a/science/PETSc/Makefile +++ b/science/PETSc/Makefile @@ -1,5 +1,6 @@ PORTNAME= PETSc DISTVERSION= 3.22.4 +PORTREVISION= 1 CATEGORIES= science devel MASTER_SITES= https://web.cels.anl.gov/projects/petsc/download/release-snapshots/ DISTNAME= ${PORTNAME:tl}-${DISTVERSION} diff --git a/science/R-cran-Epi/Makefile b/science/R-cran-Epi/Makefile index 6bdc6a33695d..371fe4129bcb 100644 --- a/science/R-cran-Epi/Makefile +++ b/science/R-cran-Epi/Makefile @@ -1,5 +1,5 @@ PORTNAME= Epi -PORTVERSION= 2.59 +PORTVERSION= 2.60 CATEGORIES= science DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/science/R-cran-Epi/distinfo b/science/R-cran-Epi/distinfo index f8021114727e..ec0e369f065d 100644 --- a/science/R-cran-Epi/distinfo +++ b/science/R-cran-Epi/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1736910907 -SHA256 (Epi_2.59.tar.gz) = 00d630908d1cd06a13d0df12d32e56840992021b6d3769e2b2b5d68078967637 -SIZE (Epi_2.59.tar.gz) = 3198148 +TIMESTAMP = 1752227410 +SHA256 (Epi_2.60.tar.gz) = 29d6d91a7a0f04369852738fce009b3aefa59c65380174b6eec24ba7046aec57 +SIZE (Epi_2.60.tar.gz) = 3976720 diff --git a/science/R-cran-eco/Makefile b/science/R-cran-eco/Makefile deleted file mode 100644 index 2967e9718267..000000000000 --- a/science/R-cran-eco/Makefile +++ /dev/null @@ -1,15 +0,0 @@ -PORTNAME= eco -PORTVERSION= 4.0.3 -CATEGORIES= science -MASTER_SITES= https://cran.r-project.org/src/contrib/Archive/eco/ -DISTNAME= ${PORTNAME}_${PORTVERSION:C/\./-/g:C/-/./1} - -MAINTAINER= wen@FreeBSD.org -COMMENT= R Package for Ecological Inference in 2x2 Tables -WWW= https://imai.princeton.edu/software/eco.html - -LICENSE= GPLv2 - -USES= cran:auto-plist,compiles - -.include <bsd.port.mk> diff --git a/science/R-cran-eco/distinfo b/science/R-cran-eco/distinfo deleted file mode 100644 index ad286ffeb822..000000000000 --- a/science/R-cran-eco/distinfo +++ /dev/null @@ -1,3 +0,0 @@ -TIMESTAMP = 1684532790 -SHA256 (eco_4.0-3.tar.gz) = 0a70fec84ed49aa30f34510493c4586dd0fcb7b05b7ab87c379324ed570f4c19 -SIZE (eco_4.0-3.tar.gz) = 176181 diff --git a/science/R-cran-eco/pkg-descr b/science/R-cran-eco/pkg-descr deleted file mode 100644 index 5d82489bddf2..000000000000 --- a/science/R-cran-eco/pkg-descr +++ /dev/null @@ -1,4 +0,0 @@ -eco is a publicly available R package that implements the Bayesian -and likelihood methods proposed in Imai, Lu, and Strauss (2008) for -ecological inference in $2 \times 2$ tables as well as the method -of bounds introduced by Duncan and Davis (1953). diff --git a/science/R-cran-udunits2/Makefile b/science/R-cran-udunits2/Makefile index 3825ea143033..c8fb34cb9bba 100644 --- a/science/R-cran-udunits2/Makefile +++ b/science/R-cran-udunits2/Makefile @@ -1,6 +1,5 @@ PORTNAME= udunits2 -PORTVERSION= 0.13.2.1 -PORTREVISION= 1 +PORTVERSION= 0.13.2.2 CATEGORIES= science DISTNAME= ${PORTNAME}_${DISTVERSION} @@ -10,8 +9,8 @@ WWW= https://cran.r-project.org/web/packages/udunits2/ LICENSE= GPLv2 -LIB_DEPENDS= libudunits2.so:science/udunits \ - libexpat.so:textproc/expat2 +LIB_DEPENDS= libexpat.so:textproc/expat2 \ + libudunits2.so:science/udunits USES= cran:auto-plist,compiles diff --git a/science/R-cran-udunits2/distinfo b/science/R-cran-udunits2/distinfo index 4049bcc2344c..095995f9577f 100644 --- a/science/R-cran-udunits2/distinfo +++ b/science/R-cran-udunits2/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1647094615 -SHA256 (udunits2_0.13.2.1.tar.gz) = 9f5429c04a24930f7d037d506e5b154b6154df69247dcdaa6261075291d7f902 -SIZE (udunits2_0.13.2.1.tar.gz) = 68485 +TIMESTAMP = 1753248089 +SHA256 (udunits2_0.13.2.2.tar.gz) = 3e6dc4a12c155fa3e77f982084adbd6cb75d7a106d0b1a49ddc50a17fa4d045b +SIZE (udunits2_0.13.2.2.tar.gz) = 68840 diff --git a/science/abinit/Makefile b/science/abinit/Makefile index 2d49adde13b9..2347581589fd 100644 --- a/science/abinit/Makefile +++ b/science/abinit/Makefile @@ -1,5 +1,5 @@ PORTNAME= abinit -DISTVERSION= 10.2.7 +DISTVERSION= 10.4.5 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/abinit/distinfo b/science/abinit/distinfo index fa923cfa81d0..3cc29d915b5d 100644 --- a/science/abinit/distinfo +++ b/science/abinit/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1739946724 -SHA256 (abinit-abinit-10.2.7_GH0.tar.gz) = 0cd5c5755d151ef6a95b107cdcf0ec496818e34356ae8d26b2b4842bf641aec4 -SIZE (abinit-abinit-10.2.7_GH0.tar.gz) = 141254516 +TIMESTAMP = 1753132807 +SHA256 (abinit-abinit-10.4.5_GH0.tar.gz) = ccb3af00603f574208b6d5bea6f857d7040be5748e7a93a689ffad84eb6a65ce +SIZE (abinit-abinit-10.4.5_GH0.tar.gz) = 153582604 diff --git a/science/afni/Makefile b/science/afni/Makefile index 4e81f12f071d..c555c6c25e04 100644 --- a/science/afni/Makefile +++ b/science/afni/Makefile @@ -1,6 +1,6 @@ PORTNAME= afni DISTVERSIONPREFIX= AFNI_ -DISTVERSION= 25.1.08 +DISTVERSION= 25.2.09 CATEGORIES= science biology graphics perl5 python MAINTAINER= fernape@FreeBSD.org diff --git a/science/afni/distinfo b/science/afni/distinfo index cc36808f49c4..4ec769ac8338 100644 --- a/science/afni/distinfo +++ b/science/afni/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1746597097 -SHA256 (afni-afni-AFNI_25.1.08_GH0.tar.gz) = 300b83cee2f9e1bb3943a3eb5a2dcb18fecca9cb33f22bc2407789ca5c1631b6 -SIZE (afni-afni-AFNI_25.1.08_GH0.tar.gz) = 53278260 +TIMESTAMP = 1756108500 +SHA256 (afni-afni-AFNI_25.2.09_GH0.tar.gz) = ff6aacf8a4f2b0b60ea584ece08e23db665488bfb1978957f05f30df6c394e05 +SIZE (afni-afni-AFNI_25.2.09_GH0.tar.gz) = 53321640 diff --git a/science/afni/pkg-plist b/science/afni/pkg-plist index 813ef69e5567..ff89f38c13a6 100644 --- a/science/afni/pkg-plist +++ b/science/afni/pkg-plist @@ -527,6 +527,7 @@ bin/afni_seeds_per_space.txt bin/afni_skeleton.py bin/afni_system_check.py bin/afni_vcheck +bin/afni_vlines_run_text.txt bin/afnisumafatcat_logo_128sq.png bin/afnisumafatcat_logo_905sq.png bin/afnisumagui_logo_128sq.jpg @@ -1296,6 +1297,7 @@ lib/afni/plug_zeropad.so %%DATADIR%%/funstuff/face_psfb_serious.jpg %%DATADIR%%/funstuff/face_psfbx.jpg %%DATADIR%%/funstuff/face_pshukla.jpg +%%DATADIR%%/funstuff/face_pt_cw_ohbm.jpg %%DATADIR%%/funstuff/face_pumpkin.jpg %%DATADIR%%/funstuff/face_qiulin.jpg %%DATADIR%%/funstuff/face_qutian.jpg diff --git a/science/agrum/Makefile b/science/agrum/Makefile index e88d1aa30b21..ff6dce0acfc3 100644 --- a/science/agrum/Makefile +++ b/science/agrum/Makefile @@ -1,5 +1,5 @@ PORTNAME= agrum -DISTVERSION= 1.17.2 +DISTVERSION= 2.2.0 CATEGORIES= science math MAINTAINER= yuri@FreeBSD.org @@ -20,7 +20,7 @@ LLD_UNSAFE= yes USE_GITLAB= yes GL_ACCOUNT= agrumery GL_PROJECT= aGrUM -GL_TAGNAME= e26d7c4bccaafd5dcd3b78e8da1198a75a8043e7 +GL_TAGNAME= cf1283f783aa6803bafbd9a3fb4991316c1b52d9 SHEBANG_FILES= act @@ -58,8 +58,10 @@ PYTHON_RUN_DEPENDS= ${PYNUMPY} \ BINARY_ALIAS= gcc=${CC} g++=${CXX} # only for tests, see https://gitlab.com/agrumery/aGrUM/-/issues/100 -do-test: # tests fail to compile, see https://gitlab.com/agrumery/aGrUM/-/issues/148 +do-test: @cd ${WRKSRC} && \ ${SETENV} ${MAKE_ENV} ./act test release agrum -t all +# tests as of 2.2.0: Failed 0 of 1483 tests + .include <bsd.port.mk> diff --git a/science/agrum/distinfo b/science/agrum/distinfo index ee433f67b97a..62c51836a6d8 100644 --- a/science/agrum/distinfo +++ b/science/agrum/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1733703562 -SHA256 (agrumery-aGrUM-e26d7c4bccaafd5dcd3b78e8da1198a75a8043e7_GL0.tar.gz) = c48276422d14483a5f8e6cce9ced3b9875fcdf2e7484594228af5320c49bb139 -SIZE (agrumery-aGrUM-e26d7c4bccaafd5dcd3b78e8da1198a75a8043e7_GL0.tar.gz) = 27395374 +TIMESTAMP = 1753632410 +SHA256 (agrumery-aGrUM-cf1283f783aa6803bafbd9a3fb4991316c1b52d9_GL0.tar.gz) = 57f7274925f64129c2f3bfcd178f75edd4cb6eaff1d06c30f20c85c41e6ca3d9 +SIZE (agrumery-aGrUM-cf1283f783aa6803bafbd9a3fb4991316c1b52d9_GL0.tar.gz) = 29175753 diff --git a/science/agrum/pkg-plist b/science/agrum/pkg-plist index eba397f95784..9fe1f9999703 100644 --- a/science/agrum/pkg-plist +++ b/science/agrum/pkg-plist @@ -77,7 +77,7 @@ include/agrum/BN/inference/tools/jointTargetedInference.h include/agrum/BN/inference/tools/jointTargetedInference_tpl.h include/agrum/BN/inference/tools/marginalTargetedInference.h include/agrum/BN/inference/tools/marginalTargetedInference_tpl.h -include/agrum/BN/inference/tools/relevantPotentialsFinderType.h +include/agrum/BN/inference/tools/relevantTensorsFinderType.h include/agrum/BN/inference/tools/samplingInference.h include/agrum/BN/inference/tools/samplingInference_tpl.h include/agrum/BN/inference/variableElimination.h @@ -170,6 +170,8 @@ include/agrum/BN/learning/constraints/structuralConstraintTabuList.h include/agrum/BN/learning/constraints/structuralConstraintTabuList_inl.h include/agrum/BN/learning/constraints/structuralConstraintUndiGraph.h include/agrum/BN/learning/constraints/structuralConstraintUndiGraph_inl.h +include/agrum/BN/learning/correctedMutualInformation.h +include/agrum/BN/learning/correctedMutualInformation_inl.h include/agrum/BN/learning/greedyHillClimbing.h include/agrum/BN/learning/greedyHillClimbing_tpl.h include/agrum/BN/learning/localSearchWithTabuList.h @@ -178,6 +180,7 @@ include/agrum/BN/learning/localSearchWithTabuList_tpl.h include/agrum/BN/learning/paramUtils/DAG2BNLearner.h include/agrum/BN/learning/paramUtils/DAG2BNLearner_inl.h include/agrum/BN/learning/paramUtils/DAG2BNLearner_tpl.h +include/agrum/BN/learning/paramUtils/EMApproximationScheme.h include/agrum/BN/learning/paramUtils/paramEstimator.h include/agrum/BN/learning/paramUtils/paramEstimatorML.h include/agrum/BN/learning/paramUtils/paramEstimatorML_inl.h @@ -214,8 +217,6 @@ include/agrum/BN/learning/scores_and_tests/scoreMDL.h include/agrum/BN/learning/scores_and_tests/score_inl.h include/agrum/BN/learning/scores_and_tests/scorefNML.h include/agrum/BN/learning/scores_and_tests/scorefNML_inl.h -include/agrum/BN/learning/scores_and_tests/scoringCache.h -include/agrum/BN/learning/scores_and_tests/scoringCache_inl.h include/agrum/BN/learning/structureUtils/IGraphChangesGenerator4DiGraph.h include/agrum/BN/learning/structureUtils/IGraphChangesGenerator4UndiGraph.h include/agrum/BN/learning/structureUtils/graphChange.h @@ -319,7 +320,7 @@ include/agrum/ID/generator/influenceDiagramGenerator_tpl.h include/agrum/ID/generator/simpleUTGenerator.h include/agrum/ID/inference/ShaferShenoyLIMIDInference.h include/agrum/ID/inference/ShaferShenoyLIMIDInference_tpl.h -include/agrum/ID/inference/tools/decisionPotential.h +include/agrum/ID/inference/tools/decisionTensor.h include/agrum/ID/inference/tools/influenceDiagramInference.h include/agrum/ID/inference/tools/influenceDiagramInference_tpl.h include/agrum/ID/influenceDiagram.h @@ -332,8 +333,6 @@ include/agrum/ID/io/IDReader.h include/agrum/ID/io/IDReader_tpl.h include/agrum/ID/io/IDWriter.h include/agrum/ID/io/IDWriter_tpl.h -include/agrum/MN/MarkovNet.h -include/agrum/MN/inference/ShaferShenoyMNInference.h include/agrum/MRF/IMarkovRandomField.h include/agrum/MRF/IMarkovRandomField_tpl.h include/agrum/MRF/MarkovRandomField.h @@ -465,543 +464,578 @@ include/agrum/PRM/o3prmr/cocoR/Scanner.h include/agrum/PRM/utils_prm.h include/agrum/PRM/utils_prm_tpl.h include/agrum/agrum.h +include/agrum/base.h +include/agrum/base/core/AVLTree.h +include/agrum/base/core/AVLTree_tpl.h +include/agrum/base/core/IThreadNumberManager.h +include/agrum/base/core/approximations/IApproximationSchemeConfiguration.h +include/agrum/base/core/approximations/IApproximationSchemeConfiguration_inl.h +include/agrum/base/core/approximations/approximationPolicy.h +include/agrum/base/core/approximations/approximationScheme.h +include/agrum/base/core/approximations/approximationSchemeListener.h +include/agrum/base/core/approximations/approximationScheme_inl.h +include/agrum/base/core/approximations/exactPolicy.h +include/agrum/base/core/approximations/exactPolicy_tpl.h +include/agrum/base/core/approximations/linearApproximationPolicy.h +include/agrum/base/core/approximations/linearApproximationPolicy_tpl.h +include/agrum/base/core/argMaxSet.h +include/agrum/base/core/argMaxSet_tpl.h +include/agrum/base/core/bijection.h +include/agrum/base/core/bijection_tpl.h +include/agrum/base/core/binSearchTree.h +include/agrum/base/core/binSearchTree_tpl.h +include/agrum/base/core/binTreeNode.h +include/agrum/base/core/binTreeNode_tpl.h +include/agrum/base/core/cast_unicode.h +include/agrum/base/core/cast_unicode_inl.h +include/agrum/base/core/cocoR/common.h +include/agrum/base/core/debug.h +include/agrum/base/core/errorsContainer.h +include/agrum/base/core/errorsContainer_inl.h +include/agrum/base/core/exceptions.h +include/agrum/base/core/functors.h +include/agrum/base/core/hashFunc.h +include/agrum/base/core/hashFunc_inl.h 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+%%PYTHON_SITELIBDIR%%/pyagrum/causal/causalEffectEstimation/_learners.py +%%PYTHON_SITELIBDIR%%/pyagrum/causal/causalEffectEstimation/_utils.py +%%PYTHON_SITELIBDIR%%/pyagrum/causal/notebook.py +%%PYTHON_SITELIBDIR%%/pyagrum/clg/CLG.py +%%PYTHON_SITELIBDIR%%/pyagrum/clg/GaussianVariable.py +%%PYTHON_SITELIBDIR%%/pyagrum/clg/SEM.py +%%PYTHON_SITELIBDIR%%/pyagrum/clg/__init__.py +%%PYTHON_SITELIBDIR%%/pyagrum/clg/canonicalForm.py +%%PYTHON_SITELIBDIR%%/pyagrum/clg/constants.py +%%PYTHON_SITELIBDIR%%/pyagrum/clg/forwardSampling.py +%%PYTHON_SITELIBDIR%%/pyagrum/clg/learning.py +%%PYTHON_SITELIBDIR%%/pyagrum/clg/notebook.py +%%PYTHON_SITELIBDIR%%/pyagrum/clg/variableElimination.py +%%PYTHON_SITELIBDIR%%/pyagrum/common.py +%%PYTHON_SITELIBDIR%%/pyagrum/config.py +%%PYTHON_SITELIBDIR%%/pyagrum/ctbn/CIM.py +%%PYTHON_SITELIBDIR%%/pyagrum/ctbn/CTBN.py +%%PYTHON_SITELIBDIR%%/pyagrum/ctbn/CTBNGenerator.py +%%PYTHON_SITELIBDIR%%/pyagrum/ctbn/CTBNInference.py +%%PYTHON_SITELIBDIR%%/pyagrum/ctbn/CTBNLearner.py +%%PYTHON_SITELIBDIR%%/pyagrum/ctbn/SamplesStats.py +%%PYTHON_SITELIBDIR%%/pyagrum/ctbn/StatsIndepTest.py +%%PYTHON_SITELIBDIR%%/pyagrum/ctbn/__init__.py +%%PYTHON_SITELIBDIR%%/pyagrum/ctbn/constants.py +%%PYTHON_SITELIBDIR%%/pyagrum/ctbn/notebook.py +%%PYTHON_SITELIBDIR%%/pyagrum/defaults.ini +%%PYTHON_SITELIBDIR%%/pyagrum/deprecated.py +%%PYTHON_SITELIBDIR%%/pyagrum/lib/__init__.py +%%PYTHON_SITELIBDIR%%/pyagrum/lib/_colors.py +%%PYTHON_SITELIBDIR%%/pyagrum/lib/bn2graph.py +%%PYTHON_SITELIBDIR%%/pyagrum/lib/bn2roc.py +%%PYTHON_SITELIBDIR%%/pyagrum/lib/bn2scores.py +%%PYTHON_SITELIBDIR%%/pyagrum/lib/bn_vs_bn.py +%%PYTHON_SITELIBDIR%%/pyagrum/lib/cn2graph.py +%%PYTHON_SITELIBDIR%%/pyagrum/lib/discreteTypeProcessor.py +%%PYTHON_SITELIBDIR%%/pyagrum/lib/discretizer.py +%%PYTHON_SITELIBDIR%%/pyagrum/lib/dynamicBN.py +%%PYTHON_SITELIBDIR%%/pyagrum/lib/explain.py +%%PYTHON_SITELIBDIR%%/pyagrum/lib/export.py +%%PYTHON_SITELIBDIR%%/pyagrum/lib/id2graph.py +%%PYTHON_SITELIBDIR%%/pyagrum/lib/image.py +%%PYTHON_SITELIBDIR%%/pyagrum/lib/ipython.py +%%PYTHON_SITELIBDIR%%/pyagrum/lib/mrf2graph.py +%%PYTHON_SITELIBDIR%%/pyagrum/lib/notebook.py +%%PYTHON_SITELIBDIR%%/pyagrum/lib/proba_histogram.py +%%PYTHON_SITELIBDIR%%/pyagrum/lib/shapley.py +%%PYTHON_SITELIBDIR%%/pyagrum/lib/utils.py +%%PYTHON_SITELIBDIR%%/pyagrum/pyagrum.py +%%PYTHON_SITELIBDIR%%/pyagrum/skbn/_MBCalcul.py +%%PYTHON_SITELIBDIR%%/pyagrum/skbn/__init__.py +%%PYTHON_SITELIBDIR%%/pyagrum/skbn/_learningMethods.py +%%PYTHON_SITELIBDIR%%/pyagrum/skbn/_utils.py +%%PYTHON_SITELIBDIR%%/pyagrum/skbn/bnclassifier.py libdata/pkgconfig/agrum.pc diff --git a/science/arbor/Makefile b/science/arbor/Makefile index 15368c1b0ac6..d2d6e0cf6ef2 100644 --- a/science/arbor/Makefile +++ b/science/arbor/Makefile @@ -1,7 +1,7 @@ PORTNAME= arbor DISTVERSIONPREFIX= v DISTVERSION= 0.10.1 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/avogadrolibs/Makefile b/science/avogadrolibs/Makefile index b6c54be01a66..96b7dc019a4f 100644 --- a/science/avogadrolibs/Makefile +++ b/science/avogadrolibs/Makefile @@ -1,5 +1,6 @@ PORTNAME= avogadrolibs DISTVERSION= 1.100.0 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/axom/Makefile b/science/axom/Makefile index 35f116e96434..58c94b7ba017 100644 --- a/science/axom/Makefile +++ b/science/axom/Makefile @@ -1,6 +1,7 @@ PORTNAME= axom DISTVERSIONPREFIX= v DISTVERSION= 0.10.1 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/bagel/Makefile b/science/bagel/Makefile index d612187af3f8..16f1638f3987 100644 --- a/science/bagel/Makefile +++ b/science/bagel/Makefile @@ -1,7 +1,7 @@ PORTNAME= bagel DISTVERSIONPREFIX= v DISTVERSION= 1.2.2-132 -PORTREVISION= 15 +PORTREVISION= 16 DISTVERSIONSUFFIX= -g2955e4d1a CATEGORIES= science diff --git a/science/bddsolve/Makefile b/science/bddsolve/Makefile index eca69ffea90a..697130a1f5fd 100644 --- a/science/bddsolve/Makefile +++ b/science/bddsolve/Makefile @@ -1,6 +1,6 @@ PORTNAME= bddsolve PORTVERSION= 1.04 -PORTREVISION= 18 +PORTREVISION= 19 CATEGORIES= science MASTER_SITES= http://www.win.tue.nl/~wieger/bddsolve/_downloads/ DISTNAME= ${PORTNAME}-source-${PORTVERSION} diff --git a/science/bout++/Makefile b/science/bout++/Makefile index 2eb36e82ec9e..43b9accad186 100644 --- a/science/bout++/Makefile +++ b/science/bout++/Makefile @@ -1,7 +1,7 @@ PORTNAME= bout++ DISTVERSIONPREFIX= v DISTVERSION= 5.1.1 -PORTREVISION= 1 +PORTREVISION= 3 CATEGORIES= science math # physics MAINTAINER= yuri@FreeBSD.org @@ -15,7 +15,7 @@ BUILD_DEPENDS= gmake:devel/gmake LIB_DEPENDS= libfftw3.so:math/fftw3 \ libfmt.so:devel/libfmt \ libopenblas.so:math/openblas \ - libuuid.so:misc/e2fsprogs-libuuid + libuuid.so:misc/libuuid RUN_DEPENDS= bash:shells/bash \ ${PYTHON_PKGNAMEPREFIX}matplotlib>=3.2.1:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}natsort>=8.1.0:devel/py-natsort@${PY_FLAVOR} \ diff --git a/science/cantera/Makefile b/science/cantera/Makefile index ebaa5cf75809..61a965965fe2 100644 --- a/science/cantera/Makefile +++ b/science/cantera/Makefile @@ -1,7 +1,7 @@ PORTNAME= cantera DISTVERSIONPREFIX= v DISTVERSION= 3.1.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science # chemistry physics MAINTAINER= yuri@FreeBSD.org diff --git a/science/cantera/pkg-plist b/science/cantera/pkg-plist index 43c08d4f98b4..516d5af0b3b4 100644 --- a/science/cantera/pkg-plist +++ b/science/cantera/pkg-plist @@ -626,7 +626,7 @@ lib/libcantera_shared.so.3.1.0 %%PYTHON%%%%PYTHON_SITELIBDIR%%/Cantera-3.1.0.dist-info/top_level.txt %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/__init__.pxd %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/__init__.py -%%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/_cantera%%PYTHON_EXT_SUFFIX%%.so +%%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/_cantera%%PYTHON_TAG%%.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/_onedim.pxd %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/_utils.pxd %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/ck2yaml.py diff --git a/science/cdf/Makefile b/science/cdf/Makefile index 803a95f11b0d..edc94cf929c9 100644 --- a/science/cdf/Makefile +++ b/science/cdf/Makefile @@ -5,7 +5,7 @@ MASTER_SITES= https://spdf.gsfc.nasa.gov/pub/software/cdf/dist/cdf39_1/ DISTNAME= cdf${VER}-dist-cdf DIST_SUBDIR= ${PORTNAME}-${PORTVERSION} -MAINTAINER= alster@vinterdalen.se +MAINTAINER= alven@FreeBSD.org COMMENT= Device independent view of the CDF data model WWW= https://cdf.gsfc.nasa.gov/ diff --git a/science/cdo/Makefile b/science/cdo/Makefile index 7051f227dae6..783eae420b68 100644 --- a/science/cdo/Makefile +++ b/science/cdo/Makefile @@ -1,7 +1,8 @@ PORTNAME= cdo -PORTVERSION= 2.5.0 +PORTVERSION= 2.5.2 +PORTREVISION= 1 CATEGORIES= science -MASTER_SITES= https://code.mpimet.mpg.de/attachments/download/29786/ \ +MASTER_SITES= https://code.mpimet.mpg.de/attachments/download/29938/ \ LOCAL/sunpoet MAINTAINER= sunpoet@FreeBSD.org @@ -26,8 +27,8 @@ CONFIGURE_ENV= PYTHON=${PYTHON_CMD} GNU_CONFIGURE= yes INSTALL_TARGET= install-strip MAKE_JOBS_UNSAFE= yes -TESTING_UNSAFE= 765 tests fail TEST_TARGET= check +TESTING_UNSAFE= 765 tests fail USE_CXXSTD= c++20 USE_LDCONFIG= yes @@ -59,7 +60,7 @@ SZIP_LIB_DEPENDS= libsz.so:science/libaec UDUNITS_CONFIGURE_WITH= udunits2 UDUNITS_LIB_DEPENDS= libudunits2.so:science/udunits UUID_CONFIGURE_OFF= ac_cv_func_uuid_create=no ac_cv_have_decl_uuid_create=no ac_cv_have_decl_uuid_generate=no ac_cv_lib_uuid_uuid_generate=no -UUID_LIB_DEPENDS= libuuid.so:misc/e2fsprogs-libuuid +UUID_LIB_DEPENDS= libuuid.so:misc/libuuid post-patch: @${REINPLACE_CMD} -e '/^SUBDIRS = / s| contrib||' ${WRKSRC}/Makefile.in diff --git a/science/cdo/distinfo b/science/cdo/distinfo index 68eeaef6c47f..fea6c9bb59e8 100644 --- a/science/cdo/distinfo +++ b/science/cdo/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1735837779 -SHA256 (cdo-2.5.0.tar.gz) = e865c05c1b52fd76b80e33421554db81b38b75210820bdc40e8690f4552f68e2 -SIZE (cdo-2.5.0.tar.gz) = 13553301 +TIMESTAMP = 1747715302 +SHA256 (cdo-2.5.2.tar.gz) = 3b28da72d75547663b1b9b08332bfe3f884d27742d0eeeb7f3c8b2c70f521fa9 +SIZE (cdo-2.5.2.tar.gz) = 13966550 diff --git a/science/cgribex/Makefile b/science/cgribex/Makefile index 0c0f443fa99d..cbc0287d6174 100644 --- a/science/cgribex/Makefile +++ b/science/cgribex/Makefile @@ -14,7 +14,6 @@ LICENSE_FILE= ${WRKSRC}/COPYING USES= libtool -CONFIGURE_ARGS= --without-grpb_api CPPFLAGS+= -DgFortran GNU_CONFIGURE= yes INSTALL_TARGET= install-strip @@ -28,9 +27,6 @@ JASPER_LIB_DEPENDS= libjasper.so:graphics/jasper SZIP_CONFIGURE_WITH= szlib=${LOCALBASE} SZIP_LIB_DEPENDS= libsz.so:science/libaec -post-configure: - @${REINPLACE_CMD} -e 's|-Ino/include||g; s|-Lno/lib||g' ${WRKSRC}/Makefile ${WRKSRC}/*/Makefile - post-install: ${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/libcgribex.so diff --git a/science/chemical-mime-data/Makefile b/science/chemical-mime-data/Makefile index 064fad3e2128..f2cf0d3ea3dd 100644 --- a/science/chemical-mime-data/Makefile +++ b/science/chemical-mime-data/Makefile @@ -1,21 +1,28 @@ PORTNAME= chemical-mime-data PORTVERSION= 0.1.94 -PORTREVISION= 11 +PORTREVISION= 12 CATEGORIES= science -MASTER_SITES= SF/chemical-mime/${PORTNAME}/${PORTVERSION} - MAINTAINER= ports@FreeBSD.org COMMENT= Collection of chemical MIME types for UNIX desktops -WWW= http://chemical-mime.sourceforge.net/ +WWW= https://github.com/dleidert/chemical-mime + +LICENSE= LGPL21 +LICENSE_FILE= ${WRKSRC}/COPYING -USES= gettext-tools gmake gnome localbase:ldflags pathfix pkgconfig \ +USES= autoreconf gettext-tools gmake gnome localbase:ldflags pathfix pkgconfig \ shared-mime-info tar:bzip2 USE_GNOME= gnomemimedata intlhack librsvg2:build libxslt:build GNU_CONFIGURE= yes -CONFIGURE_ARGS= --disable-update-database +CONFIGURE_ARGS= --disable-update-database \ + --without-kde-magic + +USE_GITHUB= yes +GH_ACCOUNT= dleidert +GH_PROJECT= chemical-mime +GH_TAGNAME= 4fd66e3b3b7d922555d1e25587908b036805c45b post-patch: - @${REINPLACE_CMD} -e 's|*-*-solaris*|*| ; s|rsvg|rsvg-convert|g' ${WRKSRC}/configure - @${REINPLACE_CMD} -e 's|-f png $$< |-f png $$< > |' ${WRKSRC}/icons/hicolor/Makefile.in + @${REINPLACE_CMD} -e 's:acronym|alias|comment|:acronym|alias|comment|generic-icon|:' \ + ${WRKSRC}/xsl/cmd_freedesktop_org.xsl .include <bsd.port.mk> diff --git a/science/chemical-mime-data/distinfo b/science/chemical-mime-data/distinfo index d00a171cc183..efec878a86be 100644 --- a/science/chemical-mime-data/distinfo +++ b/science/chemical-mime-data/distinfo @@ -1,2 +1,3 @@ -SHA256 (chemical-mime-data-0.1.94.tar.bz2) = 4907cdf60e9edca0a453f6f24e9179ae9da085b67168e932ba44a4280316bff1 -SIZE (chemical-mime-data-0.1.94.tar.bz2) = 146077 +TIMESTAMP = 1753696974 +SHA256 (dleidert-chemical-mime-0.1.94-4fd66e3b3b7d922555d1e25587908b036805c45b_GH0.tar.gz) = f40fdf56ef14c67ab59b6ebb2e6d513ddf5070929695b62e04d9f40a2baccfff +SIZE (dleidert-chemical-mime-0.1.94-4fd66e3b3b7d922555d1e25587908b036805c45b_GH0.tar.gz) = 84515 diff --git a/science/chemical-mime-data/pkg-plist b/science/chemical-mime-data/pkg-plist index c22391dc17c7..aaf1cf38383d 100644 --- a/science/chemical-mime-data/pkg-plist +++ b/science/chemical-mime-data/pkg-plist @@ -1,26 +1,14 @@ libdata/pkgconfig/chemical-mime-data.pc -share/doc/chemical-mime-data/chemical-mime-data.html -share/doc/chemical-mime-data/cmd.css -share/doc/chemical-mime-data/index.html -share/icons/hicolor/16x16/mimetypes/gnome-mime-chemical.png -share/icons/hicolor/22x22/mimetypes/gnome-mime-chemical.png -share/icons/hicolor/24x24/mimetypes/gnome-mime-chemical.png -share/icons/hicolor/32x32/mimetypes/gnome-mime-chemical.png -share/icons/hicolor/36x36/mimetypes/gnome-mime-chemical.png -share/icons/hicolor/48x48/mimetypes/gnome-mime-chemical.png -share/icons/hicolor/64x64/mimetypes/gnome-mime-chemical.png -share/icons/hicolor/72x72/mimetypes/gnome-mime-chemical.png -share/icons/hicolor/96x96/mimetypes/gnome-mime-chemical.png -share/icons/hicolor/128x128/mimetypes/gnome-mime-chemical.png -share/icons/hicolor/192x192/mimetypes/gnome-mime-chemical.png -share/icons/hicolor/scalable/mimetypes/gnome-mime-chemical.svgz +%%DATADIR%%/file/magic.mime +%%DATADIR%%/mime.types share/locale/de/LC_MESSAGES/chemical-mime-data.mo share/locale/fr/LC_MESSAGES/chemical-mime-data.mo -share/pixmaps/chemistry.png -share/pixmaps/gnome-mime-chemical.png -share/mime/packages/chemical-mime-data.xml share/mime-info/chemical-mime-data.keys share/mime-info/chemical-mime-data.mime +share/mime/packages/chemical-mime-data.xml +share/mimelnk/chemical/cml.desktop +share/mimelnk/chemical/pdb.desktop +share/mimelnk/chemical/seq-na-genbank.desktop share/mimelnk/chemical/x-alchemy.desktop share/mimelnk/chemical/x-cache.desktop share/mimelnk/chemical/x-cactvs-ascii.desktop @@ -31,11 +19,18 @@ share/mimelnk/chemical/x-cdxml.desktop share/mimelnk/chemical/x-chem3d.desktop share/mimelnk/chemical/x-cif.desktop share/mimelnk/chemical/x-cml.desktop +share/mimelnk/chemical/x-daylight-smiles.desktop share/mimelnk/chemical/x-dmol.desktop share/mimelnk/chemical/x-gamess-input.desktop share/mimelnk/chemical/x-gamess-output.desktop share/mimelnk/chemical/x-gaussian-input.desktop share/mimelnk/chemical/x-gaussian-log.desktop +share/mimelnk/chemical/x-gaussian-output.desktop +share/mimelnk/chemical/x-gaussian.desktop +share/mimelnk/chemical/x-gaussian03-output.desktop +share/mimelnk/chemical/x-gaussian92-output.desktop +share/mimelnk/chemical/x-gaussian94-output.desktop +share/mimelnk/chemical/x-gaussian98-output.desktop share/mimelnk/chemical/x-genbank.desktop share/mimelnk/chemical/x-gulp.desktop share/mimelnk/chemical/x-hin.desktop @@ -46,18 +41,24 @@ share/mimelnk/chemical/x-macromodel-input.desktop share/mimelnk/chemical/x-mdl-molfile.desktop share/mimelnk/chemical/x-mdl-rdfile.desktop share/mimelnk/chemical/x-mdl-rxnfile.desktop +share/mimelnk/chemical/x-mdl-sdfile.desktop share/mimelnk/chemical/x-mdl-tgf.desktop share/mimelnk/chemical/x-mmcif.desktop share/mimelnk/chemical/x-mol2.desktop share/mimelnk/chemical/x-mopac-graph.desktop +share/mimelnk/chemical/x-mopac-input.desktop share/mimelnk/chemical/x-mopac-out.desktop +share/mimelnk/chemical/x-mopac.desktop share/mimelnk/chemical/x-msi-car.desktop share/mimelnk/chemical/x-msi-hessian.desktop share/mimelnk/chemical/x-msi-mdf.desktop share/mimelnk/chemical/x-msi-msi.desktop +share/mimelnk/chemical/x-ncbi-asn1-ascii.desktop share/mimelnk/chemical/x-ncbi-asn1-binary.desktop share/mimelnk/chemical/x-ncbi-asn1-xml.desktop share/mimelnk/chemical/x-ncbi-asn1.desktop +share/mimelnk/chemical/x-pdb.desktop share/mimelnk/chemical/x-shelx.desktop share/mimelnk/chemical/x-vmd.desktop share/mimelnk/chemical/x-xyz.desktop +share/mimelnk/chemical/xyz.desktop diff --git a/science/chemicalfun/Makefile b/science/chemicalfun/Makefile index 1c55c5c1c2b7..9b3afed93586 100644 --- a/science/chemicalfun/Makefile +++ b/science/chemicalfun/Makefile @@ -1,6 +1,6 @@ PORTNAME= chemicalfun DISTVERSION= 0.1.8 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science # chemistry MASTER_SITES= https://bitbucket.org/${BB_ACCOUNT}/${PORTNAME}/get/${BB_COMMIT}${EXTRACT_SUFX}?dummy=/:src DISTFILES= ${PORTNAME}-${DISTVERSION}${EXTRACT_SUFX}:src @@ -45,7 +45,7 @@ post-install-PYTHON-on: @${FIND} ${STAGEDIR} -name "*.pyc" -delete @${FIND} ${STAGEDIR} -name __pycache__ -delete # strip binary - @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/chemicalfun/PyChemicalFun${PYTHON_EXT_SUFFIX}.so + @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/chemicalfun/PyChemicalFun${PYTHON_TAG}.so post-test: @${ECHO} "==> run C++ tests" diff --git a/science/chemicalfun/pkg-plist b/science/chemicalfun/pkg-plist index b730080e8561..d0fd869ad428 100644 --- a/science/chemicalfun/pkg-plist +++ b/science/chemicalfun/pkg-plist @@ -20,5 +20,5 @@ lib/libChemicalFun.so %%PYTHON_SITELIBDIR%%/chemicalfun-0.1.8.dist-info/WHEEL %%PYTHON_SITELIBDIR%%/chemicalfun-0.1.8.dist-info/direct_url.json %%PYTHON_SITELIBDIR%%/chemicalfun-0.1.8.dist-info/top_level.txt -%%PYTHON_SITELIBDIR%%/chemicalfun/PyChemicalFun%%PYTHON_EXT_SUFFIX%%.so +%%PYTHON_SITELIBDIR%%/chemicalfun/PyChemicalFun%%PYTHON_TAG%%.so %%PYTHON_SITELIBDIR%%/chemicalfun/__init__.py diff --git a/science/cif-tools/Makefile b/science/cif-tools/Makefile index 8799066a719b..401eae02834e 100644 --- a/science/cif-tools/Makefile +++ b/science/cif-tools/Makefile @@ -1,7 +1,7 @@ PORTNAME= cif-tools DISTVERSIONPREFIX= v DISTVERSION= 1.0.12 # chemistry -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/code_saturne/pkg-plist b/science/code_saturne/pkg-plist index f97fecfd65dc..21faab1e02e3 100644 --- a/science/code_saturne/pkg-plist +++ b/science/code_saturne/pkg-plist @@ -502,94 +502,94 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-%%PYTHON_SITELIBDIR%%/ple/__pycache__/pyple_coupler%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/ple/__pycache__/Coupling%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/ple/__pycache__/Coupling%%PYTHON_TAG%%.opt-2.pyc +%%PYTHON_SITELIBDIR%%/ple/__pycache__/Coupling%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/ple/__pycache__/Init%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/ple/__pycache__/Init%%PYTHON_TAG%%.opt-2.pyc +%%PYTHON_SITELIBDIR%%/ple/__pycache__/Init%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/ple/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/ple/__pycache__/__init__%%PYTHON_TAG%%.opt-2.pyc +%%PYTHON_SITELIBDIR%%/ple/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/ple/__pycache__/pyple_coupler%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/ple/__pycache__/pyple_coupler%%PYTHON_TAG%%.opt-2.pyc +%%PYTHON_SITELIBDIR%%/ple/__pycache__/pyple_coupler%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/ple/libpyplecoupling.so %%PYTHON_SITELIBDIR%%/ple/pyple_coupler.py libexec/code_saturne/cs_io_dump diff --git a/science/cp2k-data/Makefile b/science/cp2k-data/Makefile index 8bc9337cd7b9..bc2ad72bb356 100644 --- a/science/cp2k-data/Makefile +++ b/science/cp2k-data/Makefile @@ -1,6 +1,6 @@ PORTNAME= cp2k-data DISTVERSIONPREFIX= v -DISTVERSION= 2025.1 +DISTVERSION= 2025.2 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/cp2k-data/distinfo b/science/cp2k-data/distinfo index 004194f14912..264eccf26d02 100644 --- a/science/cp2k-data/distinfo +++ b/science/cp2k-data/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1735891303 -SHA256 (cp2k-cp2k-v2025.1_GH0.tar.gz) = 9b58062b9aed51de06cb1248f5dbeab2741962f03eb72c4025b9d0533af1805e -SIZE (cp2k-cp2k-v2025.1_GH0.tar.gz) = 87315415 +TIMESTAMP = 1753646804 +SHA256 (cp2k-cp2k-v2025.2_GH0.tar.gz) = 02432be1f6b56bab1d4b43e86e28ba495405d6f4015f2610f3376d56495ef74b +SIZE (cp2k-cp2k-v2025.2_GH0.tar.gz) = 88095973 diff --git a/science/cp2k-data/pkg-plist b/science/cp2k-data/pkg-plist index 3e641bb9296c..27d24338488a 100644 --- a/science/cp2k-data/pkg-plist +++ b/science/cp2k-data/pkg-plist @@ -1,6 +1,7 @@ %%DATADIR%%/ALL_BASIS_SETS %%DATADIR%%/ALL_POTENTIALS %%DATADIR%%/AcPP1_POTENTIALS +%%DATADIR%%/AcPP2_POTENTIALS %%DATADIR%%/Allegro/gra-water-deployed-neq060sp.pth %%DATADIR%%/Allegro/si-deployed-neq060dp.pth %%DATADIR%%/BASIS_ADMM @@ -12,6 +13,7 @@ %%DATADIR%%/BASIS_MINIX %%DATADIR%%/BASIS_MOLOPT %%DATADIR%%/BASIS_MOLOPT_AcPP1 +%%DATADIR%%/BASIS_MOLOPT_AcPP2 %%DATADIR%%/BASIS_MOLOPT_LnPP1 %%DATADIR%%/BASIS_MOLOPT_LnPP2 %%DATADIR%%/BASIS_MOLOPT_PSI @@ -139,7 +141,7 @@ %%DATADIR%%/DFTB/scc/zns.spl %%DATADIR%%/DFTB/scc/znzn.spl %%DATADIR%%/DFTB/uff_table -%%DATADIR%%/DeePMD/W.pb +%%DATADIR%%/DeePMD/water_dpa2.pth %%DATADIR%%/ECP_POTENTIALS %%DATADIR%%/ECP_POTENTIALS_pob-TZVP-rev2 %%DATADIR%%/EMSL_BASIS_SETS @@ -185,6 +187,17 @@ %%DATADIR%%/NNP/bulkH2O-jcp2020-cnnp/nnp-8/scaling.data %%DATADIR%%/NNP/bulkH2O-jcp2020-cnnp/nnp-8/weights.001.data %%DATADIR%%/NNP/bulkH2O-jcp2020-cnnp/nnp-8/weights.008.data +%%DATADIR%%/NNP/protH2OHelium-interaction-nnp/input.nn +%%DATADIR%%/NNP/protH2OHelium-interaction-nnp/readme.md +%%DATADIR%%/NNP/protH2OHelium-interaction-nnp/scaling.data +%%DATADIR%%/NNP/protH2OHelium-interaction-nnp/weights.001.data +%%DATADIR%%/NNP/protH2OHelium-interaction-nnp/weights.002.data +%%DATADIR%%/NNP/protH2OHelium-interaction-nnp/weights.008.data +%%DATADIR%%/NNP/protH2Ocluster-jctc2020-nnp/input.nn +%%DATADIR%%/NNP/protH2Ocluster-jctc2020-nnp/readme.md +%%DATADIR%%/NNP/protH2Ocluster-jctc2020-nnp/scaling.data +%%DATADIR%%/NNP/protH2Ocluster-jctc2020-nnp/weights.001.data +%%DATADIR%%/NNP/protH2Ocluster-jctc2020-nnp/weights.008.data %%DATADIR%%/NequIP/water-deployed-neq060dp.pth %%DATADIR%%/NequIP/water-deployed-neq060sp.pth %%DATADIR%%/POTENTIAL diff --git a/science/cp2k/Makefile b/science/cp2k/Makefile index f6b05741f098..46e7081d3302 100644 --- a/science/cp2k/Makefile +++ b/science/cp2k/Makefile @@ -1,7 +1,6 @@ PORTNAME= cp2k DISTVERSIONPREFIX= v -DISTVERSION= 2025.1 -PORTREVISION= 2 +DISTVERSION= 2025.2 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -61,5 +60,6 @@ do-test: install ./tests/do_regtest.py ${BUILD_WRKSRC}/bin ${EXE_VERSION} # build instructions: https://github.com/cp2k/cp2k/blob/master/INSTALL.md +# tests as of 2025.2: Summary: correct: 3009 / 3012; failed: 3; 141min .include <bsd.port.mk> diff --git a/science/cp2k/distinfo b/science/cp2k/distinfo index e6c365e0e377..aee1bed85e63 100644 --- a/science/cp2k/distinfo +++ b/science/cp2k/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1735886722 -SHA256 (cp2k-cp2k-v2025.1_GH0.tar.gz) = 9b58062b9aed51de06cb1248f5dbeab2741962f03eb72c4025b9d0533af1805e -SIZE (cp2k-cp2k-v2025.1_GH0.tar.gz) = 87315415 +TIMESTAMP = 1753641251 +SHA256 (cp2k-cp2k-v2025.2_GH0.tar.gz) = 02432be1f6b56bab1d4b43e86e28ba495405d6f4015f2610f3376d56495ef74b +SIZE (cp2k-cp2k-v2025.2_GH0.tar.gz) = 88095973 diff --git a/science/cp2k/files/patch-cmake_CompilerConfiguration.cmake b/science/cp2k/files/patch-cmake_CompilerConfiguration.cmake index 1ec302774635..3b5407d20736 100644 --- a/science/cp2k/files/patch-cmake_CompilerConfiguration.cmake +++ b/science/cp2k/files/patch-cmake_CompilerConfiguration.cmake @@ -1,11 +1,37 @@ ---- cmake/CompilerConfiguration.cmake.orig 2024-09-04 05:25:49 UTC +--- cmake/CompilerConfiguration.cmake.orig 2025-07-23 08:02:03 UTC +++ cmake/CompilerConfiguration.cmake -@@ -35,7 +35,7 @@ add_compile_options( - # https://github.com/cp2k/dbcsr/issues/261 eventually check compiler version - # (similar to -h system_alloc) - add_compile_options( -- "$<$<COMPILE_LANG_AND_ID:Fortran,GNU>:-mtune=native;-ffree-line-length-512;-ffree-form;-std=f2008;-fimplicit-none;-Werror=aliasing;-Werror=ampersand;-Werror=c-binding-type;-Werror=conversion;-Werror=intrinsic-shadow;-Werror=intrinsics-std;-Werror=line-truncation;-Werror=tabs;-Werror=target-lifetime;-Werror=underflow;-Werror=unused-but-set-variable;-Werror=unused-variable>" -+ "$<$<COMPILE_LANG_AND_ID:Fortran,GNU>:-ffree-line-length-512;-ffree-form;-std=f2008;-fimplicit-none;-Werror=aliasing;-Werror=ampersand;-Werror=c-binding-type;-Werror=conversion;-Werror=intrinsic-shadow;-Werror=intrinsics-std;-Werror=line-truncation;-Werror=tabs;-Werror=target-lifetime;-Werror=underflow;-Werror=unused-but-set-variable;-Werror=unused-variable>" - "$<$<AND:$<COMPILE_LANG_AND_ID:Fortran,GNU>,$<VERSION_GREATER_EQUAL:${CMAKE_Fortran_COMPILER_VERSION},11>>:-fallow-argument-mismatch>" - "$<$<COMPILE_LANG_AND_ID:Fortran,Intel>:-free -stand=f18 -fpp -heap-arrays>" - "$<$<COMPILE_LANG_AND_ID:Fortran,PGI>:-Mfreeform -Mextend -Mallocatable=03>" +@@ -53,9 +53,9 @@ add_compile_options( + + # Release + add_compile_options( +- "$<$<AND:$<CONFIG:RELEASE>,$<COMPILE_LANG_AND_ID:Fortran,GNU>>:-O3;-march=native;-mtune=native;-funroll-loops>" +- "$<$<AND:$<CONFIG:RELEASE>,$<COMPILE_LANG_AND_ID:CXX,GNU>>:-O3;-march=native;-mtune=native;-funroll-loops>" +- "$<$<AND:$<CONFIG:RELEASE>,$<COMPILE_LANG_AND_ID:C,GNU>>:-O3;-march=native;-mtune=native;-funroll-loops>" ++ "$<$<AND:$<CONFIG:RELEASE>,$<COMPILE_LANG_AND_ID:Fortran,GNU>>:-O3;-funroll-loops>" ++ "$<$<AND:$<CONFIG:RELEASE>,$<COMPILE_LANG_AND_ID:CXX,GNU>>:-O3;-funroll-loops>" ++ "$<$<AND:$<CONFIG:RELEASE>,$<COMPILE_LANG_AND_ID:C,GNU>>:-O3;-funroll-loops>" + ) + + # Generic +@@ -67,9 +67,9 @@ add_compile_options( + + # Debug + add_compile_options( +- "$<$<AND:$<CONFIG:DEBUG>,$<COMPILE_LANG_AND_ID:Fortran,GNU>>:-O1;-march=native;-mtune=native>" +- "$<$<AND:$<CONFIG:DEBUG>,$<COMPILE_LANG_AND_ID:CXX,GNU>>:-O1;-march=native;-mtune=native>" +- "$<$<AND:$<CONFIG:DEBUG>,$<COMPILE_LANG_AND_ID:C,GNU>>:-O1;-march=native;-mtune=native>" ++ "$<$<AND:$<CONFIG:DEBUG>,$<COMPILE_LANG_AND_ID:Fortran,GNU>>:-O1>" ++ "$<$<AND:$<CONFIG:DEBUG>,$<COMPILE_LANG_AND_ID:CXX,GNU>>:-O1>" ++ "$<$<AND:$<CONFIG:DEBUG>,$<COMPILE_LANG_AND_ID:C,GNU>>:-O1>" + ) + add_compile_options( + "$<$<AND:$<CONFIG:DEBUG>,$<COMPILE_LANG_AND_ID:Fortran,GNU>>:-fsanitize=leak;-Werror=realloc-lhs>" +@@ -100,7 +100,7 @@ add_compile_options( + + # Address Sanitizer + add_compile_options( +- "$<$<CONFIG:ASAN>:-fsanitize=address;-no-pie;-O3;-march=native;-mtune=native;-funroll-loops>" ++ "$<$<CONFIG:ASAN>:-fsanitize=address;-no-pie;-O3;-funroll-loops>" + ) + add_link_options("$<$<CONFIG:ASAN>:-fsanitize=address>") + diff --git a/science/cp2k/pkg-plist b/science/cp2k/pkg-plist index b502f43f6bfb..bc47f0049444 100644 --- a/science/cp2k/pkg-plist +++ b/science/cp2k/pkg-plist @@ -6,12 +6,15 @@ bin/dumpdcd%%SUFFIX%% bin/graph%%SUFFIX%% bin/grid_miniapp%%SUFFIX%% bin/grid_unittest%%SUFFIX%% +bin/gx_ac_unittest%%SUFFIX%% bin/libcp2k_unittest%%SUFFIX%% bin/memory_utilities_unittest%%SUFFIX%% bin/nequip_unittest%%SUFFIX%% bin/parallel_rng_types_unittest%%SUFFIX%% bin/xyz2dcd%%SUFFIX%% include/cp2k/libcp2k.h +include/cp2k/mod_files/ace_nlist.mod +include/cp2k/mod_files/ace_wrapper.mod include/cp2k/mod_files/admm_dm_methods.mod include/cp2k/mod_files/admm_dm_types.mod include/cp2k/mod_files/admm_methods.mod @@ -59,6 +62,7 @@ include/cp2k/mod_files/arnoldi_data_methods.mod include/cp2k/mod_files/arnoldi_geev.mod include/cp2k/mod_files/arnoldi_methods.mod include/cp2k/mod_files/arnoldi_types.mod +include/cp2k/mod_files/arnoldi_vector.mod include/cp2k/mod_files/atom.mod include/cp2k/mod_files/atom_admm_methods.mod include/cp2k/mod_files/atom_basis.mod @@ -146,6 +150,7 @@ include/cp2k/mod_files/cp_control_types.mod include/cp2k/mod_files/cp_control_utils.mod include/cp2k/mod_files/cp_dbcsr_api.mod include/cp2k/mod_files/cp_dbcsr_cholesky.mod +include/cp2k/mod_files/cp_dbcsr_contrib.mod include/cp2k/mod_files/cp_dbcsr_cp2k_link.mod include/cp2k/mod_files/cp_dbcsr_diag.mod include/cp2k/mod_files/cp_dbcsr_operations.mod @@ -209,7 +214,6 @@ include/cp2k/mod_files/ct_types.mod include/cp2k/mod_files/cube_utils.mod include/cp2k/mod_files/d3_poly.mod include/cp2k/mod_files/damping_dipole_types.mod -include/cp2k/mod_files/dbcsr_vector.mod include/cp2k/mod_files/dbm_api.mod include/cp2k/mod_files/dbm_tests.mod include/cp2k/mod_files/dbt_allocate_wrap.mod @@ -354,6 +358,7 @@ include/cp2k/mod_files/generic_os_integrals.mod include/cp2k/mod_files/generic_shg_integrals.mod include/cp2k/mod_files/generic_shg_integrals_init.mod include/cp2k/mod_files/geo_opt.mod +include/cp2k/mod_files/gfun.mod include/cp2k/mod_files/glbopt_callback.mod include/cp2k/mod_files/glbopt_history.mod include/cp2k/mod_files/glbopt_input.mod @@ -370,6 +375,7 @@ include/cp2k/mod_files/gopt_param_types.mod include/cp2k/mod_files/graph_methods.mod include/cp2k/mod_files/graph_utils.mod include/cp2k/mod_files/graphcon.mod +include/cp2k/mod_files/greenx_interface.mod include/cp2k/mod_files/grid_api.mod include/cp2k/mod_files/group_dist_types.mod include/cp2k/mod_files/grrm_utils.mod @@ -380,6 +386,7 @@ include/cp2k/mod_files/gw_large_cell_gamma.mod include/cp2k/mod_files/gw_main.mod include/cp2k/mod_files/gw_small_cell_full_kp.mod include/cp2k/mod_files/gw_utils.mod +include/cp2k/mod_files/hairy_probes.mod include/cp2k/mod_files/hartree_local_methods.mod include/cp2k/mod_files/hartree_local_types.mod include/cp2k/mod_files/hdf5_wrapper.mod @@ -505,7 +512,6 @@ include/cp2k/mod_files/kpoint_methods.mod include/cp2k/mod_files/kpoint_transitional.mod include/cp2k/mod_files/kpoint_types.mod include/cp2k/mod_files/kpsym.mod -include/cp2k/mod_files/lapack.mod include/cp2k/mod_files/lazy.mod include/cp2k/mod_files/lebedev.mod include/cp2k/mod_files/libcp2k.mod @@ -533,6 +539,7 @@ include/cp2k/mod_files/lri_optimize_ri_basis.mod include/cp2k/mod_files/lri_optimize_ri_basis_types.mod include/cp2k/mod_files/ls_matrix_exp.mod include/cp2k/mod_files/machine.mod +include/cp2k/mod_files/manybody_ace.mod include/cp2k/mod_files/manybody_allegro.mod include/cp2k/mod_files/manybody_deepmd.mod include/cp2k/mod_files/manybody_eam.mod @@ -790,6 +797,8 @@ include/cp2k/mod_files/qs_2nd_kernel_ao.mod include/cp2k/mod_files/qs_active_space_methods.mod include/cp2k/mod_files/qs_active_space_types.mod include/cp2k/mod_files/qs_active_space_utils.mod +include/cp2k/mod_files/qs_apt_fdiff_methods.mod +include/cp2k/mod_files/qs_apt_fdiff_types.mod include/cp2k/mod_files/qs_atomic_block.mod include/cp2k/mod_files/qs_band_structure.mod include/cp2k/mod_files/qs_basis_gradient.mod @@ -1001,10 +1010,6 @@ include/cp2k/mod_files/qs_tddfpt2_stda_utils.mod include/cp2k/mod_files/qs_tddfpt2_subgroups.mod include/cp2k/mod_files/qs_tddfpt2_types.mod include/cp2k/mod_files/qs_tddfpt2_utils.mod -include/cp2k/mod_files/qs_tddfpt_eigensolver.mod -include/cp2k/mod_files/qs_tddfpt_module.mod -include/cp2k/mod_files/qs_tddfpt_types.mod -include/cp2k/mod_files/qs_tddfpt_utils.mod include/cp2k/mod_files/qs_tensors.mod include/cp2k/mod_files/qs_tensors_types.mod include/cp2k/mod_files/qs_update_s_mstruct.mod @@ -1027,6 +1032,8 @@ include/cp2k/mod_files/replica_types.mod include/cp2k/mod_files/response_solver.mod include/cp2k/mod_files/restraint.mod include/cp2k/mod_files/ri_environment_methods.mod +include/cp2k/mod_files/rixs_methods.mod +include/cp2k/mod_files/rixs_types.mod include/cp2k/mod_files/rmsd.mod include/cp2k/mod_files/routine_map.mod include/cp2k/mod_files/rpa_communication.mod @@ -1135,6 +1142,9 @@ include/cp2k/mod_files/tamc_run.mod include/cp2k/mod_files/taper_types.mod include/cp2k/mod_files/task_list_methods.mod include/cp2k/mod_files/task_list_types.mod +include/cp2k/mod_files/tblite_interface.mod +include/cp2k/mod_files/tblite_ks_matrix.mod +include/cp2k/mod_files/tblite_types.mod include/cp2k/mod_files/thermal_region_types.mod include/cp2k/mod_files/thermal_region_utils.mod include/cp2k/mod_files/thermostat_mapping.mod @@ -1259,6 +1269,7 @@ include/cp2k/mod_files/xc_xbr_pbe_lda_hole_t_c_lr.mod include/cp2k/mod_files/xc_xlda_hole_t_c_lr.mod include/cp2k/mod_files/xc_xpbe_hole_t_c_lr.mod include/cp2k/mod_files/xc_xwpbe.mod +include/cp2k/mod_files/xmgrace.mod include/cp2k/mod_files/xray_diffraction.mod include/cp2k/mod_files/xtb_coulomb.mod include/cp2k/mod_files/xtb_eeq.mod @@ -1270,11 +1281,13 @@ include/cp2k/mod_files/xtb_ks_matrix.mod include/cp2k/mod_files/xtb_matrices.mod include/cp2k/mod_files/xtb_parameters.mod include/cp2k/mod_files/xtb_potentials.mod +include/cp2k/mod_files/xtb_qresp.mod include/cp2k/mod_files/xtb_types.mod lib/cmake/cp2k/cp2kConfig.cmake lib/cmake/cp2k/cp2kConfigVersion.cmake lib/cmake/cp2k/cp2kTargets-%%CMAKE_BUILD_TYPE%%.cmake lib/cmake/cp2k/cp2kTargets.cmake +lib/cmake/cp2k/modules/FindACE.cmake lib/cmake/cp2k/modules/FindArmpl.cmake lib/cmake/cp2k/modules/FindAtlas.cmake lib/cmake/cp2k/modules/FindBlas.cmake @@ -1288,28 +1301,25 @@ lib/cmake/cp2k/modules/FindGenericBLAS.cmake lib/cmake/cp2k/modules/FindLapack.cmake lib/cmake/cp2k/modules/FindLibVDWXC.cmake lib/cmake/cp2k/modules/FindLibVORI.cmake -lib/cmake/cp2k/modules/FindLibXC.cmake lib/cmake/cp2k/modules/FindLibXSMM.cmake lib/cmake/cp2k/modules/FindLibint2.cmake lib/cmake/cp2k/modules/FindMKL.cmake -lib/cmake/cp2k/modules/FindMetis.cmake lib/cmake/cp2k/modules/FindNVHPCBlas.cmake lib/cmake/cp2k/modules/FindOpenBLAS.cmake -lib/cmake/cp2k/modules/FindPEXSI.cmake lib/cmake/cp2k/modules/FindPlumed.cmake -lib/cmake/cp2k/modules/FindPtscotch.cmake -lib/cmake/cp2k/modules/FindQuip.cmake lib/cmake/cp2k/modules/FindSCALAPACK.cmake lib/cmake/cp2k/modules/FindSCI.cmake -lib/cmake/cp2k/modules/FindSuperLU.cmake +lib/cmake/cp2k/modules/FindTrexIO.cmake +lib/cmake/cp2k/modules/Findlibsmeagol.cmake lib/cmake/cp2k/modules/Finducc.cmake lib/cmake/cp2k/modules/cp2k_utils.cmake lib/libcp2k.so -lib/libcp2k.so.2025.1 +lib/libcp2k.so.2025.2 libdata/pkgconfig/libcp2k.pc %%DATADIR%%/data/ALL_BASIS_SETS %%DATADIR%%/data/ALL_POTENTIALS %%DATADIR%%/data/AcPP1_POTENTIALS +%%DATADIR%%/data/AcPP2_POTENTIALS %%DATADIR%%/data/Allegro/gra-water-deployed-neq060sp.pth %%DATADIR%%/data/Allegro/si-deployed-neq060dp.pth %%DATADIR%%/data/BASIS_ADMM @@ -1321,6 +1331,7 @@ libdata/pkgconfig/libcp2k.pc %%DATADIR%%/data/BASIS_MINIX %%DATADIR%%/data/BASIS_MOLOPT %%DATADIR%%/data/BASIS_MOLOPT_AcPP1 +%%DATADIR%%/data/BASIS_MOLOPT_AcPP2 %%DATADIR%%/data/BASIS_MOLOPT_LnPP1 %%DATADIR%%/data/BASIS_MOLOPT_LnPP2 %%DATADIR%%/data/BASIS_MOLOPT_PSI @@ -1448,7 +1459,7 @@ libdata/pkgconfig/libcp2k.pc %%DATADIR%%/data/DFTB/scc/zns.spl %%DATADIR%%/data/DFTB/scc/znzn.spl %%DATADIR%%/data/DFTB/uff_table -%%DATADIR%%/data/DeePMD/W.pb +%%DATADIR%%/data/DeePMD/water_dpa2.pth %%DATADIR%%/data/ECP_POTENTIALS %%DATADIR%%/data/ECP_POTENTIALS_pob-TZVP-rev2 %%DATADIR%%/data/EMSL_BASIS_SETS @@ -1494,6 +1505,17 @@ libdata/pkgconfig/libcp2k.pc %%DATADIR%%/data/NNP/bulkH2O-jcp2020-cnnp/nnp-8/scaling.data %%DATADIR%%/data/NNP/bulkH2O-jcp2020-cnnp/nnp-8/weights.001.data %%DATADIR%%/data/NNP/bulkH2O-jcp2020-cnnp/nnp-8/weights.008.data +%%DATADIR%%/data/NNP/protH2OHelium-interaction-nnp/input.nn +%%DATADIR%%/data/NNP/protH2OHelium-interaction-nnp/readme.md +%%DATADIR%%/data/NNP/protH2OHelium-interaction-nnp/scaling.data +%%DATADIR%%/data/NNP/protH2OHelium-interaction-nnp/weights.001.data +%%DATADIR%%/data/NNP/protH2OHelium-interaction-nnp/weights.002.data +%%DATADIR%%/data/NNP/protH2OHelium-interaction-nnp/weights.008.data +%%DATADIR%%/data/NNP/protH2Ocluster-jctc2020-nnp/input.nn +%%DATADIR%%/data/NNP/protH2Ocluster-jctc2020-nnp/readme.md +%%DATADIR%%/data/NNP/protH2Ocluster-jctc2020-nnp/scaling.data +%%DATADIR%%/data/NNP/protH2Ocluster-jctc2020-nnp/weights.001.data +%%DATADIR%%/data/NNP/protH2Ocluster-jctc2020-nnp/weights.008.data %%DATADIR%%/data/NequIP/water-deployed-neq060dp.pth %%DATADIR%%/data/NequIP/water-deployed-neq060sp.pth %%DATADIR%%/data/POTENTIAL diff --git a/science/csvtk/Makefile b/science/csvtk/Makefile index 7932341a584d..e4b2b99739a4 100644 --- a/science/csvtk/Makefile +++ b/science/csvtk/Makefile @@ -1,6 +1,6 @@ PORTNAME= csvtk DISTVERSIONPREFIX= v -DISTVERSION= 0.33.0 +DISTVERSION= 0.34.0 PORTREVISION= 1 CATEGORIES= science diff --git a/science/csvtk/distinfo b/science/csvtk/distinfo index 2baa84299593..0dfce56d9fa9 100644 --- a/science/csvtk/distinfo +++ b/science/csvtk/distinfo @@ -1,7 +1,7 @@ -TIMESTAMP = 1741868386 -SHA256 (go/science_csvtk/csvtk-v0.33.0/v0.33.0.mod) = b5fff90dd2b700db63cca9340ed60790096bd3f0e6650b0e159d9fa860fcc121 -SIZE (go/science_csvtk/csvtk-v0.33.0/v0.33.0.mod) = 2688 -SHA256 (go/science_csvtk/csvtk-v0.33.0/v0.33.0.zip) = 54d692d43c8c6dbd578355c7e810a658b52f68513e6a6246df192e139d6c1f3b -SIZE (go/science_csvtk/csvtk-v0.33.0/v0.33.0.zip) = 2617821 -SHA256 (go/science_csvtk/csvtk-v0.33.0/golang-sys-v0.6.0_GH0.tar.gz) = b4f6d17c7a128f76169964b437cb66b3f2dbf9a33361928ec19dfecf7b03fc54 -SIZE (go/science_csvtk/csvtk-v0.33.0/golang-sys-v0.6.0_GH0.tar.gz) = 1434234 +TIMESTAMP = 1753550609 +SHA256 (go/science_csvtk/csvtk-v0.34.0/v0.34.0.mod) = 485d911da4192efc1aaf72df722990fb897f03cdac18aff77fee199a3dab507f +SIZE (go/science_csvtk/csvtk-v0.34.0/v0.34.0.mod) = 2607 +SHA256 (go/science_csvtk/csvtk-v0.34.0/v0.34.0.zip) = aa1a8825b1c69e507717b825c270d9849234ee21da04f0b58d9f064056f1c971 +SIZE (go/science_csvtk/csvtk-v0.34.0/v0.34.0.zip) = 2656260 +SHA256 (go/science_csvtk/csvtk-v0.34.0/golang-sys-v0.6.0_GH0.tar.gz) = b4f6d17c7a128f76169964b437cb66b3f2dbf9a33361928ec19dfecf7b03fc54 +SIZE (go/science_csvtk/csvtk-v0.34.0/golang-sys-v0.6.0_GH0.tar.gz) = 1434234 diff --git a/science/dakota/Makefile b/science/dakota/Makefile index 1ae5bc137bc7..96e46b04e23b 100644 --- a/science/dakota/Makefile +++ b/science/dakota/Makefile @@ -1,5 +1,5 @@ PORTNAME= dakota -DISTVERSION= 6.21.0 +DISTVERSION= 6.22.0 CATEGORIES= science MASTER_SITES= https://github.com/snl-dakota/dakota/releases/download/v${DISTVERSION}/ DISTNAME= ${PORTNAME}-${DISTVERSION}-public-src-cli @@ -68,6 +68,8 @@ LDFLAGS+= -lexecinfo CONFLICTS_BUILD= dakota # self: picks up some bundled packages from the pre-installed dakota package and then fails to install them +MAKE_ARGS= VERBOSE=1 + post-extract: @${FIND} ${WRKSRC} -name "*.orig" -delete @${ECHO} ${DISTVERSION} > ${WRKSRC}/VERSION # expected by the 'install' target diff --git a/science/dakota/distinfo b/science/dakota/distinfo index 37406ed39d14..34b2e45215fb 100644 --- a/science/dakota/distinfo +++ b/science/dakota/distinfo @@ -1,5 +1,5 @@ -TIMESTAMP = 1743185006 -SHA256 (dakota-6.21.0-public-src-cli.tar.gz) = 7dcf9f93b7bc37a24dee3acda25be280c1a49774e22d53aa1e4b0a60df62ff97 -SIZE (dakota-6.21.0-public-src-cli.tar.gz) = 156415576 +TIMESTAMP = 1749739745 +SHA256 (dakota-6.22.0-public-src-cli.tar.gz) = 31d76636e4d22e6e847de3ada8cbf35a6e6c2c805ccd8677c8c4210f0ff53e07 +SIZE (dakota-6.22.0-public-src-cli.tar.gz) = 139890358 SHA256 (stan-dev-math-v2.18.0_GH0.tar.gz) = 53fbce2b28aea76695af7a91f51fdd356367153fc42b3573e2b91e6586eca91d SIZE (stan-dev-math-v2.18.0_GH0.tar.gz) = 17528084 diff --git a/science/dakota/files/fake-c++.sh b/science/dakota/files/fake-c++.sh index 743abbb92474..64e0279da6dc 100755 --- a/science/dakota/files/fake-c++.sh +++ b/science/dakota/files/fake-c++.sh @@ -1,4 +1,4 @@ #!/bin/sh -c++ "$@" -std=c++14 +c++ "$@" -std=c++17 diff --git a/science/dakota/files/patch-cmake_InstallUnixSOs.cmake.in b/science/dakota/files/patch-cmake_InstallUnixSOs.cmake.in new file mode 100644 index 000000000000..1e3a1d74203f --- /dev/null +++ b/science/dakota/files/patch-cmake_InstallUnixSOs.cmake.in @@ -0,0 +1,16 @@ +--- cmake/InstallUnixSOs.cmake.in.orig 2025-05-08 16:25:16 UTC ++++ cmake/InstallUnixSOs.cmake.in +@@ -4,6 +4,7 @@ + # NOTE: This script will only work for make install from top of build tree + # TODO: Review string quoting conventions and test with spaces in filename + ++if (FALSE) + + execute_process(COMMAND chrpath -v + OUTPUT_QUIET +@@ -78,3 +79,5 @@ endforeach() + dakota_install_dll("${dakota_dll}") + endif() + endforeach() ++ ++endif() diff --git a/science/dakota/files/patch-src_PluginInterface.hpp b/science/dakota/files/patch-src_PluginInterface.hpp new file mode 100644 index 000000000000..6e002abc8086 --- /dev/null +++ b/science/dakota/files/patch-src_PluginInterface.hpp @@ -0,0 +1,22 @@ +# https://github.com/snl-dakota/dakota/pull/195 + +--- src/PluginInterface.hpp.orig 2025-06-14 09:02:26 UTC ++++ src/PluginInterface.hpp +@@ -13,7 +13,7 @@ + #include "ApplicationInterface.hpp" + #include "plugins/DakotaInterfaceAPI.hpp" + +-#include <boost/shared_ptr.hpp> // blech ++#include <memory> + + + namespace Dakota { +@@ -54,7 +54,7 @@ class PluginInterface: public ApplicationInterface (pr + String pluginPath; + + /// the interface class loaded via plugin +- boost::shared_ptr<DakotaPlugins::DakotaInterfaceAPI> pluginInterface; ++ std::shared_ptr<DakotaPlugins::DakotaInterfaceAPI> pluginInterface; + + + /// list of drivers to perform core simulation mappings (can diff --git a/science/dakota/pkg-plist b/science/dakota/pkg-plist index 6462bd1b85e3..d9146bcf1ef3 100644 --- a/science/dakota/pkg-plist +++ b/science/dakota/pkg-plist @@ -131,6 +131,7 @@ include/DDaceZeroDivide.h include/DLSfuncs.hpp include/DLSolver.hpp include/DOTOptimizer.hpp +include/DakotaAccumulators.hpp include/DakotaActiveSet.hpp include/DakotaAnalyzer.hpp include/DakotaApproximation.hpp @@ -149,6 +150,7 @@ include/DakotaNonD.hpp include/DakotaOptimizer.hpp include/DakotaPStudyDACE.hpp include/DakotaResponse.hpp +include/DakotaResponseContainer.hpp include/DakotaSurrogates.hpp include/DakotaSurrogatesGP.hpp include/DakotaSurrogatesPoly.hpp @@ -427,6 +429,7 @@ include/MDesign.hpp include/MDriver.hpp include/MEvaluationFunctor.hpp include/MEvaluator.hpp +include/MFSolutionData.hpp include/MFitnessRecord.hpp include/MGeneticAlgorithm.hpp include/MGeneticAlgorithmEvaluator.hpp @@ -665,15 +668,6 @@ include/MainEffectsAnalyzer3.h include/MainEffectsConverter.h include/MainEffectsExcelOutput.h include/Makefile.export.Dakota -include/Makefile.export.ROL -include/Makefile.export.Teuchos -include/Makefile.export.TeuchosComm -include/Makefile.export.TeuchosCore -include/Makefile.export.TeuchosNumerics -include/Makefile.export.TeuchosParameterList -include/Makefile.export.TeuchosParser -include/Makefile.export.TeuchosRemainder -include/Makefile.export.Trilinos include/ManagedUtils.hpp include/MarginalsCorrDistribution.hpp include/Mars.h @@ -828,6 +822,7 @@ include/NullPostProcessor.hpp.inl include/NullSelector.hpp include/NullSelector.hpp.inl include/NumericGenOrthogPolynomial.hpp +include/OED_SplitComm.hpp include/OMPSolver.hpp include/OPT++_config.h include/ObjectiveFunctionInfo.hpp @@ -907,18 +902,22 @@ include/ProgramOptions.hpp include/ProjectOrthogPolyApproximation.hpp include/PseudoRandomTestsOnly.h include/Pybind11Interface.hpp -include/PythonInterface.hpp include/QMEApproximation.hpp include/QUESOImpl.hpp +include/ROL2_EnumMap.hpp +include/ROL2_Enumeration.hpp include/ROLOptimizer.hpp include/ROL_AbsoluteValue.hpp include/ROL_AffineTransformConstraint.hpp +include/ROL_AffineTransformConstraint_Def.hpp include/ROL_AffineTransformObjective.hpp +include/ROL_AffineTransformObjective_Def.hpp include/ROL_Algorithm.hpp include/ROL_AlmostSureConstraint.hpp include/ROL_Arcsine.hpp include/ROL_AtomVector.hpp include/ROL_AugmentedLagrangian.hpp +include/ROL_AugmentedLagrangianObjective.hpp include/ROL_AugmentedLagrangianStep.hpp include/ROL_AugmentedLagrangian_SimOpt.hpp include/ROL_AugmentedSystemOperator.hpp @@ -927,12 +926,16 @@ include/ROL_BLAS.hpp include/ROL_BPOE.hpp include/ROL_BVP.hpp include/ROL_BackTracking.hpp +include/ROL_BackTracking_U.hpp +include/ROL_BallIndicatorObjective.hpp include/ROL_BarzilaiBorwein.hpp include/ROL_BatchManager.hpp include/ROL_BatchStdVector.hpp include/ROL_Beale.hpp include/ROL_Beta.hpp +include/ROL_BiCGSTAB.hpp include/ROL_BinaryConstraint.hpp +include/ROL_BinaryConstraint_Def.hpp include/ROL_BinaryFunctions.hpp include/ROL_Bisection.hpp include/ROL_BisectionScalarMinimization.hpp @@ -943,53 +946,78 @@ include/ROL_BlockOperator2Diagonal.hpp include/ROL_BlockOperator2UnitLower.hpp include/ROL_BlockOperator2UnitUpper.hpp include/ROL_BoundConstraint.hpp +include/ROL_BoundConstraint_Def.hpp include/ROL_BoundConstraint_Partitioned.hpp include/ROL_BoundConstraint_SimOpt.hpp include/ROL_BoundFletcher.hpp include/ROL_BoundToConstraint.hpp +include/ROL_BoundToConstraint_Def.hpp include/ROL_Bounds.hpp +include/ROL_Bounds_Def.hpp include/ROL_Bracketing.hpp include/ROL_Brents.hpp +include/ROL_BrentsProjection.hpp +include/ROL_BrentsProjection_Def.hpp include/ROL_BrentsScalarMinimization.hpp include/ROL_Bundle.hpp include/ROL_BundleStatusTest.hpp include/ROL_BundleStep.hpp include/ROL_Bundle_AS.hpp include/ROL_Bundle_TT.hpp +include/ROL_Bundle_U.hpp +include/ROL_Bundle_U_AS.hpp +include/ROL_Bundle_U_AS_Def.hpp +include/ROL_Bundle_U_Def.hpp +include/ROL_Bundle_U_TT.hpp +include/ROL_Bundle_U_TT_Def.hpp +include/ROL_CArrayVector.hpp include/ROL_CDFObjective.hpp include/ROL_CVaR.hpp include/ROL_Cantilever.hpp include/ROL_CantileverBeam.hpp include/ROL_Cauchy.hpp include/ROL_CauchyPoint.hpp +include/ROL_CauchyPoint_U.hpp +include/ROL_ChainRuleConstraint.hpp +include/ROL_ChainRuleObjective.hpp include/ROL_ChebyshevSpectral.hpp include/ROL_Chi2Divergence.hpp include/ROL_CoherentEntropicRisk.hpp include/ROL_ColemanLiModel.hpp include/ROL_CombinedStatusTest.hpp include/ROL_CompositeConstraint_SimOpt.hpp +include/ROL_CompositeConstraint_SimOpt_Def.hpp include/ROL_CompositeObjective.hpp +include/ROL_CompositeObjective_Def.hpp include/ROL_CompositeObjective_SimOpt.hpp include/ROL_CompositeStep.hpp include/ROL_ConicApproximationModel.hpp include/ROL_ConjugateGradients.hpp include/ROL_ConjugateResiduals.hpp include/ROL_Constraint.hpp +include/ROL_ConstraintAssembler.hpp +include/ROL_ConstraintAssembler_Def.hpp include/ROL_ConstraintDef.hpp include/ROL_ConstraintFromObjective.hpp +include/ROL_ConstraintFromObjective_Def.hpp include/ROL_ConstraintManager.hpp include/ROL_ConstraintStatusTest.hpp include/ROL_Constraint_CheckInterface.hpp include/ROL_Constraint_DynamicState.hpp include/ROL_Constraint_Partitioned.hpp +include/ROL_Constraint_Partitioned_Def.hpp include/ROL_Constraint_SerialSimOpt.hpp include/ROL_Constraint_SimOpt.hpp -include/ROL_Constraint_State.hpp include/ROL_Constraint_TimeSimOpt.hpp include/ROL_ConvexCombinationRiskMeasure.hpp include/ROL_Cubic.hpp include/ROL_CubicInterp.hpp +include/ROL_CubicInterp_U.hpp include/ROL_CylinderHead.hpp +include/ROL_DaiFletcherProjection.hpp +include/ROL_DaiFletcherProjection_Def.hpp +include/ROL_DescentDirection_U.hpp +include/ROL_DescentDirection_U_Factory.hpp include/ROL_DeviationMeasureFactory.hpp include/ROL_DeviationMeasureInfo.hpp include/ROL_DiagonalOperator.hpp @@ -998,8 +1026,14 @@ include/ROL_Dirac.hpp include/ROL_Distribution.hpp include/ROL_DistributionFactory.hpp include/ROL_DogLeg.hpp +include/ROL_DogLeg_U.hpp include/ROL_DoubleDogLeg.hpp +include/ROL_DoubleDogLeg_U.hpp +include/ROL_DouglasRachfordProjection.hpp +include/ROL_DouglasRachfordProjection_Def.hpp include/ROL_DyadicOperator.hpp +include/ROL_DykstraProjection.hpp +include/ROL_DykstraProjection_Def.hpp include/ROL_DynamicConstraint.hpp include/ROL_DynamicConstraintCheck.hpp include/ROL_DynamicConstraint_CheckInterface.hpp @@ -1010,6 +1044,10 @@ include/ROL_DynamicObjectiveCheck.hpp include/ROL_DynamicObjective_CheckInterface.hpp include/ROL_DynamicTrackingFEMObjective.hpp include/ROL_DynamicTrackingObjective.hpp +include/ROL_ElasticLinearConstraint.hpp +include/ROL_ElasticLinearConstraint_Def.hpp +include/ROL_ElasticObjective.hpp +include/ROL_ElasticObjective_Def.hpp include/ROL_ElementwiseVector.hpp include/ROL_Elementwise_Function.hpp include/ROL_Elementwise_Reduce.hpp @@ -1021,7 +1059,6 @@ include/ROL_ExpectationQuadDeviation.hpp include/ROL_ExpectationQuadError.hpp include/ROL_ExpectationQuadRegret.hpp include/ROL_ExpectationQuadRisk.hpp -include/ROL_ExplicitLinearConstraint.hpp include/ROL_Exponential.hpp include/ROL_FDivergence.hpp include/ROL_Fejer2Quadrature.hpp @@ -1029,6 +1066,10 @@ include/ROL_FiniteDifference.hpp include/ROL_FiniteDifferenceDef.hpp include/ROL_Fletcher.hpp include/ROL_FletcherBase.hpp +include/ROL_FletcherObjectiveBase.hpp +include/ROL_FletcherObjectiveBase_Def.hpp +include/ROL_FletcherObjectiveE.hpp +include/ROL_FletcherObjectiveE_Def.hpp include/ROL_FletcherStatusTest.hpp include/ROL_FletcherStep.hpp include/ROL_FreudensteinRoth.hpp @@ -1041,15 +1082,19 @@ include/ROL_GaussChebyshev3Quadrature.hpp include/ROL_GaussLegendreQuadrature.hpp include/ROL_Gaussian.hpp include/ROL_GenMoreauYosidaCVaR.hpp +include/ROL_GenericFunction.hpp +include/ROL_GenericUnaryFunction.hpp include/ROL_GetTestProblems.hpp include/ROL_GoldenSection.hpp include/ROL_GoldenSectionScalarMinimization.hpp include/ROL_GradientStep.hpp +include/ROL_Gradient_U.hpp include/ROL_Gumbel.hpp include/ROL_HMCR.hpp include/ROL_HS1.hpp include/ROL_HS14.hpp include/ROL_HS2.hpp +include/ROL_HS21.hpp include/ROL_HS24.hpp include/ROL_HS25.hpp include/ROL_HS28.hpp @@ -1059,6 +1104,7 @@ include/ROL_HS32.hpp include/ROL_HS38.hpp include/ROL_HS39.hpp include/ROL_HS4.hpp +include/ROL_HS41.hpp include/ROL_HS42.hpp include/ROL_HS45.hpp include/ROL_HS48.hpp @@ -1067,6 +1113,9 @@ include/ROL_HS5.hpp include/ROL_HS50.hpp include/ROL_HS51.hpp include/ROL_HS52.hpp +include/ROL_HS53.hpp +include/ROL_HS55.hpp +include/ROL_HS63.hpp include/ROL_HS9.hpp include/ROL_HagerZhangBracketing.hpp include/ROL_HelperFunctions.hpp @@ -1074,10 +1123,12 @@ include/ROL_HouseholderReflector.hpp include/ROL_IdentityOperator.hpp include/ROL_InactiveSetVector.hpp include/ROL_InteriorPoint.hpp +include/ROL_InteriorPointObjective.hpp include/ROL_InteriorPointPenalty.hpp include/ROL_InteriorPointPrimalDualResidual.hpp include/ROL_InteriorPointStep.hpp include/ROL_IterationScaling.hpp +include/ROL_IterationScaling_U.hpp include/ROL_KLDivergence.hpp include/ROL_KelleySachsModel.hpp include/ROL_Krylov.hpp @@ -1092,11 +1143,17 @@ include/ROL_LinMoreModel.hpp include/ROL_LineSearch.hpp include/ROL_LineSearchFactory.hpp include/ROL_LineSearchStep.hpp +include/ROL_LineSearch_U.hpp +include/ROL_LineSearch_U_Factory.hpp +include/ROL_LineSearch_U_Types.hpp include/ROL_LinearAlgebra.hpp include/ROL_LinearCombinationObjective.hpp +include/ROL_LinearCombinationObjective_Def.hpp include/ROL_LinearCombinationObjective_SimOpt.hpp include/ROL_LinearConstraint.hpp +include/ROL_LinearConstraint_Def.hpp include/ROL_LinearObjective.hpp +include/ROL_LinearObjective_Def.hpp include/ROL_LinearObjective_SimOpt.hpp include/ROL_LinearOperator.hpp include/ROL_LinearOperatorFromConstraint.hpp @@ -1108,11 +1165,16 @@ include/ROL_LogExponentialQuadrangle.hpp include/ROL_LogQuantileQuadrangle.hpp include/ROL_Logistic.hpp include/ROL_LowerBoundToConstraint.hpp +include/ROL_LowerBoundToConstraint_Def.hpp include/ROL_MINRES.hpp include/ROL_MeanDeviation.hpp include/ROL_MeanDeviationFromTarget.hpp include/ROL_MeanSemiDeviation.hpp include/ROL_MeanSemiDeviationFromTarget.hpp +include/ROL_MeanValueConstraint.hpp +include/ROL_MeanValueConstraint_Def.hpp +include/ROL_MeanValueObjective.hpp +include/ROL_MeanValueObjective_Def.hpp include/ROL_MeanVariance.hpp include/ROL_MeanVarianceFromTarget.hpp include/ROL_MeanVarianceQuadrangle.hpp @@ -1123,25 +1185,88 @@ include/ROL_Minimax3.hpp include/ROL_MixedCVaR.hpp include/ROL_MomentObjective.hpp include/ROL_MonteCarloGenerator.hpp +include/ROL_MonteCarloGeneratorDef.hpp include/ROL_MoreauYosidaCVaR.hpp +include/ROL_MoreauYosidaObjective.hpp include/ROL_MoreauYosidaPenalty.hpp include/ROL_MoreauYosidaPenaltyStep.hpp +include/ROL_MultiVector.hpp +include/ROL_MultiVectorDefault.hpp +include/ROL_NewConstraintManager.hpp +include/ROL_NewConstraintManager_Def.hpp include/ROL_NewtonKrylovStep.hpp +include/ROL_NewtonKrylov_U.hpp include/ROL_NewtonStep.hpp +include/ROL_Newton_U.hpp include/ROL_NonlinearCG.hpp include/ROL_NonlinearCGStep.hpp +include/ROL_NonlinearCG_U.hpp include/ROL_NonlinearLeastSquaresObjective.hpp +include/ROL_NonlinearLeastSquaresObjective_Def.hpp include/ROL_NonlinearLeastSquaresObjective_Dynamic.hpp -include/ROL_NonlinearLeastSquaresObjective_SimOpt.hpp include/ROL_NullOperator.hpp include/ROL_NullSpaceOperator.hpp +include/ROL_OED_A_HetObjective.hpp +include/ROL_OED_A_HetObjective_Def.hpp +include/ROL_OED_A_HomObjective.hpp +include/ROL_OED_A_HomObjective_Def.hpp +include/ROL_OED_BilinearConstraint.hpp +include/ROL_OED_BilinearConstraint_Def.hpp +include/ROL_OED_C_HetObjective.hpp +include/ROL_OED_C_HetObjective_Def.hpp +include/ROL_OED_C_HomObjective.hpp +include/ROL_OED_C_HomObjective_Def.hpp +include/ROL_OED_D_HetObjective.hpp +include/ROL_OED_D_HetObjective_Def.hpp +include/ROL_OED_D_HomObjective.hpp +include/ROL_OED_D_HomObjective_Def.hpp +include/ROL_OED_DoubleWellPenalty.hpp +include/ROL_OED_DoubleWellPenalty_Def.hpp +include/ROL_OED_Factors.hpp +include/ROL_OED_Factors_Def.hpp +include/ROL_OED_Factory.hpp +include/ROL_OED_Factory_Def.hpp +include/ROL_OED_HetObjectiveBase.hpp +include/ROL_OED_HetObjectiveBase_Def.hpp +include/ROL_OED_HomObjectiveBase.hpp +include/ROL_OED_HomObjectiveBase_Def.hpp +include/ROL_OED_I_HetObjective.hpp +include/ROL_OED_I_HetObjective_Def.hpp +include/ROL_OED_I_HomObjective.hpp +include/ROL_OED_I_HomObjective_Def.hpp +include/ROL_OED_Itrace_HetObjective.hpp +include/ROL_OED_Itrace_HetObjective_Def.hpp +include/ROL_OED_Itrace_HomObjective.hpp +include/ROL_OED_Itrace_HomObjective_Def.hpp +include/ROL_OED_L1Penalty.hpp +include/ROL_OED_L1Penalty_Def.hpp +include/ROL_OED_LinearObjective.hpp +include/ROL_OED_LinearObjective_Def.hpp +include/ROL_OED_MomentOperator.hpp +include/ROL_OED_MomentOperator_Def.hpp +include/ROL_OED_Noise.hpp +include/ROL_OED_ProbabilityConstraint.hpp +include/ROL_OED_ProbabilityConstraint_Def.hpp +include/ROL_OED_ProfiledClass.hpp +include/ROL_OED_QuadraticObjective.hpp +include/ROL_OED_QuadraticObjective_Def.hpp +include/ROL_OED_Radamacher.hpp +include/ROL_OED_Radamacher_Def.hpp +include/ROL_OED_StdMomentOperator.hpp +include/ROL_OED_StdMomentOperator_Def.hpp +include/ROL_OED_Timer.hpp +include/ROL_OED_Timer_Def.hpp +include/ROL_OED_TraceSampler.hpp +include/ROL_OED_TraceSampler_Def.hpp include/ROL_Objective.hpp include/ROL_ObjectiveDef.hpp include/ROL_ObjectiveFromBoundConstraint.hpp include/ROL_ObjectiveFromConstraint.hpp +include/ROL_ObjectiveFromConstraint_Def.hpp include/ROL_ObjectiveMMA.hpp include/ROL_Objective_CheckInterface.hpp include/ROL_Objective_FSsolver.hpp +include/ROL_Objective_FSsolver_Def.hpp include/ROL_Objective_SerialSimOpt.hpp include/ROL_Objective_SimOpt.hpp include/ROL_Objective_SimOpt_CheckInterfaceDef.hpp @@ -1156,16 +1281,22 @@ include/ROL_PH_RegretObjective.hpp include/ROL_PH_RiskObjective.hpp include/ROL_PH_StatusTest.hpp include/ROL_PH_bPOEObjective.hpp +include/ROL_PQNObjective.hpp +include/ROL_PQNObjective_Def.hpp include/ROL_Parabolic.hpp include/ROL_ParaboloidCircle.hpp include/ROL_ParameterList.hpp include/ROL_ParameterListConverters.hpp include/ROL_PartitionedVector.hpp include/ROL_PathBasedTargetLevel.hpp +include/ROL_PathBasedTargetLevel_U.hpp include/ROL_PlusFunction.hpp include/ROL_PointwiseCDFObjective.hpp include/ROL_PoissonControl.hpp include/ROL_PoissonInversion.hpp +include/ROL_PolyhedralProjection.hpp +include/ROL_PolyhedralProjectionFactory.hpp +include/ROL_PolyhedralProjection_Def.hpp include/ROL_PositiveFunction.hpp include/ROL_Powell.hpp include/ROL_PrimalDualActiveSetStep.hpp @@ -1178,6 +1309,8 @@ include/ROL_PrimalDualSystemStep.hpp include/ROL_ProbabilityFactory.hpp include/ROL_ProbabilityInfo.hpp include/ROL_ProbabilityVector.hpp +include/ROL_Problem.hpp +include/ROL_Problem_Def.hpp include/ROL_ProfiledVector.hpp include/ROL_ProgressiveHedging.hpp include/ROL_ProjectedNewtonKrylovStep.hpp @@ -1185,29 +1318,42 @@ include/ROL_ProjectedNewtonStep.hpp include/ROL_ProjectedSecantStep.hpp include/ROL_Ptr.hpp include/ROL_QuadraticObjective.hpp +include/ROL_QuadraticObjective_Def.hpp include/ROL_QuadraticPenalty.hpp include/ROL_QuadraticPenalty_SimOpt.hpp include/ROL_Quadrature1D.hpp include/ROL_QuantileQuadrangle.hpp include/ROL_QuantileRadius.hpp include/ROL_Quartic.hpp +include/ROL_QuasiNewton_U.hpp include/ROL_RaisedCosine.hpp include/ROL_RandVarFunctional.hpp include/ROL_RandVarFunctionalFactory.hpp include/ROL_RandVarFunctionalInfo.hpp include/ROL_RandomVector.hpp include/ROL_RangeSpaceOperator.hpp +include/ROL_ReduceLinearConstraint.hpp +include/ROL_ReduceLinearConstraint_Def.hpp include/ROL_ReducedDynamicObjective.hpp +include/ROL_ReducedDynamicStationaryControlsObjective.hpp +include/ROL_ReducedLinearConstraint.hpp +include/ROL_ReducedLinearConstraint_Def.hpp include/ROL_Reduced_AugmentedLagrangian_SimOpt.hpp include/ROL_Reduced_Constraint_SimOpt.hpp +include/ROL_Reduced_Constraint_SimOpt_Def.hpp include/ROL_Reduced_Objective_SimOpt.hpp +include/ROL_Reduced_Objective_SimOpt_Def.hpp include/ROL_RegressionError.hpp include/ROL_RegretMeasureFactory.hpp include/ROL_RegretMeasureInfo.hpp +include/ROL_RiddersProjection.hpp +include/ROL_RiddersProjection_Def.hpp include/ROL_RieszVector.hpp include/ROL_RiskBoundConstraint.hpp include/ROL_RiskLessConstraint.hpp +include/ROL_RiskLessConstraint_Def.hpp include/ROL_RiskLessObjective.hpp +include/ROL_RiskLessObjective_Def.hpp include/ROL_RiskMeasure.hpp include/ROL_RiskMeasureFactory.hpp include/ROL_RiskMeasureInfo.hpp @@ -1215,19 +1361,26 @@ include/ROL_RiskNeutralConstraint.hpp include/ROL_RiskNeutralObjective.hpp include/ROL_RiskVector.hpp include/ROL_Rosenbrock.hpp +include/ROL_SPGTrustRegion_U.hpp include/ROL_SROMGenerator.hpp include/ROL_SROMVector.hpp include/ROL_SampleGenerator.hpp include/ROL_SampledScalar.hpp include/ROL_SampledVector.hpp +include/ROL_ScalarController.hpp +include/ROL_ScalarController_Def.hpp include/ROL_ScalarFunction.hpp include/ROL_ScalarLinearConstraint.hpp +include/ROL_ScalarLinearConstraint_Def.hpp include/ROL_ScalarMinimization.hpp include/ROL_ScalarMinimizationLineSearch.hpp +include/ROL_ScalarMinimizationLineSearch_U.hpp include/ROL_ScalarMinimizationStatusTest.hpp include/ROL_ScalarMinimizationTest.hpp include/ROL_ScalarMinimizationTest01.hpp include/ROL_ScalarTraits.hpp +include/ROL_ScaledObjective.hpp +include/ROL_ScaledObjective_Def.hpp include/ROL_ScaledStdVector.hpp include/ROL_ScaledVector.hpp include/ROL_SchurComplement.hpp @@ -1236,67 +1389,172 @@ include/ROL_SecantFactory.hpp include/ROL_SecantStep.hpp include/ROL_SecondOrderCVaR.hpp include/ROL_SemismoothNewtonDualModel.hpp +include/ROL_SemismoothNewtonProjection.hpp +include/ROL_SemismoothNewtonProjection_Def.hpp include/ROL_SerialConstraint.hpp include/ROL_SerialFunction.hpp include/ROL_SerialObjective.hpp -include/ROL_SimController.hpp +include/ROL_SimConstraint.hpp +include/ROL_SimConstraint_Def.hpp include/ROL_SimpleEqConstrained.hpp include/ROL_SimulatedBoundConstraint.hpp include/ROL_SimulatedConstraint.hpp include/ROL_SimulatedObjective.hpp include/ROL_SimulatedObjectiveCVaR.hpp include/ROL_SimulatedVector.hpp +include/ROL_SingletonTeuchosBatchManager.hpp include/ROL_SingletonVector.hpp include/ROL_Sketch.hpp +include/ROL_SlacklessConstraint.hpp +include/ROL_SlacklessConstraint_Def.hpp include/ROL_SlacklessObjective.hpp +include/ROL_SlacklessObjective_Def.hpp include/ROL_Smale.hpp include/ROL_SmoothedPOE.hpp include/ROL_SmoothedWorstCaseQuadrangle.hpp +include/ROL_Solver.hpp +include/ROL_Solver_Def.hpp include/ROL_SpectralRisk.hpp include/ROL_StatusTest.hpp include/ROL_StatusTestFactory.hpp include/ROL_StdArray.hpp include/ROL_StdBoundConstraint.hpp +include/ROL_StdBoundConstraint_Def.hpp include/ROL_StdConstraint.hpp +include/ROL_StdConstraint_Def.hpp include/ROL_StdLinearOperator.hpp include/ROL_StdLinearOperatorFactory.hpp include/ROL_StdObjective.hpp +include/ROL_StdObjective_Def.hpp +include/ROL_StdTeuchosBatchManager.hpp include/ROL_StdTridiagonalOperator.hpp include/ROL_StdVector.hpp include/ROL_Step.hpp include/ROL_StepFactory.hpp include/ROL_StochasticConstraint.hpp include/ROL_StochasticObjective.hpp +include/ROL_StochasticProblem.hpp +include/ROL_StochasticProblem_Def.hpp include/ROL_Stream.hpp include/ROL_SumOfSquares.hpp include/ROL_TestProblem.hpp +include/ROL_TeuchosBatchManager.hpp +include/ROL_TeuchosVector.hpp +include/ROL_Teuchos_Constraint.hpp +include/ROL_Teuchos_LinearOperator.hpp +include/ROL_Teuchos_Objective.hpp include/ROL_TimeStamp.hpp include/ROL_Triangle.hpp include/ROL_TruncatedCG.hpp +include/ROL_TruncatedCG_U.hpp include/ROL_TruncatedExponential.hpp include/ROL_TruncatedGaussian.hpp include/ROL_TruncatedMeanQuadrangle.hpp include/ROL_TrustRegion.hpp include/ROL_TrustRegionFactory.hpp include/ROL_TrustRegionModel.hpp +include/ROL_TrustRegionModel_U.hpp include/ROL_TrustRegionStep.hpp include/ROL_TrustRegionTypes.hpp +include/ROL_TrustRegionUtilities.hpp +include/ROL_TrustRegion_U.hpp +include/ROL_TrustRegion_U_Factory.hpp +include/ROL_TrustRegion_U_Types.hpp +include/ROL_TypeBIndicatorObjective.hpp +include/ROL_TypeB_Algorithm.hpp +include/ROL_TypeB_AlgorithmFactory.hpp +include/ROL_TypeB_Algorithm_Def.hpp +include/ROL_TypeB_ColemanLiAlgorithm.hpp +include/ROL_TypeB_ColemanLiAlgorithm_Def.hpp +include/ROL_TypeB_GradientAlgorithm.hpp +include/ROL_TypeB_GradientAlgorithm_Def.hpp +include/ROL_TypeB_InteriorPointAlgorithm.hpp +include/ROL_TypeB_InteriorPointAlgorithm_Def.hpp +include/ROL_TypeB_KelleySachsAlgorithm.hpp +include/ROL_TypeB_KelleySachsAlgorithm_Def.hpp +include/ROL_TypeB_LSecantBAlgorithm.hpp +include/ROL_TypeB_LSecantBAlgorithm_Def.hpp +include/ROL_TypeB_LinMoreAlgorithm.hpp +include/ROL_TypeB_LinMoreAlgorithm_Def.hpp +include/ROL_TypeB_MoreauYosidaAlgorithm.hpp +include/ROL_TypeB_MoreauYosidaAlgorithm_Def.hpp +include/ROL_TypeB_NewtonKrylovAlgorithm.hpp +include/ROL_TypeB_NewtonKrylovAlgorithm_Def.hpp +include/ROL_TypeB_PrimalDualActiveSetAlgorithm.hpp +include/ROL_TypeB_PrimalDualActiveSetAlgorithm_Def.hpp +include/ROL_TypeB_QuasiNewtonAlgorithm.hpp +include/ROL_TypeB_QuasiNewtonAlgorithm_Def.hpp +include/ROL_TypeB_SpectralGradientAlgorithm.hpp +include/ROL_TypeB_SpectralGradientAlgorithm_Def.hpp +include/ROL_TypeB_TrustRegionSPGAlgorithm.hpp +include/ROL_TypeB_TrustRegionSPGAlgorithm_Def.hpp +include/ROL_TypeE_Algorithm.hpp +include/ROL_TypeE_AlgorithmFactory.hpp +include/ROL_TypeE_Algorithm_Def.hpp +include/ROL_TypeE_AugmentedLagrangianAlgorithm.hpp +include/ROL_TypeE_AugmentedLagrangianAlgorithm_Def.hpp +include/ROL_TypeE_CompositeStepAlgorithm.hpp +include/ROL_TypeE_CompositeStepAlgorithm_Def.hpp +include/ROL_TypeE_FletcherAlgorithm.hpp +include/ROL_TypeE_FletcherAlgorithm_Def.hpp +include/ROL_TypeE_StabilizedLCLAlgorithm.hpp +include/ROL_TypeE_StabilizedLCLAlgorithm_Def.hpp +include/ROL_TypeG_Algorithm.hpp +include/ROL_TypeG_AlgorithmFactory.hpp +include/ROL_TypeG_Algorithm_Def.hpp +include/ROL_TypeG_AugmentedLagrangianAlgorithm.hpp +include/ROL_TypeG_AugmentedLagrangianAlgorithm_Def.hpp +include/ROL_TypeG_InteriorPointAlgorithm.hpp +include/ROL_TypeG_InteriorPointAlgorithm_Def.hpp +include/ROL_TypeG_MoreauYosidaAlgorithm.hpp +include/ROL_TypeG_MoreauYosidaAlgorithm_Def.hpp +include/ROL_TypeG_StabilizedLCLAlgorithm.hpp +include/ROL_TypeG_StabilizedLCLAlgorithm_Def.hpp +include/ROL_TypeP_Algorithm.hpp +include/ROL_TypeP_AlgorithmFactory.hpp +include/ROL_TypeP_Algorithm_Def.hpp +include/ROL_TypeP_InexactNewtonAlgorithm.hpp +include/ROL_TypeP_InexactNewtonAlgorithm_Def.hpp +include/ROL_TypeP_ProxGradientAlgorithm.hpp +include/ROL_TypeP_ProxGradientAlgorithm_Def.hpp +include/ROL_TypeP_QuasiNewtonAlgorithm.hpp +include/ROL_TypeP_QuasiNewtonAlgorithm_Def.hpp +include/ROL_TypeP_SpectralGradientAlgorithm.hpp +include/ROL_TypeP_SpectralGradientAlgorithm_Def.hpp +include/ROL_TypeP_TrustRegionAlgorithm.hpp +include/ROL_TypeP_TrustRegionAlgorithm_Def.hpp +include/ROL_TypeP_iPianoAlgorithm.hpp +include/ROL_TypeP_iPianoAlgorithm_Def.hpp +include/ROL_TypeU_Algorithm.hpp +include/ROL_TypeU_AlgorithmFactory.hpp +include/ROL_TypeU_Algorithm_Def.hpp +include/ROL_TypeU_BundleAlgorithm.hpp +include/ROL_TypeU_BundleAlgorithm_Def.hpp +include/ROL_TypeU_LineSearchAlgorithm.hpp +include/ROL_TypeU_LineSearchAlgorithm_Def.hpp +include/ROL_TypeU_TrustRegionAlgorithm.hpp +include/ROL_TypeU_TrustRegionAlgorithm_Def.hpp include/ROL_Types.hpp include/ROL_UnaryFunctions.hpp include/ROL_Uniform.hpp +include/ROL_UpdateType.hpp include/ROL_UpperBoundToConstraint.hpp +include/ROL_UpperBoundToConstraint_Def.hpp include/ROL_UserInputGenerator.hpp include/ROL_ValidParameters.hpp include/ROL_ValidateFunction.hpp include/ROL_ValidateFunctionDef.hpp include/ROL_Vector.hpp include/ROL_VectorClone.hpp +include/ROL_VectorController.hpp +include/ROL_VectorController_Def.hpp include/ROL_VectorNorms.hpp include/ROL_VectorWorkspace.hpp include/ROL_Vector_SimOpt.hpp include/ROL_WrappedVector.hpp include/ROL_Zakharov.hpp include/ROL_config.h +include/ROL_l1Objective.hpp include/ROL_lBFGS.hpp include/ROL_lDFP.hpp include/ROL_lSR1.hpp @@ -1422,6 +1680,7 @@ include/TensorProductDriver.hpp include/TestDriverInterface.hpp include/TeuchosCore_ConfigDefs.hpp include/TeuchosCore_config.h +include/TeuchosParameterList_config.h include/TeuchosRemainder_config.h include/Teuchos_AbstractFactory.hpp include/Teuchos_AbstractFactoryStd.hpp @@ -1451,7 +1710,6 @@ include/Teuchos_ConditionXMLConverter.hpp include/Teuchos_ConditionXMLConverterDB.hpp include/Teuchos_ConfigDefs.hpp include/Teuchos_ConstNonconstObjectContainer.hpp -include/Teuchos_ConstTypeTraits.hpp include/Teuchos_DLLExportMacro.h include/Teuchos_DataAccess.hpp include/Teuchos_DebugDefaultAsserts.hpp @@ -1464,6 +1722,7 @@ include/Teuchos_DependencyXMLConverterDB.hpp include/Teuchos_Describable.hpp include/Teuchos_Details_Allocator.hpp include/Teuchos_Details_Lapack128.hpp +include/Teuchos_Details_LapackLongDouble.hpp include/Teuchos_Details_MpiTypeTraits.hpp include/Teuchos_DummyObjectGetter.hpp include/Teuchos_ENull.hpp @@ -1605,7 +1864,6 @@ include/Teuchos_TreeBuildingXMLHandler.hpp include/Teuchos_Tuple.hpp include/Teuchos_TwoDArray.hpp include/Teuchos_TypeNameTraits.hpp -include/Teuchos_TypeTraits.hpp include/Teuchos_UnitTestBase.hpp include/Teuchos_UnitTestHarness.hpp include/Teuchos_UnitTestHelpers.hpp @@ -1860,6 +2118,7 @@ include/galois.h include/generator.hpp include/globals.h include/int_types.hpp +include/interface_utils.hpp include/interfaces/APPS.h include/interfaces/Cobyla.h include/interfaces/DOT.h @@ -1871,6 +2130,7 @@ include/interfaces/OPTpp.h include/interfaces/TCC.h include/ioformat.h include/iterator.hpp +include/iterator_utils.hpp include/java_util_levels.hpp include/kd_fix_rad_search.h include/kd_pr_search.h @@ -1894,6 +2154,7 @@ include/macros.hpp include/math_tools.hpp include/menu.h include/minimal_levels.hpp +include/model_utils.hpp include/mutex.hpp include/mutex.hpp.inl include/mutex_lock.hpp @@ -2194,6 +2455,7 @@ lib/cmake/ROL/ROLConfig.cmake lib/cmake/ROL/ROLTargets-%%CMAKE_BUILD_TYPE%%.cmake lib/cmake/ROL/ROLTargets.cmake lib/cmake/Teuchos/TeuchosConfig.cmake +lib/cmake/Teuchos/TeuchosTargets.cmake lib/cmake/TeuchosComm/TeuchosCommConfig.cmake lib/cmake/TeuchosComm/TeuchosCommTargets-%%CMAKE_BUILD_TYPE%%.cmake lib/cmake/TeuchosComm/TeuchosCommTargets.cmake @@ -2216,23 +2478,27 @@ lib/cmake/Trilinos/TrilinosConfig.cmake lib/cmake/Trilinos/TrilinosConfigVersion.cmake lib/cmake/ddace/ddace-config.cmake lib/cmake/nidr/nidr-config.cmake +lib/cmake/tribits/CHANGELOG.md +lib/cmake/tribits/COPYRIGHT lib/cmake/tribits/Copyright.txt +lib/cmake/tribits/LICENSE lib/cmake/tribits/README.DIRECTORY_CONTENTS.rst -lib/cmake/tribits/ReleaseNotes.txt lib/cmake/tribits/TriBITS.cmake lib/cmake/tribits/TriBITSConfig.cmake lib/cmake/tribits/Version.cmake +lib/cmake/tribits/ci_support/CDashAnalyzeReportRandomFailures.py lib/cmake/tribits/ci_support/CDashQueryAnalyzeReport.py lib/cmake/tribits/ci_support/CheckinTest.py lib/cmake/tribits/ci_support/CheckinTestConstants.py +lib/cmake/tribits/ci_support/CreateIssueTrackerFromCDashQuery.py lib/cmake/tribits/ci_support/FindGeneralScriptSupport.py lib/cmake/tribits/ci_support/TribitsDependencies.py lib/cmake/tribits/ci_support/TribitsDumpDepsXmlScript.cmake -lib/cmake/tribits/ci_support/TribitsDumpXmlDependenciesFiles.cmake lib/cmake/tribits/ci_support/TribitsGetExtraReposForCheckinTest.cmake lib/cmake/tribits/ci_support/TribitsPackageFilePathUtils.py lib/cmake/tribits/ci_support/TribitsPackageTestNameUtils.py lib/cmake/tribits/ci_support/TribitsStripCommentsFromCMakeCacheFile.cmake +lib/cmake/tribits/ci_support/TribitsWriteXmlDependenciesFiles.cmake lib/cmake/tribits/ci_support/cdash_analyze_and_report.py lib/cmake/tribits/ci_support/cdash_build_testing_date.py lib/cmake/tribits/ci_support/checkin-test.py @@ -2247,12 +2513,16 @@ lib/cmake/tribits/common_tpls/FindTPLBLAS.cmake lib/cmake/tribits/common_tpls/FindTPLBinUtils.cmake lib/cmake/tribits/common_tpls/FindTPLBoost.cmake lib/cmake/tribits/common_tpls/FindTPLCGNS.cmake +lib/cmake/tribits/common_tpls/FindTPLCGNSDependencies.cmake lib/cmake/tribits/common_tpls/FindTPLHDF5.cmake lib/cmake/tribits/common_tpls/FindTPLHYPRE.cmake lib/cmake/tribits/common_tpls/FindTPLLAPACK.cmake +lib/cmake/tribits/common_tpls/FindTPLLAPACKDependencies.cmake lib/cmake/tribits/common_tpls/FindTPLNetcdf.cmake +lib/cmake/tribits/common_tpls/FindTPLNetcdfDependencies.cmake lib/cmake/tribits/common_tpls/FindTPLPETSC.cmake lib/cmake/tribits/common_tpls/FindTPLPnetcdf.cmake +lib/cmake/tribits/common_tpls/FindTPLProjectLastLib.cmake lib/cmake/tribits/common_tpls/find_modules/FindCGNS.cmake lib/cmake/tribits/common_tpls/find_modules/FindHDF5.cmake lib/cmake/tribits/common_tpls/find_modules/FindNetCDF.cmake @@ -2260,7 +2530,8 @@ lib/cmake/tribits/common_tpls/find_modules/FindPNetCDF.cmake lib/cmake/tribits/common_tpls/utils/AddImportedLibrary.cmake lib/cmake/tribits/common_tpls/utils/AddPackageDependency.cmake lib/cmake/tribits/common_tpls/utils/ParseLibraryList.cmake -lib/cmake/tribits/core/add_install_group_and_perms_fixups/CMakeLists.txt +lib/cmake/tribits/core/common/TribitsCMakePolicies.cmake +lib/cmake/tribits/core/common/TribitsConstants.cmake lib/cmake/tribits/core/config_tests/BLASMangling.cmake lib/cmake/tribits/core/config_tests/FiniteValue.cmake lib/cmake/tribits/core/config_tests/FortranMangling.cmake @@ -2273,67 +2544,86 @@ lib/cmake/tribits/core/config_tests/fmangle/fmangle.f lib/cmake/tribits/core/installation/TribitsConfigInclude.cmake.in lib/cmake/tribits/core/installation/TribitsInstallationTestingMacros.cmake lib/cmake/tribits/core/installation/TribitsPackageConfigTemplate.cmake.in -lib/cmake/tribits/core/installation/TribitsPackageConfigTemplate.export.in lib/cmake/tribits/core/installation/TribitsProjectConfigTemplate.cmake.in -lib/cmake/tribits/core/installation/TribitsProjectConfigTemplate.export.in +lib/cmake/tribits/core/installation/add_install_group_and_perms_fixups/CMakeLists.txt +lib/cmake/tribits/core/installation/add_project_install_commands/CMakeLists.txt lib/cmake/tribits/core/installation/cmake_pbp_install.cmake.in lib/cmake/tribits/core/installation/set_installed_group_and_permissions.cmake.in -lib/cmake/tribits/core/package_arch/TribitsAddAdvancedTest.cmake -lib/cmake/tribits/core/package_arch/TribitsAddAdvancedTestHelpers.cmake lib/cmake/tribits/core/package_arch/TribitsAddExecutable.cmake lib/cmake/tribits/core/package_arch/TribitsAddExecutableAndTest.cmake -lib/cmake/tribits/core/package_arch/TribitsAddExecutableTestHelpers.cmake lib/cmake/tribits/core/package_arch/TribitsAddInstallGroupAndPermsFixups.cmake +lib/cmake/tribits/core/package_arch/TribitsAddLibrary.cmake lib/cmake/tribits/core/package_arch/TribitsAddOptionAndDefine.cmake -lib/cmake/tribits/core/package_arch/TribitsAddTest.cmake -lib/cmake/tribits/core/package_arch/TribitsAddTestHelpers.cmake lib/cmake/tribits/core/package_arch/TribitsAdjustPackageEnables.cmake lib/cmake/tribits/core/package_arch/TribitsBLASMangling.cmake -lib/cmake/tribits/core/package_arch/TribitsCMakePolicies.cmake lib/cmake/tribits/core/package_arch/TribitsCommonArgsHelpers.cmake lib/cmake/tribits/core/package_arch/TribitsConfigureCTestCustom.cmake -lib/cmake/tribits/core/package_arch/TribitsConstants.cmake +lib/cmake/tribits/core/package_arch/TribitsConfigureFile.cmake +lib/cmake/tribits/core/package_arch/TribitsConfigureTiming.cmake lib/cmake/tribits/core/package_arch/TribitsCopyFilesToBinaryDir.cmake lib/cmake/tribits/core/package_arch/TribitsCreateClientTemplateHeaders.cmake lib/cmake/tribits/core/package_arch/TribitsDefineStandardCompileVars.cmake lib/cmake/tribits/core/package_arch/TribitsETISupport.cmake +lib/cmake/tribits/core/package_arch/TribitsExternalPackageWithImportedTargetsFindTplModuleHelpers.cmake +lib/cmake/tribits/core/package_arch/TribitsExternalPackageWriteConfigFile.cmake lib/cmake/tribits/core/package_arch/TribitsFindMostRecentFileTimestamp.cmake lib/cmake/tribits/core/package_arch/TribitsFindPythonInterp.cmake lib/cmake/tribits/core/package_arch/TribitsFortranMangling.cmake lib/cmake/tribits/core/package_arch/TribitsGeneralMacros.cmake lib/cmake/tribits/core/package_arch/TribitsGenerateResourceSpecFile.cmake +lib/cmake/tribits/core/package_arch/TribitsGetPackageEnableStatus.cmake +lib/cmake/tribits/core/package_arch/TribitsGetPackageSublists.cmake lib/cmake/tribits/core/package_arch/TribitsGetVersionDate.cmake lib/cmake/tribits/core/package_arch/TribitsGlobalMacros.cmake lib/cmake/tribits/core/package_arch/TribitsHostType.cmake lib/cmake/tribits/core/package_arch/TribitsIncludeDirectories.cmake lib/cmake/tribits/core/package_arch/TribitsInstallHeaders.cmake +lib/cmake/tribits/core/package_arch/TribitsInternalPackageWriteConfigFile.cmake +lib/cmake/tribits/core/package_arch/TribitsLibIsTestOnly.cmake lib/cmake/tribits/core/package_arch/TribitsLibraryMacros.cmake lib/cmake/tribits/core/package_arch/TribitsListHelpers.cmake 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lib/cmake/tribits/core/package_arch/TribitsProjectImpl.cmake +lib/cmake/tribits/core/package_arch/TribitsProjectWriteConfigFile.cmake +lib/cmake/tribits/core/package_arch/TribitsReadAllProjectDepsFilesCreateDepsGraph.cmake +lib/cmake/tribits/core/package_arch/TribitsReadDepsFilesCreateDepsGraph.cmake lib/cmake/tribits/core/package_arch/TribitsReportInvalidTribitsUsage.cmake +lib/cmake/tribits/core/package_arch/TribitsSetAndIncDirs.cmake +lib/cmake/tribits/core/package_arch/TribitsSetUpEnabledOnlyDependencies.cmake lib/cmake/tribits/core/package_arch/TribitsSetupBasicCompileLinkFlags.cmake lib/cmake/tribits/core/package_arch/TribitsSetupMPI.cmake lib/cmake/tribits/core/package_arch/TribitsSetupStrongCompileWarnings.cmake -lib/cmake/tribits/core/package_arch/TribitsSortListAccordingToMasterList.cmake lib/cmake/tribits/core/package_arch/TribitsSubPackageMacros.cmake -lib/cmake/tribits/core/package_arch/TribitsTestCategories.cmake +lib/cmake/tribits/core/package_arch/TribitsSystemDataStructuresMacrosFunctions.rst lib/cmake/tribits/core/package_arch/TribitsTplDeclareLibraries.cmake lib/cmake/tribits/core/package_arch/TribitsTplFindIncludeDirsAndLibraries.cmake lib/cmake/tribits/core/package_arch/TribitsVerbosePrintVar.cmake -lib/cmake/tribits/core/package_arch/TribitsWriteClientExportFiles.cmake +lib/cmake/tribits/core/package_arch/TribitsWritePackageConfigFileHelpers.cmake lib/cmake/tribits/core/package_arch/Tribits_version.h.in lib/cmake/tribits/core/package_arch/Tribits_version_date.h.in lib/cmake/tribits/core/package_arch/VersionDate.cmake.in lib/cmake/tribits/core/package_arch/tribits_get_version_date.cmake lib/cmake/tribits/core/std_tpls/FindTPLCUDA.cmake lib/cmake/tribits/core/std_tpls/FindTPLMPI.cmake +lib/cmake/tribits/core/test_support/TribitsAddAdvancedTest.cmake +lib/cmake/tribits/core/test_support/TribitsAddAdvancedTestHelpers.cmake +lib/cmake/tribits/core/test_support/TribitsAddExecutableTestHelpers.cmake +lib/cmake/tribits/core/test_support/TribitsAddTest.cmake +lib/cmake/tribits/core/test_support/TribitsAddTestHelpers.cmake +lib/cmake/tribits/core/test_support/TribitsSetTribitsPackageName.cmake +lib/cmake/tribits/core/test_support/TribitsTestCategories.cmake lib/cmake/tribits/core/utils/AddSubdirectories.cmake lib/cmake/tribits/core/utils/AdvancedOption.cmake lib/cmake/tribits/core/utils/AdvancedSet.cmake @@ -2346,7 +2636,6 @@ lib/cmake/tribits/core/utils/AppendStringVarWithSep.cmake lib/cmake/tribits/core/utils/AssertAndTouchDefined.cmake lib/cmake/tribits/core/utils/AssertDefined.cmake lib/cmake/tribits/core/utils/CMakeBuildTypesList.cmake -lib/cmake/tribits/core/utils/CMakeOverrides.cmake lib/cmake/tribits/core/utils/CombinedOption.cmake lib/cmake/tribits/core/utils/ConcatStrings.cmake lib/cmake/tribits/core/utils/DriveAdvancedTest.cmake @@ -2372,16 +2661,26 @@ lib/cmake/tribits/core/utils/PrependSet.cmake lib/cmake/tribits/core/utils/PrintNonemptyVar.cmake lib/cmake/tribits/core/utils/PrintNonemptyVarWithSpaces.cmake lib/cmake/tribits/core/utils/PrintVar.cmake +lib/cmake/tribits/core/utils/PrintVarWithSpaces.cmake lib/cmake/tribits/core/utils/RemoveGlobalDuplicates.cmake -lib/cmake/tribits/core/utils/SetAndIncDirs.cmake lib/cmake/tribits/core/utils/SetCacheOnOffEmpty.cmake lib/cmake/tribits/core/utils/SetDefault.cmake lib/cmake/tribits/core/utils/SetDefaultAndFromEnv.cmake lib/cmake/tribits/core/utils/SetNotFound.cmake lib/cmake/tribits/core/utils/Split.cmake lib/cmake/tribits/core/utils/TimingUtils.cmake +lib/cmake/tribits/core/utils/TribitsAddEnumCacheVar.cmake +lib/cmake/tribits/core/utils/TribitsCreateReverseList.cmake +lib/cmake/tribits/core/utils/TribitsDeprecatedHelpers.cmake lib/cmake/tribits/core/utils/TribitsFilepathHelpers.cmake +lib/cmake/tribits/core/utils/TribitsGatherBuildTargets.cmake lib/cmake/tribits/core/utils/TribitsGetCategoriesString.cmake +lib/cmake/tribits/core/utils/TribitsGetImportedLocationProperty.cmake +lib/cmake/tribits/core/utils/TribitsGitRepoVersionInfo.cmake +lib/cmake/tribits/core/utils/TribitsParseArgumentsHelpers.cmake +lib/cmake/tribits/core/utils/TribitsPrintList.cmake +lib/cmake/tribits/core/utils/TribitsSetCacheVarAndDefault.cmake +lib/cmake/tribits/core/utils/TribitsSortListAccordingToMasterList.cmake lib/cmake/tribits/core/utils/TribitsStandardizePaths.cmake lib/cmake/tribits/core/utils/TribitsStripQuotesFromStr.cmake lib/cmake/tribits/core/utils/UnitTestHelpers.cmake @@ -2390,6 +2689,7 @@ lib/cmake/tribits/ctest_driver/README lib/cmake/tribits/ctest_driver/TribitsAddDashboardTarget.cmake lib/cmake/tribits/ctest_driver/TribitsCTestDriverCore.cmake lib/cmake/tribits/ctest_driver/TribitsCTestDriverCoreHelpers.cmake +lib/cmake/tribits/ctest_driver/TribitsGetCDashUrlsInsideCTestS.cmake lib/cmake/tribits/ctest_driver/TribitsGetCTestTestXmlDir.cmake lib/cmake/tribits/ctest_driver/TribitsReadTagFile.cmake lib/cmake/tribits/ctest_driver/dump-cdash-deps-xml-file.py @@ -2403,7 +2703,6 @@ lib/cmake/tribits/dashboard_driver/TribitsDriverCMakeLists.cmake lib/cmake/tribits/dashboard_driver/TribitsDriverDashboard.cmake lib/cmake/tribits/dashboard_driver/TribitsDriverSupport.cmake lib/cmake/tribits/dashboard_driver/tdd_driver.py -lib/cmake/tribits/devtools_install/0001-CTest-Add-CTEST_RESOURCE_SPEC_FILE-variable.patch lib/cmake/tribits/devtools_install/FindGeneralScriptSupport.py lib/cmake/tribits/devtools_install/InstallProgramDriver.py lib/cmake/tribits/devtools_install/install-autoconf.py @@ -2415,7 +2714,6 @@ lib/cmake/tribits/devtools_install/install-openmpi.py lib/cmake/tribits/devtools_install/install_devtools.py lib/cmake/tribits/devtools_install/load_dev_env.csh.in lib/cmake/tribits/devtools_install/load_dev_env.sh.in -lib/cmake/tribits/doc/README.DEPENDENCIES lib/cmake/tribits/doc/build_docs.sh lib/cmake/tribits/doc/build_ref/Makefile lib/cmake/tribits/doc/build_ref/README @@ -2423,25 +2721,59 @@ lib/cmake/tribits/doc/build_ref/TribitsBuildReferenceBody.rst lib/cmake/tribits/doc/build_ref/TribitsBuildReferenceTemplate.rst lib/cmake/tribits/doc/build_ref/create-build-ref.sh lib/cmake/tribits/doc/build_ref/create-project-build-ref.py -lib/cmake/tribits/doc/developers_guide/ExtraReposList.cmake -lib/cmake/tribits/doc/developers_guide/Makefile -lib/cmake/tribits/doc/developers_guide/README -lib/cmake/tribits/doc/developers_guide/ReducedMockTrilinosOutput/EnableAllPackages.txt -lib/cmake/tribits/doc/developers_guide/ReducedMockTrilinosOutput/EnableEpetra_EnableRTOp_DisableTeuchos.txt -lib/cmake/tribits/doc/developers_guide/ReducedMockTrilinosOutput/EnableEpetra_EnableRTOp_DisableTeuchos_DisableEnabledFwdDepPackages.txt -lib/cmake/tribits/doc/developers_guide/ReducedMockTrilinosOutput/EnableThyra_DisableEpetra_EnableTests.txt -lib/cmake/tribits/doc/developers_guide/ReducedMockTrilinosOutput/EnableThyra_EnableTests.txt -lib/cmake/tribits/doc/developers_guide/ReducedMockTrilinosOutput/EnableThyra_EnableTests_EnableBoost_ST.txt -lib/cmake/tribits/doc/developers_guide/ReducedMockTrilinosOutput/EnableThyra_EnableTests_EnableBoost_ST_RequiredOnly.txt -lib/cmake/tribits/doc/developers_guide/ReducedMockTrilinosOutput/ExpectedDependencies.txt -lib/cmake/tribits/doc/developers_guide/ReducedMockTrilinosOutput/NoEnables.txt -lib/cmake/tribits/doc/developers_guide/TribitsDevelopersGuide.rst -lib/cmake/tribits/doc/developers_guide/TribitsMacroFunctionDocTemplate.rst -lib/cmake/tribits/doc/developers_guide/UtilsMacroFunctionDocTemplate.rst -lib/cmake/tribits/doc/developers_guide/generate-dev-guide.sh -lib/cmake/tribits/doc/developers_guide/rst2latex.tex -lib/cmake/tribits/doc/developers_guide/scripts/dummy_test_commit.sh +lib/cmake/tribits/doc/guides/ExtraReposList.cmake +lib/cmake/tribits/doc/guides/Makefile.common_generated_files +lib/cmake/tribits/doc/guides/README +lib/cmake/tribits/doc/guides/ReducedMockTrilinosOutput/EnableAllPackages.txt +lib/cmake/tribits/doc/guides/ReducedMockTrilinosOutput/EnableEpetra_EnableRTOp_DisableTeuchos.txt +lib/cmake/tribits/doc/guides/ReducedMockTrilinosOutput/EnableEpetra_EnableRTOp_DisableTeuchos_DisableEnabledFwdDepPackages.txt +lib/cmake/tribits/doc/guides/ReducedMockTrilinosOutput/EnableThyraCoreLibs_EnableTests.txt +lib/cmake/tribits/doc/guides/ReducedMockTrilinosOutput/EnableThyraEpetra_EnableTests.txt +lib/cmake/tribits/doc/guides/ReducedMockTrilinosOutput/EnableThyra_DisableEpetra_EnableTests.txt +lib/cmake/tribits/doc/guides/ReducedMockTrilinosOutput/EnableThyra_EnableTests.txt +lib/cmake/tribits/doc/guides/ReducedMockTrilinosOutput/EnableThyra_EnableTests_EnableBoost_ST.txt +lib/cmake/tribits/doc/guides/ReducedMockTrilinosOutput/EnableThyra_EnableTests_EnableBoost_ST_RequiredOnly.txt +lib/cmake/tribits/doc/guides/ReducedMockTrilinosOutput/ExpectedDependencies.txt +lib/cmake/tribits/doc/guides/ReducedMockTrilinosOutput/NoEnables.txt +lib/cmake/tribits/doc/guides/TribitsCMakeLanguageOverviewAndGotchas.rst +lib/cmake/tribits/doc/guides/TribitsCoreDetailedReference.rst +lib/cmake/tribits/doc/guides/TribitsDesignConsiderations.rst +lib/cmake/tribits/doc/guides/TribitsFAQ.rst +lib/cmake/tribits/doc/guides/TribitsGuidesBody.rst +lib/cmake/tribits/doc/guides/TribitsGuidesReferences.rst +lib/cmake/tribits/doc/guides/TribitsHistory.rst +lib/cmake/tribits/doc/guides/TribitsMacroFunctionDocTemplate.rst +lib/cmake/tribits/doc/guides/TribitsPackageNotCMakePackage.rst +lib/cmake/tribits/doc/guides/TribitsSystemMacroFunctionDocTemplate.rst +lib/cmake/tribits/doc/guides/TribitsToolsDocumentation.rst +lib/cmake/tribits/doc/guides/UtilsMacroFunctionDocTemplate.rst +lib/cmake/tribits/doc/guides/generate-guide.sh +lib/cmake/tribits/doc/guides/maintainers_guide/Makefile +lib/cmake/tribits/doc/guides/maintainers_guide/TribitsCoreDetailedReference.rst +lib/cmake/tribits/doc/guides/maintainers_guide/TribitsMaintainersGuide.rst +lib/cmake/tribits/doc/guides/rst2latex.tex +lib/cmake/tribits/doc/guides/scripts/dummy_test_commit.sh +lib/cmake/tribits/doc/guides/users_guide/Makefile +lib/cmake/tribits/doc/guides/users_guide/TribitsCoreDetailedReference.rst +lib/cmake/tribits/doc/guides/users_guide/TribitsUsersGuide.rst lib/cmake/tribits/doc/publish_docs.sh +lib/cmake/tribits/doc/sphinx/build_ref/Makefile +lib/cmake/tribits/doc/sphinx/build_ref/__init__.py +lib/cmake/tribits/doc/sphinx/build_ref/conf.py +lib/cmake/tribits/doc/sphinx/build_ref/make.bat +lib/cmake/tribits/doc/sphinx/build_sphinx_docs.sh +lib/cmake/tribits/doc/sphinx/combined_docs/index.html +lib/cmake/tribits/doc/sphinx/index.rst +lib/cmake/tribits/doc/sphinx/maintainers_guide/Makefile +lib/cmake/tribits/doc/sphinx/maintainers_guide/__init__.py +lib/cmake/tribits/doc/sphinx/maintainers_guide/conf.py +lib/cmake/tribits/doc/sphinx/maintainers_guide/make.bat +lib/cmake/tribits/doc/sphinx/requirements.txt +lib/cmake/tribits/doc/sphinx/sphinx_rst_generator.py +lib/cmake/tribits/doc/sphinx/users_guide/Makefile +lib/cmake/tribits/doc/sphinx/users_guide/__init__.py +lib/cmake/tribits/doc/sphinx/users_guide/conf.py +lib/cmake/tribits/doc/sphinx/users_guide/make.bat lib/cmake/tribits/doc/tutorial/README.md lib/cmake/tribits/doc/tutorial/generate-tutorial.sh lib/cmake/tribits/doc/tutorial/src/TribitsTutorial_ConvertAProject.rst @@ -2476,7 +2808,6 @@ lib/cmake/tribits/examples/MixedSharedStaticLibs/static_only/StaticOnly.hpp lib/cmake/tribits/examples/MixedSharedStaticLibs/static_only/cmake/Dependencies.cmake lib/cmake/tribits/examples/MockTrilinos/CMakeLists.txt lib/cmake/tribits/examples/MockTrilinos/CTestConfig.cmake -lib/cmake/tribits/examples/MockTrilinos/Copyright.txt lib/cmake/tribits/examples/MockTrilinos/PackagesList.cmake lib/cmake/tribits/examples/MockTrilinos/ProjectName.cmake lib/cmake/tribits/examples/MockTrilinos/TPLsList.cmake @@ -2487,6 +2818,10 @@ lib/cmake/tribits/examples/MockTrilinos/cmake/NativeRepositoriesList1.cmake lib/cmake/tribits/examples/MockTrilinos/cmake/ProjectDependenciesSetup.cmake lib/cmake/tribits/examples/MockTrilinos/cmake/Reduced_preCopyrightTrilinos_PackagesList.cmake lib/cmake/tribits/examples/MockTrilinos/cmake/RepositoryDependenciesSetup.cmake +lib/cmake/tribits/examples/MockTrilinos/cmake/TPLs/FindTPLLAPACKDependencies.cmake +lib/cmake/tribits/examples/MockTrilinos/cmake/TPLs/FindTPLParMETISDependencies.cmake +lib/cmake/tribits/examples/MockTrilinos/cmake/TPLs/FindTPLSuperLUDependencies.cmake +lib/cmake/tribits/examples/MockTrilinos/cmake/TPLs/FindTPLSuperLUDistDependencies.cmake lib/cmake/tribits/examples/MockTrilinos/cmake/cmake/Dependencies.cmake lib/cmake/tribits/examples/MockTrilinos/extraRepoOnePackage/PackagesList.cmake lib/cmake/tribits/examples/MockTrilinos/extraRepoOnePackage/TPLsList.cmake @@ -2565,6 +2900,9 @@ lib/cmake/tribits/examples/ReducedMockTrilinos/CMakeLists.txt lib/cmake/tribits/examples/ReducedMockTrilinos/PackagesList.cmake lib/cmake/tribits/examples/ReducedMockTrilinos/ProjectName.cmake lib/cmake/tribits/examples/ReducedMockTrilinos/TPLsList.cmake +lib/cmake/tribits/examples/ReducedMockTrilinos/extraRepos/DependsOnLAPACK/PackagesList.cmake +lib/cmake/tribits/examples/ReducedMockTrilinos/extraRepos/DependsOnLAPACK/TPLsList.cmake +lib/cmake/tribits/examples/ReducedMockTrilinos/extraRepos/DependsOnLAPACK/cmake/Dependencies.cmake lib/cmake/tribits/examples/ReducedMockTrilinos/packages/epetra/cmake/Dependencies.cmake lib/cmake/tribits/examples/ReducedMockTrilinos/packages/epetraext/cmake/Dependencies.cmake lib/cmake/tribits/examples/ReducedMockTrilinos/packages/rtop/cmake/Dependencies.cmake @@ -2586,6 +2924,14 @@ lib/cmake/tribits/examples/TargetDefinesPkg/cmake/Dependencies.cmake lib/cmake/tribits/examples/TargetDefinesPkg/test/CMakeLists.txt lib/cmake/tribits/examples/TargetDefinesPkg/test/TargetDefinesPkg_test.cpp lib/cmake/tribits/examples/TargetDefinesPkg/test/deprecated_defines/CMakeLists.txt +lib/cmake/tribits/examples/TribitsExampleApp/AppHelperFuncs.cmake +lib/cmake/tribits/examples/TribitsExampleApp/CMakeLists.txt +lib/cmake/tribits/examples/TribitsExampleApp/README.md +lib/cmake/tribits/examples/TribitsExampleApp/app.cpp +lib/cmake/tribits/examples/TribitsExampleApp2/AppHelperFuncs.cmake +lib/cmake/tribits/examples/TribitsExampleApp2/CMakeLists.txt +lib/cmake/tribits/examples/TribitsExampleApp2/README.md +lib/cmake/tribits/examples/TribitsExampleApp2/app.cpp lib/cmake/tribits/examples/TribitsExampleMetaProject/CMakeLists.txt lib/cmake/tribits/examples/TribitsExampleMetaProject/CTestConfig.cmake lib/cmake/tribits/examples/TribitsExampleMetaProject/PackagesList.cmake @@ -2603,7 +2949,7 @@ lib/cmake/tribits/examples/TribitsExampleProject/Copyright.txt lib/cmake/tribits/examples/TribitsExampleProject/LICENSE lib/cmake/tribits/examples/TribitsExampleProject/PackagesList.cmake lib/cmake/tribits/examples/TribitsExampleProject/ProjectName.cmake -lib/cmake/tribits/examples/TribitsExampleProject/README +lib/cmake/tribits/examples/TribitsExampleProject/README.md lib/cmake/tribits/examples/TribitsExampleProject/TPLsList.cmake lib/cmake/tribits/examples/TribitsExampleProject/Version.cmake lib/cmake/tribits/examples/TribitsExampleProject/cmake/CallbackDefineProjectPackaging.cmake @@ -2627,7 +2973,8 @@ lib/cmake/tribits/examples/TribitsExampleProject/packages/mixed_lang/src/Ray.hh lib/cmake/tribits/examples/TribitsExampleProject/packages/mixed_lang/src/Ray_Tracer.cc lib/cmake/tribits/examples/TribitsExampleProject/packages/mixed_lang/src/Ray_Tracer.hh lib/cmake/tribits/examples/TribitsExampleProject/packages/mixed_lang/src/Ray_Tracer_Kernel.f90 -lib/cmake/tribits/examples/TribitsExampleProject/packages/mixed_lang/src/Vector_Lite.hh +lib/cmake/tribits/examples/TribitsExampleProject/packages/mixed_lang/src/vector/CMakeLists.txt +lib/cmake/tribits/examples/TribitsExampleProject/packages/mixed_lang/src/vector/Vector_Lite.hh lib/cmake/tribits/examples/TribitsExampleProject/packages/mixed_lang/test/CMakeLists.txt lib/cmake/tribits/examples/TribitsExampleProject/packages/mixed_lang/test/tstRay_Tracer.cc lib/cmake/tribits/examples/TribitsExampleProject/packages/simple_cxx/CMakeLists.txt @@ -2640,16 +2987,20 @@ lib/cmake/tribits/examples/TribitsExampleProject/packages/simple_cxx/src/SimpleC lib/cmake/tribits/examples/TribitsExampleProject/packages/simple_cxx/src/SimpleCxx_HelloWorld_Prog.cpp lib/cmake/tribits/examples/TribitsExampleProject/packages/simple_cxx/test/CMakeLists.txt lib/cmake/tribits/examples/TribitsExampleProject/packages/simple_cxx/test/SimpleCxx_HelloWorld_Tests.cpp +lib/cmake/tribits/examples/TribitsExampleProject/packages/simple_cxx/test/inc/SimpleCxx_HelloWorld_Tests.hpp lib/cmake/tribits/examples/TribitsExampleProject/packages/with_subpackages/CMakeLists.txt lib/cmake/tribits/examples/TribitsExampleProject/packages/with_subpackages/a/A.cpp lib/cmake/tribits/examples/TribitsExampleProject/packages/with_subpackages/a/A.hpp lib/cmake/tribits/examples/TribitsExampleProject/packages/with_subpackages/a/CMakeLists.txt lib/cmake/tribits/examples/TribitsExampleProject/packages/with_subpackages/a/cmake/Dependencies.cmake +lib/cmake/tribits/examples/TribitsExampleProject/packages/with_subpackages/a/cmake/WithSubpackagesA_config.h.in lib/cmake/tribits/examples/TribitsExampleProject/packages/with_subpackages/a/tests/CMakeLists.txt lib/cmake/tribits/examples/TribitsExampleProject/packages/with_subpackages/a/tests/a_test.cpp lib/cmake/tribits/examples/TribitsExampleProject/packages/with_subpackages/b/CMakeLists.txt +lib/cmake/tribits/examples/TribitsExampleProject/packages/with_subpackages/b/ExcludeFromRelease.txt lib/cmake/tribits/examples/TribitsExampleProject/packages/with_subpackages/b/cmake/Dependencies.cmake lib/cmake/tribits/examples/TribitsExampleProject/packages/with_subpackages/b/cmake/WithSubpackagesB_config.h.in +lib/cmake/tribits/examples/TribitsExampleProject/packages/with_subpackages/b/src/AlsoExcludeFromTarball.txt lib/cmake/tribits/examples/TribitsExampleProject/packages/with_subpackages/b/src/B.cpp lib/cmake/tribits/examples/TribitsExampleProject/packages/with_subpackages/b/src/B.hpp lib/cmake/tribits/examples/TribitsExampleProject/packages/with_subpackages/b/src/CMakeLists.txt @@ -2688,6 +3039,52 @@ lib/cmake/tribits/examples/TribitsExampleProject/packages/wrap_external/run_exte lib/cmake/tribits/examples/TribitsExampleProject/project-checkin-test-config.py lib/cmake/tribits/examples/TribitsExampleProject/sampleScripts/linux-mpi-debug.sh lib/cmake/tribits/examples/TribitsExampleProject/sampleScripts/linux-serial-debug.sh +lib/cmake/tribits/examples/TribitsExampleProject2/CMakeLists.txt +lib/cmake/tribits/examples/TribitsExampleProject2/PackagesList.cmake +lib/cmake/tribits/examples/TribitsExampleProject2/ProjectName.cmake +lib/cmake/tribits/examples/TribitsExampleProject2/TPLsList.cmake +lib/cmake/tribits/examples/TribitsExampleProject2/Version.cmake +lib/cmake/tribits/examples/TribitsExampleProject2/cmake/tpls/FindTPLTpl1.cmake +lib/cmake/tribits/examples/TribitsExampleProject2/cmake/tpls/FindTPLTpl2.cmake +lib/cmake/tribits/examples/TribitsExampleProject2/cmake/tpls/FindTPLTpl2Dependencies.cmake +lib/cmake/tribits/examples/TribitsExampleProject2/cmake/tpls/FindTPLTpl3.cmake +lib/cmake/tribits/examples/TribitsExampleProject2/cmake/tpls/FindTPLTpl3Dependencies.cmake +lib/cmake/tribits/examples/TribitsExampleProject2/cmake/tpls/FindTPLTpl4.cmake +lib/cmake/tribits/examples/TribitsExampleProject2/cmake/tpls/FindTPLTpl4Dependencies.cmake +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package1/CMakeLists.raw.cmake +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package1/CMakeLists.tribits.cmake +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package1/CMakeLists.txt +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package1/cmake/Dependencies.cmake +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package1/cmake/raw/DefineAllLibsTarget.cmake +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package1/cmake/raw/EnableTribitsTestSupport.cmake +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package1/cmake/raw/GeneratePackageConfigFileForBuildDir.cmake +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package1/cmake/raw/GeneratePackageConfigFileForInstallDir.cmake +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package1/cmake/raw/Package1Config.cmake.in +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package1/src/CMakeLists.raw.cmake +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package1/src/CMakeLists.tribits.cmake +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package1/src/CMakeLists.txt +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package1/src/Package1.cpp +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package1/src/Package1.hpp +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package1/src/Package1_Prg.cpp +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package1/test/CMakeLists.raw.cmake +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package1/test/CMakeLists.tribits.cmake +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package1/test/CMakeLists.txt +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package2/CMakeLists.txt +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package2/cmake/Dependencies.cmake +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package2/cmake/Package2_config.h.in +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package2/src/CMakeLists.txt +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package2/src/Package2.cpp +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package2/src/Package2.hpp +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package2/src/Package2_Prg.cpp +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package2/test/CMakeLists.txt +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package3/CMakeLists.txt +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package3/cmake/Dependencies.cmake +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package3/cmake/Package3_config.h.in +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package3/src/CMakeLists.txt +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package3/src/Package3.cpp +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package3/src/Package3.hpp +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package3/src/Package3_Prg.cpp +lib/cmake/tribits/examples/TribitsExampleProject2/packages/package3/test/CMakeLists.txt lib/cmake/tribits/examples/TribitsExampleProjectAddons/CMakeLists.txt lib/cmake/tribits/examples/TribitsExampleProjectAddons/PackagesList.cmake lib/cmake/tribits/examples/TribitsExampleProjectAddons/ProjectName.cmake @@ -2713,14 +3110,39 @@ lib/cmake/tribits/examples/TribitsHelloWorld/hello_world/hello_world_lib.cpp lib/cmake/tribits/examples/TribitsHelloWorld/hello_world/hello_world_lib.hpp lib/cmake/tribits/examples/TribitsHelloWorld/hello_world/hello_world_main.cpp lib/cmake/tribits/examples/TribitsHelloWorld/hello_world/hello_world_unit_tests.cpp +lib/cmake/tribits/examples/TribitsOldSimpleExampleApp/CMakeLists.txt +lib/cmake/tribits/examples/TribitsOldSimpleExampleApp/README.md +lib/cmake/tribits/examples/TribitsOldSimpleExampleApp/app.cpp +lib/cmake/tribits/examples/TribitsOldSimpleExampleApp/util.cpp +lib/cmake/tribits/examples/TribitsSimpleExampleApp/CMakeLists.txt +lib/cmake/tribits/examples/TribitsSimpleExampleApp/README.md +lib/cmake/tribits/examples/TribitsSimpleExampleApp/app.cpp +lib/cmake/tribits/examples/TribitsSimpleExampleApp/util.cpp lib/cmake/tribits/examples/tpls/HeaderOnlyTpl/HeaderOnlyTpl_stuff.hpp lib/cmake/tribits/examples/tpls/SimpleTpl/CMakeLists.txt lib/cmake/tribits/examples/tpls/SimpleTpl/SimpleTpl.cpp lib/cmake/tribits/examples/tpls/SimpleTpl/SimpleTpl.hpp +lib/cmake/tribits/examples/tpls/Tpl1/CMakeLists.txt +lib/cmake/tribits/examples/tpls/Tpl1/Tpl1.cpp +lib/cmake/tribits/examples/tpls/Tpl1/Tpl1.hpp +lib/cmake/tribits/examples/tpls/Tpl2/CMakeLists.txt +lib/cmake/tribits/examples/tpls/Tpl2/Tpl2Config.cmake.in +lib/cmake/tribits/examples/tpls/Tpl2/Tpl2a.cpp +lib/cmake/tribits/examples/tpls/Tpl2/Tpl2a.hpp +lib/cmake/tribits/examples/tpls/Tpl2/Tpl2b.cpp +lib/cmake/tribits/examples/tpls/Tpl2/Tpl2b.hpp +lib/cmake/tribits/examples/tpls/Tpl3/CMakeLists.txt +lib/cmake/tribits/examples/tpls/Tpl3/Tpl3.cpp +lib/cmake/tribits/examples/tpls/Tpl3/Tpl3.hpp +lib/cmake/tribits/examples/tpls/Tpl3/Tpl3Config.cmake.in +lib/cmake/tribits/examples/tpls/Tpl4/CMakeLists.txt +lib/cmake/tribits/examples/tpls/Tpl4/Tpl4.hpp +lib/cmake/tribits/examples/tpls/Tpl4/Tpl4Config.cmake.in lib/cmake/tribits/python_utils/CMakeBinaries.py lib/cmake/tribits/python_utils/CMakeVersions.py lib/cmake/tribits/python_utils/GeneralScriptSupport.py lib/cmake/tribits/python_utils/GenerateDocUtilsOutput.py +lib/cmake/tribits/python_utils/Python2and3.py lib/cmake/tribits/python_utils/SnapshotDir.py lib/cmake/tribits/python_utils/download-cmake.py lib/cmake/tribits/python_utils/extract_rst_cmake_doc.py @@ -2730,10 +3152,15 @@ lib/cmake/tribits/python_utils/git-config-alias.sh lib/cmake/tribits/python_utils/gitdist lib/cmake/tribits/python_utils/gitdist-setup.sh lib/cmake/tribits/python_utils/gitdist.py +lib/cmake/tribits/python_utils/lower_case_cmake.py lib/cmake/tribits/python_utils/mailmsg.py lib/cmake/tribits/python_utils/mockprogram.py lib/cmake/tribits/python_utils/snapshot-dir.py lib/cmake/tribits/python_utils/tree.py +lib/cmake/tribits/refactoring/lower-case-cmake-tree.sh +lib/cmake/tribits/refactoring/string-replace.py +lib/cmake/tribits/refactoring/to-python3.sh +lib/cmake/tribits/refactoring/token-replace.py lib/cmake/tribits/snapshot_tribits.py lib/cmake/tribits/tpls/FindTPLCUDA.cmake lib/cmake/tribits/tpls/FindTPLMPI.cmake @@ -2745,6 +3172,10 @@ lib/cmake/tribits/win_interface/include/unistd.h lib/cmake/tribits/win_interface/include/winmath.h lib/cmake/tribits/win_interface/include/winprocess.h lib/cmake/tribits/xsdk/XSDKDefaults.cmake +lib/external_packages/BLAS/BLASConfig.cmake +lib/external_packages/BLAS/BLASConfigVersion.cmake +lib/external_packages/LAPACK/LAPACKConfig.cmake +lib/external_packages/LAPACK/LAPACKConfigVersion.cmake lib/lib3po.so lib/libamplsolver.so lib/libapproxnn.so @@ -2783,8 +3214,8 @@ lib/libpecos_util.so lib/libpsuade.so lib/libqueso.so lib/librol.so -lib/librol.so.13 -lib/librol.so.13.0 +lib/librol.so.16 +lib/librol.so.16.1.0 lib/libscolib.so lib/libsoga.so lib/libsparsegrid.so @@ -2793,23 +3224,23 @@ lib/libsurfpack_c_interface.so lib/libsurfpack_fortran.so lib/libsurfpack_interpreter.so lib/libteuchoscomm.so -lib/libteuchoscomm.so.13 -lib/libteuchoscomm.so.13.0 +lib/libteuchoscomm.so.16 +lib/libteuchoscomm.so.16.1.0 lib/libteuchoscore.so -lib/libteuchoscore.so.13 -lib/libteuchoscore.so.13.0 +lib/libteuchoscore.so.16 +lib/libteuchoscore.so.16.1.0 lib/libteuchosnumerics.so -lib/libteuchosnumerics.so.13 -lib/libteuchosnumerics.so.13.0 +lib/libteuchosnumerics.so.16 +lib/libteuchosnumerics.so.16.1.0 lib/libteuchosparameterlist.so -lib/libteuchosparameterlist.so.13 -lib/libteuchosparameterlist.so.13.0 +lib/libteuchosparameterlist.so.16 +lib/libteuchosparameterlist.so.16.1.0 lib/libteuchosparser.so -lib/libteuchosparser.so.13 -lib/libteuchosparser.so.13.0 +lib/libteuchosparser.so.16 +lib/libteuchosparser.so.16.1.0 lib/libteuchosremainder.so -lib/libteuchosremainder.so.13 -lib/libteuchosremainder.so.13.0 +lib/libteuchosremainder.so.16 +lib/libteuchosremainder.so.16.1.0 lib/libtinyxml.so lib/libutilib.so lib/libutilities.so diff --git a/science/dlib-cpp/Makefile b/science/dlib-cpp/Makefile index 617844a38ab6..98c6d4828563 100644 --- a/science/dlib-cpp/Makefile +++ b/science/dlib-cpp/Makefile @@ -1,6 +1,7 @@ PORTNAME= dlib DISTVERSIONPREFIX=v -DISTVERSION= 19.24.8 +DISTVERSION= 20.0 +PORTREVISION= 1 CATEGORIES= science devel math PKGNAMESUFFIX= -cpp @@ -14,13 +15,16 @@ LICENSE_FILE= ${WRKSRC}/dlib/LICENSE.txt LIB_DEPENDS= libpng.so:graphics/png \ libgif.so:graphics/giflib -USES= cmake compiler:c++11-lang pkgconfig sqlite tar:bzip2 xorg +USES= cmake compiler:c++11-lang jpeg pkgconfig sqlite tar:bzip2 xorg USE_LDCONFIG= yes USE_XORG= ice sm x11 xext USE_GITHUB= yes GH_ACCOUNT= davisking +EXTRACT_AFTER_ARGS= --exclude=${PORTNAME}-${DISTVERSION}/dlib/external \ + --no-same-owner --no-same-permissions + CMAKE_ON= BUILD_SHARED_LIBS OPTIONS_DEFINE= BLASLAPACK FFMPEG diff --git a/science/dlib-cpp/distinfo b/science/dlib-cpp/distinfo index 8f3862fa286a..5beba767785f 100644 --- a/science/dlib-cpp/distinfo +++ b/science/dlib-cpp/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1741012083 -SHA256 (davisking-dlib-v19.24.8_GH0.tar.gz) = 819cfd28639fe80ca28039f591a15e01772b7ada479de4a002b95bcb8077ce80 -SIZE (davisking-dlib-v19.24.8_GH0.tar.gz) = 18965261 +TIMESTAMP = 1748714072 +SHA256 (davisking-dlib-v20.0_GH0.tar.gz) = 705749801c7896f5c19c253b6be639f4cef2c1831a9606955f01b600b3d86d80 +SIZE (davisking-dlib-v20.0_GH0.tar.gz) = 18977636 diff --git a/science/dlib-cpp/pkg-plist b/science/dlib-cpp/pkg-plist index 2efa18ced207..a2a920512e2a 100644 --- a/science/dlib-cpp/pkg-plist +++ b/science/dlib-cpp/pkg-plist @@ -215,78 +215,6 @@ include/dlib/entropy_encoder_model/entropy_encoder_model_kernel_6.h include/dlib/entropy_encoder_model/entropy_encoder_model_kernel_abstract.h include/dlib/entropy_encoder_model/entropy_encoder_model_kernel_c.h include/dlib/error.h -include/dlib/external/cblas/cblas.h -include/dlib/external/cblas/cblas_f77.h -include/dlib/external/libjpeg/cderror.h -include/dlib/external/libjpeg/cdjpeg.h -include/dlib/external/libjpeg/jconfig.h -include/dlib/external/libjpeg/jdct.h -include/dlib/external/libjpeg/jerror.h -include/dlib/external/libjpeg/jinclude.h -include/dlib/external/libjpeg/jmemsys.h -include/dlib/external/libjpeg/jmorecfg.h -include/dlib/external/libjpeg/jpegint.h -include/dlib/external/libjpeg/jpeglib.h -include/dlib/external/libjpeg/jversion.h -include/dlib/external/libjpeg/transupp.h -include/dlib/external/libpng/png.h -include/dlib/external/libpng/pngconf.h -include/dlib/external/libpng/pngdebug.h -include/dlib/external/libpng/pnginfo.h -include/dlib/external/libpng/pnglibconf.h -include/dlib/external/libpng/pngpriv.h -include/dlib/external/libpng/pngstruct.h -include/dlib/external/pybind11/include/pybind11/attr.h -include/dlib/external/pybind11/include/pybind11/buffer_info.h -include/dlib/external/pybind11/include/pybind11/cast.h -include/dlib/external/pybind11/include/pybind11/chrono.h -include/dlib/external/pybind11/include/pybind11/common.h -include/dlib/external/pybind11/include/pybind11/complex.h -include/dlib/external/pybind11/include/pybind11/detail/class.h -include/dlib/external/pybind11/include/pybind11/detail/common.h -include/dlib/external/pybind11/include/pybind11/detail/descr.h -include/dlib/external/pybind11/include/pybind11/detail/init.h -include/dlib/external/pybind11/include/pybind11/detail/internals.h -include/dlib/external/pybind11/include/pybind11/detail/type_caster_base.h -include/dlib/external/pybind11/include/pybind11/detail/typeid.h -include/dlib/external/pybind11/include/pybind11/eigen.h -include/dlib/external/pybind11/include/pybind11/eigen/common.h -include/dlib/external/pybind11/include/pybind11/eigen/matrix.h -include/dlib/external/pybind11/include/pybind11/eigen/tensor.h -include/dlib/external/pybind11/include/pybind11/embed.h -include/dlib/external/pybind11/include/pybind11/eval.h -include/dlib/external/pybind11/include/pybind11/functional.h -include/dlib/external/pybind11/include/pybind11/gil.h -include/dlib/external/pybind11/include/pybind11/gil_safe_call_once.h -include/dlib/external/pybind11/include/pybind11/iostream.h -include/dlib/external/pybind11/include/pybind11/numpy.h -include/dlib/external/pybind11/include/pybind11/operators.h -include/dlib/external/pybind11/include/pybind11/options.h -include/dlib/external/pybind11/include/pybind11/pybind11.h -include/dlib/external/pybind11/include/pybind11/pytypes.h -include/dlib/external/pybind11/include/pybind11/stl.h -include/dlib/external/pybind11/include/pybind11/stl/filesystem.h -include/dlib/external/pybind11/include/pybind11/stl_bind.h -include/dlib/external/pybind11/include/pybind11/type_caster_pyobject_ptr.h -include/dlib/external/pybind11/include/pybind11/typing.h -include/dlib/external/pybind11/tools/FindCatch.cmake -include/dlib/external/pybind11/tools/FindEigen3.cmake -include/dlib/external/pybind11/tools/FindPythonLibsNew.cmake -include/dlib/external/pybind11/tools/JoinPaths.cmake -include/dlib/external/pybind11/tools/pybind11Common.cmake -include/dlib/external/pybind11/tools/pybind11NewTools.cmake -include/dlib/external/pybind11/tools/pybind11Tools.cmake -include/dlib/external/zlib/crc32.h -include/dlib/external/zlib/deflate.h -include/dlib/external/zlib/gzguts.h -include/dlib/external/zlib/inffast.h -include/dlib/external/zlib/inffixed.h -include/dlib/external/zlib/inflate.h -include/dlib/external/zlib/inftrees.h -include/dlib/external/zlib/trees.h -include/dlib/external/zlib/zconf.h -include/dlib/external/zlib/zlib.h -include/dlib/external/zlib/zutil.h include/dlib/fft/fft.h include/dlib/fft/fft_size.h include/dlib/fft/fft_stl.h @@ -1051,6 +979,8 @@ include/dlib/timer/timer_abstract.h include/dlib/timer/timer_heavy.h include/dlib/timing.h include/dlib/tokenizer.h +include/dlib/tokenizer/bpe_tokenizer.h +include/dlib/tokenizer/bpe_tokenizer_abstract.h include/dlib/tokenizer/tokenizer_kernel_1.h include/dlib/tokenizer/tokenizer_kernel_abstract.h include/dlib/tokenizer/tokenizer_kernel_c.h @@ -1082,7 +1012,7 @@ lib/cmake/dlib/dlib.cmake lib/cmake/dlib/dlibConfig.cmake lib/cmake/dlib/dlibConfigVersion.cmake lib/libdlib.so -lib/libdlib.so.19.24.8 +lib/libdlib.so.20.0.0 libdata/pkgconfig/dlib-1.pc @dir include/dlib/all @dir include/dlib/cmake_utils/test_for_avx @@ -1094,7 +1024,6 @@ libdata/pkgconfig/dlib-1.pc @dir include/dlib/cmake_utils/test_for_libwebp @dir include/dlib/cmake_utils/test_for_neon @dir include/dlib/cmake_utils/test_for_sse4 -@dir include/dlib/external/libpng/arm @dir include/dlib/test/blas_bindings @dir include/dlib/test/examples @dir include/dlib/test/ffmpeg_data diff --git a/science/dssp/Makefile b/science/dssp/Makefile index 7f52f5e5c342..2b65378d1409 100644 --- a/science/dssp/Makefile +++ b/science/dssp/Makefile @@ -1,6 +1,7 @@ PORTNAME= dssp DISTVERSIONPREFIX= v DISTVERSION= 4.4.11 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/dvc/Makefile b/science/dvc/Makefile deleted file mode 100644 index 4cad61186841..000000000000 --- a/science/dvc/Makefile +++ /dev/null @@ -1,40 +0,0 @@ -PORTNAME= dvc -DISTVERSION= 0.30.1 -PORTREVISION= 7 -CATEGORIES= science python -MASTER_SITES= PYPI - -MAINTAINER= yuri@FreeBSD.org -COMMENT= Git for data scientists: manage code and data together -WWW= https://dvc.org/ - -LICENSE= APACHE20 - -DEPRECATED= Depends on expired math/py-grandalf -EXPIRATION_DATE=2025-06-01 - -RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}appdirs>=1.4.3:devel/py-appdirs@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}asciimatics>=1.10.0:devel/py-asciimatics@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}colorama>=0.3.9:devel/py-colorama@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}configobj>=5.0.6:devel/py-configobj@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}configparser>=3.5.0:devel/py-configparser@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}distro>=1.3.0:sysutils/py-distro@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}future>=0.16.0:devel/py-future@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}gitpython>=2.1.8:devel/py-gitpython@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}grandalf>=0.7:math/py-grandalf@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}jsonpath-rw>0:devel/py-jsonpath-rw@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}nanotime>=0.5.2:devel/py-nanotime@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}networkx>=2.1:math/py-networkx@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}ply>=3.9:devel/py-ply@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}pyasn1>=0.4.1:devel/py-pyasn1@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}pyyaml>=3.12:devel/py-pyyaml@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}requests>=2.18.4:www/py-requests@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}schema>=0.6.7:devel/py-schema@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}zc.lockfile>0:devel/py-zc.lockfile@${PY_FLAVOR} - -USES= python -USE_PYTHON= distutils autoplist noflavors - -NO_ARCH= yes - -.include <bsd.port.mk> diff --git a/science/dvc/distinfo b/science/dvc/distinfo deleted file mode 100644 index 4c2fab04b2c1..000000000000 --- a/science/dvc/distinfo +++ /dev/null @@ -1,3 +0,0 @@ -TIMESTAMP = 1551843995 -SHA256 (dvc-0.30.1.tar.gz) = a223d011edab4e3e5227e62aa834e9fd311522070232890e55a4dd37500c4b2e -SIZE (dvc-0.30.1.tar.gz) = 91286 diff --git a/science/dvc/pkg-descr b/science/dvc/pkg-descr deleted file mode 100644 index a66a0f5bee82..000000000000 --- a/science/dvc/pkg-descr +++ /dev/null @@ -1,12 +0,0 @@ -Data Science Version Control or DVC is an open-source tool for data science and -machine learning projects. With a simple and flexible Git-like architecture and -interface it helps data scientists: -* manage machine learning models - versioning, including data sets and - transformations (scripts) that were used to generate models; -* make projects reproducible; -* make projects shareable; -* manage experiments with branching and metrics tracking. - -It aims to replace tools like Excel and Docs that are being commonly used as a -knowledge repo and a ledger for the team, ad-hoc scripts to track and move -deploy different model versions, ad-hoc data file suffixes and prefixes. diff --git a/science/dynare/Makefile b/science/dynare/Makefile index 0856cc00a8ed..d0babbf623e3 100644 --- a/science/dynare/Makefile +++ b/science/dynare/Makefile @@ -1,6 +1,6 @@ PORTNAME= dynare DISTVERSION= 5.4 -PORTREVISION= 13 +PORTREVISION= 14 CATEGORIES= science # economics MASTER_SITES= https://www.dynare.org/release/source/ diff --git a/science/eccodes/Makefile b/science/eccodes/Makefile index 621246ad0f47..9d4fac3000af 100644 --- a/science/eccodes/Makefile +++ b/science/eccodes/Makefile @@ -1,5 +1,5 @@ PORTNAME= eccodes -PORTVERSION= 2.41.0 +PORTVERSION= 2.42.0 DISTVERSIONSUFFIX= -Source CATEGORIES= science MASTER_SITES= https://confluence.ecmwf.int/download/attachments/45757960/ \ diff --git a/science/eccodes/distinfo b/science/eccodes/distinfo index 5623a88647de..4347e3129fb3 100644 --- a/science/eccodes/distinfo +++ b/science/eccodes/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1745177938 -SHA256 (eccodes-2.41.0-Source.tar.gz) = a1467842e11ed7f62a2f5cc1982e04eec62398f4962e6ba03ace7646f32cf270 -SIZE (eccodes-2.41.0-Source.tar.gz) = 12637191 +TIMESTAMP = 1751375037 +SHA256 (eccodes-2.42.0-Source.tar.gz) = 60371b357cb011dee546db2eabace5b7e27f0f87d3ea4a5adde7891371b3c128 +SIZE (eccodes-2.42.0-Source.tar.gz) = 12279749 diff --git a/science/eccodes/pkg-plist b/science/eccodes/pkg-plist index bdba82c7be1c..52d540fa23dd 100644 --- a/science/eccodes/pkg-plist +++ b/science/eccodes/pkg-plist @@ -492,3606 +492,35 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/bufr/tables/0/local/8/78/0/codetables/8199.table %%DATADIR%%/definitions/bufr/tables/0/local/8/78/0/element.table %%DATADIR%%/definitions/bufr/tables/0/local/8/78/0/sequence.def -%%DATADIR%%/definitions/bufr/tables/0/local/8/78/1/codetables/11199.table -%%DATADIR%%/definitions/bufr/tables/0/local/8/78/1/codetables/11200.table -%%DATADIR%%/definitions/bufr/tables/0/local/8/78/1/codetables/11201.table -%%DATADIR%%/definitions/bufr/tables/0/local/8/78/1/codetables/11208.table -%%DATADIR%%/definitions/bufr/tables/0/local/8/78/1/codetables/11209.table -%%DATADIR%%/definitions/bufr/tables/0/local/8/78/1/codetables/1193.table -%%DATADIR%%/definitions/bufr/tables/0/local/8/78/1/codetables/1194.table -%%DATADIR%%/definitions/bufr/tables/0/local/8/78/1/codetables/1200.table -%%DATADIR%%/definitions/bufr/tables/0/local/8/78/1/codetables/12195.table 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%%DATADIR%%/definitions/grib2/boot_multifield.def %%DATADIR%%/definitions/grib2/cfName.def %%DATADIR%%/definitions/grib2/cfVarName.def +%%DATADIR%%/definitions/grib2/chemFormula.def +%%DATADIR%%/definitions/grib2/chemId.def +%%DATADIR%%/definitions/grib2/chemName.def +%%DATADIR%%/definitions/grib2/chemShortName.def %%DATADIR%%/definitions/grib2/combinationOfAttributesOfTileConcept.def %%DATADIR%%/definitions/grib2/crraLocalVersion.table +%%DATADIR%%/definitions/grib2/crra_ci_suiteName.table %%DATADIR%%/definitions/grib2/crra_suiteName.table %%DATADIR%%/definitions/grib2/destineLocalVersion.table %%DATADIR%%/definitions/grib2/destine_activity.table @@ -19935,18 +15885,18 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/grib2/local/ecmf/template.4.65533.def %%DATADIR%%/definitions/grib2/local/ecmf/template.4.65534.def %%DATADIR%%/definitions/grib2/local/kwbc/template.3.32769.def -%%DATADIR%%/definitions/grib2/localConcepts/cerise/MTG2SwitchViaTablesVersionConcept.def +%%DATADIR%%/definitions/grib2/localConcepts/cerise/MTG2SwitchConcept.def %%DATADIR%%/definitions/grib2/localConcepts/cerise/cfName.def %%DATADIR%%/definitions/grib2/localConcepts/cerise/cfVarName.def -%%DATADIR%%/definitions/grib2/localConcepts/cerise/name.def -%%DATADIR%%/definitions/grib2/localConcepts/cerise/paramId.def -%%DATADIR%%/definitions/grib2/localConcepts/cerise/shortName.def -%%DATADIR%%/definitions/grib2/localConcepts/cerise/units.def +%%DATADIR%%/definitions/grib2/localConcepts/cerise/name.lte33.def +%%DATADIR%%/definitions/grib2/localConcepts/cerise/paramId.lte33.def +%%DATADIR%%/definitions/grib2/localConcepts/cerise/shortName.lte33.def +%%DATADIR%%/definitions/grib2/localConcepts/cerise/units.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/cnmc/name.def %%DATADIR%%/definitions/grib2/localConcepts/cnmc/paramId.def %%DATADIR%%/definitions/grib2/localConcepts/cnmc/shortName.def %%DATADIR%%/definitions/grib2/localConcepts/cnmc/units.def -%%DATADIR%%/definitions/grib2/localConcepts/destine/MTG2SwitchConcept.def +%%DATADIR%%/definitions/grib2/localConcepts/destine/MTG2SwitchViaTablesVersionConcept.def %%DATADIR%%/definitions/grib2/localConcepts/destine/cfName.def %%DATADIR%%/definitions/grib2/localConcepts/destine/destineOriginConcept.def %%DATADIR%%/definitions/grib2/localConcepts/destine/gridSpecificationConcept.def @@ -19957,9 +15907,13 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/grib2/localConcepts/destine/modelVersionConcept.HARMONIE-AROME.def %%DATADIR%%/definitions/grib2/localConcepts/destine/modelVersionConcept.IFS.def %%DATADIR%%/definitions/grib2/localConcepts/destine/name.def +%%DATADIR%%/definitions/grib2/localConcepts/destine/name.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/destine/paramId.def +%%DATADIR%%/definitions/grib2/localConcepts/destine/paramId.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/destine/shortName.def +%%DATADIR%%/definitions/grib2/localConcepts/destine/shortName.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/destine/units.def +%%DATADIR%%/definitions/grib2/localConcepts/destine/units.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/destinegen1/MTG2SwitchConcept.def %%DATADIR%%/definitions/grib2/localConcepts/destinegen1/destineOriginConcept.def %%DATADIR%%/definitions/grib2/localConcepts/destinegen1/gridSpecificationConcept.def @@ -19969,6 +15923,10 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/grib2/localConcepts/ecmf/cfName.legacy.def %%DATADIR%%/definitions/grib2/localConcepts/ecmf/cfVarName.def %%DATADIR%%/definitions/grib2/localConcepts/ecmf/cfVarName.legacy.def +%%DATADIR%%/definitions/grib2/localConcepts/ecmf/chemFormula.def +%%DATADIR%%/definitions/grib2/localConcepts/ecmf/chemId.def +%%DATADIR%%/definitions/grib2/localConcepts/ecmf/chemName.def +%%DATADIR%%/definitions/grib2/localConcepts/ecmf/chemShortName.def %%DATADIR%%/definitions/grib2/localConcepts/ecmf/marsLevtypeConcept.def %%DATADIR%%/definitions/grib2/localConcepts/ecmf/modelNameConcept.def %%DATADIR%%/definitions/grib2/localConcepts/ecmf/modelVersionConcept.IFS.def @@ -19977,15 +15935,24 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/grib2/localConcepts/ecmf/modelVersionConcept.aifs-ens.def %%DATADIR%%/definitions/grib2/localConcepts/ecmf/modelVersionConcept.aifs-single-mse.def %%DATADIR%%/definitions/grib2/localConcepts/ecmf/modelVersionConcept.aifs-single.def +%%DATADIR%%/definitions/grib2/localConcepts/ecmf/name.chemsplit.def %%DATADIR%%/definitions/grib2/localConcepts/ecmf/name.def %%DATADIR%%/definitions/grib2/localConcepts/ecmf/name.legacy.def +%%DATADIR%%/definitions/grib2/localConcepts/ecmf/name.lte33.def +%%DATADIR%%/definitions/grib2/localConcepts/ecmf/paramId.chemsplit.def %%DATADIR%%/definitions/grib2/localConcepts/ecmf/paramId.def %%DATADIR%%/definitions/grib2/localConcepts/ecmf/paramId.legacy.def +%%DATADIR%%/definitions/grib2/localConcepts/ecmf/paramId.lte33.def +%%DATADIR%%/definitions/grib2/localConcepts/ecmf/shortName.chemsplit.def %%DATADIR%%/definitions/grib2/localConcepts/ecmf/shortName.def %%DATADIR%%/definitions/grib2/localConcepts/ecmf/shortName.legacy.def +%%DATADIR%%/definitions/grib2/localConcepts/ecmf/shortName.lte33.def +%%DATADIR%%/definitions/grib2/localConcepts/ecmf/timespanConcept.def %%DATADIR%%/definitions/grib2/localConcepts/ecmf/typeOfLevelConcept.def +%%DATADIR%%/definitions/grib2/localConcepts/ecmf/units.chemsplit.def %%DATADIR%%/definitions/grib2/localConcepts/ecmf/units.def %%DATADIR%%/definitions/grib2/localConcepts/ecmf/units.legacy.def +%%DATADIR%%/definitions/grib2/localConcepts/ecmf/units.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/ecmf/unstructuredGrid.def %%DATADIR%%/definitions/grib2/localConcepts/ecmf/unstructuredGridSubtype.def %%DATADIR%%/definitions/grib2/localConcepts/ecmf/unstructuredGridType.def @@ -20001,23 +15968,27 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/grib2/localConcepts/efkl/units.def %%DATADIR%%/definitions/grib2/localConcepts/egrr/cfVarName.def %%DATADIR%%/definitions/grib2/localConcepts/egrr/name.def +%%DATADIR%%/definitions/grib2/localConcepts/egrr/name.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/egrr/paramId.def +%%DATADIR%%/definitions/grib2/localConcepts/egrr/paramId.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/egrr/shortName.def +%%DATADIR%%/definitions/grib2/localConcepts/egrr/shortName.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/egrr/units.def +%%DATADIR%%/definitions/grib2/localConcepts/egrr/units.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/ekmi/name.def %%DATADIR%%/definitions/grib2/localConcepts/ekmi/paramId.def %%DATADIR%%/definitions/grib2/localConcepts/ekmi/shortName.def %%DATADIR%%/definitions/grib2/localConcepts/ekmi/units.def %%DATADIR%%/definitions/grib2/localConcepts/era/MTG2SwitchConcept.def %%DATADIR%%/definitions/grib2/localConcepts/era/cfName.def -%%DATADIR%%/definitions/grib2/localConcepts/era/name.def %%DATADIR%%/definitions/grib2/localConcepts/era/name.legacy.def -%%DATADIR%%/definitions/grib2/localConcepts/era/paramId.def +%%DATADIR%%/definitions/grib2/localConcepts/era/name.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/era/paramId.legacy.def -%%DATADIR%%/definitions/grib2/localConcepts/era/shortName.def +%%DATADIR%%/definitions/grib2/localConcepts/era/paramId.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/era/shortName.legacy.def -%%DATADIR%%/definitions/grib2/localConcepts/era/units.def +%%DATADIR%%/definitions/grib2/localConcepts/era/shortName.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/era/units.legacy.def +%%DATADIR%%/definitions/grib2/localConcepts/era/units.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/era6/MTG2SwitchConcept.def %%DATADIR%%/definitions/grib2/localConcepts/era6/cfName.def %%DATADIR%%/definitions/grib2/localConcepts/era6/marsLevtypeConcept.def @@ -20033,67 +16004,97 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/grib2/localConcepts/eswi/paramId.def %%DATADIR%%/definitions/grib2/localConcepts/eswi/shortName.def %%DATADIR%%/definitions/grib2/localConcepts/eswi/units.def +%%DATADIR%%/definitions/grib2/localConcepts/fire/MTG2SwitchViaTablesVersionConcept.def %%DATADIR%%/definitions/grib2/localConcepts/hydro/MTG2SwitchConcept.def %%DATADIR%%/definitions/grib2/localConcepts/hydro/cfVarName.def -%%DATADIR%%/definitions/grib2/localConcepts/hydro/name.def -%%DATADIR%%/definitions/grib2/localConcepts/hydro/paramId.def -%%DATADIR%%/definitions/grib2/localConcepts/hydro/shortName.def -%%DATADIR%%/definitions/grib2/localConcepts/hydro/units.def +%%DATADIR%%/definitions/grib2/localConcepts/hydro/name.lte33.def +%%DATADIR%%/definitions/grib2/localConcepts/hydro/paramId.lte33.def +%%DATADIR%%/definitions/grib2/localConcepts/hydro/shortName.lte33.def +%%DATADIR%%/definitions/grib2/localConcepts/hydro/units.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/kwbc/cfVarName.def %%DATADIR%%/definitions/grib2/localConcepts/kwbc/name.def +%%DATADIR%%/definitions/grib2/localConcepts/kwbc/name.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/kwbc/paramId.def +%%DATADIR%%/definitions/grib2/localConcepts/kwbc/paramId.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/kwbc/shortName.def +%%DATADIR%%/definitions/grib2/localConcepts/kwbc/shortName.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/kwbc/typeOfLevelConcept.def %%DATADIR%%/definitions/grib2/localConcepts/kwbc/units.def +%%DATADIR%%/definitions/grib2/localConcepts/kwbc/units.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/lfpw/faFieldName.def %%DATADIR%%/definitions/grib2/localConcepts/lfpw/faLevelName.def %%DATADIR%%/definitions/grib2/localConcepts/lfpw/faModelName.def %%DATADIR%%/definitions/grib2/localConcepts/lfpw/name.def +%%DATADIR%%/definitions/grib2/localConcepts/lfpw/name.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/lfpw/paramId.def +%%DATADIR%%/definitions/grib2/localConcepts/lfpw/paramId.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/lfpw/shortName.def +%%DATADIR%%/definitions/grib2/localConcepts/lfpw/shortName.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/lfpw/units.def +%%DATADIR%%/definitions/grib2/localConcepts/lfpw/units.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/lfpw1/name.def %%DATADIR%%/definitions/grib2/localConcepts/lfpw1/paramId.def %%DATADIR%%/definitions/grib2/localConcepts/lfpw1/shortName.def %%DATADIR%%/definitions/grib2/localConcepts/lfpw1/units.def -%%DATADIR%%/definitions/grib2/localConcepts/nextgems/MTG2SwitchConcept.def +%%DATADIR%%/definitions/grib2/localConcepts/nextgems/MTG2SwitchViaTablesVersionConcept.def %%DATADIR%%/definitions/grib2/localConcepts/nextgems/cfName.def %%DATADIR%%/definitions/grib2/localConcepts/nextgems/marsLevtypeConcept.def %%DATADIR%%/definitions/grib2/localConcepts/nextgems/name.def +%%DATADIR%%/definitions/grib2/localConcepts/nextgems/name.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/nextgems/paramId.def +%%DATADIR%%/definitions/grib2/localConcepts/nextgems/paramId.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/nextgems/shortName.def +%%DATADIR%%/definitions/grib2/localConcepts/nextgems/shortName.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/nextgems/units.def +%%DATADIR%%/definitions/grib2/localConcepts/nextgems/units.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/s2s/MTG2SwitchViaTablesVersionConcept.def %%DATADIR%%/definitions/grib2/localConcepts/s2s/cfName.def %%DATADIR%%/definitions/grib2/localConcepts/s2s/cfVarName.def %%DATADIR%%/definitions/grib2/localConcepts/s2s/name.def +%%DATADIR%%/definitions/grib2/localConcepts/s2s/name.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/s2s/paramId.def +%%DATADIR%%/definitions/grib2/localConcepts/s2s/paramId.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/s2s/shortName.def +%%DATADIR%%/definitions/grib2/localConcepts/s2s/shortName.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/s2s/units.def +%%DATADIR%%/definitions/grib2/localConcepts/s2s/units.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/tigge/MTG2SwitchViaTablesVersionConcept.def %%DATADIR%%/definitions/grib2/localConcepts/tigge/cfVarName.def %%DATADIR%%/definitions/grib2/localConcepts/tigge/name.def +%%DATADIR%%/definitions/grib2/localConcepts/tigge/name.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/tigge/paramId.def +%%DATADIR%%/definitions/grib2/localConcepts/tigge/paramId.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/tigge/shortName.def +%%DATADIR%%/definitions/grib2/localConcepts/tigge/shortName.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/tigge/units.def +%%DATADIR%%/definitions/grib2/localConcepts/tigge/units.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/uerra/MTG2SwitchViaTablesVersionConcept.def %%DATADIR%%/definitions/grib2/localConcepts/uerra/cfName.def %%DATADIR%%/definitions/grib2/localConcepts/uerra/cfVarName.def %%DATADIR%%/definitions/grib2/localConcepts/uerra/marsLevtypeConcept.def %%DATADIR%%/definitions/grib2/localConcepts/uerra/name.def +%%DATADIR%%/definitions/grib2/localConcepts/uerra/name.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/uerra/paramId.def +%%DATADIR%%/definitions/grib2/localConcepts/uerra/paramId.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/uerra/shortName.def +%%DATADIR%%/definitions/grib2/localConcepts/uerra/shortName.lte33.def %%DATADIR%%/definitions/grib2/localConcepts/uerra/units.def +%%DATADIR%%/definitions/grib2/localConcepts/uerra/units.lte33.def %%DATADIR%%/definitions/grib2/ls_labeling.82.def %%DATADIR%%/definitions/grib2/marsLevtypeConcept.def %%DATADIR%%/definitions/grib2/mars_labeling.82.def %%DATADIR%%/definitions/grib2/mars_labeling.def %%DATADIR%%/definitions/grib2/modelNameConcept.def +%%DATADIR%%/definitions/grib2/name.chemsplit.def %%DATADIR%%/definitions/grib2/name.def %%DATADIR%%/definitions/grib2/name.legacy.def +%%DATADIR%%/definitions/grib2/name.lte33.def +%%DATADIR%%/definitions/grib2/paramId.chemsplit.def %%DATADIR%%/definitions/grib2/paramId.def %%DATADIR%%/definitions/grib2/paramId.legacy.def +%%DATADIR%%/definitions/grib2/paramId.lte33.def %%DATADIR%%/definitions/grib2/parameters.def +%%DATADIR%%/definitions/grib2/paramtypeConcept.def %%DATADIR%%/definitions/grib2/postProcessingConcept.def %%DATADIR%%/definitions/grib2/post_meta_data.hook.products_12.def %%DATADIR%%/definitions/grib2/productDefinitionTemplateConcept.def @@ -20125,111 +16126,12 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/grib2/section.7.def %%DATADIR%%/definitions/grib2/section.8.def %%DATADIR%%/definitions/grib2/sections.def 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-%%DATADIR%%/definitions/grib2/tables/0/4.91.table -%%DATADIR%%/definitions/grib2/tables/0/5.0.table -%%DATADIR%%/definitions/grib2/tables/0/5.1.table -%%DATADIR%%/definitions/grib2/tables/0/5.2.table -%%DATADIR%%/definitions/grib2/tables/0/5.3.table -%%DATADIR%%/definitions/grib2/tables/0/5.4.table -%%DATADIR%%/definitions/grib2/tables/0/5.40.table -%%DATADIR%%/definitions/grib2/tables/0/5.5.table -%%DATADIR%%/definitions/grib2/tables/0/5.6.table -%%DATADIR%%/definitions/grib2/tables/0/5.7.table -%%DATADIR%%/definitions/grib2/tables/0/5.8.table -%%DATADIR%%/definitions/grib2/tables/0/5.9.table -%%DATADIR%%/definitions/grib2/tables/0/6.0.table %%DATADIR%%/definitions/grib2/tables/1.0.table %%DATADIR%%/definitions/grib2/tables/1/0.0.table %%DATADIR%%/definitions/grib2/tables/1/1.0.table @@ -23984,6 +19886,188 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/grib2/tables/34/5.6.table %%DATADIR%%/definitions/grib2/tables/34/5.7.table %%DATADIR%%/definitions/grib2/tables/34/6.0.table +%%DATADIR%%/definitions/grib2/tables/35/5.40.table +%%DATADIR%%/definitions/grib2/tables/35/0.0.table +%%DATADIR%%/definitions/grib2/tables/35/1.0.table +%%DATADIR%%/definitions/grib2/tables/35/1.1.table +%%DATADIR%%/definitions/grib2/tables/35/1.2.table +%%DATADIR%%/definitions/grib2/tables/35/1.3.table +%%DATADIR%%/definitions/grib2/tables/35/1.4.table +%%DATADIR%%/definitions/grib2/tables/35/1.5.table +%%DATADIR%%/definitions/grib2/tables/35/1.6.table +%%DATADIR%%/definitions/grib2/tables/35/3.0.table +%%DATADIR%%/definitions/grib2/tables/35/3.1.table +%%DATADIR%%/definitions/grib2/tables/35/3.10.table +%%DATADIR%%/definitions/grib2/tables/35/3.11.table +%%DATADIR%%/definitions/grib2/tables/35/3.12.table +%%DATADIR%%/definitions/grib2/tables/35/3.13.table +%%DATADIR%%/definitions/grib2/tables/35/3.15.table +%%DATADIR%%/definitions/grib2/tables/35/3.2.table +%%DATADIR%%/definitions/grib2/tables/35/3.20.table 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+%%DATADIR%%/definitions/grib2/tables/35/4.236.table +%%DATADIR%%/definitions/grib2/tables/35/4.238.table +%%DATADIR%%/definitions/grib2/tables/35/4.239.table +%%DATADIR%%/definitions/grib2/tables/35/4.240.table +%%DATADIR%%/definitions/grib2/tables/35/4.241.table +%%DATADIR%%/definitions/grib2/tables/35/4.242.table +%%DATADIR%%/definitions/grib2/tables/35/4.243.table +%%DATADIR%%/definitions/grib2/tables/35/4.244.table +%%DATADIR%%/definitions/grib2/tables/35/4.246.table +%%DATADIR%%/definitions/grib2/tables/35/4.247.table +%%DATADIR%%/definitions/grib2/tables/35/4.248.table +%%DATADIR%%/definitions/grib2/tables/35/4.249.table +%%DATADIR%%/definitions/grib2/tables/35/4.250.table +%%DATADIR%%/definitions/grib2/tables/35/4.251.table +%%DATADIR%%/definitions/grib2/tables/35/4.252.table +%%DATADIR%%/definitions/grib2/tables/35/4.253.table +%%DATADIR%%/definitions/grib2/tables/35/4.3.table +%%DATADIR%%/definitions/grib2/tables/35/4.333.table +%%DATADIR%%/definitions/grib2/tables/35/4.335.table +%%DATADIR%%/definitions/grib2/tables/35/4.336.table +%%DATADIR%%/definitions/grib2/tables/35/4.4.table +%%DATADIR%%/definitions/grib2/tables/35/4.5.table +%%DATADIR%%/definitions/grib2/tables/35/4.6.table +%%DATADIR%%/definitions/grib2/tables/35/4.7.table +%%DATADIR%%/definitions/grib2/tables/35/4.8.table +%%DATADIR%%/definitions/grib2/tables/35/4.9.table +%%DATADIR%%/definitions/grib2/tables/35/4.91.table +%%DATADIR%%/definitions/grib2/tables/35/5.0.table +%%DATADIR%%/definitions/grib2/tables/35/5.1.table +%%DATADIR%%/definitions/grib2/tables/35/5.2.table +%%DATADIR%%/definitions/grib2/tables/35/5.25.table +%%DATADIR%%/definitions/grib2/tables/35/5.26.table +%%DATADIR%%/definitions/grib2/tables/35/5.3.table +%%DATADIR%%/definitions/grib2/tables/35/5.4.table +%%DATADIR%%/definitions/grib2/tables/35/5.5.table +%%DATADIR%%/definitions/grib2/tables/35/5.6.table +%%DATADIR%%/definitions/grib2/tables/35/5.7.table +%%DATADIR%%/definitions/grib2/tables/35/6.0.table %%DATADIR%%/definitions/grib2/tables/4/0.0.table %%DATADIR%%/definitions/grib2/tables/4/1.0.table %%DATADIR%%/definitions/grib2/tables/4/1.1.table @@ -25035,11 +21119,14 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/grib2/templates/template.7.second_order.def %%DATADIR%%/definitions/grib2/tiggeLocalVersion.table %%DATADIR%%/definitions/grib2/tigge_suiteName.table +%%DATADIR%%/definitions/grib2/timespanConcept.def %%DATADIR%%/definitions/grib2/typeOfLevelConcept.def %%DATADIR%%/definitions/grib2/typeOfUnstructuredGridConcept.def %%DATADIR%%/definitions/grib2/uerraLocalVersion.table +%%DATADIR%%/definitions/grib2/units.chemsplit.def %%DATADIR%%/definitions/grib2/units.def %%DATADIR%%/definitions/grib2/units.legacy.def +%%DATADIR%%/definitions/grib2/units.lte33.def %%DATADIR%%/definitions/grib2/unstructuredGridConcept.def %%DATADIR%%/definitions/grib2/unstructuredGridSubtype.def %%DATADIR%%/definitions/grib2/unstructuredGridType.def @@ -25872,7 +21959,6 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/mars/stream.table %%DATADIR%%/definitions/mars/type.table %%DATADIR%%/definitions/mars/wave_domain.def -%%DATADIR%%/definitions/mars_param.table %%DATADIR%%/definitions/metar/CCCC.txt %%DATADIR%%/definitions/metar/boot.def %%DATADIR%%/definitions/metar/boot.flexible.def @@ -25934,7 +22020,6 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/metar/wind_Trend4.def %%DATADIR%%/definitions/metar/wind_shear.def %%DATADIR%%/definitions/metar/wrong_delayed.def -%%DATADIR%%/definitions/param_id.table %%DATADIR%%/definitions/param_limits.def %%DATADIR%%/definitions/parameters_version.def %%DATADIR%%/definitions/stepUnits.table diff --git a/science/elk/Makefile b/science/elk/Makefile index a092be431179..3901d4ab49f2 100644 --- a/science/elk/Makefile +++ b/science/elk/Makefile @@ -1,6 +1,6 @@ PORTNAME= elk DISTVERSION= 10.3.12 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science MASTER_SITES= SF/${PORTNAME} PKGNAMESUFFIX= -chemistry diff --git a/science/elmerfem/Makefile b/science/elmerfem/Makefile index 0e5a8d54d2dc..6922d8d4b4eb 100644 --- a/science/elmerfem/Makefile +++ b/science/elmerfem/Makefile @@ -1,7 +1,7 @@ PORTNAME= elmerfem DISTVERSIONPREFIX= release- DISTVERSION= 9.0 -PORTREVISION= 21 +PORTREVISION= 22 CATEGORIES= science PATCH_SITES= https://github.com/ElmerCSC/${PORTNAME}/commit/ @@ -9,10 +9,12 @@ PATCHFILES= 48e9430c.patch:-p1 # https://github.com/ElmerCSC/elmerfem/pull/294 MAINTAINER= henrik@gulbra.net COMMENT= Multiphysical simulation software -WWW= https://www.csc.fi/web/elmer +WWW= https://www.elmerfem.org/blog/ LICENSE= GPLv2 +BROKEN= fails to build with vtk-9.5.0, see https://github.com/ElmerCSC/elmerfem/issues/677 + LIB_DEPENDS= libblas.so:math/blas \ libhdf5.so:science/hdf5 \ libmetis.so:math/metis \ diff --git a/science/fastjet/Makefile b/science/fastjet/Makefile index 8990a1950f62..00a5ee17b4c4 100644 --- a/science/fastjet/Makefile +++ b/science/fastjet/Makefile @@ -1,5 +1,5 @@ PORTNAME= fastjet -DISTVERSION= 3.4.3 +DISTVERSION= 3.5.1 CATEGORIES= science MASTER_SITES= https://fastjet.fr/repo/ @@ -46,7 +46,7 @@ post-install: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/lib*.so* post-install-PYTHON-on: - @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/_fastjet.so.0.0.0 + @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/_fastjet_swig.so.0.0.0 do-test: # python tests diff --git a/science/fastjet/distinfo b/science/fastjet/distinfo index c318c545d2f6..896e7e12357e 100644 --- a/science/fastjet/distinfo +++ b/science/fastjet/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1730346663 -SHA256 (fastjet-3.4.3.tar.gz) = cc175471bfab8656b8c6183a8e5e9ad05d5f7506e46f3212a9a8230905b8f6a3 -SIZE (fastjet-3.4.3.tar.gz) = 2984798 +TIMESTAMP = 1755888400 +SHA256 (fastjet-3.5.1.tar.gz) = 9a4154163e72041dee3fdde9cb24e814625e178091a8734a6ad5375e5371b423 +SIZE (fastjet-3.5.1.tar.gz) = 3069022 diff --git a/science/fastjet/pkg-plist b/science/fastjet/pkg-plist index e3e4ce7ab677..5f83019a7641 100644 --- a/science/fastjet/pkg-plist +++ b/science/fastjet/pkg-plist @@ -128,12 +128,13 @@ lib/libsiscone_spherical.a lib/libsiscone_spherical.so lib/libsiscone_spherical.so.0 lib/libsiscone_spherical.so.0.0.0 -%%PYTHON%%%%PYTHON_SITELIBDIR%%/__pycache__/fastjet%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/__pycache__/fastjet%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/_fastjet.a -%%PYTHON%%%%PYTHON_SITELIBDIR%%/_fastjet.so -%%PYTHON%%%%PYTHON_SITELIBDIR%%/_fastjet.so.0 -%%PYTHON%%%%PYTHON_SITELIBDIR%%/_fastjet.so.0.0.0 +%%PYTHON%%%%PYTHON_SITELIBDIR%%/__pycache__/fastjet%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/__pycache__/fastjet%%PYTHON_TAG%%.opt-2.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/__pycache__/fastjet%%PYTHON_TAG%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/_fastjet_swig.a +%%PYTHON%%%%PYTHON_SITELIBDIR%%/_fastjet_swig.so +%%PYTHON%%%%PYTHON_SITELIBDIR%%/_fastjet_swig.so.0 +%%PYTHON%%%%PYTHON_SITELIBDIR%%/_fastjet_swig.so.0.0.0 %%PYTHON%%%%PYTHON_SITELIBDIR%%/fastjet.py %%PYTHON%%%%DATADIR%%/pyinterface/FastJetPythonExtensions.hh %%PYTHON%%%%DATADIR%%/pyinterface/fastjet-doc.i diff --git a/science/fleur/Makefile b/science/fleur/Makefile index f8e5cc7bf64b..062471209bd4 100644 --- a/science/fleur/Makefile +++ b/science/fleur/Makefile @@ -1,6 +1,6 @@ PORTNAME= fleur DISTVERSION= 7.2 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science # chemistry MAINTAINER= yuri@FreeBSD.org diff --git a/science/gchemutils/Makefile b/science/gchemutils/Makefile index 7c54225e49b6..644ef599a5f7 100644 --- a/science/gchemutils/Makefile +++ b/science/gchemutils/Makefile @@ -1,6 +1,6 @@ PORTNAME= gchemutils PORTVERSION= 0.14.17 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science MASTER_SITES= SAVANNAH/${PORTNAME}/${PORTVERSION:R} DISTNAME= gnome-chemistry-utils-${PORTVERSION} diff --git a/science/gemmi/Makefile b/science/gemmi/Makefile index bca3ebaed373..aa0f3083bca2 100644 --- a/science/gemmi/Makefile +++ b/science/gemmi/Makefile @@ -1,11 +1,12 @@ PORTNAME= gemmi DISTVERSIONPREFIX= v -DISTVERSION= 0.7.1 +DISTVERSION= 0.7.3 CATEGORIES= science # chemistry MAINTAINER= yuri@FreeBSD.org COMMENT= Macromolecular crystallography library and utilities -WWW= https://gemmi.readthedocs.io/en/latest/ +WWW= https://gemmi.readthedocs.io/en/latest/ \ + https://github.com/project-gemmi/gemmi LICENSE= MPL20 LICENSE_FILE= ${WRKSRC}/LICENSE.txt @@ -25,7 +26,7 @@ FORTRAN_USES= fortran FORTRAN_CMAKE_BOOL= USE_FORTRAN FORTRAN_BROKEN= project option doesn't do anything, see https://github.com/project-gemmi/gemmi/issues/232 -# tests as of 0.7.1 (run work/.build/cpptest): +# tests as of 0.7.3 (run work/.build/cpptest): # [doctest] test cases: 14 | 14 passed | 0 failed | 0 skipped # [doctest] assertions: 129 | 129 passed | 0 failed | # [doctest] Status: SUCCESS! diff --git a/science/gemmi/distinfo b/science/gemmi/distinfo index 49c83ebc50e8..a7884ddf53a9 100644 --- a/science/gemmi/distinfo +++ b/science/gemmi/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1742884325 -SHA256 (project-gemmi-gemmi-v0.7.1_GH0.tar.gz) = 5d87c3e82ee159f5642d7c083a74e00ca9cc038ccf9be2522d7ae985f3377393 -SIZE (project-gemmi-gemmi-v0.7.1_GH0.tar.gz) = 1910265 +TIMESTAMP = 1753139349 +SHA256 (project-gemmi-gemmi-v0.7.3_GH0.tar.gz) = ed5e1d0665f27d623d877fa36f6c99a5de21310cc8715337ff9f6b545bd2e9d3 +SIZE (project-gemmi-gemmi-v0.7.3_GH0.tar.gz) = 1924234 diff --git a/science/gemmi/pkg-plist b/science/gemmi/pkg-plist index c28c9d130ae7..965571f541a2 100644 --- a/science/gemmi/pkg-plist +++ b/science/gemmi/pkg-plist @@ -23,6 +23,7 @@ include/gemmi/crd.hpp include/gemmi/ddl.hpp include/gemmi/dencalc.hpp include/gemmi/dirwalk.hpp +include/gemmi/dssp.hpp include/gemmi/ecalc.hpp include/gemmi/eig3.hpp include/gemmi/elem.hpp diff --git a/science/ghemical/Makefile b/science/ghemical/Makefile index 0d393aa81339..3900f5d87dc8 100644 --- a/science/ghemical/Makefile +++ b/science/ghemical/Makefile @@ -1,6 +1,6 @@ PORTNAME= ghemical PORTVERSION= 3.0.0 -PORTREVISION= 28 +PORTREVISION= 29 CATEGORIES= science MASTER_SITES= http://bioinformatics.org/ghemical/download/%SUBDIR%/ MASTER_SITE_SUBDIR= release20111012 current diff --git a/science/ghmm/Makefile b/science/ghmm/Makefile index b665afc62876..2b596af2cb00 100644 --- a/science/ghmm/Makefile +++ b/science/ghmm/Makefile @@ -1,6 +1,6 @@ PORTNAME= ghmm DISTVERSION= 0.9-rc3 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science math MASTER_SITES= SF/${PORTNAME}/${PORTNAME}/${PORTNAME}%20${DISTVERSION} diff --git a/science/gnudatalanguage/Makefile b/science/gnudatalanguage/Makefile index cc3068fab6eb..bcc3ee4ec241 100644 --- a/science/gnudatalanguage/Makefile +++ b/science/gnudatalanguage/Makefile @@ -1,5 +1,6 @@ PORTNAME= gnudatalanguage PORTVERSION= 1.1.1 +PORTREVISION= 1 DISTVERSIONPREFIX= v CATEGORIES= science lang MASTER_SITES= https://github.com/${PORTNAME}/gdl/releases/download/v${PORTVERSION}/ diff --git a/science/gramps/Makefile b/science/gramps/Makefile index 327654ad23ee..f261cd0a1aa4 100644 --- a/science/gramps/Makefile +++ b/science/gramps/Makefile @@ -1,5 +1,5 @@ PORTNAME= gramps -DISTVERSION= 6.0.1 +DISTVERSION= 6.0.4 CATEGORIES= science gnome python MASTER_SITES= PYPI diff --git a/science/gramps/distinfo b/science/gramps/distinfo index 3ba83716f73f..30016e379016 100644 --- a/science/gramps/distinfo +++ b/science/gramps/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1745218089 -SHA256 (gramps-6.0.1.tar.gz) = b4dfa633f2f8736826cd10143935b9b3ceb950b66191e9c35aebe80c62e883db -SIZE (gramps-6.0.1.tar.gz) = 21650631 +TIMESTAMP = 1754945114 +SHA256 (gramps-6.0.4.tar.gz) = ebabb1cfa8dc61859ee0e9c4ad0b54c94ccff2809dd1b0895a38a46b80382692 +SIZE (gramps-6.0.4.tar.gz) = 21963080 diff --git a/science/hypre/Makefile b/science/hypre/Makefile index d5df638850a3..a439de1d4f3c 100644 --- a/science/hypre/Makefile +++ b/science/hypre/Makefile @@ -1,6 +1,7 @@ PORTNAME= hypre DISTVERSIONPREFIX= v DISTVERSION= 2.33.0 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/kalzium/distinfo b/science/kalzium/distinfo index 95a697f2ede1..dc9bdf4527dc 100644 --- a/science/kalzium/distinfo +++ b/science/kalzium/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1746557949 -SHA256 (KDE/release-service/25.04.1/kalzium-25.04.1.tar.xz) = 31a31a45dc2d7c5581066d5e6654c2038e2c73b15126328170e39fdf361a1b64 -SIZE (KDE/release-service/25.04.1/kalzium-25.04.1.tar.xz) = 22660736 +TIMESTAMP = 1754646547 +SHA256 (KDE/release-service/25.08.0/kalzium-25.08.0.tar.xz) = 8765737e7baeb7fb0d0c16112ce11694ddb90a102e8e6b3e723dae9d595b8529 +SIZE (KDE/release-service/25.08.0/kalzium-25.08.0.tar.xz) = 22650880 diff --git a/science/kalzium/pkg-plist b/science/kalzium/pkg-plist index 6d96ce611615..08dc853471f9 100644 --- a/science/kalzium/pkg-plist +++ b/science/kalzium/pkg-plist @@ -10,6 +10,9 @@ include/libkdeedu/psetables.h include/libkdeedu/science_export.h include/libkdeedu/spectrum.h include/libkdeedu/spectrumparser.h +lib/libcompoundviewer.so +lib/libcompoundviewer.so.5 +lib/libcompoundviewer.so.5.0.0 lib/libscience.so lib/libscience.so.5 lib/libscience.so.5.0.0 @@ -348,6 +351,7 @@ share/icons/hicolor/scalable/apps/kalzium.svgz %%DATADIR%%/icons/hicolor/scalable/actions/statematter.svgz %%DATADIR%%/icons/hicolor/scalable/actions/timeline.svgz %%DATADIR%%/icons/hicolor/scalable/actions/tooltip.svgz +share/knsrcfiles/kalzium.knsrc share/libkdeedu/data/elements.xml share/libkdeedu/data/isotopes.xml share/libkdeedu/data/spectra.xml @@ -383,6 +387,7 @@ share/locale/hi/LC_MESSAGES/kalzium.mo share/locale/hne/LC_MESSAGES/kalzium.mo share/locale/hr/LC_MESSAGES/kalzium.mo share/locale/hu/LC_MESSAGES/kalzium.mo +share/locale/ia/LC_MESSAGES/kalzium.mo share/locale/is/LC_MESSAGES/kalzium.mo share/locale/it/LC_MESSAGES/kalzium.mo share/locale/ja/LC_MESSAGES/kalzium.mo @@ -424,6 +429,21 @@ share/locale/uk/LC_MESSAGES/kalzium.mo share/locale/xh/LC_MESSAGES/kalzium.mo share/locale/zh_CN/LC_MESSAGES/kalzium.mo share/locale/zh_TW/LC_MESSAGES/kalzium.mo +share/man/ca/man1/kalzium.1.gz +share/man/da/man1/kalzium.1.gz +share/man/de/man1/kalzium.1.gz +share/man/es/man1/kalzium.1.gz +share/man/et/man1/kalzium.1.gz +share/man/fr/man1/kalzium.1.gz +share/man/gl/man1/kalzium.1.gz +share/man/it/man1/kalzium.1.gz share/man/man1/kalzium.1.gz +share/man/nl/man1/kalzium.1.gz +share/man/pl/man1/kalzium.1.gz +share/man/pt/man1/kalzium.1.gz +share/man/pt_BR/man1/kalzium.1.gz +share/man/ru/man1/kalzium.1.gz +share/man/sv/man1/kalzium.1.gz +share/man/uk/man1/kalzium.1.gz share/metainfo/org.kde.kalzium.appdata.xml share/qlogging-categories6/kalzium.categories diff --git a/science/lammps/Makefile b/science/lammps/Makefile index 1bdf467a781d..ca1ee8bb2653 100644 --- a/science/lammps/Makefile +++ b/science/lammps/Makefile @@ -1,6 +1,6 @@ PORTNAME= lammps PORTVERSION= ${GH_TAGNAME:C/(stable|patch)_([0-9]{1,2})([A-Z][a-z][a-z])([0-9]{4})/\4.\3.\2/S/Jan/01/S/Feb/02/S/Mar/03/S/Apr/04/S/May/05/S/Jun/06/S/Jul/07/S/Aug/08/S/Sep/09/S/Oct/10/S/Nov/11/S/Dec/12/S/_update/./:C/\.([1-9])$/.0\1/:S/.//g} -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/libaec/Makefile b/science/libaec/Makefile index 8df9c8eecaa7..4c96052c3035 100644 --- a/science/libaec/Makefile +++ b/science/libaec/Makefile @@ -1,5 +1,5 @@ PORTNAME= libaec -PORTVERSION= 1.1.3 +PORTVERSION= 1.1.4 CATEGORIES= science MASTER_SITES= https://github.com/MathisRosenhauer/libaec/releases/download/v${PORTVERSION}/ @@ -13,7 +13,11 @@ LICENSE_FILE= ${WRKSRC}/LICENSE.txt USES= cmake:testing -CMAKE_OFF= AEC_FUZZING BUILD_TESTING +CMAKE_OFF= AEC_FUZZING \ + BUILD_TESTING +CMAKE_ON= BUILD_SHARED_LIBS \ + BUILD_STATIC_LIBS \ + libaec_INCLUDE_PACKAGING USE_LDCONFIG= yes .include <bsd.port.mk> diff --git a/science/libaec/distinfo b/science/libaec/distinfo index 608c4223f5e4..d36e3dc23478 100644 --- a/science/libaec/distinfo +++ b/science/libaec/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1711541240 -SHA256 (libaec-1.1.3.tar.gz) = bd8bea8b69ca602796b2daf17b0a7de019ce3c3bd0ad56fa9ef4a631a4088058 -SIZE (libaec-1.1.3.tar.gz) = 3137647 +TIMESTAMP = 1750188012 +SHA256 (libaec-1.1.4.tar.gz) = 1b9f3b913d9111469a83820ab62bb6a9f3ec7a5f9b6d681761776aecbc7fefbe +SIZE (libaec-1.1.4.tar.gz) = 3148407 diff --git a/science/libaec/pkg-plist b/science/libaec/pkg-plist index 703f76e3068c..c325028be7b8 100644 --- a/science/libaec/pkg-plist +++ b/science/libaec/pkg-plist @@ -1,11 +1,13 @@ -cmake/libaec-config-version.cmake -cmake/libaec-config.cmake include/libaec.h include/szlib.h +lib/cmake/libaec/libaec-config-version.cmake +lib/cmake/libaec/libaec-config.cmake +lib/cmake/libaec/libaec-targets-%%CMAKE_BUILD_TYPE%%.cmake +lib/cmake/libaec/libaec-targets.cmake lib/libaec.a lib/libaec.so lib/libaec.so.0 -lib/libaec.so.0.1.3 +lib/libaec.so.0.1.4 lib/libsz.a lib/libsz.so lib/libsz.so.2 diff --git a/science/libcifpp/Makefile b/science/libcifpp/Makefile index 7e532ad196e9..08680c8e05d4 100644 --- a/science/libcifpp/Makefile +++ b/science/libcifpp/Makefile @@ -1,7 +1,7 @@ PORTNAME= libcifpp DISTVERSIONPREFIX= v DISTVERSION= 7.0.8 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MASTER_SITES= https://files.wwpdb.org/pub/pdb/data/monomers/:components DISTFILES= components.cif.gz:components diff --git a/science/libcint/Makefile b/science/libcint/Makefile index af528fdf2ec6..030c5de31ee3 100644 --- a/science/libcint/Makefile +++ b/science/libcint/Makefile @@ -1,7 +1,6 @@ PORTNAME= libcint DISTVERSIONPREFIX= v -DISTVERSION= 6.1.2 -PORTREVISION= 2 +DISTVERSION= 6.1.3 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -24,7 +23,7 @@ PLIST_FILES= include/cint.h \ include/cint_funcs.h \ lib/libcint.so \ lib/libcint.so.${PORTVERSION:R:R} \ - lib/libcint.so.6.1.1 # see https://github.com/sunqm/libcint/issues/106 + lib/libcint.so.${PORTVERSION} #lib/libcint.so.${PORTVERSION} post-patch: @@ -39,4 +38,6 @@ do-test: # needs science/py-pyscf, pending https://github.com/pyscf/pyscf/issues ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} test +# tests as of 6.1.3: 100% tests passed, 0 tests failed out of 2 + .include <bsd.port.mk> diff --git a/science/libcint/distinfo b/science/libcint/distinfo index 947086b18216..c2d4cf4a3f83 100644 --- a/science/libcint/distinfo +++ b/science/libcint/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1710384136 -SHA256 (sunqm-libcint-v6.1.2_GH0.tar.gz) = 8287e1eaf2b8c8e19eb7a8ea92fd73898f0884023c503b84624610400adb25c4 -SIZE (sunqm-libcint-v6.1.2_GH0.tar.gz) = 50862041 +TIMESTAMP = 1755587717 +SHA256 (sunqm-libcint-v6.1.3_GH0.tar.gz) = e4d977d4aeb4d5b87639ea57a2d2f1d5c1001f3f94e480b08c297a6cbc186f27 +SIZE (sunqm-libcint-v6.1.3_GH0.tar.gz) = 50867546 diff --git a/science/libcint/files/patch-src_c2f.h b/science/libcint/files/patch-src_c2f.h deleted file mode 100644 index b7d3deccc865..000000000000 --- a/science/libcint/files/patch-src_c2f.h +++ /dev/null @@ -1,10 +0,0 @@ ---- src/c2f.h.orig 2018-03-21 00:24:56 UTC -+++ src/c2f.h -@@ -4,6 +4,7 @@ - */ - - #include "config.h" -+#include <sys/types.h> - - #define ALL_CINT_FORTRAN_(NAME) \ - int c##NAME##_sph_(double *out, int *shls, int *atm, int *natm, \ diff --git a/science/libint2-psi4/Makefile b/science/libint2-psi4/Makefile index 1894026c3442..3ac7e76bd463 100644 --- a/science/libint2-psi4/Makefile +++ b/science/libint2-psi4/Makefile @@ -1,6 +1,6 @@ PORTNAME= libint2-psi4 DISTVERSION= 0.1-${VERSION} -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science MASTER_SITES= https://github.com/loriab/libint/releases/download/v${DISTVERSION:C/-.*//}/ DISTFILES= libint-${VERSION}-post1-5-4-3-6-5-4_mm4f12ob2_1.tgz diff --git a/science/libint2/Makefile b/science/libint2/Makefile index 3ce2d7b5b56c..49d12c0e9529 100644 --- a/science/libint2/Makefile +++ b/science/libint2/Makefile @@ -1,6 +1,7 @@ PORTNAME= libint DISTVERSIONPREFIX= v DISTVERSION= 2.11.0 +PORTREVISION= 1 CATEGORIES= science PKGNAMESUFFIX= 2 diff --git a/science/libkml/Makefile b/science/libkml/Makefile index 7079f2ce974f..7a1d72729c2a 100644 --- a/science/libkml/Makefile +++ b/science/libkml/Makefile @@ -1,6 +1,6 @@ PORTNAME= libkml PORTVERSION= 1.3.0 -PORTREVISION= 29 +PORTREVISION= 30 CATEGORIES= science MAINTAINER= sunpoet@FreeBSD.org diff --git a/science/liblinear/Makefile b/science/liblinear/Makefile index 47e270f7bd40..def48c0f720a 100644 --- a/science/liblinear/Makefile +++ b/science/liblinear/Makefile @@ -1,5 +1,5 @@ PORTNAME= liblinear -PORTVERSION= 2.48 +PORTVERSION= 2.49 CATEGORIES= science math MASTER_SITES= https://www.csie.ntu.edu.tw/~cjlin/liblinear/ \ https://www.csie.ntu.edu.tw/~cjlin/liblinear/oldfiles/ diff --git a/science/liblinear/distinfo b/science/liblinear/distinfo index 8038611ce025..d48db96c0dda 100644 --- a/science/liblinear/distinfo +++ b/science/liblinear/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1738088850 -SHA256 (liblinear-2.48.tar.gz) = 72ea3853a9fb430b49c3196177d8acdffd2dadb5901832ee323465792087e8cc -SIZE (liblinear-2.48.tar.gz) = 73035 +TIMESTAMP = 1748495705 +SHA256 (liblinear-2.49.tar.gz) = 166ca3c741b2207a74978cdb55077261be43b1e58e55f2b4c4f40e6ec1d8a347 +SIZE (liblinear-2.49.tar.gz) = 74356 diff --git a/science/liggghts/Makefile b/science/liggghts/Makefile index dadf1e6ed49b..d088170996e3 100644 --- a/science/liggghts/Makefile +++ b/science/liggghts/Makefile @@ -1,6 +1,6 @@ PORTNAME= liggghts DISTVERSION= 3.8.0-58 -PORTREVISION= 6 +PORTREVISION= 7 DISTVERSIONSUFFIX= -g6e28cfe3 CATEGORIES= science diff --git a/science/maeparser/Makefile b/science/maeparser/Makefile index 268fa5cc87ac..20538a1eac85 100644 --- a/science/maeparser/Makefile +++ b/science/maeparser/Makefile @@ -1,6 +1,6 @@ PORTNAME= maeparser DISTVERSIONPREFIX= v -DISTVERSION= 1.3.2 +DISTVERSION= 1.3.3 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -18,4 +18,6 @@ USE_GITHUB= yes GH_ACCOUNT= schrodinger USE_LDCONFIG= yes +# 100% tests passed, 0 tests failed out of 1 + .include <bsd.port.mk> diff --git a/science/maeparser/distinfo b/science/maeparser/distinfo index 7bc14e5f0eb7..7c04a6e20f93 100644 --- a/science/maeparser/distinfo +++ b/science/maeparser/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1743488608 -SHA256 (schrodinger-maeparser-v1.3.2_GH0.tar.gz) = 431ae029957534324b59eb3974486f3cad97d06e9bacd88ec94dc598046dfcd3 -SIZE (schrodinger-maeparser-v1.3.2_GH0.tar.gz) = 39847 +TIMESTAMP = 1749275276 +SHA256 (schrodinger-maeparser-v1.3.3_GH0.tar.gz) = 78e7571a779ea4952e752ecef57c62fb26463947e29ef7f4b31b11988d88ca07 +SIZE (schrodinger-maeparser-v1.3.3_GH0.tar.gz) = 39896 diff --git a/science/maeparser/pkg-plist b/science/maeparser/pkg-plist index 3bd5854903b0..e44bcd4ac59e 100644 --- a/science/maeparser/pkg-plist +++ b/science/maeparser/pkg-plist @@ -9,4 +9,4 @@ lib/cmake/maeparser-config-%%CMAKE_BUILD_TYPE%%.cmake lib/cmake/maeparser-config.cmake lib/libmaeparser.so lib/libmaeparser.so.1 -lib/libmaeparser.so.1.3.2 +lib/libmaeparser.so.1.3.3 diff --git a/science/mbdyn/Makefile b/science/mbdyn/Makefile index c65f1560bb54..4ac211eda4e6 100644 --- a/science/mbdyn/Makefile +++ b/science/mbdyn/Makefile @@ -1,6 +1,6 @@ PORTNAME= mbdyn DISTVERSION= 1.7.3 -PORTREVISION= 18 +PORTREVISION= 19 CATEGORIES= science MASTER_SITES= https://www.mbdyn.org/userfiles/downloads/ diff --git a/science/mcpl/Makefile b/science/mcpl/Makefile index c9a1ab93c9d6..25c22bb8a36c 100644 --- a/science/mcpl/Makefile +++ b/science/mcpl/Makefile @@ -1,6 +1,6 @@ PORTNAME= mcpl DISTVERSIONPREFIX= v -DISTVERSION= 2.0.0 +DISTVERSION= 2.2.0 CATEGORIES= science # physics MAINTAINER= yuri@FreeBSD.org @@ -11,6 +11,9 @@ WWW= https://mctools.github.io/mcpl/ \ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE +NOT_FOR_ARCHS= armv7 powerpc i386 +NOT_FOR_ARCHS_REASON= MCPL does not support 32 bit platforms + BROKEN_i386= compilation fails, see https://github.com/mctools/mcpl/issues/88 USES= cmake:testing @@ -22,6 +25,6 @@ GH_ACCOUNT= mctools CMAKE_OFF= MCPL_ENABLE_TESTING CMAKE_TESTING_ON= MCPL_ENABLE_TESTING -# tests as of 2.0.0: 100% tests passed, 0 tests failed out of 27 +# tests as of 2.2.0: 100% tests passed, 0 tests failed out of 32 .include <bsd.port.mk> diff --git a/science/mcpl/distinfo b/science/mcpl/distinfo index 34a50e9299ba..b2b747457b55 100644 --- a/science/mcpl/distinfo +++ b/science/mcpl/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1745570645 -SHA256 (mctools-mcpl-v2.0.0_GH0.tar.gz) = c451d86abf17181edb8c36cf77b6dcbbe22f1d3c30df84321f8c17eda7c5a873 -SIZE (mctools-mcpl-v2.0.0_GH0.tar.gz) = 338436 +TIMESTAMP = 1748077643 +SHA256 (mctools-mcpl-v2.2.0_GH0.tar.gz) = 0cd926621d7d45d2bb39fab64732448b67f622cda9434a105de4c9d942a3db5c +SIZE (mctools-mcpl-v2.2.0_GH0.tar.gz) = 374448 diff --git a/science/meep/pkg-plist b/science/meep/pkg-plist index 9070caf99d57..e58a530b2aac 100644 --- a/science/meep/pkg-plist +++ b/science/meep/pkg-plist @@ -15,71 +15,71 @@ lib/libpympb.so lib/libpympb.so.33 lib/libpympb.so.33.0.0 %%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__init__.py -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-2.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/binary_partition_utils%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/binary_partition_utils%%PYTHON_EXT_SUFFIX%%.opt-2.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/binary_partition_utils%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/chunk_balancer%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/chunk_balancer%%PYTHON_EXT_SUFFIX%%.opt-2.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/chunk_balancer%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/geom%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/geom%%PYTHON_EXT_SUFFIX%%.opt-2.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/geom%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/materials%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/materials%%PYTHON_EXT_SUFFIX%%.opt-2.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/materials%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/simulation%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/simulation%%PYTHON_EXT_SUFFIX%%.opt-2.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/simulation%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/source%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/source%%PYTHON_EXT_SUFFIX%%.opt-2.pyc 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+%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/__init__%%PYTHON_TAG%%.opt-2.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/binary_partition_utils%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/binary_partition_utils%%PYTHON_TAG%%.opt-2.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/binary_partition_utils%%PYTHON_TAG%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/chunk_balancer%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/chunk_balancer%%PYTHON_TAG%%.opt-2.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/chunk_balancer%%PYTHON_TAG%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/geom%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/geom%%PYTHON_TAG%%.opt-2.pyc 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+%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/timing_measurements%%PYTHON_TAG%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/verbosity_mgr%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/verbosity_mgr%%PYTHON_TAG%%.opt-2.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/verbosity_mgr%%PYTHON_TAG%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/visualization%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/visualization%%PYTHON_TAG%%.opt-2.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/__pycache__/visualization%%PYTHON_TAG%%.pyc %%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/_meep.a %%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/_meep.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/_meep.so.33 %%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/_meep.so.33.0.0 %%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/adjoint/__init__.py -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/adjoint/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc 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+%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/adjoint/__pycache__/filters%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/adjoint/__pycache__/filters%%PYTHON_TAG%%.opt-2.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/adjoint/__pycache__/filters%%PYTHON_TAG%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/adjoint/__pycache__/objective%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/adjoint/__pycache__/objective%%PYTHON_TAG%%.opt-2.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/adjoint/__pycache__/objective%%PYTHON_TAG%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/adjoint/__pycache__/optimization_problem%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/adjoint/__pycache__/optimization_problem%%PYTHON_TAG%%.opt-2.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/adjoint/__pycache__/optimization_problem%%PYTHON_TAG%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/adjoint/__pycache__/unfilter_design%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/adjoint/__pycache__/unfilter_design%%PYTHON_TAG%%.opt-2.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/adjoint/__pycache__/unfilter_design%%PYTHON_TAG%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/adjoint/__pycache__/utils%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/adjoint/__pycache__/utils%%PYTHON_TAG%%.opt-2.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/adjoint/__pycache__/utils%%PYTHON_TAG%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/adjoint/__pycache__/wrapper%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/adjoint/__pycache__/wrapper%%PYTHON_TAG%%.opt-2.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/adjoint/__pycache__/wrapper%%PYTHON_TAG%%.pyc %%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/adjoint/basis.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/adjoint/connectivity.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/adjoint/filter_source.py @@ -94,15 +94,15 @@ lib/libpympb.so.33.0.0 %%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/geom.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/materials.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/mpb/__init__.py -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/mpb/__pycache__/mpb%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/mpb/__pycache__/mpb%%PYTHON_EXT_SUFFIX%%.opt-2.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/mpb/__pycache__/mpb%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/mpb/__pycache__/mpb_data%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/mpb/__pycache__/mpb_data%%PYTHON_EXT_SUFFIX%%.opt-2.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/mpb/__pycache__/mpb_data%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/mpb/__pycache__/solver%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/mpb/__pycache__/solver%%PYTHON_EXT_SUFFIX%%.opt-2.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/mpb/__pycache__/solver%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/mpb/__pycache__/mpb%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/mpb/__pycache__/mpb%%PYTHON_TAG%%.opt-2.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/mpb/__pycache__/mpb%%PYTHON_TAG%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/mpb/__pycache__/mpb_data%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/mpb/__pycache__/mpb_data%%PYTHON_TAG%%.opt-2.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/mpb/__pycache__/mpb_data%%PYTHON_TAG%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/mpb/__pycache__/solver%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/mpb/__pycache__/solver%%PYTHON_TAG%%.opt-2.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/mpb/__pycache__/solver%%PYTHON_TAG%%.pyc %%PYTHON%%%%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/mpb/_mpb.a %%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/mpb/_mpb.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/meep/mpb/_mpb.so.33 diff --git a/science/mmg/Makefile b/science/mmg/Makefile index 20acba012afe..a3bf8dc89a09 100644 --- a/science/mmg/Makefile +++ b/science/mmg/Makefile @@ -1,6 +1,7 @@ PORTNAME= mmg DISTVERSIONPREFIX= v DISTVERSION= 5.7.3 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= ports@FreeBSD.org diff --git a/science/molgif/Makefile b/science/molgif/Makefile index 19ebca83657a..280dc2503615 100644 --- a/science/molgif/Makefile +++ b/science/molgif/Makefile @@ -1,6 +1,6 @@ PORTNAME= molgif DISTVERSION= g20180108 -PORTREVISION= 25 +PORTREVISION= 29 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/molsketch/Makefile b/science/molsketch/Makefile index 36882dc5b57b..c071685b4325 100644 --- a/science/molsketch/Makefile +++ b/science/molsketch/Makefile @@ -1,5 +1,5 @@ PORTNAME= molsketch -DISTVERSION= 0.8.1 +DISTVERSION= 0.8.2 DISTVERSIONSUFFIX= -src CATEGORIES= science MASTER_SITES= SF/${PORTNAME}/Molsketch/ @@ -7,19 +7,21 @@ DISTNAME= Molsketch-${DISTVERSIONFULL} MAINTAINER= yuri@FreeBSD.org COMMENT= 2D molecule editor -WWW= https://molsketch.sourceforge.net/ +WWW= https://molsketch.sourceforge.io/ LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libopenbabel.so:science/openbabel -USES= cmake:noninja compiler:c++17-lang desktop-file-utils localbase:ldflags \ - pkgconfig qt:5 shared-mime-info # build fails with ninja, see https://sourceforge.net/p/molsketch/bugs/41/ -USE_QT= core gui network printsupport svg widgets buildtools:build linguisttools:build qmake:build +USES= cmake compiler:c++20-lang desktop-file-utils gl localbase:ldflags \ + pkgconfig qt:6 shared-mime-info # build fails with ninja, see https://sourceforge.net/p/molsketch/bugs/41/ +USE_QT= base svg tools:build USE_LDCONFIG= ${PREFIX}/lib/molsketch +USE_GL= gl opengl CMAKE_ARGS= -DMSK_PREFIX:STRING=${PREFIX} +CMAKE_ON= MSK_QT6 OPTIONS_DEFINE= DOCS diff --git a/science/molsketch/distinfo b/science/molsketch/distinfo index 43a093c33158..5b8402170fc9 100644 --- a/science/molsketch/distinfo +++ b/science/molsketch/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1737708866 -SHA256 (Molsketch-0.8.1-src.tar.gz) = eb016f977024b6ff11804748d8436c29a9652a5632fdff13b26e42d0507f8a02 -SIZE (Molsketch-0.8.1-src.tar.gz) = 1852967 +TIMESTAMP = 1750672153 +SHA256 (Molsketch-0.8.2-src.tar.gz) = 5a8a18e4eb8e927f5c4bf97eb44ab191f4fa996298123630e8751c0b9e7de5e2 +SIZE (Molsketch-0.8.2-src.tar.gz) = 1855799 diff --git a/science/molsketch/pkg-plist b/science/molsketch/pkg-plist index fe9d00f0e4db..181e835ac162 100644 --- a/science/molsketch/pkg-plist +++ b/science/molsketch/pkg-plist @@ -46,9 +46,6 @@ include/libmolsketch/constants.h include/libmolsketch/coordinatedelegate.h include/libmolsketch/coordinatemodel.h include/libmolsketch/coordinatetableview.h -include/libmolsketch/core/coreatom.h -include/libmolsketch/core/corebond.h -include/libmolsketch/core/coremolecule.h include/libmolsketch/debuggable.h include/libmolsketch/electronsystem.h include/libmolsketch/element.h @@ -92,6 +89,11 @@ include/libmolsketch/stringify.h include/libmolsketch/sumformula.h include/libmolsketch/textitem.h include/libmolsketch/xmlobjectinterface.h +include/libmskcore/coreatom.h +include/libmskcore/corebond.h +include/libmskcore/coremolecule.h +include/libmskcore/position.h +lib/molsketch/libmolsketch.so lib/molsketch/libmskcore.so lib/molsketch/libobabeliface.so share/applications/molsketch.desktop diff --git a/science/ncrystal/Makefile b/science/ncrystal/Makefile index b08c32516014..8738797874bd 100644 --- a/science/ncrystal/Makefile +++ b/science/ncrystal/Makefile @@ -1,6 +1,6 @@ PORTNAME= ncrystal DISTVERSIONPREFIX= v -DISTVERSION= 4.1.6 +DISTVERSION= 4.2.8 CATEGORIES= science # physics MAINTAINER= yuri@FreeBSD.org @@ -21,9 +21,6 @@ SHEBANG_FILES= tests/scripts/* CMAKE_TESTING_ON= NCRYSTAL_ENABLE_TESTING \ NCRYSTAL_ENABLE_CORE_TEST -post-install: # workaround for https://github.com/mctools/ncrystal/issues/150 - @${RM} ${STAGEDIR}${PREFIX}/*.sh - -# tests as of 4.1.4: 54% tests passed, 37 tests failed out of 80, see https://github.com/mctools/ncrystal/issues/231 +# tests as of 4.2.6: 51% tests passed, 43 tests failed out of 88 (only py_xx tests fail) .include <bsd.port.mk> diff --git a/science/ncrystal/distinfo b/science/ncrystal/distinfo index fe3708884b1d..ebf4e8a8d01a 100644 --- a/science/ncrystal/distinfo +++ b/science/ncrystal/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1743578912 -SHA256 (mctools-ncrystal-v4.1.6_GH0.tar.gz) = 4fc1be0503c6e68a110b6da13963bd2bf53154794a727c63f1218a56f6241eff -SIZE (mctools-ncrystal-v4.1.6_GH0.tar.gz) = 2719484 +TIMESTAMP = 1754558330 +SHA256 (mctools-ncrystal-v4.2.8_GH0.tar.gz) = 499e355e8cb534954101241c5af1f3d4f729aa87f4d63734b05570033a5d6dbd +SIZE (mctools-ncrystal-v4.2.8_GH0.tar.gz) = 2822048 diff --git a/science/nest/Makefile b/science/nest/Makefile index 6214e7641122..49b9c6090721 100644 --- a/science/nest/Makefile +++ b/science/nest/Makefile @@ -1,7 +1,7 @@ PORTNAME= nest DISTVERSIONPREFIX= v DISTVERSION= 3.8 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science biology # NEST is used in neuroscience MAINTAINER= yuri@FreeBSD.org diff --git a/science/openbabel/Makefile b/science/openbabel/Makefile index d18e08b964b3..b14fb8f12ff0 100644 --- a/science/openbabel/Makefile +++ b/science/openbabel/Makefile @@ -1,6 +1,6 @@ PORTNAME= openbabel DISTVERSION= 3-1-1-178 -PORTREVISION= 3 +PORTREVISION= 5 #DISTVERSIONSUFFIX= -source DISTVERSIONSUFFIX= -g2b211d6ac CATEGORIES= science diff --git a/science/openems/Makefile b/science/openems/Makefile index 9b9a734a10a5..04c0f0305e74 100644 --- a/science/openems/Makefile +++ b/science/openems/Makefile @@ -1,7 +1,7 @@ PORTNAME= openems DISTVERSIONPREFIX= v DISTVERSION= 0.0.36 -PORTREVISION= 4 +PORTREVISION= 6 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/openmc/Makefile b/science/openmc/Makefile index 9481907cdec7..dd31d577e3d7 100644 --- a/science/openmc/Makefile +++ b/science/openmc/Makefile @@ -1,6 +1,7 @@ PORTNAME= openmc DISTVERSIONPREFIX= v DISTVERSION= 0.15.0 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -12,7 +13,7 @@ WWW= https://openmc.org/ \ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE -BROKEN_FreeBSD_15= compilation fails with clang-19, see https://github.com/openmc-dev/openmc/issues/3183 +BROKEN= compilation fails with clang-19, see https://github.com/openmc-dev/openmc/issues/3183 BUILD_DEPENDS= xtensor>0:math/xtensor LIB_DEPENDS= libfmt.so:devel/libfmt \ diff --git a/science/openmodelica/Makefile b/science/openmodelica/Makefile index 0140a1415d77..fd76e7f0a190 100644 --- a/science/openmodelica/Makefile +++ b/science/openmodelica/Makefile @@ -1,6 +1,6 @@ PORTNAME= openmodelica DISTVERSIONPREFIX= v -DISTVERSION= 1.25.0 +DISTVERSION= 1.25.2 CATEGORIES= science cad java DIST_SUBDIR= ${PORTNAME}-${PORTVERSION} @@ -17,7 +17,7 @@ LICENSE_NAME= Public license for OpenModelica LICENSE_TEXT= See https://github.com/OpenModelica/OpenModelica/blob/master/OSMC-License.txt LICENSE_PERMS= auto-accept dist-mirror dist-sell pkg-mirror pkg-sell -BROKEN_aarch64= compilation fails: gcc13 doesn't install libquadmath.so, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=285692 +BROKEN_aarch64= compilation fails: OpenModelica expects libquadmath.so, which does not exist on aarch64 (PR 285692) BROKEN_armv7= link fails: ld: cannot find -lquadmath: No such file or directory BROKEN_i386= compilation fails: /wrkdirs/usr/ports/science/openmodelica/work/OpenModelica-1.20.0/OMCompiler/3rdParty/libffi/src/x86/sysv.S:841:1: error: changed section flags for .eh_frame, expected: 0x2 @@ -32,7 +32,7 @@ LIB_DEPENDS= libboost_filesystem.so:devel/boost-libs \ libcurl.so:ftp/curl \ libicuuc.so:devel/icu \ libosg.so:graphics/osg \ - libuuid.so:misc/e2fsprogs-libuuid + libuuid.so:misc/libuuid RUN_DEPENDS= bash:shells/bash \ gmake:devel/gmake @@ -53,15 +53,15 @@ GH_PROJECT= OpenModelica SHEBANG_GLOB= *.sh *.in *.ac GH_TUPLE= \ - OpenModelica:OMOptim:f1036f43db18c5015da259771004cfb80e08a110:OpenModelica_OMOptim/OMOptim \ - OpenModelica:OMSimulator:46fa40f:OpenModelica_OMSimulator/OMSimulator \ + OpenModelica:OMOptim:d53288b:OpenModelica_OMOptim/OMOptim \ + OpenModelica:OMSimulator:e3a3aeb:OpenModelica_OMSimulator/OMSimulator \ OpenModelica:OMSimulator-3rdParty:5c10de1648d1134a577d9284b58580a72383d89f:OpenModelica_OMSimulator_3rdParty/OMSimulator/3rdParty \ OpenModelica:OMCompiler-3rdParty:520663f:OpenModelica_OMCompiler_3rdParty/OMCompiler/3rdParty \ OpenModelica:OMSens:093ad11:OpenModelica_OMSens/OMSens \ OpenModelica:OMSens_Qt:bab329a:OpenModelica_OMSens_Qt/OMSens_Qt \ OpenModelica:OpenModelica-common:08a01802db5ba5edb540383c46718b89ff229ef2:OpenModelica_OpenModelica_common/OMOptim/common \ OpenModelica:OpenModelica-common:08a01802db5ba5edb540383c46718b89ff229ef2:OpenModelica_OpenModelica_common/OMSens_Qt/common -GH_TUPLE+= OpenModelica:OMBootstrapping:91938f0acbdc6e9ba91114376e3640ca6147b579:bootstrapping/OMCompiler/Compiler/boot/bomc # downloaded by cmake +GH_TUPLE+= OpenModelica:OMBootstrapping:04d16f7461e5401321f0f72613daf466ae2f76be:bootstrapping/OMCompiler/Compiler/boot/bomc # downloaded by cmake # this should change make program everywhere, but it doesn't, # hence the patches in OMCompiler/Compiler/runtime/CMakeLists.txt, OMEdit/OMEditLIB/Simulation/SimulationOutputWidget.cpp @@ -69,6 +69,7 @@ CMAKE_ARGS= -DCMAKE_MAKE_PROGRAM=gmake \ -DPython_EXECUTABLE=${PYTHON_CMD} CMAKE_ARGS+= -DOM_USE_CCACHE:BOOL=${CCACHE_ENABLED:S/yes/ON/:S/no/OFF/} # if refuses to build w/out ccache by default +#CMAKE_ARGS+= -DOM_QT_MAJOR_VERSION=6 # broken, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=287596 CMAKE_ON= OM_OMEDIT_ENABLE_QTWEBENGINE LDFLAGS+= -lexecinfo -lintl -pthread diff --git a/science/openmodelica/distinfo b/science/openmodelica/distinfo index 7311a47a4919..56ac7fddde4b 100644 --- a/science/openmodelica/distinfo +++ b/science/openmodelica/distinfo @@ -1,19 +1,19 @@ -TIMESTAMP = 1743866725 -SHA256 (openmodelica-1.25.0/OpenModelica-OpenModelica-v1.25.0_GH0.tar.gz) = 77c810ca3a1b72f7f96af2bfbf7bba0162136c76b3e83771b7d82db16c65a1a0 -SIZE (openmodelica-1.25.0/OpenModelica-OpenModelica-v1.25.0_GH0.tar.gz) = 148273042 -SHA256 (openmodelica-1.25.0/OpenModelica-OMOptim-f1036f43db18c5015da259771004cfb80e08a110_GH0.tar.gz) = 11189c8ab3fb9d22ed805271ef53b9698b0d41007a1708d7a77ef074a5b20447 -SIZE (openmodelica-1.25.0/OpenModelica-OMOptim-f1036f43db18c5015da259771004cfb80e08a110_GH0.tar.gz) = 4022842 -SHA256 (openmodelica-1.25.0/OpenModelica-OMSimulator-46fa40f_GH0.tar.gz) = eb5fbb88b2cf6a3556c43ee4c0b446fb26a70be06ddfb4031e50636dc1af1048 -SIZE (openmodelica-1.25.0/OpenModelica-OMSimulator-46fa40f_GH0.tar.gz) = 92370094 -SHA256 (openmodelica-1.25.0/OpenModelica-OMSimulator-3rdParty-5c10de1648d1134a577d9284b58580a72383d89f_GH0.tar.gz) = ea57e90ea76eca2657e8ddaa6c87301a16661200b3e8a00347a12bfdbb5f973d -SIZE (openmodelica-1.25.0/OpenModelica-OMSimulator-3rdParty-5c10de1648d1134a577d9284b58580a72383d89f_GH0.tar.gz) = 7637943 -SHA256 (openmodelica-1.25.0/OpenModelica-OMCompiler-3rdParty-520663f_GH0.tar.gz) = 37c82357fc1e862eb13d79cf1ff2d143f263502472db9bb2c350c0c551022954 -SIZE (openmodelica-1.25.0/OpenModelica-OMCompiler-3rdParty-520663f_GH0.tar.gz) = 50256095 -SHA256 (openmodelica-1.25.0/OpenModelica-OMSens-093ad11_GH0.tar.gz) = 335512c08f94902bb07e75278cea791370a551336272f7bebef8c707ef5e5e2b -SIZE (openmodelica-1.25.0/OpenModelica-OMSens-093ad11_GH0.tar.gz) = 8871049 -SHA256 (openmodelica-1.25.0/OpenModelica-OMSens_Qt-bab329a_GH0.tar.gz) = 2f2dcba4defd7f13e9fd5e0c26bb4951b9f1fcc7da64960a6ad1cee32a628efa -SIZE (openmodelica-1.25.0/OpenModelica-OMSens_Qt-bab329a_GH0.tar.gz) = 211270 -SHA256 (openmodelica-1.25.0/OpenModelica-OpenModelica-common-08a01802db5ba5edb540383c46718b89ff229ef2_GH0.tar.gz) = fdb5bb442da0375373ef221cf26195114bf149511c1c2be051caad6301c21c9a -SIZE (openmodelica-1.25.0/OpenModelica-OpenModelica-common-08a01802db5ba5edb540383c46718b89ff229ef2_GH0.tar.gz) = 36148 -SHA256 (openmodelica-1.25.0/OpenModelica-OMBootstrapping-91938f0acbdc6e9ba91114376e3640ca6147b579_GH0.tar.gz) = 1a0327dabedd09dab3aa872af194b6d4e79bacc45659ea3154076e7f1f54b2cc -SIZE (openmodelica-1.25.0/OpenModelica-OMBootstrapping-91938f0acbdc6e9ba91114376e3640ca6147b579_GH0.tar.gz) = 3328929 +TIMESTAMP = 1756357301 +SHA256 (openmodelica-1.25.2/OpenModelica-OpenModelica-v1.25.2_GH0.tar.gz) = a56f60074842f8b10c05d8ad323e89937b38ecbea0c9f062858f57d5ab8dbf7c +SIZE (openmodelica-1.25.2/OpenModelica-OpenModelica-v1.25.2_GH0.tar.gz) = 148277183 +SHA256 (openmodelica-1.25.2/OpenModelica-OMOptim-d53288b_GH0.tar.gz) = d5012951f43e90dce03d7866d221278ee11ddfbdac4db20fe43d93adbc3748e7 +SIZE (openmodelica-1.25.2/OpenModelica-OMOptim-d53288b_GH0.tar.gz) = 4024177 +SHA256 (openmodelica-1.25.2/OpenModelica-OMSimulator-e3a3aeb_GH0.tar.gz) = 6192d933c258950fb0171f5d0ddac0353632d17ee99f6974ba53dd654f547e49 +SIZE (openmodelica-1.25.2/OpenModelica-OMSimulator-e3a3aeb_GH0.tar.gz) = 95557541 +SHA256 (openmodelica-1.25.2/OpenModelica-OMSimulator-3rdParty-5c10de1648d1134a577d9284b58580a72383d89f_GH0.tar.gz) = ea57e90ea76eca2657e8ddaa6c87301a16661200b3e8a00347a12bfdbb5f973d +SIZE (openmodelica-1.25.2/OpenModelica-OMSimulator-3rdParty-5c10de1648d1134a577d9284b58580a72383d89f_GH0.tar.gz) = 7637943 +SHA256 (openmodelica-1.25.2/OpenModelica-OMCompiler-3rdParty-520663f_GH0.tar.gz) = 37c82357fc1e862eb13d79cf1ff2d143f263502472db9bb2c350c0c551022954 +SIZE (openmodelica-1.25.2/OpenModelica-OMCompiler-3rdParty-520663f_GH0.tar.gz) = 50256095 +SHA256 (openmodelica-1.25.2/OpenModelica-OMSens-093ad11_GH0.tar.gz) = 335512c08f94902bb07e75278cea791370a551336272f7bebef8c707ef5e5e2b +SIZE (openmodelica-1.25.2/OpenModelica-OMSens-093ad11_GH0.tar.gz) = 8871049 +SHA256 (openmodelica-1.25.2/OpenModelica-OMSens_Qt-bab329a_GH0.tar.gz) = 2f2dcba4defd7f13e9fd5e0c26bb4951b9f1fcc7da64960a6ad1cee32a628efa +SIZE (openmodelica-1.25.2/OpenModelica-OMSens_Qt-bab329a_GH0.tar.gz) = 211270 +SHA256 (openmodelica-1.25.2/OpenModelica-OpenModelica-common-08a01802db5ba5edb540383c46718b89ff229ef2_GH0.tar.gz) = fdb5bb442da0375373ef221cf26195114bf149511c1c2be051caad6301c21c9a +SIZE (openmodelica-1.25.2/OpenModelica-OpenModelica-common-08a01802db5ba5edb540383c46718b89ff229ef2_GH0.tar.gz) = 36148 +SHA256 (openmodelica-1.25.2/OpenModelica-OMBootstrapping-04d16f7461e5401321f0f72613daf466ae2f76be_GH0.tar.gz) = 9ac6d28be6a331dfb61a57b033f2bcf984448cd63bc1a4cd140d60c2f5c64a79 +SIZE (openmodelica-1.25.2/OpenModelica-OMBootstrapping-04d16f7461e5401321f0f72613daf466ae2f76be_GH0.tar.gz) = 3346859 diff --git a/science/openmodelica/pkg-plist b/science/openmodelica/pkg-plist index 2f3a85526399..9c08ba4f8e0a 100644 --- a/science/openmodelica/pkg-plist +++ b/science/openmodelica/pkg-plist @@ -778,12 +778,15 @@ share/OMSimulator/schema/fmi3/fmi3Type.xsd share/OMSimulator/schema/fmi3/fmi3Unit.xsd share/OMSimulator/schema/fmi3/fmi3Variable.xsd share/OMSimulator/schema/fmi3/fmi3VariableDependency.xsd +share/OMSimulator/schema/ssp/SSPTraceabilityCommon.xsd +share/OMSimulator/schema/ssp/SimulationResourceMetaData.xsd share/OMSimulator/schema/ssp/SystemStructureCommon.xsd share/OMSimulator/schema/ssp/SystemStructureDescription.xsd share/OMSimulator/schema/ssp/SystemStructureDescription11.xsd share/OMSimulator/schema/ssp/SystemStructureParameterMapping.xsd share/OMSimulator/schema/ssp/SystemStructureParameterValues.xsd share/OMSimulator/schema/ssp/SystemStructureSignalDictionary.xsd +share/OMSimulator/schema/ssp/xlink.xsd share/OMSimulator/scripts/OMSimulatorServer.py share/cmake/ZeroMQ/ZeroMQConfig.cmake share/cmake/ZeroMQ/ZeroMQConfigVersion.cmake diff --git a/science/opensph/Makefile b/science/opensph/Makefile index a200d2cc9e12..8550bb4472b0 100644 --- a/science/opensph/Makefile +++ b/science/opensph/Makefile @@ -1,6 +1,6 @@ PORTNAME= OpenSPH DISTVERSION= 0.4.1 -PORTREVISION= 7 +PORTREVISION= 9 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/orthanc-dicomweb/Makefile b/science/orthanc-dicomweb/Makefile index e134921637b1..9c049433aab3 100644 --- a/science/orthanc-dicomweb/Makefile +++ b/science/orthanc-dicomweb/Makefile @@ -1,6 +1,6 @@ PORTNAME= orthanc-dicomweb DISTVERSION= 1.8 -PORTREVISION= 13 +PORTREVISION= 14 CATEGORIES= science MASTER_SITES= https://www.orthanc-server.com/downloads/get.php?path=/plugin-dicom-web/:main \ https://www.orthanc-server.com/downloads/get.php?path=/orthanc/:framework \ diff --git a/science/orthanc-mysql/Makefile b/science/orthanc-mysql/Makefile index ce6691e06642..f963cfd53313 100644 --- a/science/orthanc-mysql/Makefile +++ b/science/orthanc-mysql/Makefile @@ -1,6 +1,6 @@ PORTNAME= orthanc-mysql DISTVERSION= 4.3 -PORTREVISION= 10 +PORTREVISION= 11 CATEGORIES= science MASTER_SITES= https://www.orthanc-server.com/downloads/get.php?path=/plugin-mysql/:main \ https://www.orthanc-server.com/downloads/get.php?path=/orthanc/:framework \ diff --git a/science/orthanc-postgresql/Makefile b/science/orthanc-postgresql/Makefile index 897e54d1fb7e..044e5ef0a822 100644 --- a/science/orthanc-postgresql/Makefile +++ b/science/orthanc-postgresql/Makefile @@ -1,6 +1,6 @@ PORTNAME= orthanc-postgresql DISTVERSION= 4.0 -PORTREVISION= 10 +PORTREVISION= 11 CATEGORIES= science MASTER_SITES= https://www.orthanc-server.com/downloads/get.php?path=/plugin-postgresql/:main \ https://www.orthanc-server.com/downloads/get.php?path=/orthanc/:framework \ diff --git a/science/orthanc-webviewer/Makefile b/science/orthanc-webviewer/Makefile index 935acee20db1..71b7598926a0 100644 --- a/science/orthanc-webviewer/Makefile +++ b/science/orthanc-webviewer/Makefile @@ -1,5 +1,6 @@ PORTNAME= orthanc-webviewer DISTVERSION= 2.9 +PORTREVISION= 1 CATEGORIES= science MASTER_SITES= https://orthanc.uclouvain.be/downloads/sources/orthanc-webviewer/:main \ https://orthanc.uclouvain.be/downloads/sources/orthanc/:framework \ diff --git a/science/orthanc/Makefile b/science/orthanc/Makefile index e2a87f603b28..515e49a5a4fb 100644 --- a/science/orthanc/Makefile +++ b/science/orthanc/Makefile @@ -1,6 +1,6 @@ PORTNAME= orthanc DISTVERSION= 1.12.6 -PORTREVISION= 1 +PORTREVISION= 3 CATEGORIES= science MASTER_SITES= https://orthanc.uclouvain.be/downloads/sources/orthanc/ DISTNAME= Orthanc-${PORTVERSION} @@ -25,7 +25,7 @@ LIB_DEPENDS= libboost_atomic.so:devel/boost-libs \ libprotobuf.so:devel/protobuf \ libpugixml.so:textproc/pugixml \ libtiff.so:graphics/tiff \ - libuuid.so:misc/e2fsprogs-libuuid + libuuid.so:misc/libuuid USES= cmake gnome iconv jpeg lua python:build sqlite ssl USE_GNOME= libxml2 diff --git a/science/packmol/Makefile b/science/packmol/Makefile index 258cb4887b23..8f1bef5e46ce 100644 --- a/science/packmol/Makefile +++ b/science/packmol/Makefile @@ -1,6 +1,6 @@ PORTNAME= packmol DISTVERSIONPREFIX= v -DISTVERSION= 21.0.2 +DISTVERSION= 21.1.0 CATEGORIES= science MAINTAINER= eduardo@FreeBSD.org diff --git a/science/packmol/distinfo b/science/packmol/distinfo index a29aecb117ea..a62a7e08f6a6 100644 --- a/science/packmol/distinfo +++ b/science/packmol/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1746477631 -SHA256 (m3g-packmol-v21.0.2_GH0.tar.gz) = 4b63d73400f7702347d9ff0cc4d0009be5a752afa7af00ad612554e8918f00fd -SIZE (m3g-packmol-v21.0.2_GH0.tar.gz) = 630603 +TIMESTAMP = 1755694551 +SHA256 (m3g-packmol-v21.1.0_GH0.tar.gz) = bcb64849bd490c329018210cf91375871108004ac8bf3e8cf9463e42e551fe46 +SIZE (m3g-packmol-v21.1.0_GH0.tar.gz) = 634772 diff --git a/science/pagmo2/Makefile b/science/pagmo2/Makefile index 3d2cbe37a4f1..dd0ecbe367c2 100644 --- a/science/pagmo2/Makefile +++ b/science/pagmo2/Makefile @@ -1,7 +1,7 @@ PORTNAME= pagmo2 DISTVERSIONPREFIX= v DISTVERSION= 2.19.1 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/paje/Makefile b/science/paje/Makefile index 6c6a554a8b5b..0d73a91fe8bf 100644 --- a/science/paje/Makefile +++ b/science/paje/Makefile @@ -1,6 +1,6 @@ PORTNAME= paje PORTVERSION= 1.97 -PORTREVISION= 12 +PORTREVISION= 13 CATEGORIES= science gnustep MASTER_SITES= SF/${PORTNAME}/Releases DISTNAME= Paje_${PORTVERSION} diff --git a/science/paraview/Makefile b/science/paraview/Makefile index 95df05404a9c..4e69796ed499 100644 --- a/science/paraview/Makefile +++ b/science/paraview/Makefile @@ -1,6 +1,6 @@ PORTNAME= paraview DISTVERSION= ${PARAVIEW_VER}.3 -PORTREVISION= 1 +PORTREVISION= 4 CATEGORIES= science graphics MASTER_SITES= http://www.paraview.org/files/v${PARAVIEW_VER}/ DISTNAME= ParaView-v${PORTVERSION} @@ -63,7 +63,7 @@ RUN_DEPENDS= ${PYNUMPY} \ ${PYTHON_SITELIBDIR}/matplotlib/pyplot.py:math/py-matplotlib@${PY_FLAVOR} USES= alias cmake compiler:c++17-lang desktop-file-utils eigen:3 fortran gl gnome \ - jpeg localbase pkgconfig python qt:6 shebangfix sqlite tar:xz xorg + jpeg localbase llvm:min=19 pkgconfig python qt:6 shebangfix sqlite tar:xz xorg USE_GL= glew opengl USE_GNOME= libxml2 USE_QT= 5compat base svg tools webengine diff --git a/science/pastix/Makefile b/science/pastix/Makefile index 6bca922f6246..4520f4c93ef1 100644 --- a/science/pastix/Makefile +++ b/science/pastix/Makefile @@ -10,9 +10,6 @@ WWW= https://solverstack.gitlabpages.inria.fr/pastix/ LICENSE= LGPL3 -DEPRECATED= Depends on expired lang/julia -EXPIRATION_DATE=2025-06-01 - BUILD_DEPENDS= bash:shells/bash \ ${PYNUMPY} LIB_DEPENDS= libmetis.so:math/metis \ diff --git a/science/phonopy/Makefile b/science/phonopy/Makefile index 79dae27c15f8..87062e5bc90e 100644 --- a/science/phonopy/Makefile +++ b/science/phonopy/Makefile @@ -1,6 +1,6 @@ PORTNAME= phonopy DISTVERSIONPREFIX= v -DISTVERSION= 2.38.0 +DISTVERSION= 2.42.0 CATEGORIES= science python MAINTAINER= yuri@FreeBSD.org diff --git a/science/phonopy/distinfo b/science/phonopy/distinfo index fd9b3ed7de36..7a515ee74037 100644 --- a/science/phonopy/distinfo +++ b/science/phonopy/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1741068945 -SHA256 (phonopy-phonopy-v2.38.0_GH0.tar.gz) = e98c2b63f5cd847aa2efe6aa714ed1e656a3a2dba6f167830fc3149ee6bef4f1 -SIZE (phonopy-phonopy-v2.38.0_GH0.tar.gz) = 7712107 +TIMESTAMP = 1753085727 +SHA256 (phonopy-phonopy-v2.42.0_GH0.tar.gz) = db7efd4acb881114a9679a8f6730f127c196090d82077009746325ad2bc53041 +SIZE (phonopy-phonopy-v2.42.0_GH0.tar.gz) = 7718436 diff --git a/science/precice/Makefile b/science/precice/Makefile index 6871148ce6f9..7f6315a778c2 100644 --- a/science/precice/Makefile +++ b/science/precice/Makefile @@ -1,7 +1,7 @@ PORTNAME= precice DISTVERSIONPREFIX= v DISTVERSION= 3.1.2 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science # physics MAINTAINER= yuri@FreeBSD.org diff --git a/science/psi4/pkg-plist b/science/psi4/pkg-plist index 7fa115b01889..7992f2f14c22 100644 --- a/science/psi4/pkg-plist +++ b/science/psi4/pkg-plist @@ -148,7 +148,7 @@ include/psi4/psifiles.h include/psi4/pybind11.h include/psi4/times.h %%PYTHON_SITELIBDIR%%/psi4/__init__.py -%%PYTHON_SITELIBDIR%%/psi4/core%%PYTHON_EXT_SUFFIX%%.so +%%PYTHON_SITELIBDIR%%/psi4/core%%PYTHON_TAG%%.so %%PYTHON_SITELIBDIR%%/psi4/driver/__init__.py %%PYTHON_SITELIBDIR%%/psi4/driver/aliases.py %%PYTHON_SITELIBDIR%%/psi4/driver/constants.py diff --git a/science/pulseview/Makefile b/science/pulseview/Makefile index ba9d698a4050..3caf31619525 100644 --- a/science/pulseview/Makefile +++ b/science/pulseview/Makefile @@ -1,6 +1,6 @@ PORTNAME= pulseview PORTVERSION= 0.4.2 -PORTREVISION= 6 +PORTREVISION= 7 CATEGORIES= science cad MASTER_SITES= http://sigrok.org/download/source/pulseview/ diff --git a/science/py-DendroPy/Makefile b/science/py-DendroPy/Makefile deleted file mode 100644 index c92414b1f2d8..000000000000 --- a/science/py-DendroPy/Makefile +++ /dev/null @@ -1,24 +0,0 @@ -PORTNAME= DendroPy -PORTVERSION= 5.0.1 -PORTREVISION= 1 -CATEGORIES= science python -MASTER_SITES= PYPI -PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} - -MAINTAINER= wen@FreeBSD.org -COMMENT= Phylogenetic computing library -WWW= http://packages.python.org/DendroPy/ - -LICENSE= BSD3CLAUSE - -DEPRECATED= Depends on expired devel/py-pytest-runner -EXPIRATION_DATE=2025-03-31 - -BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pip>0:devel/py-pip@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}pytest-runner>0:devel/py-pytest-runner@${PY_FLAVOR} - -USES= python -USE_PYTHON= distutils autoplist - -.include <bsd.port.mk> diff --git a/science/py-DendroPy/distinfo b/science/py-DendroPy/distinfo deleted file mode 100644 index 0db0c8397580..000000000000 --- a/science/py-DendroPy/distinfo +++ /dev/null @@ -1,3 +0,0 @@ -TIMESTAMP = 1717397726 -SHA256 (DendroPy-5.0.1.tar.gz) = f2815e7649a6fe2924ff3fdf00a660c948dc6f3316e303b8b022f74cc75ca42e -SIZE (DendroPy-5.0.1.tar.gz) = 395057 diff --git a/science/py-DendroPy/pkg-descr b/science/py-DendroPy/pkg-descr deleted file mode 100644 index 7a507db67459..000000000000 --- a/science/py-DendroPy/pkg-descr +++ /dev/null @@ -1,2 +0,0 @@ -py-DendroPy is a python library for phylogenetic scripting, -simulation, data processing and manipulation. diff --git a/science/py-DendroPy/pkg-message b/science/py-DendroPy/pkg-message deleted file mode 100644 index 1f71993d6f73..000000000000 --- a/science/py-DendroPy/pkg-message +++ /dev/null @@ -1,11 +0,0 @@ -[ -{ type: install - message: <<EOM -If you use this library either in whole or in part in your analysis, or -use any code derived from it, please cite it as: - - Sukumaran, J. and Mark T. Holder. 2010. DendroPy: A Python library - for phylogenetic computing. Bioinformatics 26: 1569-1571. -EOM -} -] diff --git a/science/py-GPy/Makefile b/science/py-GPy/Makefile index 9c443094cf47..6a87dce87266 100644 --- a/science/py-GPy/Makefile +++ b/science/py-GPy/Makefile @@ -31,8 +31,8 @@ POST_PLIST= fix-plist post-install: @${STRIP_CMD} \ - ${STAGEDIR}${PYTHON_SITELIBDIR}/GPy/*/*${PYTHON_EXT_SUFFIX}.so \ - ${STAGEDIR}${PYTHON_SITELIBDIR}/GPy/*/*/*${PYTHON_EXT_SUFFIX}.so + ${STAGEDIR}${PYTHON_SITELIBDIR}/GPy/*/*${PYTHON_TAG}.so \ + ${STAGEDIR}${PYTHON_SITELIBDIR}/GPy/*/*/*${PYTHON_TAG}.so fix-plist: # workaroud for /usr/ports/science/py-GPy/work-py311/.PLIST.mktmp @${REINPLACE_CMD} -e "s|.*__pycache__/mpi_test__.*$$||" ${TMPPLIST} diff --git a/science/py-OpenFermion/Makefile b/science/py-OpenFermion/Makefile index 142909380720..6505d132d2ad 100644 --- a/science/py-OpenFermion/Makefile +++ b/science/py-OpenFermion/Makefile @@ -1,7 +1,6 @@ PORTNAME= OpenFermion DISTVERSIONPREFIX= v -DISTVERSION= 1.6.1 -PORTREVISION= 1 +DISTVERSION= 1.7.1 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -22,6 +21,7 @@ RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}cirq-core>=1.0:science/py-cirq-core@${PY_FLA ${PYTHON_PKGNAMEPREFIX}requests>=2.18:www/py-requests@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.1.0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}sympy>0:math/py-sympy@${PY_FLAVOR} +TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}nbformat>0:devel/py-nbformat@${PY_FLAVOR} USES= python USE_PYTHON= distutils autoplist pytest # 1 tests fails, see https://github.com/quantumlib/OpenFermion/issues/879 @@ -33,4 +33,6 @@ NO_ARCH= yes BINARY_ALIAS= python3=${PYTHON_CMD} # only for tests +# tests as of 1.7.1: 2 failed, 2157 passed, 60 skipped, 218 warnings in 3296.13s (0:54:56) + .include <bsd.port.mk> diff --git a/science/py-OpenFermion/distinfo b/science/py-OpenFermion/distinfo index 82454570bd5e..29cc8a58888d 100644 --- a/science/py-OpenFermion/distinfo +++ b/science/py-OpenFermion/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1714198243 -SHA256 (quantumlib-OpenFermion-v1.6.1_GH0.tar.gz) = d1b6fd254efa12dd3eb08c7877c4b9e04bb12e4ead4ec809b8e370b25c898ed6 -SIZE (quantumlib-OpenFermion-v1.6.1_GH0.tar.gz) = 45081688 +TIMESTAMP = 1749274853 +SHA256 (quantumlib-OpenFermion-v1.7.1_GH0.tar.gz) = bee119b0c25dc50900634ef79ef963ea518eef29625e73886e5241bbe849b30c +SIZE (quantumlib-OpenFermion-v1.7.1_GH0.tar.gz) = 45123000 diff --git a/science/py-OpenMC/Makefile b/science/py-OpenMC/Makefile index 6a295606f93b..77f10b2454d9 100644 --- a/science/py-OpenMC/Makefile +++ b/science/py-OpenMC/Makefile @@ -1,7 +1,7 @@ PORTNAME= OpenMC DISTVERSIONPREFIX= v DISTVERSION= 0.15.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -15,7 +15,7 @@ LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}ipython>0:devel/ipython@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}lxml>0:devel/py-lxml@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}lxml5>0:devel/py-lxml5@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \ diff --git a/science/py-PyNE/pkg-plist b/science/py-PyNE/pkg-plist index 5e6baa1151b7..9cd1ff49c348 100644 --- a/science/py-PyNE/pkg-plist +++ b/science/py-PyNE/pkg-plist @@ -44,44 +44,44 @@ lib/libpyne.so %%PYTHON_SITELIBDIR%%/pyne-0.7.8-py%%PYTHON_VER%%.egg-info/top_level.txt %%PYTHON_SITELIBDIR%%/pyne/__init__.pxd %%PYTHON_SITELIBDIR%%/pyne/__init__.py -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/_argparse%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/alara%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/api%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/binaryreader%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/cccc%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/decay_tape9%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/endl%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/ensdf%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/ensdf_processing%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/fispact%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/fluka%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/gammaspec%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/mcnp%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/mesh%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/njoy%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/openmc_utils%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/origen22%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/partisn%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/ptrac_to_hdf5%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/pyne_version%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/r2s%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/rxdata%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/serpent%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/spatialsolver%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/spectanalysis%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/utils%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/__pycache__/variancereduction%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/_argparse%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/alara%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/api%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/binaryreader%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/cccc%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/decay_tape9%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/endl%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/ensdf%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/ensdf_processing%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/fispact%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/fluka%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/gammaspec%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/mcnp%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/mesh%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/njoy%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/openmc_utils%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/origen22%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/partisn%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/ptrac_to_hdf5%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/pyne_version%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/r2s%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/rxdata%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/serpent%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/spatialsolver%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/spectanalysis%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/utils%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/variancereduction%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/pyne/_argparse.py %%PYTHON_SITELIBDIR%%/pyne/_utils.so %%PYTHON_SITELIBDIR%%/pyne/ace.so %%PYTHON_SITELIBDIR%%/pyne/alara.py %%PYTHON_SITELIBDIR%%/pyne/api.py %%PYTHON_SITELIBDIR%%/pyne/apigen/__init__.py -%%PYTHON_SITELIBDIR%%/pyne/apigen/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/apigen/__pycache__/enrich_multi_sym%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/apigen/__pycache__/main%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/apigen/__pycache__/utils%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/apigen/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/apigen/__pycache__/enrich_multi_sym%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/apigen/__pycache__/main%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/apigen/__pycache__/utils%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/pyne/apigen/enrich_multi_sym.py %%PYTHON_SITELIBDIR%%/pyne/apigen/main.py %%PYTHON_SITELIBDIR%%/pyne/apigen/utils.py @@ -91,8 +91,8 @@ lib/libpyne.so %%PYTHON_SITELIBDIR%%/pyne/c_cram.pxd %%PYTHON_SITELIBDIR%%/pyne/cccc.py %%PYTHON_SITELIBDIR%%/pyne/cli/__init__.py -%%PYTHON_SITELIBDIR%%/pyne/cli/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/cli/__pycache__/tape9%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/cli/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/cli/__pycache__/tape9%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/pyne/cli/tape9.py %%PYTHON_SITELIBDIR%%/pyne/cpp_dagmc_bridge.pxd %%PYTHON_SITELIBDIR%%/pyne/cpp_data.pxd @@ -112,23 +112,23 @@ lib/libpyne.so %%PYTHON_SITELIBDIR%%/pyne/data.pxd %%PYTHON_SITELIBDIR%%/pyne/data.so %%PYTHON_SITELIBDIR%%/pyne/dbgen/__init__.py -%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/api%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/atomic_mass%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/cinder%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/decay%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/dosefactors%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/eaf%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/hashtools%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/isotopic_abundance%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/kaeri%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/materials_library%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/ndsfpy%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/nuc_data_make%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/q_val%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/scattering_lengths%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/simple_xs%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/wimsdfpy%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/api%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/atomic_mass%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/cinder%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/decay%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/dosefactors%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/eaf%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/hashtools%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/isotopic_abundance%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/kaeri%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/materials_library%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/ndsfpy%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/nuc_data_make%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/q_val%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/scattering_lengths%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/simple_xs%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/wimsdfpy%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/pyne/dbgen/abundances.txt %%PYTHON_SITELIBDIR%%/pyne/dbgen/api.py %%PYTHON_SITELIBDIR%%/pyne/dbgen/atomic_mass.py @@ -174,17 +174,17 @@ lib/libpyne.so %%PYTHON_SITELIBDIR%%/pyne/fortranformat/FortranRecordReader.py %%PYTHON_SITELIBDIR%%/pyne/fortranformat/FortranRecordWriter.py %%PYTHON_SITELIBDIR%%/pyne/fortranformat/__init__.py -%%PYTHON_SITELIBDIR%%/pyne/fortranformat/__pycache__/FortranRecordReader%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/fortranformat/__pycache__/FortranRecordWriter%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/fortranformat/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/fortranformat/__pycache__/_edit_descriptors%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/fortranformat/__pycache__/_exceptions%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/fortranformat/__pycache__/_input%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/fortranformat/__pycache__/_lexer%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/fortranformat/__pycache__/_misc%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/fortranformat/__pycache__/_output%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/fortranformat/__pycache__/_parser%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/fortranformat/__pycache__/config%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/fortranformat/__pycache__/FortranRecordReader%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/fortranformat/__pycache__/FortranRecordWriter%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/fortranformat/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/fortranformat/__pycache__/_edit_descriptors%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/fortranformat/__pycache__/_exceptions%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/fortranformat/__pycache__/_input%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/fortranformat/__pycache__/_lexer%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/fortranformat/__pycache__/_misc%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/fortranformat/__pycache__/_output%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/fortranformat/__pycache__/_parser%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/fortranformat/__pycache__/config%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/pyne/fortranformat/_edit_descriptors.py %%PYTHON_SITELIBDIR%%/pyne/fortranformat/_exceptions.py %%PYTHON_SITELIBDIR%%/pyne/fortranformat/_input.py @@ -195,10 +195,10 @@ lib/libpyne.so %%PYTHON_SITELIBDIR%%/pyne/fortranformat/config.py %%PYTHON_SITELIBDIR%%/pyne/gammaspec.py %%PYTHON_SITELIBDIR%%/pyne/gui/__init__.py -%%PYTHON_SITELIBDIR%%/pyne/gui/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/gui/__pycache__/aceviewer%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/gui/__pycache__/decaychain%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/gui/__pycache__/spectplots%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/gui/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/gui/__pycache__/aceviewer%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/gui/__pycache__/decaychain%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/gui/__pycache__/spectplots%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/pyne/gui/aceviewer.py %%PYTHON_SITELIBDIR%%/pyne/gui/decaychain.py %%PYTHON_SITELIBDIR%%/pyne/gui/spectplots.py @@ -238,20 +238,20 @@ lib/libpyne.so %%PYTHON_SITELIBDIR%%/pyne/tally.pxd %%PYTHON_SITELIBDIR%%/pyne/tally.so %%PYTHON_SITELIBDIR%%/pyne/transmute/__init__.py -%%PYTHON_SITELIBDIR%%/pyne/transmute/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/transmute/__pycache__/chainsolve%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/transmute/__pycache__/origen22%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/transmute/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/transmute/__pycache__/chainsolve%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/transmute/__pycache__/origen22%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/pyne/transmute/chainsolve.py %%PYTHON_SITELIBDIR%%/pyne/transmute/origen22.py %%PYTHON_SITELIBDIR%%/pyne/transmuters.so %%PYTHON_SITELIBDIR%%/pyne/utils.py %%PYTHON_SITELIBDIR%%/pyne/variancereduction.py %%PYTHON_SITELIBDIR%%/pyne/xs/__init__.py -%%PYTHON_SITELIBDIR%%/pyne/xs/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/xs/__pycache__/api%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/xs/__pycache__/cache%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/xs/__pycache__/channels%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pyne/xs/__pycache__/data_source%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/xs/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/xs/__pycache__/api%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/xs/__pycache__/cache%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/xs/__pycache__/channels%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/xs/__pycache__/data_source%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/pyne/xs/api.py %%PYTHON_SITELIBDIR%%/pyne/xs/cache.py %%PYTHON_SITELIBDIR%%/pyne/xs/channels.py diff --git a/science/py-arbor/Makefile b/science/py-arbor/Makefile index 7823bff44fbf..c7bf63b0a7b6 100644 --- a/science/py-arbor/Makefile +++ b/science/py-arbor/Makefile @@ -39,7 +39,7 @@ post-patch: @${ECHO} ${DISTVERSION} > ${WRKSRC}/VERSION post-install: - @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/arbor/_arbor${PYTHON_EXT_SUFFIX}.so + @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/arbor/_arbor${PYTHON_TAG}.so do-test: # some tests fail with 'make'-related errors @cd ${BUILD_WRKSRC} && \ diff --git a/science/py-arbor/pkg-plist b/science/py-arbor/pkg-plist index c4ff5834b200..4df3dc59a2f1 100644 --- a/science/py-arbor/pkg-plist +++ b/science/py-arbor/pkg-plist @@ -1,3 +1,3 @@ %%PYTHON_SITELIBDIR%%/arbor/VERSION %%PYTHON_SITELIBDIR%%/arbor/__init__.py -%%PYTHON_SITELIBDIR%%/arbor/_arbor%%PYTHON_EXT_SUFFIX%%.so +%%PYTHON_SITELIBDIR%%/arbor/_arbor%%PYTHON_TAG%%.so diff --git a/science/py-arch/Makefile b/science/py-arch/Makefile index a2e8e0244061..1208ad8f6fec 100644 --- a/science/py-arch/Makefile +++ b/science/py-arch/Makefile @@ -30,7 +30,7 @@ TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} post-install: @${STRIP_CMD} \ - ${STAGEDIR}${PYTHON_SITELIBDIR}/arch/bootstrap/_samplers${PYTHON_EXT_SUFFIX}.so \ - ${STAGEDIR}${PYTHON_SITELIBDIR}/arch/univariate/recursions${PYTHON_EXT_SUFFIX}.so + ${STAGEDIR}${PYTHON_SITELIBDIR}/arch/bootstrap/_samplers${PYTHON_TAG}.so \ + ${STAGEDIR}${PYTHON_SITELIBDIR}/arch/univariate/recursions${PYTHON_TAG}.so .include <bsd.port.mk> diff --git a/science/py-asdf-standard/Makefile b/science/py-asdf-standard/Makefile index 5d9f5c50b8e9..9283d803ac3f 100644 --- a/science/py-asdf-standard/Makefile +++ b/science/py-asdf-standard/Makefile @@ -1,5 +1,5 @@ PORTNAME= asdf-standard -PORTVERSION= 1.1.1 +PORTVERSION= 1.3.0 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -7,7 +7,8 @@ DISTNAME= asdf_standard-${PORTVERSION} MAINTAINER= sunpoet@FreeBSD.org COMMENT= ASDF Standard schemas -WWW= https://github.com/asdf-format/asdf-standard +WWW= https://www.asdf-format.org/projects/asdf-standard/en/latest/ \ + https://github.com/asdf-format/asdf-standard LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE @@ -16,7 +17,7 @@ BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=61:devel/py-setuptools@${PY_FL ${PYTHON_PKGNAMEPREFIX}setuptools-scm>=3.4:devel/py-setuptools-scm@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} -USES= python:3.9+ +USES= python USE_PYTHON= autoplist concurrent pep517 NO_ARCH= yes diff --git a/science/py-asdf-standard/distinfo b/science/py-asdf-standard/distinfo index f530ea1078a2..b0cc521e77a1 100644 --- a/science/py-asdf-standard/distinfo +++ b/science/py-asdf-standard/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1710712522 -SHA256 (asdf_standard-1.1.1.tar.gz) = 01535bc2b15bfc09ec8a62d4999f9cf32dc49dc71660c8425640228fd8776102 -SIZE (asdf_standard-1.1.1.tar.gz) = 114823 +TIMESTAMP = 1750188132 +SHA256 (asdf_standard-1.3.0.tar.gz) = 5958961f399dead2000a78724da37f5aeeb0499a780bbd9ae4fc3ecbe3eaed64 +SIZE (asdf_standard-1.3.0.tar.gz) = 273495 diff --git a/science/py-asdf-standard/files/patch-pyproject.toml b/science/py-asdf-standard/files/patch-pyproject.toml new file mode 100644 index 000000000000..5038faf2d1d0 --- /dev/null +++ b/science/py-asdf-standard/files/patch-pyproject.toml @@ -0,0 +1,20 @@ +--- pyproject.toml.orig 2025-05-21 16:47:38 UTC ++++ pyproject.toml +@@ -3,7 +3,7 @@ requires-python = '>=3.9' + description = 'The ASDF Standard schemas' + readme = 'README.md' + requires-python = '>=3.9' +-license-files = ['LICENSE'] ++license = { file = 'LICENSE' } + authors = [{ name = 'The ASDF Developers', email = 'help@stsci.edu' }] + classifiers = [ + 'Programming Language :: Python', +@@ -41,7 +41,7 @@ requires = [ + + [build-system] + requires = [ +- "setuptools >=77", ++ "setuptools >=61", + "setuptools_scm[toml] >=3.4", + "wheel", + ] diff --git a/science/py-asdf-transform-schemas/Makefile b/science/py-asdf-transform-schemas/Makefile index a41c58ee6590..50b0113ca45f 100644 --- a/science/py-asdf-transform-schemas/Makefile +++ b/science/py-asdf-transform-schemas/Makefile @@ -1,5 +1,5 @@ PORTNAME= asdf-transform-schemas -PORTVERSION= 0.5.0 +PORTVERSION= 0.6.0 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -7,7 +7,8 @@ DISTNAME= asdf_transform_schemas-${PORTVERSION} MAINTAINER= sunpoet@FreeBSD.org COMMENT= ASDF schemas for transforms -WWW= https://github.com/asdf-format/asdf-transform-schemas +WWW= https://www.asdf-format.org/projects/asdf-transform-schemas/en/latest/ \ + https://github.com/asdf-format/asdf-transform-schemas LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE @@ -17,7 +18,7 @@ BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=42:devel/py-setuptools@${PY_FL ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}asdf-standard>=1.1.0:science/py-asdf-standard@${PY_FLAVOR} -USES= python:3.9+ +USES= python USE_PYTHON= autoplist concurrent pep517 NO_ARCH= yes diff --git a/science/py-asdf-transform-schemas/distinfo b/science/py-asdf-transform-schemas/distinfo index 875ad58c6670..c05367274e94 100644 --- a/science/py-asdf-transform-schemas/distinfo +++ b/science/py-asdf-transform-schemas/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1710712524 -SHA256 (asdf_transform_schemas-0.5.0.tar.gz) = 82cf4c782575734a895327f25ff583ce9499d7e2b836fe8880b2d7961c6b462b -SIZE (asdf_transform_schemas-0.5.0.tar.gz) = 109226 +TIMESTAMP = 1748495845 +SHA256 (asdf_transform_schemas-0.6.0.tar.gz) = 0f50f8e096fffd2d14b9c82995901266ef25b23d0dffc30ad41bba46851a9732 +SIZE (asdf_transform_schemas-0.6.0.tar.gz) = 223330 diff --git a/science/py-asdf-transform-schemas/files/patch-pyproject.toml b/science/py-asdf-transform-schemas/files/patch-pyproject.toml new file mode 100644 index 000000000000..19255e15dec5 --- /dev/null +++ b/science/py-asdf-transform-schemas/files/patch-pyproject.toml @@ -0,0 +1,20 @@ +--- pyproject.toml.orig 2025-05-27 23:00:35 UTC ++++ pyproject.toml +@@ -3,7 +3,7 @@ requires-python = '>=3.9' + description = 'ASDF schemas for transforms' + readme = 'README.md' + requires-python = '>=3.9' +-license-files = ['LICENSE'] ++license = { file = 'LICENSE' } + authors = [{ name = 'The ASDF Developers', email = 'help@stsci.edu' }] + classifiers = [ + 'Programming Language :: Python', +@@ -44,7 +44,7 @@ requires = [ + + [build-system] + requires = [ +- "setuptools >77", ++ "setuptools >=42", + "setuptools_scm[toml] >=3.4", + "wheel", + ] diff --git a/science/py-asdf/Makefile b/science/py-asdf/Makefile index f6c7539035f4..3986edee3d15 100644 --- a/science/py-asdf/Makefile +++ b/science/py-asdf/Makefile @@ -1,12 +1,12 @@ PORTNAME= asdf -PORTVERSION= 4.1.0 +PORTVERSION= 4.3.0 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= Python tools to handle ASDF files -WWW= https://asdf.readthedocs.io/en/latest/ \ +WWW= https://www.asdf-format.org/projects/asdf/en/latest/ \ https://github.com/asdf-format/asdf LICENSE= BSD3CLAUSE @@ -31,18 +31,23 @@ TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}fsspec>=2022.8.2:filesystems/py-fsspec@${PY # fsspec[http] TEST_DEPENDS+= ${PYTHON_PKGNAMEPREFIX}aiohttp>=0:www/py-aiohttp@${PY_FLAVOR} -USES= python:3.9+ shebangfix +USES= python shebangfix USE_PYTHON= autoplist concurrent pep517 pytest NO_ARCH= yes SHEBANG_FILES= asdf/_jsonschema/json/bin/jsonschema_suite -OPTIONS_DEFINE= ALL -OPTIONS_DEFAULT=ALL -ALL_DESC= Lz4 compression algorithm support +OPTIONS_DEFINE= ALL HTTP LZ4 +OPTIONS_DEFAULT=ALL HTTP LZ4 +ALL_IMPLIES= HTTP LZ4 +ALL_DESC= All optional dependencies +HTTP_DESC= HTTP support via fsspec +LZ4_DESC= Lz4 compression algorithm support -ALL_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lz4>=0.10:archivers/py-lz4@${PY_FLAVOR} +HTTP_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}aiohttp>=0:www/py-aiohttp@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}fsspec>=2022.8.2:filesystems/py-fsspec@${PY_FLAVOR} +LZ4_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lz4>=0.10:archivers/py-lz4@${PY_FLAVOR} .include <bsd.port.pre.mk> diff --git a/science/py-asdf/distinfo b/science/py-asdf/distinfo index 32ed0b5a80d7..f3a2707208d2 100644 --- a/science/py-asdf/distinfo +++ b/science/py-asdf/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1738606491 -SHA256 (asdf-4.1.0.tar.gz) = 0ff44992c85fd768bd9a9512ab7f012afb52ddcee390e9caf67e30d404122da1 -SIZE (asdf-4.1.0.tar.gz) = 905128 +TIMESTAMP = 1753265788 +SHA256 (asdf-4.3.0.tar.gz) = 961d75fb1f1c4868b4533f885655b7ea9a3f0d257c65b49d728da53fe6df087d +SIZE (asdf-4.3.0.tar.gz) = 897816 diff --git a/science/py-asdf/files/patch-pyproject.toml b/science/py-asdf/files/patch-pyproject.toml new file mode 100644 index 000000000000..be3ddaa30ee5 --- /dev/null +++ b/science/py-asdf/files/patch-pyproject.toml @@ -0,0 +1,11 @@ +--- pyproject.toml.orig 2025-05-30 20:49:07 UTC ++++ pyproject.toml +@@ -2,7 +2,7 @@ readme = 'README.rst' + name = "asdf" + description = "Python implementation of the ASDF Standard" + readme = 'README.rst' +-license-files = ['LICENSE'] ++license = { file = 'LICENSE' } + authors = [{ name = 'The ASDF Developers', email = 'help@stsci.edu' }] + requires-python = '>=3.9' + classifiers = [ diff --git a/science/py-avogadrolibs/Makefile b/science/py-avogadrolibs/Makefile index 31fbec7c419d..1b745afc3b79 100644 --- a/science/py-avogadrolibs/Makefile +++ b/science/py-avogadrolibs/Makefile @@ -26,7 +26,7 @@ CMAKE_ARGS= -DINSTALL_LIBRARY_DIR:STRING=${PYTHON_SITELIBDIR} PLIST_FILES= ${PYTHON_SITELIBDIR}/avogadro/__init__.py \ ${PYTHON_SITELIBDIR}/avogadro/cjson.py \ ${PYTHON_SITELIBDIR}/avogadro/connect.py \ - ${PYTHON_SITELIBDIR}/avogadro/core${PYTHON_EXT_SUFFIX}.so \ - ${PYTHON_SITELIBDIR}/avogadro/io${PYTHON_EXT_SUFFIX}.so + ${PYTHON_SITELIBDIR}/avogadro/core${PYTHON_TAG}.so \ + ${PYTHON_SITELIBDIR}/avogadro/io${PYTHON_TAG}.so .include <bsd.port.mk> diff --git a/science/py-dftd4/Makefile b/science/py-dftd4/Makefile index cac71ffd1a33..bd89908e3afd 100644 --- a/science/py-dftd4/Makefile +++ b/science/py-dftd4/Makefile @@ -22,6 +22,6 @@ USES= pkgconfig python USE_PYTHON= pep517 autoplist post-install: - @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/dftd4/_libdftd4${PYTHON_EXT_SUFFIX}.so + @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/dftd4/_libdftd4${PYTHON_TAG}.so .include <bsd.port.mk> diff --git a/science/py-dimod/Makefile b/science/py-dimod/Makefile index be947d42048c..74fe1a102445 100644 --- a/science/py-dimod/Makefile +++ b/science/py-dimod/Makefile @@ -25,7 +25,7 @@ TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} TEST_WRKSRC= ${WRKSRC}/tests post-install: - @${FIND} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME} -name "*${PYTHON_EXT_SUFFIX}.so" | ${XARGS} ${STRIP_CMD} + @${FIND} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME} -name "*${PYTHON_TAG}.so" | ${XARGS} ${STRIP_CMD} # tests as of 0.12.20: Ran 2913 tests in 34.742s diff --git a/science/py-dipy/pkg-plist b/science/py-dipy/pkg-plist index 8db59397f174..8342bf1ffb0f 100644 --- a/science/py-dipy/pkg-plist +++ b/science/py-dipy/pkg-plist @@ -45,81 +45,81 @@ bin/dipy_track_pft %%PYTHON_SITELIBDIR%%/dipy-1.10.0.dist-info/WHEEL %%PYTHON_SITELIBDIR%%/dipy-1.10.0.dist-info/entry_points.txt %%PYTHON_SITELIBDIR%%/dipy/__init__.py -%%PYTHON_SITELIBDIR%%/dipy/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dipy/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc 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+%%PYTHON_SITELIBDIR%%/dipy/workflows/tests/__pycache__/test_utils%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dipy/workflows/tests/__pycache__/test_utils%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dipy/workflows/tests/__pycache__/test_viz%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dipy/workflows/tests/__pycache__/test_viz%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dipy/workflows/tests/__pycache__/test_workflow%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dipy/workflows/tests/__pycache__/test_workflow%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dipy/workflows/tests/__pycache__/workflow_tests_utils%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dipy/workflows/tests/__pycache__/workflow_tests_utils%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/dipy/workflows/tests/test_align.py %%PYTHON_SITELIBDIR%%/dipy/workflows/tests/test_denoise.py %%PYTHON_SITELIBDIR%%/dipy/workflows/tests/test_docstring_parser.py diff --git a/science/py-dlib/Makefile b/science/py-dlib/Makefile index 520f5dc60851..18631607cec6 100644 --- a/science/py-dlib/Makefile +++ b/science/py-dlib/Makefile @@ -1,6 +1,6 @@ PORTNAME= dlib -DISTVERSION= 19.24.6 -PORTREVISION= 2 +DISTVERSION= 20.0.0 +PORTREVISION= 1 CATEGORIES= science devel math python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -16,8 +16,8 @@ LIB_DEPENDS= ${PY_BOOST} \ libpng.so:graphics/png \ libgif.so:graphics/giflib -USES= cmake:indirect compiler:c++11-lang pkgconfig python shebangfix \ - sqlite xorg +USES= cmake:indirect compiler:c++11-lang jpeg pkgconfig python \ + shebangfix sqlite xorg USE_PYTHON= autoplist distutils USE_XORG= ice sm x11 xext SHEBANG_FILES= python_examples/*.py @@ -29,7 +29,10 @@ BLASLAPACK_DESC= Use OpenBLAS for matrix operations BLASLAPACK_USES= blaslapack:openblas BLASLAPACK_VARS_OFF= blaslapackargs="--no DLIB_USE_BLAS --no DLIB_USE_LAPACK" -PYDISTUTILS_BUILDARGS= --set BOOST_PYTHON_SUFFIX:STRING=${PYTHON_SUFFIX} ${X11ARGS} ${JPEGARGS} ${PNGARGS} ${GIFARGS} ${SQLITEARGS} ${BLASLAPACKARGS} ${AVXARGS} ${BLASLAPACK} +PYDISTUTILS_BUILDARGS= --set BOOST_PYTHON_SUFFIX:STRING=${PYTHON_SUFFIX} ${BLASLAPACKARGS} + +post-extract: + ${FIND} ${WRKSRC}/dlib/external -d 1 -not -name pybind11 -exec rm -rf {} + # due to a build system bug the code gets recompiled twice during "build" and "stage" do-build: diff --git a/science/py-dlib/distinfo b/science/py-dlib/distinfo index 93f2a9e4be33..fd5ff331d522 100644 --- a/science/py-dlib/distinfo +++ b/science/py-dlib/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1729934493 -SHA256 (dlib-19.24.6.tar.gz) = 77e3c28ac2c66141514b07cbb74b7c7f80381c019ce5fec99007980bc6490d7d -SIZE (dlib-19.24.6.tar.gz) = 3374495 +TIMESTAMP = 1748764373 +SHA256 (dlib-20.0.0.tar.gz) = 9ab6a6fe113cc36a20c3f611c57fa6a07f18d1169bd04efb85c32e21b23b7d2b +SIZE (dlib-20.0.0.tar.gz) = 3310015 diff --git a/science/py-dlib/files/patch-dlib_serialize.h b/science/py-dlib/files/patch-dlib_serialize.h deleted file mode 100644 index 94306df64159..000000000000 --- a/science/py-dlib/files/patch-dlib_serialize.h +++ /dev/null @@ -1,11 +0,0 @@ ---- dlib/serialize.h.orig 2024-02-17 21:44:22 UTC -+++ dlib/serialize.h -@@ -639,6 +639,8 @@ namespace dlib - USE_DEFAULT_INT_SERIALIZATION_FOR(wchar_t) - #endif - -+ USE_DEFAULT_INT_SERIALIZATION_FOR(char32_t) -+ - // ---------------------------------------------------------------------------------------- - - inline void serialize( diff --git a/science/py-dlib/files/patch-dlib_unicode_unicode.h b/science/py-dlib/files/patch-dlib_unicode_unicode.h deleted file mode 100644 index 4527fdc054b0..000000000000 --- a/science/py-dlib/files/patch-dlib_unicode_unicode.h +++ /dev/null @@ -1,11 +0,0 @@ ---- dlib/unicode/unicode.h.orig 2024-02-17 21:44:22 UTC -+++ dlib/unicode/unicode.h -@@ -16,7 +16,7 @@ namespace dlib - - // ---------------------------------------------------------------------------------------- - -- using unichar = uint32; -+ using unichar = char32_t; - using ustring = std::basic_string<unichar>; - - // ---------------------------------------------------------------------------------------- diff --git a/science/py-dlib/pkg-plist b/science/py-dlib/pkg-plist index 6dd59d547748..a63f7353953e 100644 --- a/science/py-dlib/pkg-plist +++ b/science/py-dlib/pkg-plist @@ -1,5 +1,3 @@ %%PYTHON_SITELIBDIR%%/dlib/__init__.py -%%PYTHON2%%%%PYTHON_SITELIBDIR%%/dlib/__init__.pyc -%%PYTHON2%%%%PYTHON_SITELIBDIR%%/dlib/__init__.pyo %%PYTHON3%%%%PYTHON_SITELIBDIR%%/dlib/__pycache__/__init__.cpython-%%PYTHON_SUFFIX%%.opt-1.pyc %%PYTHON3%%%%PYTHON_SITELIBDIR%%/dlib/__pycache__/__init__.cpython-%%PYTHON_SUFFIX%%.pyc diff --git a/science/py-dwave-inspector/pkg-plist b/science/py-dwave-inspector/pkg-plist index f8f6c5a27501..2672c9bffd1b 100644 --- a/science/py-dwave-inspector/pkg-plist +++ b/science/py-dwave-inspector/pkg-plist @@ -1,22 +1,22 @@ %%PYTHON_SITELIBDIR%%/dwave/inspector/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/adapters%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/adapters%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/config%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/config%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/package_info%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/package_info%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/proxies%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/proxies%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/server%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/server%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/storage%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/storage%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/utils%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/utils%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/viewers%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/viewers%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/adapters%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/adapters%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/config%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/config%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/package_info%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/package_info%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/proxies%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/proxies%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/server%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/server%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/storage%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/storage%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/utils%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/utils%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/viewers%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/inspector/__pycache__/viewers%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/dwave/inspector/adapters.py %%PYTHON_SITELIBDIR%%/dwave/inspector/config.py %%PYTHON_SITELIBDIR%%/dwave/inspector/package_info.py diff --git a/science/py-dwave-optimization/Makefile b/science/py-dwave-optimization/Makefile index 3b289fc324a8..9afc4936d88d 100644 --- a/science/py-dwave-optimization/Makefile +++ b/science/py-dwave-optimization/Makefile @@ -26,8 +26,8 @@ post-install: # strip binaries @${STRIP_CMD} \ ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/optimization/libdwave-optimization.so \ - ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/optimization/model${PYTHON_EXT_SUFFIX}.so \ - ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/optimization/symbols${PYTHON_EXT_SUFFIX}.so + ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/optimization/model${PYTHON_TAG}.so \ + ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/optimization/symbols${PYTHON_TAG}.so # remove conflicting __init__.py, see https://github.com/dwavesystems/dwave-system/issues/462 @${RM} -r \ ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/__init__.py \ diff --git a/science/py-dwave-preprocessing/Makefile b/science/py-dwave-preprocessing/Makefile index 4f73fe34f2b9..a7fc27a649bb 100644 --- a/science/py-dwave-preprocessing/Makefile +++ b/science/py-dwave-preprocessing/Makefile @@ -27,8 +27,8 @@ TEST_WRKSRC= ${WRKSRC}/tests post-install: # strip binaries @${STRIP_CMD} \ - ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/preprocessing/cyfix_variables${PYTHON_EXT_SUFFIX}.so \ - ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/preprocessing/presolve/cypresolve${PYTHON_EXT_SUFFIX}.so + ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/preprocessing/cyfix_variables${PYTHON_TAG}.so \ + ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/preprocessing/presolve/cypresolve${PYTHON_TAG}.so # remove conflicting __init__.py, see https://github.com/dwavesystems/dwave-preprocessing/issues/45 @${RM} -r \ ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/__init__.py \ diff --git a/science/py-dwave-preprocessing/pkg-plist b/science/py-dwave-preprocessing/pkg-plist index 93a7865b4dcf..ad7fa6653841 100644 --- a/science/py-dwave-preprocessing/pkg-plist +++ b/science/py-dwave-preprocessing/pkg-plist @@ -1,28 +1,28 @@ %%PYTHON_SITELIBDIR%%/dwave/preprocessing/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/preprocessing/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/preprocessing/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/preprocessing/__pycache__/lower_bounds%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/preprocessing/__pycache__/lower_bounds%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/preprocessing/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/preprocessing/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/preprocessing/__pycache__/lower_bounds%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/preprocessing/__pycache__/lower_bounds%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/__pycache__/clip%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/__pycache__/clip%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/__pycache__/connected_components%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/__pycache__/connected_components%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/__pycache__/fix_variables%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/__pycache__/fix_variables%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/__pycache__/scale%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/__pycache__/scale%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/__pycache__/spin_reversal_transform%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/__pycache__/spin_reversal_transform%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/__pycache__/clip%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/__pycache__/clip%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/__pycache__/connected_components%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/__pycache__/connected_components%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/__pycache__/fix_variables%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/__pycache__/fix_variables%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/__pycache__/scale%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/__pycache__/scale%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/__pycache__/spin_reversal_transform%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/__pycache__/spin_reversal_transform%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/clip.py %%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/connected_components.py %%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/fix_variables.py %%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/scale.py %%PYTHON_SITELIBDIR%%/dwave/preprocessing/composites/spin_reversal_transform.py %%PYTHON_SITELIBDIR%%/dwave/preprocessing/cyfix_variables.cpp -%%PYTHON_SITELIBDIR%%/dwave/preprocessing/cyfix_variables%%PYTHON_EXT_SUFFIX%%.so +%%PYTHON_SITELIBDIR%%/dwave/preprocessing/cyfix_variables%%PYTHON_TAG%%.so %%PYTHON_SITELIBDIR%%/dwave/preprocessing/cyfix_variables.pyx %%PYTHON_SITELIBDIR%%/dwave/preprocessing/include/dwave-preprocessing/fix_variables.hpp %%PYTHON_SITELIBDIR%%/dwave/preprocessing/include/dwave-preprocessing/helper_data_structures.hpp @@ -38,14 +38,14 @@ %%PYTHON_SITELIBDIR%%/dwave/preprocessing/lower_bounds.py %%PYTHON_SITELIBDIR%%/dwave/preprocessing/presolve/__init__.pxd %%PYTHON_SITELIBDIR%%/dwave/preprocessing/presolve/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/preprocessing/presolve/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/preprocessing/presolve/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/preprocessing/presolve/__pycache__/exceptions%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/preprocessing/presolve/__pycache__/exceptions%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/preprocessing/presolve/__pycache__/pypresolve%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/preprocessing/presolve/__pycache__/pypresolve%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/preprocessing/presolve/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/preprocessing/presolve/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/preprocessing/presolve/__pycache__/exceptions%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/preprocessing/presolve/__pycache__/exceptions%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/preprocessing/presolve/__pycache__/pypresolve%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/preprocessing/presolve/__pycache__/pypresolve%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/dwave/preprocessing/presolve/cypresolve.cpp -%%PYTHON_SITELIBDIR%%/dwave/preprocessing/presolve/cypresolve%%PYTHON_EXT_SUFFIX%%.so +%%PYTHON_SITELIBDIR%%/dwave/preprocessing/presolve/cypresolve%%PYTHON_TAG%%.so %%PYTHON_SITELIBDIR%%/dwave/preprocessing/presolve/cypresolve.pxd %%PYTHON_SITELIBDIR%%/dwave/preprocessing/presolve/cypresolve.pyx %%PYTHON_SITELIBDIR%%/dwave/preprocessing/presolve/exceptions.py diff --git a/science/py-dwave-samplers/Makefile b/science/py-dwave-samplers/Makefile index 1f613a7c0dd7..e7ec7a9d766c 100644 --- a/science/py-dwave-samplers/Makefile +++ b/science/py-dwave-samplers/Makefile @@ -37,7 +37,7 @@ post-install: ${RM} -r samplers; \ ) # strip binaries - @${FIND} ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/samplers -name "*${PYTHON_EXT_SUFFIX}.so" | ${XARGS} ${STRIP_CMD} + @${FIND} ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/samplers -name "*${PYTHON_TAG}.so" | ${XARGS} ${STRIP_CMD} # remove conflicting __init__.py, see https://github.com/dwavesystems/dwave-system/issues/462 @${RM} -r \ ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/__init__.py \ diff --git a/science/py-dwave-samplers/pkg-plist b/science/py-dwave-samplers/pkg-plist index 515ec9a250b2..d9aa3ff38972 100644 --- a/science/py-dwave-samplers/pkg-plist +++ b/science/py-dwave-samplers/pkg-plist @@ -1,60 +1,60 @@ %%PYTHON_SITELIBDIR%%/dwave/samplers/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/samplers/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/samplers/__pycache__/__init__%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/__pycache__/composite%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/__pycache__/composite%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/__pycache__/sampler%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/__pycache__/sampler%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/__pycache__/composite%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/__pycache__/composite%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/__pycache__/sampler%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/__pycache__/sampler%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/composite.py %%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/decl.pxd %%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/descent.cpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/descent%%PYTHON_EXT_SUFFIX%%.so +%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/descent%%PYTHON_TAG%%.so %%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/descent.pyx %%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/sampler.py %%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/src/descent.cpp %%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/src/descent.h %%PYTHON_SITELIBDIR%%/dwave/samplers/planar/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/__pycache__/planar%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/__pycache__/planar%%PYTHON_EXT_SUFFIX%%.pyc 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+%%PYTHON_SITELIBDIR%%/dwave/samplers/sa/__pycache__/sampler%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/samplers/sa/__pycache__/sampler%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/dwave/samplers/sa/sampler.py %%PYTHON_SITELIBDIR%%/dwave/samplers/sa/simulated_annealing.cpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/sa/simulated_annealing%%PYTHON_EXT_SUFFIX%%.so +%%PYTHON_SITELIBDIR%%/dwave/samplers/sa/simulated_annealing%%PYTHON_TAG%%.so %%PYTHON_SITELIBDIR%%/dwave/samplers/sa/simulated_annealing.pyx %%PYTHON_SITELIBDIR%%/dwave/samplers/sa/src/cpu_sa.cpp %%PYTHON_SITELIBDIR%%/dwave/samplers/sa/src/cpu_sa.h %%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/__pycache__/sampler%%PYTHON_EXT_SUFFIX%%.opt-1.pyc 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%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/src/tabu_utils.h %%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/tabu.pxd %%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/tabu_search.cpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/tabu_search%%PYTHON_EXT_SUFFIX%%.so +%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/tabu_search%%PYTHON_TAG%%.so %%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/tabu_search.pyx %%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/utils.py %%PYTHON_SITELIBDIR%%/dwave/samplers/tree/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/__pycache__/samplers%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/__pycache__/samplers%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/__pycache__/samplers%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/__pycache__/samplers%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/dwave/samplers/tree/orang.pxd %%PYTHON_SITELIBDIR%%/dwave/samplers/tree/sample.cpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/sample%%PYTHON_EXT_SUFFIX%%.so +%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/sample%%PYTHON_TAG%%.so %%PYTHON_SITELIBDIR%%/dwave/samplers/tree/sample.pyx %%PYTHON_SITELIBDIR%%/dwave/samplers/tree/samplers.py %%PYTHON_SITELIBDIR%%/dwave/samplers/tree/solve.cpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/solve%%PYTHON_EXT_SUFFIX%%.so +%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/solve%%PYTHON_TAG%%.so %%PYTHON_SITELIBDIR%%/dwave/samplers/tree/solve.pyx %%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/base.h %%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/buckettree.h @@ -101,5 +101,5 @@ %%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/utils.hpp %%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/varorder.h %%PYTHON_SITELIBDIR%%/dwave/samplers/tree/utilities.cpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/utilities%%PYTHON_EXT_SUFFIX%%.so +%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/utilities%%PYTHON_TAG%%.so %%PYTHON_SITELIBDIR%%/dwave/samplers/tree/utilities.pyx diff --git a/science/py-dwave-system/pkg-plist b/science/py-dwave-system/pkg-plist index 2979d624307b..b55d9993ee26 100644 --- a/science/py-dwave-system/pkg-plist +++ b/science/py-dwave-system/pkg-plist @@ -1,28 +1,28 @@ %%PYTHON_SITELIBDIR%%/dwave/embedding/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/chain_breaks%%PYTHON_EXT_SUFFIX%%.opt-1.pyc 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%%PYTHON_SITELIBDIR%%/dwave/embedding/chain_strength.py %%PYTHON_SITELIBDIR%%/dwave/embedding/chimera.py @@ -35,51 +35,51 @@ %%PYTHON_SITELIBDIR%%/dwave/embedding/utils.py %%PYTHON_SITELIBDIR%%/dwave/embedding/zephyr.py %%PYTHON_SITELIBDIR%%/dwave/system/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/coupling_groups%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/coupling_groups%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/exceptions%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/exceptions%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/flux_bias_offsets%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/flux_bias_offsets%%PYTHON_EXT_SUFFIX%%.pyc 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-%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/warnings%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/coupling_groups%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/coupling_groups%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/exceptions%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/exceptions%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/flux_bias_offsets%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/flux_bias_offsets%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/package_info%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/package_info%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/schedules%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/schedules%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/temperatures%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/temperatures%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/testing%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/testing%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/utilities%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/utilities%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/warnings%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/warnings%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/dwave/system/cache/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/cache_manager%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/cache_manager%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/database_manager%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/database_manager%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/schema%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/schema%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/cache_manager%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/cache_manager%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/database_manager%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/database_manager%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/schema%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/schema%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/dwave/system/cache/cache_manager.py %%PYTHON_SITELIBDIR%%/dwave/system/cache/database_manager.py %%PYTHON_SITELIBDIR%%/dwave/system/cache/schema.py %%PYTHON_SITELIBDIR%%/dwave/system/composites/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/cutoffcomposite%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/cutoffcomposite%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/embedding%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/embedding%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/reversecomposite%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/reversecomposite%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/tiling%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/tiling%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/virtual_graph%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/virtual_graph%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/cutoffcomposite%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/cutoffcomposite%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/embedding%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/embedding%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/reversecomposite%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/reversecomposite%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/tiling%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/tiling%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/virtual_graph%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/virtual_graph%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/dwave/system/composites/cutoffcomposite.py %%PYTHON_SITELIBDIR%%/dwave/system/composites/embedding.py %%PYTHON_SITELIBDIR%%/dwave/system/composites/reversecomposite.py @@ -90,14 +90,14 @@ %%PYTHON_SITELIBDIR%%/dwave/system/flux_bias_offsets.py %%PYTHON_SITELIBDIR%%/dwave/system/package_info.py %%PYTHON_SITELIBDIR%%/dwave/system/samplers/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/clique%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/clique%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/dwave_sampler%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/dwave_sampler%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/leap_hybrid_sampler%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/leap_hybrid_sampler%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/clique%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/clique%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/dwave_sampler%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/dwave_sampler%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/leap_hybrid_sampler%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/leap_hybrid_sampler%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/dwave/system/samplers/clique.py %%PYTHON_SITELIBDIR%%/dwave/system/samplers/dwave_sampler.py %%PYTHON_SITELIBDIR%%/dwave/system/samplers/leap_hybrid_sampler.py diff --git a/science/py-eccodes/Makefile b/science/py-eccodes/Makefile index d76393714ea3..044eb813edc2 100644 --- a/science/py-eccodes/Makefile +++ b/science/py-eccodes/Makefile @@ -1,5 +1,5 @@ PORTNAME= eccodes -PORTVERSION= 2.41.0 +PORTVERSION= 2.43.0 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-eccodes/distinfo b/science/py-eccodes/distinfo index 6c4b4266664a..e37fc89abc25 100644 --- a/science/py-eccodes/distinfo +++ b/science/py-eccodes/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1745177940 -SHA256 (eccodes-2.41.0.tar.gz) = f3e209f5da5a7fcee4942295db4ee7888e077bd2e0342e6170ec5fedb9b29840 -SIZE (eccodes-2.41.0.tar.gz) = 2268345 +TIMESTAMP = 1753796092 +SHA256 (eccodes-2.43.0.tar.gz) = b99c41aaa64b20291452297a3d513e0b08cc96bcedfe364d8f58348159c48faa +SIZE (eccodes-2.43.0.tar.gz) = 2269307 diff --git a/science/py-eccodes/files/patch-setup.py b/science/py-eccodes/files/patch-setup.py new file mode 100644 index 000000000000..8a15aeac70e2 --- /dev/null +++ b/science/py-eccodes/files/patch-setup.py @@ -0,0 +1,10 @@ +--- setup.py.orig 2025-07-25 10:03:25 UTC ++++ setup.py +@@ -90,7 +90,6 @@ install_requires += [ + "attrs", + "cffi", + "findlibs", +- "eccodeslib;platform_system!='Windows'", + ] + + setuptools.setup( diff --git a/science/py-fresnel/pkg-plist b/science/py-fresnel/pkg-plist index 09ef36e04193..4007accf32bb 100644 --- a/science/py-fresnel/pkg-plist +++ b/science/py-fresnel/pkg-plist @@ -1,6 +1,6 @@ %%PYTHON_SITELIBDIR%%/fresnel/__init__.py -%%PYTHON_SITELIBDIR%%/fresnel/_common%%PYTHON_EXT_SUFFIX%%.so -%%PYTHON_SITELIBDIR%%/fresnel/_cpu%%PYTHON_EXT_SUFFIX%%.so +%%PYTHON_SITELIBDIR%%/fresnel/_common%%PYTHON_TAG%%.so +%%PYTHON_SITELIBDIR%%/fresnel/_cpu%%PYTHON_TAG%%.so %%PYTHON_SITELIBDIR%%/fresnel/camera.py %%PYTHON_SITELIBDIR%%/fresnel/color.py %%PYTHON_SITELIBDIR%%/fresnel/conftest.py diff --git a/science/py-gemmi/Makefile b/science/py-gemmi/Makefile index 2aac5d8717f0..9e7f9f8d7544 100644 --- a/science/py-gemmi/Makefile +++ b/science/py-gemmi/Makefile @@ -1,12 +1,13 @@ PORTNAME= gemmi DISTVERSIONPREFIX= v -DISTVERSION= 0.7.1 +DISTVERSION= 0.7.3 CATEGORIES= science python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Macromolecular crystallography library and utilities -WWW= https://gemmi.readthedocs.io/en/latest/ +WWW= https://gemmi.readthedocs.io/en/latest/ \ + https://github.com/project-gemmi/gemmi LICENSE= MPL20 LICENSE_FILE= ${WRKSRC}/LICENSE.txt @@ -36,4 +37,6 @@ PLIST_SUB= VER=${PORTVERSION} do-test: @cd ${WRKSRC} && ${SETENV} ${TEST_ENV} ${PYTHON_CMD} -m unittest discover -v tests/ +# tests as of 0.7.3: test 'test_syntax_error' fails with syntax error, see https://github.com/project-gemmi/gemmi/issues/384 + .include <bsd.port.mk> diff --git a/science/py-gemmi/distinfo b/science/py-gemmi/distinfo index 9050772d8cc8..b40d35b8cada 100644 --- a/science/py-gemmi/distinfo +++ b/science/py-gemmi/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1742885714 -SHA256 (project-gemmi-gemmi-v0.7.1_GH0.tar.gz) = 5d87c3e82ee159f5642d7c083a74e00ca9cc038ccf9be2522d7ae985f3377393 -SIZE (project-gemmi-gemmi-v0.7.1_GH0.tar.gz) = 1910265 +TIMESTAMP = 1753140186 +SHA256 (project-gemmi-gemmi-v0.7.3_GH0.tar.gz) = ed5e1d0665f27d623d877fa36f6c99a5de21310cc8715337ff9f6b545bd2e9d3 +SIZE (project-gemmi-gemmi-v0.7.3_GH0.tar.gz) = 1924234 diff --git a/science/py-gemmi/files/patch-CMakeLists.txt b/science/py-gemmi/files/patch-CMakeLists.txt index d75096e3228b..62637e7014cd 100644 --- a/science/py-gemmi/files/patch-CMakeLists.txt +++ b/science/py-gemmi/files/patch-CMakeLists.txt @@ -1,4 +1,4 @@ ---- CMakeLists.txt.orig 2025-03-24 16:35:30 UTC +--- CMakeLists.txt.orig 2025-07-05 13:51:16 UTC +++ CMakeLists.txt @@ -6,7 +6,7 @@ string(REGEX REPLACE ".+\"([0-9]+\.[0-9]+\.[0-9]+)(-de string(REGEX REPLACE ".+\"([0-9]+\.[0-9]+\.[0-9]+)(-dev)?\"" "\\1" @@ -27,7 +27,7 @@ -target_include_directories(gemmi_headers INTERFACE - "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>" - "$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>") --target_compile_features(gemmi_headers INTERFACE cxx_std_17) +-target_compile_features(gemmi_headers INTERFACE cxx_std_14) -set_target_properties(gemmi_headers PROPERTIES EXPORT_NAME headers) - -add_library(gemmi_cpp @@ -37,7 +37,7 @@ - src/monlib.cpp src/mtz.cpp src/mtz2cif.cpp - src/pdb.cpp src/polyheur.cpp src/read_cif.cpp - src/resinfo.cpp src/riding_h.cpp -- src/select.cpp src/sprintf.cpp src/symmetry.cpp +- src/select.cpp src/sprintf.cpp src/dssp.cpp src/symmetry.cpp - src/to_json.cpp src/to_mmcif.cpp src/to_pdb.cpp src/topo.cpp - src/xds_ascii.cpp) -add_library(gemmi::gemmi_cpp ALIAS gemmi_cpp) @@ -98,8 +98,8 @@ target_include_directories(gemmi-${target} PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party") endfunction() -@@ -336,7 +274,7 @@ add_executable(gemmi::prog ALIAS gemmi_prog) - prog/xds2mtz.cpp +@@ -337,7 +275,7 @@ add_executable(gemmi::prog ALIAS gemmi_prog) + prog/wcn.cpp prog/xds2mtz.cpp $<TARGET_OBJECTS:options>) add_executable(gemmi::prog ALIAS gemmi_prog) -target_link_libraries(gemmi_prog PRIVATE gemmi_cpp) @@ -107,7 +107,7 @@ target_include_directories(gemmi_prog PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party") target_compile_definitions(gemmi_prog PRIVATE GEMMI_ALL_IN_ONE=1) set_target_properties(gemmi_prog PROPERTIES OUTPUT_NAME gemmi EXPORT_NAME prog) -@@ -376,7 +314,7 @@ target_compile_definitions(cpptest PRIVATE USE_STD_SNP +@@ -377,17 +315,17 @@ target_compile_definitions(cpptest PRIVATE USE_STD_SNP add_executable(cpptest EXCLUDE_FROM_ALL tests/main.cpp tests/cif.cpp tests/windowsh.cpp) target_compile_definitions(cpptest PRIVATE USE_STD_SNPRINTF=1) @@ -115,11 +115,9 @@ +target_link_libraries(cpptest PRIVATE gemmi) target_include_directories(cpptest PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party") - add_executable(hello EXCLUDE_FROM_ALL examples/hello.cpp) -@@ -384,11 +322,11 @@ add_executable(doc_example EXCLUDE_FROM_ALL add_executable(doc_example EXCLUDE_FROM_ALL docs/code/sym.cpp docs/code/elem.cpp docs/code/resinfo.cpp - docs/code/cell.cpp docs/code/mutate.cpp src/resinfo.cpp) + docs/code/cell.cpp docs/code/mutate.cpp) -target_link_libraries(doc_example PRIVATE gemmi_cpp) +target_link_libraries(doc_example PRIVATE gemmi) add_executable(doc_example2 EXCLUDE_FROM_ALL docs/code/cif_cc.cpp) @@ -130,7 +128,7 @@ # always compile these tests with assertions enabled if (CMAKE_CXX_COMPILER_ID MATCHES "Clang|GNU|Intel") -@@ -396,14 +334,14 @@ add_executable(test_disulf EXCLUDE_FROM_ALL tests/disu +@@ -395,14 +333,14 @@ add_executable(test_disulf EXCLUDE_FROM_ALL tests/disu endif() add_executable(test_disulf EXCLUDE_FROM_ALL tests/disulf.cpp) @@ -148,16 +146,16 @@ enable_testing() -@@ -440,7 +378,7 @@ if (benchmark_FOUND) +@@ -439,7 +377,7 @@ if (benchmark_FOUND) foreach(b stoi elem mod niggli pdb resinfo round sym writecif) add_executable(${b}-bm EXCLUDE_FROM_ALL benchmarks/${b}.cpp) - if (b MATCHES "elem|resinfo|pdb|writecif") + if (b MATCHES "elem|resinfo|pdb|sym|writecif") - target_link_libraries(${b}-bm PRIVATE gemmi_cpp) + target_link_libraries(${b}-bm PRIVATE gemmi) endif() target_link_libraries(${b}-bm PRIVATE gemmi_headers benchmark::benchmark) set_property(TARGET ${b}-bm PROPERTY RUNTIME_OUTPUT_DIRECTORY -@@ -481,11 +419,11 @@ if (USE_PYTHON) +@@ -480,11 +418,11 @@ if (USE_PYTHON) python/unitcell.cpp python/write.cpp) if (STANDALONE_PYTHON_MODULE) @@ -172,7 +170,7 @@ endif() set_property(TARGET gemmi_py PROPERTY OUTPUT_NAME gemmi_ext) if (CMAKE_CONFIGURATION_TYPES) -@@ -568,19 +506,19 @@ endif() +@@ -567,19 +505,19 @@ endif() install(TARGETS gemmi_prog EXPORT GemmiTargets) endif() diff --git a/science/py-gemmi/pkg-plist b/science/py-gemmi/pkg-plist index 52ebda9cb374..9201705db9d6 100644 --- a/science/py-gemmi/pkg-plist +++ b/science/py-gemmi/pkg-plist @@ -7,7 +7,6 @@ %%PYTHON_SITELIBDIR%%/gemmi/examples/cif_i_sigi.py %%PYTHON_SITELIBDIR%%/gemmi/examples/col_order.py %%PYTHON_SITELIBDIR%%/gemmi/examples/from_json.py -%%PYTHON_SITELIBDIR%%/gemmi/examples/hello.py %%PYTHON_SITELIBDIR%%/gemmi/examples/long_geom.py %%PYTHON_SITELIBDIR%%/gemmi/examples/map2mtz.py %%PYTHON_SITELIBDIR%%/gemmi/examples/maskcheck.py @@ -22,10 +21,11 @@ %%PYTHON_SITELIBDIR%%/gemmi/examples/qq-plot.py %%PYTHON_SITELIBDIR%%/gemmi/examples/rama_gather.py %%PYTHON_SITELIBDIR%%/gemmi/examples/rama_plot.py +%%PYTHON_SITELIBDIR%%/gemmi/examples/read_cif.py %%PYTHON_SITELIBDIR%%/gemmi/examples/refln-stats.py %%PYTHON_SITELIBDIR%%/gemmi/examples/simple_search.py %%PYTHON_SITELIBDIR%%/gemmi/examples/sub_ccd.py %%PYTHON_SITELIBDIR%%/gemmi/examples/to_rdkit.py %%PYTHON_SITELIBDIR%%/gemmi/examples/weight.py -%%PYTHON_SITELIBDIR%%/gemmi/gemmi_ext%%PYTHON_EXT_SUFFIX%%.so +%%PYTHON_SITELIBDIR%%/gemmi/gemmi_ext%%PYTHON_TAG%%.so %%PYTHON_SITELIBDIR%%/gemmi/py.typed diff --git a/science/py-geometer/Makefile b/science/py-geometer/Makefile index 22d1404b8f58..e4d0aaf184a2 100644 --- a/science/py-geometer/Makefile +++ b/science/py-geometer/Makefile @@ -1,6 +1,5 @@ PORTNAME= geometer -PORTVERSION= 0.3.5 -PORTREVISION= 2 +PORTVERSION= 0.4.1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -12,9 +11,9 @@ WWW= https://github.com/jan-mue/geometer LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE -BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} -RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=1.15,1:math/py-numpy@${PY_FLAVOR} +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}hatchling>=0:devel/py-hatchling@${PY_FLAVOR} +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=0,1:math/py-numpy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}typing-extensions>=4.6.1<5.0.0:devel/py-typing-extensions@${PY_FLAVOR} USES= python USE_PYTHON= autoplist concurrent pep517 diff --git a/science/py-geometer/distinfo b/science/py-geometer/distinfo index 382d1ff5ad23..911086479111 100644 --- a/science/py-geometer/distinfo +++ b/science/py-geometer/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1679498804 -SHA256 (geometer-0.3.5.tar.gz) = 016aaf625650ea8841812c1a93d6dd65b2a71d188149f646ad84f4d2c2914451 -SIZE (geometer-0.3.5.tar.gz) = 52886 +TIMESTAMP = 1749813104 +SHA256 (geometer-0.4.1.tar.gz) = 1701124dea9f748f00b50adad91a1a471af96571ae8d5ff9b73858a1cbdb9822 +SIZE (geometer-0.4.1.tar.gz) = 114402 diff --git a/science/py-geometer/files/patch-pyproject.toml b/science/py-geometer/files/patch-pyproject.toml new file mode 100644 index 000000000000..a09e31fd2ff8 --- /dev/null +++ b/science/py-geometer/files/patch-pyproject.toml @@ -0,0 +1,11 @@ +--- pyproject.toml.orig 2020-02-02 00:00:00 UTC ++++ pyproject.toml +@@ -25,7 +25,7 @@ dependencies = [ + "Programming Language :: Python", + ] + dependencies = [ +- "numpy>=2.0", ++ "numpy", + "typing-extensions>=4.6.1,<5.0.0", + ] + diff --git a/science/py-hoomd-blue/pkg-plist b/science/py-hoomd-blue/pkg-plist index 3d9ea65fcbd2..004601c86f0c 100644 --- a/science/py-hoomd-blue/pkg-plist +++ b/science/py-hoomd-blue/pkg-plist @@ -6,7 +6,7 @@ lib/cmake/hoomd/hoomd-macros.cmake lib/cmake/hoomd/hoomd-targets-%%CMAKE_BUILD_TYPE%%.cmake lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/__init__.py -%%PYTHON_SITELIBDIR%%/hoomd/_hoomd%%PYTHON_EXT_SUFFIX%%.so +%%PYTHON_SITELIBDIR%%/hoomd/_hoomd%%PYTHON_TAG%%.so %%PYTHON_SITELIBDIR%%/hoomd/box.py %%PYTHON_SITELIBDIR%%/hoomd/communicator.py %%PYTHON_SITELIBDIR%%/hoomd/conftest.py @@ -37,7 +37,7 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/filter/tags.py %%PYTHON_SITELIBDIR%%/hoomd/filter/type_.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/__init__.py -%%PYTHON_SITELIBDIR%%/hoomd/hpmc/_hpmc%%PYTHON_EXT_SUFFIX%%.so +%%PYTHON_SITELIBDIR%%/hoomd/hpmc/_hpmc%%PYTHON_TAG%%.so %%PYTHON_SITELIBDIR%%/hoomd/hpmc/compute.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/external/__init__.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/external/external.py @@ -690,7 +690,7 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/libquickhull.so %%PYTHON_SITELIBDIR%%/hoomd/logging.py %%PYTHON_SITELIBDIR%%/hoomd/md/__init__.py -%%PYTHON_SITELIBDIR%%/hoomd/md/_md%%PYTHON_EXT_SUFFIX%%.so +%%PYTHON_SITELIBDIR%%/hoomd/md/_md%%PYTHON_TAG%%.so %%PYTHON_SITELIBDIR%%/hoomd/md/alchemy/__init__.py %%PYTHON_SITELIBDIR%%/hoomd/md/alchemy/methods.py %%PYTHON_SITELIBDIR%%/hoomd/md/alchemy/pair.py @@ -781,7 +781,7 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/md/update.py %%PYTHON_SITELIBDIR%%/hoomd/mesh.py %%PYTHON_SITELIBDIR%%/hoomd/mpcd/__init__.py -%%PYTHON_SITELIBDIR%%/hoomd/mpcd/_mpcd%%PYTHON_EXT_SUFFIX%%.so +%%PYTHON_SITELIBDIR%%/hoomd/mpcd/_mpcd%%PYTHON_TAG%%.so %%PYTHON_SITELIBDIR%%/hoomd/mpcd/collide.py %%PYTHON_SITELIBDIR%%/hoomd/mpcd/fill.py %%PYTHON_SITELIBDIR%%/hoomd/mpcd/force.py diff --git a/science/py-kimpy/Makefile b/science/py-kimpy/Makefile index fe599fe87dfa..442b5c9a82d3 100644 --- a/science/py-kimpy/Makefile +++ b/science/py-kimpy/Makefile @@ -20,6 +20,6 @@ USES= compiler:c++20-lang pkgconfig python USE_PYTHON= distutils autoplist pytest # tests fail to run, see https://github.com/openkim/kimpy/issues/16 post-install: - @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/kimpy/*${PYTHON_EXT_SUFFIX}.so + @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/kimpy/*${PYTHON_TAG}.so .include <bsd.port.mk> diff --git a/science/py-kpLib/Makefile b/science/py-kpLib/Makefile index ea502313a16c..bc5206c29439 100644 --- a/science/py-kpLib/Makefile +++ b/science/py-kpLib/Makefile @@ -25,6 +25,6 @@ USE_LDCONFIG= yes USE_PYTHON= distutils concurrent autoplist post-install: - @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/kpLib/lib${PYTHON_EXT_SUFFIX}.so + @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/kpLib/lib${PYTHON_TAG}.so .include <bsd.port.mk> diff --git a/science/py-libgetar/Makefile b/science/py-libgetar/Makefile index ee65a32b0538..3d9881305244 100644 --- a/science/py-libgetar/Makefile +++ b/science/py-libgetar/Makefile @@ -26,7 +26,7 @@ GH_ACCOUNT= glotzerlab TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} post-install: - @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/gtar/_gtar${PYTHON_EXT_SUFFIX}.so + @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/gtar/_gtar${PYTHON_TAG}.so do-test: @cd ${WRKSRC}/test && ${SETENV} ${TEST_ENV} ${PYTHON_CMD} -m unittest discover diff --git a/science/py-meshio/pkg-plist b/science/py-meshio/pkg-plist index 15ca0bda9cd3..f3a0677c6f8e 100644 --- a/science/py-meshio/pkg-plist +++ b/science/py-meshio/pkg-plist @@ -7,39 +7,39 @@ bin/meshio %%PYTHON_SITELIBDIR%%/meshio-%%VER%%.dist-info/top_level.txt %%PYTHON_SITELIBDIR%%/meshio/__about__.py %%PYTHON_SITELIBDIR%%/meshio/__init__.py -%%PYTHON_SITELIBDIR%%/meshio/__pycache__/__about__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/meshio/__pycache__/__about__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/meshio/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/meshio/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/meshio/__pycache__/_common%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/meshio/__pycache__/_common%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/meshio/__pycache__/_exceptions%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/meshio/__pycache__/_exceptions%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/meshio/__pycache__/_files%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/meshio/__pycache__/_files%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/meshio/__pycache__/_helpers%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/meshio/__pycache__/_helpers%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/meshio/__pycache__/_mesh%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/meshio/__pycache__/_mesh%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/meshio/__pycache__/_vtk_common%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/meshio/__pycache__/_vtk_common%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/meshio/__pycache__/__about__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/meshio/__pycache__/__about__%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/meshio/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/meshio/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/meshio/__pycache__/_common%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/meshio/__pycache__/_common%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/meshio/__pycache__/_exceptions%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/meshio/__pycache__/_exceptions%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/meshio/__pycache__/_files%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/meshio/__pycache__/_files%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/meshio/__pycache__/_helpers%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/meshio/__pycache__/_helpers%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/meshio/__pycache__/_mesh%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/meshio/__pycache__/_mesh%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/meshio/__pycache__/_vtk_common%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/meshio/__pycache__/_vtk_common%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/meshio/_cli/__init__.py -%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_ascii%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_ascii%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_binary%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_binary%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_compress%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_compress%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_convert%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_convert%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_decompress%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_decompress%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_info%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_info%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_main%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_main%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_ascii%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_ascii%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_binary%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_binary%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_compress%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_compress%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_convert%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_convert%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_decompress%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_decompress%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_info%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_info%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_main%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/meshio/_cli/__pycache__/_main%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/meshio/_cli/_ascii.py %%PYTHON_SITELIBDIR%%/meshio/_cli/_binary.py %%PYTHON_SITELIBDIR%%/meshio/_cli/_compress.py @@ -49,10 +49,10 @@ bin/meshio %%PYTHON_SITELIBDIR%%/meshio/_cli/_main.py %%PYTHON_SITELIBDIR%%/meshio/_common.py %%PYTHON_SITELIBDIR%%/meshio/_cxml/__init__.py -%%PYTHON_SITELIBDIR%%/meshio/_cxml/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/meshio/_cxml/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/meshio/_cxml/__pycache__/etree%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/meshio/_cxml/__pycache__/etree%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/meshio/_cxml/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/meshio/_cxml/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/meshio/_cxml/__pycache__/etree%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/meshio/_cxml/__pycache__/etree%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/meshio/_cxml/etree.py %%PYTHON_SITELIBDIR%%/meshio/_exceptions.py %%PYTHON_SITELIBDIR%%/meshio/_files.py @@ -60,209 +60,209 @@ bin/meshio %%PYTHON_SITELIBDIR%%/meshio/_mesh.py %%PYTHON_SITELIBDIR%%/meshio/_vtk_common.py %%PYTHON_SITELIBDIR%%/meshio/abaqus/__init__.py -%%PYTHON_SITELIBDIR%%/meshio/abaqus/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/meshio/abaqus/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/meshio/abaqus/__pycache__/_abaqus%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/meshio/abaqus/__pycache__/_abaqus%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/meshio/abaqus/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/meshio/abaqus/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/meshio/abaqus/__pycache__/_abaqus%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/meshio/abaqus/__pycache__/_abaqus%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/meshio/abaqus/_abaqus.py %%PYTHON_SITELIBDIR%%/meshio/ansys/__init__.py 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-%%PYTHON_SITELIBDIR%%/meshio/xdmf/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/meshio/xdmf/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/meshio/xdmf/__pycache__/common%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/meshio/xdmf/__pycache__/common%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/meshio/xdmf/__pycache__/main%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/meshio/xdmf/__pycache__/main%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/meshio/xdmf/__pycache__/time_series%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/meshio/xdmf/__pycache__/time_series%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/meshio/xdmf/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/meshio/xdmf/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/meshio/xdmf/__pycache__/common%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/meshio/xdmf/__pycache__/common%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/meshio/xdmf/__pycache__/main%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/meshio/xdmf/__pycache__/main%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/meshio/xdmf/__pycache__/time_series%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/meshio/xdmf/__pycache__/time_series%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/meshio/xdmf/common.py %%PYTHON_SITELIBDIR%%/meshio/xdmf/main.py %%PYTHON_SITELIBDIR%%/meshio/xdmf/time_series.py diff --git a/science/py-ncrystal/Makefile b/science/py-ncrystal/Makefile index 31735ffb8f3f..c6a90d0c973f 100644 --- a/science/py-ncrystal/Makefile +++ b/science/py-ncrystal/Makefile @@ -1,6 +1,6 @@ PORTNAME= ncrystal DISTVERSIONPREFIX= v -DISTVERSION= 4.1.6 +DISTVERSION= 4.2.8 CATEGORIES= science # physics PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -32,7 +32,7 @@ post-install: # strip binary #@${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/NCrystal/ncrystal_pyinst_data/lib/libNCrystal.so -do-test: # the third test fails for an unknown reason +do-test: @cd ${TEST_WRKSRC} && \ ${SETENV} ${TEST_ENV} ${PYTHON_CMD} -m NCrystal.test all diff --git a/science/py-ncrystal/distinfo b/science/py-ncrystal/distinfo index 21654bc9942b..335765086002 100644 --- a/science/py-ncrystal/distinfo +++ b/science/py-ncrystal/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1743584261 -SHA256 (mctools-ncrystal-v4.1.6_GH0.tar.gz) = 4fc1be0503c6e68a110b6da13963bd2bf53154794a727c63f1218a56f6241eff -SIZE (mctools-ncrystal-v4.1.6_GH0.tar.gz) = 2719484 +TIMESTAMP = 1754559207 +SHA256 (mctools-ncrystal-v4.2.8_GH0.tar.gz) = 499e355e8cb534954101241c5af1f3d4f729aa87f4d63734b05570033a5d6dbd +SIZE (mctools-ncrystal-v4.2.8_GH0.tar.gz) = 2822048 diff --git a/science/py-obspy/Makefile b/science/py-obspy/Makefile index 682927b7f136..b0a3b8b4c973 100644 --- a/science/py-obspy/Makefile +++ b/science/py-obspy/Makefile @@ -1,5 +1,6 @@ PORTNAME= obspy PORTVERSION= 1.4.2 +PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -14,7 +15,7 @@ BUILD_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.7.0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}future>=0.12.4:devel/py-future@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>=3.3.0:math/py-matplotlib@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}lxml>=2.2:devel/py-lxml@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}lxml5>=2.2:devel/py-lxml5@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}requests>=0:www/py-requests@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}decorator>=0:devel/py-decorator@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}sqlalchemy10>=0:databases/py-sqlalchemy10@${PY_FLAVOR} diff --git a/science/py-openEMS/Makefile b/science/py-openEMS/Makefile index 61fcb3a01b33..51720a486db1 100644 --- a/science/py-openEMS/Makefile +++ b/science/py-openEMS/Makefile @@ -35,7 +35,7 @@ post-patch: post-install: .for name in _nf2ff openEMS - @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/openEMS/${name}${PYTHON_EXT_SUFFIX}.so + @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/openEMS/${name}${PYTHON_TAG}.so .endfor .include <bsd.port.mk> diff --git a/science/py-openbabel/Makefile b/science/py-openbabel/Makefile index ea17e5ca77c9..16ecbeb51eee 100644 --- a/science/py-openbabel/Makefile +++ b/science/py-openbabel/Makefile @@ -28,6 +28,6 @@ post-patch: .endif post-install: - @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/openbabel/_openbabel${PYTHON_EXT_SUFFIX}.so + @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/openbabel/_openbabel${PYTHON_TAG}.so .include <bsd.port.mk> diff --git a/science/py-phonopy/Makefile b/science/py-phonopy/Makefile index 9cb61a29d3be..b298e416ecf5 100644 --- a/science/py-phonopy/Makefile +++ b/science/py-phonopy/Makefile @@ -1,5 +1,5 @@ PORTNAME= phonopy -DISTVERSION= 2.38.0 +DISTVERSION= 2.42.0 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -34,8 +34,8 @@ TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} TEST_WRKSRC= ${WRKSRC}/test post-install: - @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/phonopy/_phonopy${PYTHON_EXT_SUFFIX}.so + @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/phonopy/_phonopy${PYTHON_TAG}.so -# tests as of 2.37.0: 3 failed, 270 passed, 4 skipped, 4 warnings, 5 errors in 1448.81s (0:24:08) (failures are likely in science/py-symfc with -9999 error) +# tests as of 2.41.2: 6 failed, 159 passed, 5 skipped, 21 warnings, 130 errors in 502.46s (0:08:22) (failures are likely in science/py-symfc with -9999 error) .include <bsd.port.mk> diff --git a/science/py-phonopy/distinfo b/science/py-phonopy/distinfo index 73eee825c0b9..fa7a9f63de51 100644 --- a/science/py-phonopy/distinfo +++ b/science/py-phonopy/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1741068971 -SHA256 (phonopy-2.38.0.tar.gz) = f2c285affe76b45fcef59d6323c7da727bbcfcdf25e0684cbdae46fccdcf40cf -SIZE (phonopy-2.38.0.tar.gz) = 4712135 +TIMESTAMP = 1753085744 +SHA256 (phonopy-2.42.0.tar.gz) = f157afabc461d6b86c3ff09b139534890ca365ac4fd468cad1a0d0e9233776ce +SIZE (phonopy-2.42.0.tar.gz) = 4715307 diff --git a/science/py-pycsw/Makefile b/science/py-pycsw/Makefile index be76bccd65c7..0e08e20fb106 100644 --- a/science/py-pycsw/Makefile +++ b/science/py-pycsw/Makefile @@ -1,5 +1,6 @@ PORTNAME= pycsw PORTVERSION= 2.6.2 +PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -15,7 +16,7 @@ LICENSE_FILE= ${WRKSRC}/LICENSE.txt BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}geolinks>=0:science/py-geolinks@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}lxml>=0:devel/py-lxml@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}lxml5>=0:devel/py-lxml5@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}OWSLib>=0:graphics/py-OWSLib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyproj>=0:graphics/py-pyproj@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}shapely>=0:devel/py-shapely@${PY_FLAVOR} \ diff --git a/science/py-pygeometa/Makefile b/science/py-pygeometa/Makefile index dd1b60da1fc8..df12a82e2163 100644 --- a/science/py-pygeometa/Makefile +++ b/science/py-pygeometa/Makefile @@ -1,6 +1,6 @@ PORTNAME= pygeometa PORTVERSION= 0.15.3 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -18,7 +18,7 @@ BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLA RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}click>=0:devel/py-click@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}Jinja2>=0:devel/py-Jinja2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}jsonschema>=0:devel/py-jsonschema@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}lxml>=0:devel/py-lxml@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}lxml5>=0:devel/py-lxml5@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}OWSLib>=0:graphics/py-OWSLib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyyaml>=0:devel/py-pyyaml@${PY_FLAVOR} diff --git a/science/py-pygmo2/Makefile b/science/py-pygmo2/Makefile index 00f56445e7ad..a7ed3634ffd4 100644 --- a/science/py-pygmo2/Makefile +++ b/science/py-pygmo2/Makefile @@ -1,7 +1,7 @@ PORTNAME= pygmo2 DISTVERSIONPREFIX= v DISTVERSION= 2.19.7 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= science graphics PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-pygmo2/pkg-plist b/science/py-pygmo2/pkg-plist index c4cc5ac853af..83353e3c6136 100644 --- a/science/py-pygmo2/pkg-plist +++ b/science/py-pygmo2/pkg-plist @@ -21,6 +21,6 @@ %%PYTHON_SITELIBDIR%%/pygmo/_s_policy_test.py %%PYTHON_SITELIBDIR%%/pygmo/_topology_test.py %%PYTHON_SITELIBDIR%%/pygmo/_version.py -%%PYTHON_SITELIBDIR%%/pygmo/core%%PYTHON_EXT_SUFFIX%%.so +%%PYTHON_SITELIBDIR%%/pygmo/core%%PYTHON_TAG%%.so %%PYTHON_SITELIBDIR%%/pygmo/plotting/__init__.py %%PYTHON_SITELIBDIR%%/pygmo/test.py diff --git a/science/py-pymatgen/Makefile b/science/py-pymatgen/Makefile index 33b459c57ce1..dc428fc53ede 100644 --- a/science/py-pymatgen/Makefile +++ b/science/py-pymatgen/Makefile @@ -1,6 +1,6 @@ PORTNAME= pymatgen DISTVERSIONPREFIX= v -DISTVERSION= 2025.3.10 +DISTVERSION= 2025.6.14 CATEGORIES= science python #MASTER_SITES= PYPI # no tests PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -16,29 +16,30 @@ LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${PY_SETUPTOOLS} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} -RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}beautifulsoup>0:www/py-beautifulsoup@${PY_FLAVOR} \ +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}bibtexparser>=1.4.0:textproc/py-bibtexparser@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}joblib>=1:devel/py-joblib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>=3.8:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}monty>=2025.1.9:devel/py-monty@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}networkx>=2.7:math/py-networkx@${PY_FLAVOR} \ ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}orjson>=3.10:devel/py-orjson@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}palettable>=3.3.3:misc/py-palettable@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>=2:math/py-pandas@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}plotly>=4.5.0:graphics/py-plotly@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}plotly>=5.0.0:graphics/py-plotly@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pybtex>=0.24.0:textproc/py-pybtex@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}requests>=2.32:www/py-requests@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}ruamel.yaml>=0.17.0:devel/py-ruamel.yaml@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.13.0:science/py-scipy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}spglib>=2.5.0:science/py-spglib@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}spglib>=2.5:science/py-spglib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}sympy>=1.3:math/py-sympy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}tabulate>=0.9:devel/py-tabulate@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}tqdm>=4.60:misc/py-tqdm@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}uncertainties>=3.1.4:math/py-uncertainties@${PY_FLAVOR} -RUN_DEPENDS+= ${PYTHON_PKGNAMEPREFIX}ase>0:science/py-ase@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}icet>0:science/py-icet@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}openbabel>0:science/py-openbabel@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}phonopy>0:science/py-phonopy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}seekpath>0:science/py-seekpath@${PY_FLAVOR} # optional dependencies +RUN_DEPENDS+= ${PYTHON_PKGNAMEPREFIX}ase>=3.23.0:science/py-ase@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}beautifulsoup>0:www/py-beautifulsoup@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}h5py>=3.11.0:science/py-h5py@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}phonopy>=2.33.3:science/py-phonopy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}seekpath>=2.0.1:science/py-seekpath@${PY_FLAVOR} # optional dependencies TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pybtex>0:textproc/py-pybtex@${PY_FLAVOR} USES= compiler:c++11-lang python @@ -60,5 +61,6 @@ post-install: # strip binaries util/coord_cython*.so # tests as of 2025.2.18: 56 failed, 2912 passed, 149 skipped, 1980 warnings in 11080.55s (3:04:40), see https://github.com/materialsproject/pymatgen/issues/4264 +# tests as of 2025.5.28: 56 failed, 3015 passed, 161 skipped, 131 warnings, 7 errors in 5700.13s (1:35:00) .include <bsd.port.mk> diff --git a/science/py-pymatgen/distinfo b/science/py-pymatgen/distinfo index b86f67b1dd9f..8258c6d8ccd7 100644 --- a/science/py-pymatgen/distinfo +++ b/science/py-pymatgen/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1741670459 -SHA256 (materialsproject-pymatgen-v2025.3.10_GH0.tar.gz) = e04c32df88d92c46a07bf23205cd36f33e1c8b760ccf7d6c975abc2b2f1db238 -SIZE (materialsproject-pymatgen-v2025.3.10_GH0.tar.gz) = 271898854 +TIMESTAMP = 1750130703 +SHA256 (materialsproject-pymatgen-v2025.6.14_GH0.tar.gz) = 5fb34d91889816240e93888a64bdf0b8d17ae23c51b9f6f9dcd5c940a90f47a6 +SIZE (materialsproject-pymatgen-v2025.6.14_GH0.tar.gz) = 272204087 diff --git a/science/py-pymol/Makefile b/science/py-pymol/Makefile index 35810048bbd2..a5d83df2c640 100644 --- a/science/py-pymol/Makefile +++ b/science/py-pymol/Makefile @@ -1,7 +1,7 @@ PORTNAME= pymol DISTVERSIONPREFIX= v DISTVERSION= 3.0.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science biology python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-pymol/pkg-plist b/science/py-pymol/pkg-plist index 3363a43e5cb1..d83b8833bccb 100644 --- a/science/py-pymol/pkg-plist +++ b/science/py-pymol/pkg-plist @@ -1,91 +1,91 @@ bin/pymol %%PYTHON_SITELIBDIR%%/chempy/__init__.py -%%PYTHON_SITELIBDIR%%/chempy/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/chempy/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/chempy/__pycache__/arc%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/chempy/__pycache__/arc%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/chempy/__pycache__/bond_amber%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/chempy/__pycache__/bond_amber%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/chempy/__pycache__/bond_mmff%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/chempy/__pycache__/bond_mmff%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/chempy/__pycache__/bonds%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/chempy/__pycache__/bonds%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/chempy/__pycache__/brick%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/chempy/__pycache__/brick%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/chempy/__pycache__/cc1%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/chempy/__pycache__/cc1%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/chempy/__pycache__/charge%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/chempy/__pycache__/charge%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/chempy/__pycache__/cif%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/chempy/__pycache__/cif%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/chempy/__pycache__/cpv%%PYTHON_EXT_SUFFIX%%.opt-1.pyc 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+%%PYTHON_SITELIBDIR%%/pymol/wizard/__pycache__/message%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/pymol/wizard/__pycache__/message%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pymol/wizard/__pycache__/mutagenesis%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/pymol/wizard/__pycache__/mutagenesis%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pymol/wizard/__pycache__/nucmutagenesis%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/pymol/wizard/__pycache__/nucmutagenesis%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pymol/wizard/__pycache__/openvr%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/pymol/wizard/__pycache__/openvr%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pymol/wizard/__pycache__/pair_fit%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/pymol/wizard/__pycache__/pair_fit%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pymol/wizard/__pycache__/pseudoatom%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/pymol/wizard/__pycache__/pseudoatom%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pymol/wizard/__pycache__/renaming%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/pymol/wizard/__pycache__/renaming%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pymol/wizard/__pycache__/sculpting%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/pymol/wizard/__pycache__/sculpting%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pymol/wizard/__pycache__/security%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/pymol/wizard/__pycache__/security%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pymol/wizard/__pycache__/stereodemo%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/pymol/wizard/__pycache__/stereodemo%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pymol/wizard/__pycache__/toggle%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/pymol/wizard/__pycache__/toggle%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/pymol/wizard/annotation.py %%PYTHON_SITELIBDIR%%/pymol/wizard/appearance.py %%PYTHON_SITELIBDIR%%/pymol/wizard/benchmark.py @@ -922,8 +922,8 @@ bin/pymol %%PYTHON_SITELIBDIR%%/pymol/xray.py %%PYTHON_SITELIBDIR%%/pymol/xwin.py %%PYTHON_SITELIBDIR%%/pymol2/__init__.py -%%PYTHON_SITELIBDIR%%/pymol2/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/pymol2/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/pymol2/__pycache__/cmd2%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/pymol2/__pycache__/cmd2%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/pymol2/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/pymol2/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/pymol2/__pycache__/cmd2%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/pymol2/__pycache__/cmd2%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/pymol2/cmd2.py diff --git a/science/py-pysal/Makefile b/science/py-pysal/Makefile deleted file mode 100644 index 9fb0d4ef1b18..000000000000 --- a/science/py-pysal/Makefile +++ /dev/null @@ -1,63 +0,0 @@ -PORTNAME= pysal -PORTVERSION= 24.1 -CATEGORIES= science python -MASTER_SITES= PYPI -PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} - -MAINTAINER= sunpoet@FreeBSD.org -COMMENT= Cross-platform library of spatial analysis functions -WWW= https://pysal.org/ \ - https://github.com/pysal/pysal/releases - -LICENSE= BSD3CLAUSE -LICENSE_FILE= ${WRKSRC}/LICENSE.txt - -DEPRECATED= Depends on expired math/py-spvcm -EXPIRATION_DATE=2025-06-04 - -BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} -RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}access>=1.1.8:science/py-access@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}esda>=2.4.1:science/py-esda@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}giddy>=2.3.3:graphics/py-giddy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}inequality>=1.0.0:science/py-inequality@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}libpysal>=4.6.2:science/py-libpysal@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}mapclassify>=2.4.3:graphics/py-mapclassify@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}mgwr>=2.1.2:graphics/py-mgwr@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}momepy>=0.5.3:graphics/py-momepy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}pointpats>=2.2.0:graphics/py-pointpats@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}segregation>=2.3.1:science/py-segregation@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}spaghetti>=1.6.6:science/py-spaghetti@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}spglm>=1.0.8:math/py-spglm@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}spint>=1.0.7:math/py-spint@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}splot>=1.1.5.post1:math/py-splot@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}spopt>=0.4.1:math/py-spopt@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}spreg>=1.2.4:math/py-spreg@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}spvcm>=0.3.0:math/py-spvcm@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}tobler>=0.8.2:science/py-tobler@${PY_FLAVOR} - -USES= python -USE_PYTHON= autoplist concurrent pep517 - -NO_ARCH= yes - -OPTIONS_DEFINE= PLUS -PLUS_DESC= Extra features - -PLUS_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}bokeh>=0.11.1:www/py-bokeh@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}descartes>=0:graphics/py-descartes@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}folium>=0.2.1:www/py-folium@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}geojson>=1.3.2:devel/py-geojson@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}geopandas>=0.2:graphics/py-geopandas@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}mapclassify>=0:graphics/py-mapclassify@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}matplotlib>=1.5.1:math/py-matplotlib@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}numba>=0:devel/py-numba@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}numexpr>=0:math/py-numexpr@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}palettable>=0:misc/py-palettable@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}pandana>=0:graphics/py-pandana@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}scikit-learn>=0.17.1:science/py-scikit-learn@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}seaborn>=0.7.0:math/py-seaborn@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}statsmodels>=0.6.1:math/py-statsmodels@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}urbanaccess>=0:graphics/py-urbanaccess@${PY_FLAVOR} - -.include <bsd.port.mk> diff --git a/science/py-pysal/distinfo b/science/py-pysal/distinfo deleted file mode 100644 index b9d40d0a82d9..000000000000 --- a/science/py-pysal/distinfo +++ /dev/null @@ -1,3 +0,0 @@ -TIMESTAMP = 1721280228 -SHA256 (pysal-24.1.tar.gz) = ed84c663c8daf73f5d83daa1ce01f14915fde3cf21b5d46259905cc733336dfb -SIZE (pysal-24.1.tar.gz) = 37876 diff --git a/science/py-pysal/pkg-descr b/science/py-pysal/pkg-descr deleted file mode 100644 index 52b55e84fa5d..000000000000 --- a/science/py-pysal/pkg-descr +++ /dev/null @@ -1,3 +0,0 @@ -PySAL is a cross-platform library of spatial analysis functions written in -Python. It is intended to support the development of high level applications for -spatial analysis. diff --git a/science/py-pyteomics/Makefile b/science/py-pyteomics/Makefile index cbcc08f885f8..6ef21f18727d 100644 --- a/science/py-pyteomics/Makefile +++ b/science/py-pyteomics/Makefile @@ -1,5 +1,6 @@ PORTNAME= pyteomics PORTVERSION= 4.7.5 +PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -30,9 +31,9 @@ XML_DESC= XML support DF_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pandas>=0.17,1:math/py-pandas@${PY_FLAVOR} GRAPHICS_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}matplotlib>=0:math/py-matplotlib@${PY_FLAVOR} TDA_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=0,1:math/py-numpy@${PY_FLAVOR} -UNIMOD_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lxml>=0:devel/py-lxml@${PY_FLAVOR} \ +UNIMOD_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lxml5>=0:devel/py-lxml5@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}sqlalchemy14>=0:databases/py-sqlalchemy14@${PY_FLAVOR} -XML_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lxml>=0:devel/py-lxml@${PY_FLAVOR} \ +XML_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lxml5>=0:devel/py-lxml5@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}numpy>=0,1:math/py-numpy@${PY_FLAVOR} .include <bsd.port.mk> diff --git a/science/py-qiskit/Makefile b/science/py-qiskit/Makefile index a3ef41863553..c55d7b2e49e3 100644 --- a/science/py-qiskit/Makefile +++ b/science/py-qiskit/Makefile @@ -1,5 +1,5 @@ PORTNAME= qiskit -DISTVERSION= 2.0.0 +DISTVERSION= 2.1.1 CATEGORIES= science python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-qiskit/Makefile.crates b/science/py-qiskit/Makefile.crates index ff8fa8febab4..790b3238b85a 100644 --- a/science/py-qiskit/Makefile.crates +++ b/science/py-qiskit/Makefile.crates @@ -1,5 +1,5 @@ -CARGO_CRATES= ahash-0.7.8 \ - ahash-0.8.11 \ +CARGO_CRATES= ahash-0.7.0 \ + ahash-0.8.12 \ aho-corasick-1.1.3 \ allocator-api2-0.2.21 \ anstream-0.6.18 \ @@ -10,15 +10,16 @@ CARGO_CRATES= ahash-0.7.8 \ approx-0.5.1 \ ariadne-0.3.0 \ autocfg-1.4.0 \ + bincode-1.3.3 \ bitfield-struct-0.9.5 \ bitflags-1.3.2 \ bitflags-2.9.0 \ block-buffer-0.10.4 \ boolenum-0.1.0 \ - bytemuck-1.22.0 \ + bytemuck-1.23.0 \ bytemuck_derive-1.8.1 \ byteorder-1.5.0 \ - cbindgen-0.28.0 \ + cbindgen-0.29.0 \ cfg-if-1.0.0 \ clap-4.5.31 \ clap_builder-4.5.31 \ @@ -66,19 +67,20 @@ CARGO_CRATES= ahash-0.7.8 \ getrandom-0.2.15 \ getrandom-0.3.1 \ half-2.4.1 \ + hash32-0.3.1 \ hashbrown-0.12.3 \ hashbrown-0.14.5 \ hashbrown-0.15.2 \ - heck-0.4.1 \ + heapless-0.8.0 \ heck-0.5.0 \ - hermit-abi-0.4.0 \ - indexmap-2.7.1 \ + hermit-abi-0.5.1 \ + indexmap-2.9.0 \ indoc-2.0.6 \ - is-terminal-0.4.15 \ + is-terminal-0.4.16 \ is_terminal_polyfill-1.70.1 \ itertools-0.10.5 \ itertools-0.11.0 \ - itertools-0.13.0 \ + itertools-0.14.0 \ itoa-1.0.15 \ lazy_static-1.5.0 \ libc-0.2.170 \ @@ -90,6 +92,7 @@ CARGO_CRATES= ahash-0.7.8 \ matrixmultiply-0.3.9 \ memchr-2.7.4 \ memoffset-0.9.1 \ + minimal-lexical-0.2.1 \ nalgebra-0.33.2 \ nalgebra-macros-0.2.2 \ nano-gemm-0.1.2 \ @@ -101,43 +104,44 @@ CARGO_CRATES= ahash-0.7.8 \ nano-gemm-f64-0.1.0 \ ndarray-0.16.1 \ ndarray-einsum-0.8.0 \ - npyz-0.8.3 \ + nom-7.1.3 \ + nom-unicode-0.3.0 \ + npyz-0.8.4 \ num-bigint-0.4.6 \ num-complex-0.4.6 \ num-integer-0.1.46 \ num-rational-0.4.2 \ num-traits-0.2.19 \ - numpy-0.23.0 \ - once_cell-1.20.3 \ + numpy-0.25.0 \ + once_cell-1.21.3 \ oq3_lexer-0.7.0 \ oq3_parser-0.7.0 \ oq3_semantics-0.7.0 \ oq3_source_file-0.7.0 \ oq3_syntax-0.7.0 \ paste-1.0.15 \ - pest-2.7.15 \ - pest_derive-2.7.15 \ - pest_generator-2.7.15 \ - pest_meta-2.7.15 \ + pest-2.8.0 \ + pest_derive-2.8.0 \ + pest_generator-2.8.0 \ + pest_meta-2.8.0 \ petgraph-0.6.5 \ petgraph-0.7.1 \ portable-atomic-1.11.0 \ portable-atomic-util-0.2.4 \ - ppv-lite86-0.2.20 \ + ppv-lite86-0.2.21 \ priority-queue-2.1.2 \ proc-macro-error-1.0.4 \ proc-macro-error-attr-1.0.4 \ proc-macro2-1.0.94 \ pulp-0.18.22 \ - pulp-0.21.4 \ + pulp-0.21.5 \ pulp-macro-0.1.1 \ py_literal-0.4.0 \ - pyo3-0.23.5 \ - pyo3-build-config-0.23.5 \ - pyo3-build-config-0.24.0 \ - pyo3-ffi-0.23.5 \ - pyo3-macros-0.23.5 \ - pyo3-macros-backend-0.23.5 \ + pyo3-0.25.0 \ + pyo3-build-config-0.25.0 \ + pyo3-ffi-0.25.0 \ + pyo3-macros-0.25.0 \ + pyo3-macros-backend-0.25.0 \ quote-1.0.39 \ ra_ap_limit-0.0.188 \ rand-0.8.5 \ @@ -160,9 +164,10 @@ CARGO_CRATES= ahash-0.7.8 \ regex-automata-0.4.9 \ regex-syntax-0.8.5 \ rowan-0.15.15 \ + rstar-0.12.2 \ rustc-hash-1.1.0 \ rustc-hash-2.1.1 \ - rustiq-core-0.0.10 \ + rustiq-core-0.0.11 \ rustix-0.38.44 \ rustversion-1.0.20 \ rustworkx-core-0.16.0 \ @@ -170,14 +175,15 @@ CARGO_CRATES= ahash-0.7.8 \ safe_arch-0.7.4 \ same-file-1.0.6 \ seq-macro-0.3.6 \ - serde-1.0.218 \ - serde_derive-1.0.218 \ + serde-1.0.219 \ + serde_derive-1.0.219 \ serde_json-1.0.140 \ serde_spanned-0.6.8 \ sha2-0.10.8 \ simba-0.9.0 \ - smallvec-1.14.0 \ + smallvec-1.15.0 \ smol_str-0.2.2 \ + stable_deref_trait-1.2.0 \ strsim-0.11.1 \ syn-1.0.109 \ syn-2.0.99 \ @@ -202,6 +208,7 @@ CARGO_CRATES= ahash-0.7.8 \ unicode-xid-0.2.6 \ unindent-0.2.4 \ utf8parse-0.2.2 \ + uuid-1.17.0 \ version_check-0.9.5 \ walkdir-2.5.0 \ wasi-0.11.0+wasi-snapshot-preview1 \ @@ -232,7 +239,5 @@ CARGO_CRATES= ahash-0.7.8 \ xshell-0.2.7 \ xshell-macros-0.2.7 \ yansi-0.5.1 \ - zerocopy-0.7.35 \ - zerocopy-0.8.21 \ - zerocopy-derive-0.7.35 \ - zerocopy-derive-0.8.21 + zerocopy-0.8.25 \ + zerocopy-derive-0.8.25 diff --git a/science/py-qiskit/distinfo b/science/py-qiskit/distinfo index 5614a20c079c..f1f98a1c4ce5 100644 --- a/science/py-qiskit/distinfo +++ b/science/py-qiskit/distinfo @@ -1,8 +1,8 @@ -TIMESTAMP = 1745542321 -SHA256 (rust/crates/ahash-0.7.8.crate) = 891477e0c6a8957309ee5c45a6368af3ae14bb510732d2684ffa19af310920f9 -SIZE (rust/crates/ahash-0.7.8.crate) = 38550 -SHA256 (rust/crates/ahash-0.8.11.crate) = e89da841a80418a9b391ebaea17f5c112ffaaa96f621d2c285b5174da76b9011 -SIZE (rust/crates/ahash-0.8.11.crate) = 43607 +TIMESTAMP = 1753430083 +SHA256 (rust/crates/ahash-0.7.0.crate) = efa60d2eadd8b12a996add391db32bd1153eac697ba4869660c0016353611426 +SIZE (rust/crates/ahash-0.7.0.crate) = 55813 +SHA256 (rust/crates/ahash-0.8.12.crate) = 5a15f179cd60c4584b8a8c596927aadc462e27f2ca70c04e0071964a73ba7a75 +SIZE (rust/crates/ahash-0.8.12.crate) = 43413 SHA256 (rust/crates/aho-corasick-1.1.3.crate) = 8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916 SIZE (rust/crates/aho-corasick-1.1.3.crate) = 183311 SHA256 (rust/crates/allocator-api2-0.2.21.crate) = 683d7910e743518b0e34f1186f92494becacb047c7b6bf616c96772180fef923 @@ -23,6 +23,8 @@ SHA256 (rust/crates/ariadne-0.3.0.crate) = 72fe02fc62033df9ba41cba57ee19acf5e742 SIZE (rust/crates/ariadne-0.3.0.crate) = 21829 SHA256 (rust/crates/autocfg-1.4.0.crate) = ace50bade8e6234aa140d9a2f552bbee1db4d353f69b8217bc503490fc1a9f26 SIZE (rust/crates/autocfg-1.4.0.crate) = 17712 +SHA256 (rust/crates/bincode-1.3.3.crate) = b1f45e9417d87227c7a56d22e471c6206462cba514c7590c09aff4cf6d1ddcad +SIZE (rust/crates/bincode-1.3.3.crate) = 28958 SHA256 (rust/crates/bitfield-struct-0.9.5.crate) = b2869c63ccf4f8bf0d485070b880e60e097fb7aeea80ee82a0a94a957e372a0b SIZE (rust/crates/bitfield-struct-0.9.5.crate) = 15953 SHA256 (rust/crates/bitflags-1.3.2.crate) = bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a @@ -33,14 +35,14 @@ SHA256 (rust/crates/block-buffer-0.10.4.crate) = 3078c7629b62d3f0439517fa394996a SIZE (rust/crates/block-buffer-0.10.4.crate) = 10538 SHA256 (rust/crates/boolenum-0.1.0.crate) = a6c8abd585d7026df20a9ae12982127ba5e81cc7a09397b957e71659da8c5de8 SIZE (rust/crates/boolenum-0.1.0.crate) = 3444 -SHA256 (rust/crates/bytemuck-1.22.0.crate) = b6b1fc10dbac614ebc03540c9dbd60e83887fda27794998c6528f1782047d540 -SIZE (rust/crates/bytemuck-1.22.0.crate) = 52451 +SHA256 (rust/crates/bytemuck-1.23.0.crate) = 9134a6ef01ce4b366b50689c94f82c14bc72bc5d0386829828a2e2752ef7958c +SIZE (rust/crates/bytemuck-1.23.0.crate) = 52534 SHA256 (rust/crates/bytemuck_derive-1.8.1.crate) = 3fa76293b4f7bb636ab88fd78228235b5248b4d05cc589aed610f954af5d7c7a SIZE (rust/crates/bytemuck_derive-1.8.1.crate) = 23100 SHA256 (rust/crates/byteorder-1.5.0.crate) = 1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b SIZE (rust/crates/byteorder-1.5.0.crate) = 23288 -SHA256 (rust/crates/cbindgen-0.28.0.crate) = eadd868a2ce9ca38de7eeafdcec9c7065ef89b42b32f0839278d55f35c54d1ff -SIZE (rust/crates/cbindgen-0.28.0.crate) = 223401 +SHA256 (rust/crates/cbindgen-0.29.0.crate) = 975982cdb7ad6a142be15bdf84aea7ec6a9e5d4d797c004d43185b24cfe4e684 +SIZE (rust/crates/cbindgen-0.29.0.crate) = 226905 SHA256 (rust/crates/cfg-if-1.0.0.crate) = baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd SIZE (rust/crates/cfg-if-1.0.0.crate) = 7934 SHA256 (rust/crates/clap-4.5.31.crate) = 027bb0d98429ae334a8698531da7077bdf906419543a35a55c2cb1b66437d767 @@ -135,32 +137,34 @@ SHA256 (rust/crates/getrandom-0.3.1.crate) = 43a49c392881ce6d5c3b8cb70f98717b7c0 SIZE (rust/crates/getrandom-0.3.1.crate) = 42449 SHA256 (rust/crates/half-2.4.1.crate) = 6dd08c532ae367adf81c312a4580bc67f1d0fe8bc9c460520283f4c0ff277888 SIZE (rust/crates/half-2.4.1.crate) = 50892 +SHA256 (rust/crates/hash32-0.3.1.crate) = 47d60b12902ba28e2730cd37e95b8c9223af2808df9e902d4df49588d1470606 +SIZE (rust/crates/hash32-0.3.1.crate) = 10273 SHA256 (rust/crates/hashbrown-0.12.3.crate) = 8a9ee70c43aaf417c914396645a0fa852624801b24ebb7ae78fe8272889ac888 SIZE (rust/crates/hashbrown-0.12.3.crate) = 102968 SHA256 (rust/crates/hashbrown-0.14.5.crate) = e5274423e17b7c9fc20b6e7e208532f9b19825d82dfd615708b70edd83df41f1 SIZE (rust/crates/hashbrown-0.14.5.crate) = 141498 SHA256 (rust/crates/hashbrown-0.15.2.crate) = bf151400ff0baff5465007dd2f3e717f3fe502074ca563069ce3a6629d07b289 SIZE (rust/crates/hashbrown-0.15.2.crate) = 138478 -SHA256 (rust/crates/heck-0.4.1.crate) = 95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8 -SIZE (rust/crates/heck-0.4.1.crate) = 11567 +SHA256 (rust/crates/heapless-0.8.0.crate) = 0bfb9eb618601c89945a70e254898da93b13be0388091d42117462b265bb3fad +SIZE (rust/crates/heapless-0.8.0.crate) = 77802 SHA256 (rust/crates/heck-0.5.0.crate) = 2304e00983f87ffb38b55b444b5e3b60a884b5d30c0fca7d82fe33449bbe55ea SIZE (rust/crates/heck-0.5.0.crate) = 11517 -SHA256 (rust/crates/hermit-abi-0.4.0.crate) = fbf6a919d6cf397374f7dfeeea91d974c7c0a7221d0d0f4f20d859d329e53fcc -SIZE (rust/crates/hermit-abi-0.4.0.crate) = 16310 -SHA256 (rust/crates/indexmap-2.7.1.crate) = 8c9c992b02b5b4c94ea26e32fe5bccb7aa7d9f390ab5c1221ff895bc7ea8b652 -SIZE (rust/crates/indexmap-2.7.1.crate) = 88644 +SHA256 (rust/crates/hermit-abi-0.5.1.crate) = f154ce46856750ed433c8649605bf7ed2de3bc35fd9d2a9f30cddd873c80cb08 +SIZE (rust/crates/hermit-abi-0.5.1.crate) = 17549 +SHA256 (rust/crates/indexmap-2.9.0.crate) = cea70ddb795996207ad57735b50c5982d8844f38ba9ee5f1aedcfb708a2aa11e +SIZE (rust/crates/indexmap-2.9.0.crate) = 91214 SHA256 (rust/crates/indoc-2.0.6.crate) = f4c7245a08504955605670dbf141fceab975f15ca21570696aebe9d2e71576bd SIZE (rust/crates/indoc-2.0.6.crate) = 17164 -SHA256 (rust/crates/is-terminal-0.4.15.crate) = e19b23d53f35ce9f56aebc7d1bb4e6ac1e9c0db7ac85c8d1760c04379edced37 -SIZE (rust/crates/is-terminal-0.4.15.crate) = 7770 +SHA256 (rust/crates/is-terminal-0.4.16.crate) = e04d7f318608d35d4b61ddd75cbdaee86b023ebe2bd5a66ee0915f0bf93095a9 +SIZE (rust/crates/is-terminal-0.4.16.crate) = 7811 SHA256 (rust/crates/is_terminal_polyfill-1.70.1.crate) = 7943c866cc5cd64cbc25b2e01621d07fa8eb2a1a23160ee81ce38704e97b8ecf SIZE (rust/crates/is_terminal_polyfill-1.70.1.crate) = 7492 SHA256 (rust/crates/itertools-0.10.5.crate) = b0fd2260e829bddf4cb6ea802289de2f86d6a7a690192fbe91b3f46e0f2c8473 SIZE (rust/crates/itertools-0.10.5.crate) = 115354 SHA256 (rust/crates/itertools-0.11.0.crate) = b1c173a5686ce8bfa551b3563d0c2170bf24ca44da99c7ca4bfdab5418c3fe57 SIZE (rust/crates/itertools-0.11.0.crate) = 125074 -SHA256 (rust/crates/itertools-0.13.0.crate) = 413ee7dfc52ee1a4949ceeb7dbc8a33f2d6c088194d9f922fb8318faf1f01186 -SIZE (rust/crates/itertools-0.13.0.crate) = 146261 +SHA256 (rust/crates/itertools-0.14.0.crate) = 2b192c782037fadd9cfa75548310488aabdbf3d2da73885b31bd0abd03351285 +SIZE (rust/crates/itertools-0.14.0.crate) = 152715 SHA256 (rust/crates/itoa-1.0.15.crate) = 4a5f13b858c8d314ee3e8f639011f7ccefe71f97f96e50151fb991f267928e2c SIZE (rust/crates/itoa-1.0.15.crate) = 11231 SHA256 (rust/crates/lazy_static-1.5.0.crate) = bbd2bcb4c963f2ddae06a2efc7e9f3591312473c50c6685e1f298068316e66fe @@ -183,6 +187,8 @@ SHA256 (rust/crates/memchr-2.7.4.crate) = 78ca9ab1a0babb1e7d5695e3530886289c18cf SIZE (rust/crates/memchr-2.7.4.crate) = 96670 SHA256 (rust/crates/memoffset-0.9.1.crate) = 488016bfae457b036d996092f6cb448677611ce4449e970ceaf42695203f218a SIZE (rust/crates/memoffset-0.9.1.crate) = 9032 +SHA256 (rust/crates/minimal-lexical-0.2.1.crate) = 68354c5c6bd36d73ff3feceb05efa59b6acb7626617f4962be322a825e61f79a +SIZE (rust/crates/minimal-lexical-0.2.1.crate) = 94841 SHA256 (rust/crates/nalgebra-0.33.2.crate) = 26aecdf64b707efd1310e3544d709c5c0ac61c13756046aaaba41be5c4f66a3b SIZE (rust/crates/nalgebra-0.33.2.crate) = 385768 SHA256 (rust/crates/nalgebra-macros-0.2.2.crate) = 254a5372af8fc138e36684761d3c0cdb758a4410e938babcff1c860ce14ddbfc @@ -205,8 +211,12 @@ SHA256 (rust/crates/ndarray-0.16.1.crate) = 882ed72dce9365842bf196bdeedf5055305f SIZE (rust/crates/ndarray-0.16.1.crate) = 291026 SHA256 (rust/crates/ndarray-einsum-0.8.0.crate) = f4b2d52dfff9b24d072b6080eab1587cbd54ae24da7b8370072c3a84db221e05 SIZE (rust/crates/ndarray-einsum-0.8.0.crate) = 34449 -SHA256 (rust/crates/npyz-0.8.3.crate) = 13f27ea175875c472b3df61ece89a6d6ef4e0627f43704e400c782f174681ebd -SIZE (rust/crates/npyz-0.8.3.crate) = 75073 +SHA256 (rust/crates/nom-7.1.3.crate) = d273983c5a657a70a3e8f2a01329822f3b8c8172b73826411a55751e404a0a4a +SIZE (rust/crates/nom-7.1.3.crate) = 117570 +SHA256 (rust/crates/nom-unicode-0.3.0.crate) = a5c03a4d71ab9740c752c165329e9df13a808093b146dfbef6170ac260771ffe +SIZE (rust/crates/nom-unicode-0.3.0.crate) = 9378 +SHA256 (rust/crates/npyz-0.8.4.crate) = 9f0e759e014e630f90af745101b614f761306ddc541681e546649068e25ec1b9 +SIZE (rust/crates/npyz-0.8.4.crate) = 77220 SHA256 (rust/crates/num-bigint-0.4.6.crate) = a5e44f723f1133c9deac646763579fdb3ac745e418f2a7af9cd0c431da1f20b9 SIZE (rust/crates/num-bigint-0.4.6.crate) = 102801 SHA256 (rust/crates/num-complex-0.4.6.crate) = 73f88a1307638156682bada9d7604135552957b7818057dcef22705b4d509495 @@ -217,10 +227,10 @@ SHA256 (rust/crates/num-rational-0.4.2.crate) = f83d14da390562dca69fc84082e73e54 SIZE (rust/crates/num-rational-0.4.2.crate) = 28159 SHA256 (rust/crates/num-traits-0.2.19.crate) = 071dfc062690e90b734c0b2273ce72ad0ffa95f0c74596bc250dcfd960262841 SIZE (rust/crates/num-traits-0.2.19.crate) = 51631 -SHA256 (rust/crates/numpy-0.23.0.crate) = b94caae805f998a07d33af06e6a3891e38556051b8045c615470a71590e13e78 -SIZE (rust/crates/numpy-0.23.0.crate) = 79034 -SHA256 (rust/crates/once_cell-1.20.3.crate) = 945462a4b81e43c4e3ba96bd7b49d834c6f61198356aa858733bc4acf3cbe62e -SIZE (rust/crates/once_cell-1.20.3.crate) = 33456 +SHA256 (rust/crates/numpy-0.25.0.crate) = 29f1dee9aa8d3f6f8e8b9af3803006101bb3653866ef056d530d53ae68587191 +SIZE (rust/crates/numpy-0.25.0.crate) = 81623 +SHA256 (rust/crates/once_cell-1.21.3.crate) = 42f5e15c9953c5e4ccceeb2e7382a716482c34515315f7b03532b8b4e8393d2d +SIZE (rust/crates/once_cell-1.21.3.crate) = 34534 SHA256 (rust/crates/oq3_lexer-0.7.0.crate) = a27bbc91e3e9d6193a44aac8f5d62c1507c41669af71a4e7e0ef66fd6470e960 SIZE (rust/crates/oq3_lexer-0.7.0.crate) = 16877 SHA256 (rust/crates/oq3_parser-0.7.0.crate) = 9a72022fcb414e8a0912920a1cf46417b6aa95f19d4b38778df7450f8a3c17fa @@ -233,14 +243,14 @@ SHA256 (rust/crates/oq3_syntax-0.7.0.crate) = 42c754ce1d9da28d6c0334c212d64b5212 SIZE (rust/crates/oq3_syntax-0.7.0.crate) = 63066 SHA256 (rust/crates/paste-1.0.15.crate) = 57c0d7b74b563b49d38dae00a0c37d4d6de9b432382b2892f0574ddcae73fd0a SIZE (rust/crates/paste-1.0.15.crate) = 18374 -SHA256 (rust/crates/pest-2.7.15.crate) = 8b7cafe60d6cf8e62e1b9b2ea516a089c008945bb5a275416789e7db0bc199dc -SIZE (rust/crates/pest-2.7.15.crate) = 127895 -SHA256 (rust/crates/pest_derive-2.7.15.crate) = 816518421cfc6887a0d62bf441b6ffb4536fcc926395a69e1a85852d4363f57e -SIZE (rust/crates/pest_derive-2.7.15.crate) = 40745 -SHA256 (rust/crates/pest_generator-2.7.15.crate) = 7d1396fd3a870fc7838768d171b4616d5c91f6cc25e377b673d714567d99377b -SIZE (rust/crates/pest_generator-2.7.15.crate) = 18417 -SHA256 (rust/crates/pest_meta-2.7.15.crate) = e1e58089ea25d717bfd31fb534e4f3afcc2cc569c70de3e239778991ea3b7dea -SIZE (rust/crates/pest_meta-2.7.15.crate) = 42121 +SHA256 (rust/crates/pest-2.8.0.crate) = 198db74531d58c70a361c42201efde7e2591e976d518caf7662a47dc5720e7b6 +SIZE (rust/crates/pest-2.8.0.crate) = 128955 +SHA256 (rust/crates/pest_derive-2.8.0.crate) = d725d9cfd79e87dccc9341a2ef39d1b6f6353d68c4b33c177febbe1a402c97c5 +SIZE (rust/crates/pest_derive-2.8.0.crate) = 42196 +SHA256 (rust/crates/pest_generator-2.8.0.crate) = db7d01726be8ab66ab32f9df467ae8b1148906685bbe75c82d1e65d7f5b3f841 +SIZE (rust/crates/pest_generator-2.8.0.crate) = 18617 +SHA256 (rust/crates/pest_meta-2.8.0.crate) = 7f9f832470494906d1fca5329f8ab5791cc60beb230c74815dff541cbd2b5ca0 +SIZE (rust/crates/pest_meta-2.8.0.crate) = 42931 SHA256 (rust/crates/petgraph-0.6.5.crate) = b4c5cc86750666a3ed20bdaf5ca2a0344f9c67674cae0515bec2da16fbaa47db SIZE (rust/crates/petgraph-0.6.5.crate) = 710970 SHA256 (rust/crates/petgraph-0.7.1.crate) = 3672b37090dbd86368a4145bc067582552b29c27377cad4e0a306c97f9bd7772 @@ -249,8 +259,8 @@ SHA256 (rust/crates/portable-atomic-1.11.0.crate) = 350e9b48cbc6b0e028b0473b1144 SIZE (rust/crates/portable-atomic-1.11.0.crate) = 181258 SHA256 (rust/crates/portable-atomic-util-0.2.4.crate) = d8a2f0d8d040d7848a709caf78912debcc3f33ee4b3cac47d73d1e1069e83507 SIZE (rust/crates/portable-atomic-util-0.2.4.crate) = 47043 -SHA256 (rust/crates/ppv-lite86-0.2.20.crate) = 77957b295656769bb8ad2b6a6b09d897d94f05c41b069aede1fcdaa675eaea04 -SIZE (rust/crates/ppv-lite86-0.2.20.crate) = 22478 +SHA256 (rust/crates/ppv-lite86-0.2.21.crate) = 85eae3c4ed2f50dcfe72643da4befc30deadb458a9b590d720cde2f2b1e97da9 +SIZE (rust/crates/ppv-lite86-0.2.21.crate) = 22522 SHA256 (rust/crates/priority-queue-2.1.2.crate) = 090ded312ed32a928fb49cb91ab4db6523ae3767225e61fbf6ceaaec3664ed26 SIZE (rust/crates/priority-queue-2.1.2.crate) = 36557 SHA256 (rust/crates/proc-macro-error-1.0.4.crate) = da25490ff9892aab3fcf7c36f08cfb902dd3e71ca0f9f9517bea02a73a5ce38c @@ -261,24 +271,22 @@ SHA256 (rust/crates/proc-macro2-1.0.94.crate) = a31971752e70b8b2686d7e46ec17fb38 SIZE (rust/crates/proc-macro2-1.0.94.crate) = 52391 SHA256 (rust/crates/pulp-0.18.22.crate) = a0a01a0dc67cf4558d279f0c25b0962bd08fc6dec0137699eae304103e882fe6 SIZE (rust/crates/pulp-0.18.22.crate) = 117838 -SHA256 (rust/crates/pulp-0.21.4.crate) = 95fb7a99b37aaef4c7dd2fd15a819eb8010bfc7a2c2155230d51f497316cad6d -SIZE (rust/crates/pulp-0.21.4.crate) = 135569 +SHA256 (rust/crates/pulp-0.21.5.crate) = 96b86df24f0a7ddd5e4b95c94fc9ed8a98f1ca94d3b01bdce2824097e7835907 +SIZE (rust/crates/pulp-0.21.5.crate) = 136353 SHA256 (rust/crates/pulp-macro-0.1.1.crate) = d315b3197b780e4873bc0e11251cb56a33f65a6032a3d39b8d1405c255513766 SIZE (rust/crates/pulp-macro-0.1.1.crate) = 3268 SHA256 (rust/crates/py_literal-0.4.0.crate) = 102df7a3d46db9d3891f178dcc826dc270a6746277a9ae6436f8d29fd490a8e1 SIZE (rust/crates/py_literal-0.4.0.crate) = 16747 -SHA256 (rust/crates/pyo3-0.23.5.crate) = 7778bffd85cf38175ac1f545509665d0b9b92a198ca7941f131f85f7a4f9a872 -SIZE (rust/crates/pyo3-0.23.5.crate) = 1088533 -SHA256 (rust/crates/pyo3-build-config-0.23.5.crate) = 94f6cbe86ef3bf18998d9df6e0f3fc1050a8c5efa409bf712e661a4366e010fb -SIZE (rust/crates/pyo3-build-config-0.23.5.crate) = 33885 -SHA256 (rust/crates/pyo3-build-config-0.24.0.crate) = e9b6c2b34cf71427ea37c7001aefbaeb85886a074795e35f161f5aecc7620a7a -SIZE (rust/crates/pyo3-build-config-0.24.0.crate) = 33982 -SHA256 (rust/crates/pyo3-ffi-0.23.5.crate) = e9f1b4c431c0bb1c8fb0a338709859eed0d030ff6daa34368d3b152a63dfdd8d -SIZE (rust/crates/pyo3-ffi-0.23.5.crate) = 74867 -SHA256 (rust/crates/pyo3-macros-0.23.5.crate) = fbc2201328f63c4710f68abdf653c89d8dbc2858b88c5d88b0ff38a75288a9da -SIZE (rust/crates/pyo3-macros-0.23.5.crate) = 8856 -SHA256 (rust/crates/pyo3-macros-backend-0.23.5.crate) = fca6726ad0f3da9c9de093d6f116a93c1a38e417ed73bf138472cf4064f72028 -SIZE (rust/crates/pyo3-macros-backend-0.23.5.crate) = 70938 +SHA256 (rust/crates/pyo3-0.25.0.crate) = f239d656363bcee73afef85277f1b281e8ac6212a1d42aa90e55b90ed43c47a4 +SIZE (rust/crates/pyo3-0.25.0.crate) = 1120850 +SHA256 (rust/crates/pyo3-build-config-0.25.0.crate) = 755ea671a1c34044fa165247aaf6f419ca39caa6003aee791a0df2713d8f1b6d +SIZE (rust/crates/pyo3-build-config-0.25.0.crate) = 34122 +SHA256 (rust/crates/pyo3-ffi-0.25.0.crate) = fc95a2e67091e44791d4ea300ff744be5293f394f1bafd9f78c080814d35956e +SIZE (rust/crates/pyo3-ffi-0.25.0.crate) = 77991 +SHA256 (rust/crates/pyo3-macros-0.25.0.crate) = a179641d1b93920829a62f15e87c0ed791b6c8db2271ba0fd7c2686090510214 +SIZE (rust/crates/pyo3-macros-0.25.0.crate) = 8876 +SHA256 (rust/crates/pyo3-macros-backend-0.25.0.crate) = 9dff85ebcaab8c441b0e3f7ae40a6963ecea8a9f5e74f647e33fcf5ec9a1e89e +SIZE (rust/crates/pyo3-macros-backend-0.25.0.crate) = 75089 SHA256 (rust/crates/quote-1.0.39.crate) = c1f1914ce909e1658d9907913b4b91947430c7d9be598b15a1912935b8c04801 SIZE (rust/crates/quote-1.0.39.crate) = 31206 SHA256 (rust/crates/ra_ap_limit-0.0.188.crate) = 92d33758724f997689f84146e5401e28d875a061804f861f113696f44f5232aa @@ -323,12 +331,14 @@ SHA256 (rust/crates/regex-syntax-0.8.5.crate) = 2b15c43186be67a4fd63bee50d0303af SIZE (rust/crates/regex-syntax-0.8.5.crate) = 357541 SHA256 (rust/crates/rowan-0.15.15.crate) = 32a58fa8a7ccff2aec4f39cc45bf5f985cec7125ab271cf681c279fd00192b49 SIZE (rust/crates/rowan-0.15.15.crate) = 39971 +SHA256 (rust/crates/rstar-0.12.2.crate) = 421400d13ccfd26dfa5858199c30a5d76f9c54e0dba7575273025b43c5175dbb +SIZE (rust/crates/rstar-0.12.2.crate) = 43756 SHA256 (rust/crates/rustc-hash-1.1.0.crate) = 08d43f7aa6b08d49f382cde6a7982047c3426db949b1424bc4b7ec9ae12c6ce2 SIZE (rust/crates/rustc-hash-1.1.0.crate) = 9331 SHA256 (rust/crates/rustc-hash-2.1.1.crate) = 357703d41365b4b27c590e3ed91eabb1b663f07c4c084095e60cbed4362dff0d SIZE (rust/crates/rustc-hash-2.1.1.crate) = 14154 -SHA256 (rust/crates/rustiq-core-0.0.10.crate) = 666b580cb45b60a39f5a17b284bbe8343cfcd67929931729b4afee19ec94d308 -SIZE (rust/crates/rustiq-core-0.0.10.crate) = 40292 +SHA256 (rust/crates/rustiq-core-0.0.11.crate) = 51bfa802a80a4fa591941e4caaf2d6d7793ae3ffd307022afe0739453fae07a6 +SIZE (rust/crates/rustiq-core-0.0.11.crate) = 41963 SHA256 (rust/crates/rustix-0.38.44.crate) = fdb5bc1ae2baa591800df16c9ca78619bf65c0488b41b96ccec5d11220d8c154 SIZE (rust/crates/rustix-0.38.44.crate) = 379347 SHA256 (rust/crates/rustversion-1.0.20.crate) = eded382c5f5f786b989652c49544c4877d9f015cc22e145a5ea8ea66c2921cd2 @@ -343,10 +353,10 @@ SHA256 (rust/crates/same-file-1.0.6.crate) = 93fc1dc3aaa9bfed95e02e6eadabb4baf7e SIZE (rust/crates/same-file-1.0.6.crate) = 10183 SHA256 (rust/crates/seq-macro-0.3.6.crate) = 1bc711410fbe7399f390ca1c3b60ad0f53f80e95c5eb935e52268a0e2cd49acc SIZE (rust/crates/seq-macro-0.3.6.crate) = 16031 -SHA256 (rust/crates/serde-1.0.218.crate) = e8dfc9d19bdbf6d17e22319da49161d5d0108e4188e8b680aef6299eed22df60 -SIZE (rust/crates/serde-1.0.218.crate) = 78968 -SHA256 (rust/crates/serde_derive-1.0.218.crate) = f09503e191f4e797cb8aac08e9a4a4695c5edf6a2e70e376d961ddd5c969f82b -SIZE (rust/crates/serde_derive-1.0.218.crate) = 57782 +SHA256 (rust/crates/serde-1.0.219.crate) = 5f0e2c6ed6606019b4e29e69dbaba95b11854410e5347d525002456dbbb786b6 +SIZE (rust/crates/serde-1.0.219.crate) = 78983 +SHA256 (rust/crates/serde_derive-1.0.219.crate) = 5b0276cf7f2c73365f7157c8123c21cd9a50fbbd844757af28ca1f5925fc2a00 +SIZE (rust/crates/serde_derive-1.0.219.crate) = 57798 SHA256 (rust/crates/serde_json-1.0.140.crate) = 20068b6e96dc6c9bd23e01df8827e6c7e1f2fddd43c21810382803c136b99373 SIZE (rust/crates/serde_json-1.0.140.crate) = 154852 SHA256 (rust/crates/serde_spanned-0.6.8.crate) = 87607cb1398ed59d48732e575a4c28a7a8ebf2454b964fe3f224f2afc07909e1 @@ -355,10 +365,12 @@ SHA256 (rust/crates/sha2-0.10.8.crate) = 793db75ad2bcafc3ffa7c68b215fee268f53798 SIZE (rust/crates/sha2-0.10.8.crate) = 26357 SHA256 (rust/crates/simba-0.9.0.crate) = b3a386a501cd104797982c15ae17aafe8b9261315b5d07e3ec803f2ea26be0fa SIZE (rust/crates/simba-0.9.0.crate) = 52680 -SHA256 (rust/crates/smallvec-1.14.0.crate) = 7fcf8323ef1faaee30a44a340193b1ac6814fd9b7b4e88e9d4519a3e4abe1cfd -SIZE (rust/crates/smallvec-1.14.0.crate) = 35561 +SHA256 (rust/crates/smallvec-1.15.0.crate) = 8917285742e9f3e1683f0a9c4e6b57960b7314d0b08d30d1ecd426713ee2eee9 +SIZE (rust/crates/smallvec-1.15.0.crate) = 38113 SHA256 (rust/crates/smol_str-0.2.2.crate) = dd538fb6910ac1099850255cf94a94df6551fbdd602454387d0adb2d1ca6dead SIZE (rust/crates/smol_str-0.2.2.crate) = 15840 +SHA256 (rust/crates/stable_deref_trait-1.2.0.crate) = a8f112729512f8e442d81f95a8a7ddf2b7c6b8a1a6f509a95864142b30cab2d3 +SIZE (rust/crates/stable_deref_trait-1.2.0.crate) = 8054 SHA256 (rust/crates/strsim-0.11.1.crate) = 7da8b5736845d9f2fcb837ea5d9e2628564b3b043a70948a3f0b778838c5fb4f SIZE (rust/crates/strsim-0.11.1.crate) = 14266 SHA256 (rust/crates/syn-1.0.109.crate) = 72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237 @@ -407,6 +419,8 @@ SHA256 (rust/crates/unindent-0.2.4.crate) = 7264e107f553ccae879d21fbea1d6724ac78 SIZE (rust/crates/unindent-0.2.4.crate) = 7422 SHA256 (rust/crates/utf8parse-0.2.2.crate) = 06abde3611657adf66d383f00b093d7faecc7fa57071cce2578660c9f1010821 SIZE (rust/crates/utf8parse-0.2.2.crate) = 13499 +SHA256 (rust/crates/uuid-1.17.0.crate) = 3cf4199d1e5d15ddd86a694e4d0dffa9c323ce759fea589f00fef9d81cc1931d +SIZE (rust/crates/uuid-1.17.0.crate) = 59014 SHA256 (rust/crates/version_check-0.9.5.crate) = 0b928f33d975fc6ad9f86c8f283853ad26bdd5b10b7f1542aa2fa15e2289105a SIZE (rust/crates/version_check-0.9.5.crate) = 15554 SHA256 (rust/crates/walkdir-2.5.0.crate) = 29790946404f91d9c5d06f9874efddea1dc06c5efe94541a7d6863108e3a5e4b @@ -467,13 +481,9 @@ SHA256 (rust/crates/xshell-macros-0.2.7.crate) = 32ac00cd3f8ec9c1d33fb3e7958a82d SIZE (rust/crates/xshell-macros-0.2.7.crate) = 2890 SHA256 (rust/crates/yansi-0.5.1.crate) = 09041cd90cf85f7f8b2df60c646f853b7f535ce68f85244eb6731cf89fa498ec SIZE (rust/crates/yansi-0.5.1.crate) = 16525 -SHA256 (rust/crates/zerocopy-0.7.35.crate) = 1b9b4fd18abc82b8136838da5d50bae7bdea537c574d8dc1a34ed098d6c166f0 -SIZE (rust/crates/zerocopy-0.7.35.crate) = 152645 -SHA256 (rust/crates/zerocopy-0.8.21.crate) = dcf01143b2dd5d134f11f545cf9f1431b13b749695cb33bcce051e7568f99478 -SIZE (rust/crates/zerocopy-0.8.21.crate) = 238506 -SHA256 (rust/crates/zerocopy-derive-0.7.35.crate) = fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e -SIZE (rust/crates/zerocopy-derive-0.7.35.crate) = 37829 -SHA256 (rust/crates/zerocopy-derive-0.8.21.crate) = 712c8386f4f4299382c9abee219bee7084f78fb939d88b6840fcc1320d5f6da2 -SIZE (rust/crates/zerocopy-derive-0.8.21.crate) = 83886 -SHA256 (Qiskit-qiskit-2.0.0_GH0.tar.gz) = 563938d0f2c353b0a79ea8b7a1c9a3d7d915972b282ddad48e0ffd1079edaeaa -SIZE (Qiskit-qiskit-2.0.0_GH0.tar.gz) = 7911127 +SHA256 (rust/crates/zerocopy-0.8.25.crate) = a1702d9583232ddb9174e01bb7c15a2ab8fb1bc6f227aa1233858c351a3ba0cb +SIZE (rust/crates/zerocopy-0.8.25.crate) = 252714 +SHA256 (rust/crates/zerocopy-derive-0.8.25.crate) = 28a6e20d751156648aa063f3800b706ee209a32c0b4d9f24be3d980b01be55ef +SIZE (rust/crates/zerocopy-derive-0.8.25.crate) = 87671 +SHA256 (Qiskit-qiskit-2.1.1_GH0.tar.gz) = 96cd5725ea5f99a6527885e9ef4436bcb34e6388c6ab1bf43d48b9dab80f429f +SIZE (Qiskit-qiskit-2.1.1_GH0.tar.gz) = 7095152 diff --git a/science/py-quantities/Makefile b/science/py-quantities/Makefile index 74a45beef3b2..dddaaa22df9e 100644 --- a/science/py-quantities/Makefile +++ b/science/py-quantities/Makefile @@ -1,6 +1,5 @@ PORTNAME= quantities -DISTVERSION= 0.16.1 -PORTREVISION= 1 +DISTVERSION= 0.16.2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -21,6 +20,6 @@ TEST_WRKSRC= ${WRKSRC}/quantities/tests NO_ARCH= yes -# tests: 173 passed, 3 xfailed in 33.50s +# tests as of 0.16.2: 175 passed, 3 xfailed in 30.81s .include <bsd.port.mk> diff --git a/science/py-quantities/distinfo b/science/py-quantities/distinfo index 26529773f059..eb191c3bbb35 100644 --- a/science/py-quantities/distinfo +++ b/science/py-quantities/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1731110912 -SHA256 (quantities-0.16.1.tar.gz) = c9d688e8719720654187a6a83425e7d54f427d7465e03c49f3da53befd20074b -SIZE (quantities-0.16.1.tar.gz) = 101045 +TIMESTAMP = 1753137018 +SHA256 (quantities-0.16.2.tar.gz) = 1f7c24f10d9ff57ddf751a358ea2fdfa9914516722f06a788ef4a2924c77d21c +SIZE (quantities-0.16.2.tar.gz) = 101862 diff --git a/science/py-rmf/Makefile b/science/py-rmf/Makefile index 1d13d19df62c..dbe6e2950396 100644 --- a/science/py-rmf/Makefile +++ b/science/py-rmf/Makefile @@ -6,7 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Library to support reading and writing of Rich Molecular Format files WWW= https://integrativemodeling.org/rmf/ \ - https://github.com/open-rmf/rmf + https://github.com/salilab/rmf LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/COPYING diff --git a/science/py-scikit-sparse/Makefile b/science/py-scikit-sparse/Makefile index ecc38f90c432..e80c63af51fe 100644 --- a/science/py-scikit-sparse/Makefile +++ b/science/py-scikit-sparse/Makefile @@ -1,6 +1,7 @@ PORTNAME= scikit-sparse DISTVERSIONPREFIX= v DISTVERSION= 0.4.16 +PORTREVISION= 1 CATEGORIES= science python #MASTER_SITES= PYPI # missing files under tests/ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-spglib/Makefile b/science/py-spglib/Makefile index 14ad98f6aa4a..01e37fba4057 100644 --- a/science/py-spglib/Makefile +++ b/science/py-spglib/Makefile @@ -1,7 +1,6 @@ PORTNAME= spglib DISTVERSIONPREFIX= v -DISTVERSION= 2.5.0 -PORTREVISION= 1 +DISTVERSION= 2.6.0 CATEGORIES= science python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -19,10 +18,12 @@ BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools-scm>0:devel/py-setuptools-scm@$ ${PYNUMPY} \ ${PY_SETUPTOOLS} LIB_DEPENDS= libsymspg.so:science/spglib -RUN_DEPENDS= ${PYNUMPY} +RUN_DEPENDS= ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}typing-extensions>=4.9.0:devel/py-typing-extensions@${PY_FLAVOR} +TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest-benchmark>0:devel/py-pytest-benchmark@${PY_FLAVOR} USES= python -USE_PYTHON= pep517 autoplist pytest # tests fail to run, see https://github.com/spglib/spglib/issues/192 +USE_PYTHON= pep517 autoplist pytest USE_GITHUB= yes CMAKE_ARGS= -DPython3_EXECUTABLE=${PYTHON_CMD} @@ -32,4 +33,6 @@ MAKE_ENV= SETUPTOOLS_SCM_PRETEND_VERSION=${DISTVERSION} TEST_WRKSRC= ${WRKSRC} TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} +# tests as of 2.6.0: 3024 passed in 149.52s (0:02:29) + .include <bsd.port.mk> diff --git a/science/py-spglib/distinfo b/science/py-spglib/distinfo index 48711790a26d..b88216427863 100644 --- a/science/py-spglib/distinfo +++ b/science/py-spglib/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1720768210 -SHA256 (spglib-spglib-v2.5.0_GH0.tar.gz) = b6026f5e85106c0c9ee57e54b9399890d0f29982e20e96ede0428b3efbe6b914 -SIZE (spglib-spglib-v2.5.0_GH0.tar.gz) = 2926427 +TIMESTAMP = 1753137266 +SHA256 (spglib-spglib-v2.6.0_GH0.tar.gz) = c65af71136c915352eb82444b165ec83289877eb8e46593033f199801b43dbf7 +SIZE (spglib-spglib-v2.6.0_GH0.tar.gz) = 2438640 diff --git a/science/py-spglib/files/patch-pyproject.toml b/science/py-spglib/files/patch-pyproject.toml index 38d350736f4d..d7417075f4d6 100644 --- a/science/py-spglib/files/patch-pyproject.toml +++ b/science/py-spglib/files/patch-pyproject.toml @@ -1,21 +1,21 @@ - removal of license-files is a workaround for https://github.com/spglib/spglib/issues/560 ---- pyproject.toml.orig 2024-07-11 08:36:56 UTC +--- pyproject.toml.orig 2025-03-06 12:33:46 UTC +++ pyproject.toml @@ -1,7 +1,7 @@ [build-system] # Numpy build and runtime dependencies are linked to ABI compatibility # A new wheel rebuild is needed when changing these --requires = ["scikit-build-core", "numpy~=2.0"] -+requires = ["scikit-build-core", "numpy"] +-requires = ["scikit-build-core>=0.11", "numpy~=2.0"] ++requires = ["scikit-build-core>=0.11", "numpy"] build-backend = "scikit_build_core.build" [project] -@@ -9,7 +9,6 @@ license = { text = "BSD-3-Clause" } +@@ -9,7 +9,6 @@ license = "BSD-3-Clause" requires-python = ">=3.9" description = "This is the spglib module." - license = { text = "BSD-3-Clause" } --license-files = { paths = ["COPYING"] } + license = "BSD-3-Clause" +-license-files = ["COPYING"] readme = "python/README.rst" dynamic = ["version"] dependencies = [ diff --git a/science/py-tensorflow/Makefile b/science/py-tensorflow/Makefile index ce89ebf4ad00..15489d182e8c 100644 --- a/science/py-tensorflow/Makefile +++ b/science/py-tensorflow/Makefile @@ -1,12 +1,14 @@ PORTNAME= tensorflow DISTVERSIONPREFIX= v -DISTVERSION= 2.9.1 -PORTREVISION= 21 +DISTVERSION= 2.13.1 CATEGORIES= science python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} DIST_SUBDIR= ${PORTNAME} EXTRACT_ONLY= ${DISTNAME}.tar.gz +PATCH_SITES= https://github.com/${GH_ACCOUNT}/${GH_PROJECT}/commit/ +PATCHFILES= ba7501696cc.patch:-p1 667cf3ed2d7.patch:-p1 + MAINTAINER= amzo1337@gmail.com COMMENT= Computation using data flow graphs for scalable machine learning WWW= https://www.tensorflow.org @@ -14,61 +16,56 @@ WWW= https://www.tensorflow.org LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE -BROKEN= variable has incomplete type 'StateSaver' ONLY_FOR_ARCHS= amd64 BUILD_DEPENDS= ${RUN_DEPENDS} \ ${PYTHON_PKGNAMEPREFIX}grpcio-tools>=1.22.0:devel/py-grpcio-tools@${PY_FLAVOR} \ bash:shells/bash \ - cython:lang/cython \ - swig:devel/swig \ bazel:devel/bazel5 \ - git:devel/git + cython:lang/cython \ + git:devel/git \ + patchelf:sysutils/patchelf \ + swig:devel/swig LIB_DEPENDS= libnsync.so:devel/nsync \ libgpr.so:devel/grpc \ libpng.so:graphics/png \ libsnappy.so:archivers/snappy \ - liblmdb.so:databases/lmdb \ + libabsl_base.so:devel/abseil \ libsqlite3.so:databases/sqlite3 \ libicuio.so:devel/icu \ libjsoncpp.so:devel/jsoncpp \ - libpcre.so:devel/pcre \ - libnsync.so:devel/nsync \ libprotobuf.so:devel/protobuf \ - libprotobuf-c.so:devel/protobuf-c \ - libre2.so:devel/re2 \ libgif.so:graphics/giflib \ libcurl.so:ftp/curl \ - libflatbuffers.so:devel/flatbuffers \ libdouble-conversion.so:devel/double-conversion RUN_DEPENDS= pybind11>=2.6.2:devel/pybind11 \ - ${PYTHON_PKGNAMEPREFIX}absl-py>=1.0.0:devel/py-absl-py \ - ${PYTHON_PKGNAMEPREFIX}astunparse>=1.6.3:devel/py-astunparse@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}typing-extensions>=4.3.0:devel/py-typing-extensions@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}absl-py>=1.0.0:devel/py-absl-py@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}astunparse>=1.6.0:devel/py-astunparse@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}flatbuffers>=23.1.21:devel/py-flatbuffers@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}gast>=0.2.1:devel/py-gast@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}google-pasta>=0.1.1:devel/py-google-pasta@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}h5py>=2.9.0:science/py-h5py@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}flatbuffers>=2.0:devel/py-flatbuffers@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}gast>=0.5.3:devel/py-gast@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}numpy>=1.20.0:math/py-numpy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}google-pasta>=0.1.7:devel/py-google-pasta@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}protobuf>=3.7.1:devel/py-protobuf@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}six>=1.10.0:devel/py-six@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}termcolor>=1.1.0:devel/py-termcolor@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}grpcio>=1.22.0:devel/py-grpcio@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}keras-preprocessing>=1.1.1:math/py-keras-preprocessing@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}wrapt>=1.14.1:devel/py-wrapt@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}wheel>=0.30.0:devel/py-wheel@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}opt-einsum>=3.3.0:math/py-opt-einsum@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}numpy>=1.22.0:math/py-numpy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}opt-einsum>=2.3.2:math/py-opt-einsum@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}packaging>=21.3:devel/py-packaging@${PY_FLAVOR} \ - pybind11>=2.6.2:devel/pybind11 + ${PYTHON_PKGNAMEPREFIX}requests>=2.21.0:www/py-requests@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}protobuf>=3.20.3:devel/py-protobuf@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}six>=1.12.0:devel/py-six@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}termcolor>=1.1.0:devel/py-termcolor@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}typing-extensions>=3.6.6:devel/py-typing-extensions@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}wrapt>=1.11.0:devel/py-wrapt@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}grpcio>=1.24.3:devel/py-grpcio@${PY_FLAVOR} -USES= jpeg llvm:16 python shebangfix ssl -USE_CXXSTD= c++17 +USES= jpeg perl5 python shebangfix ssl +USE_CXXSTD= c++17 USE_GITHUB= yes +USE_LDCONFIG= yes +USE_PERL5= build USE_PYTHON= distutils SHEBANG_GLOB= *.py -BAZEL_BOOT= --output_user_root=${WRKDIR}/bazel_out +BINARY_ALIAS= python3=${PYTHON_CMD} PLIST_SUB= TF_PORT_VERSION=${PORTVERSION} @@ -95,13 +92,17 @@ XLA_VARS_OFF= XLA_OPT="0" .include "Makefile.MASTER_SITES" +BAZEL_BOOT= --output_user_root=${WRKDIR}/bazel_out +.if !defined(WITH_DEBUG) +# For the reason why the linker is used for the strip, see PR 280234. +BAZEL_LINKOPT= --linkopt=-Wl,--strip-all +.endif + post-patch: # Set up a local repository with our pre-downloaded packages # This prevents bazel downloading the files without modifying # the bzl files. - @${MKDIR} ${WRKDIR}/bazel-cache @${MKDIR} ${WRKDIR}/bazel-dist - @${MKDIR} ${WRKDIR}/.bin .for file in ${DISTFILES:C/\:(.*)//} @${ECHO} "Moving ${file} to ${WRKDIR}/bazel-dist" @@ -112,24 +113,8 @@ post-patch: @${CP} -R ${PATCHDIR}/bazel/* \ ${WRKSRC}/third_party/ - @${LN} -s ${PYTHON_CMD} ${WRKDIR}/.bin/python3 - - @cd ${WRKSRC} && \ - ${REINPLACE_CMD} "s#--batch#${BAZEL_BOOT}\', \'--batch#" \ - configure.py - - ${REINPLACE_CMD} "s#%%PYTHON%%#${PYTHON_VERSION}#" ${WRKSRC}/configure \ - ${WRKSRC}/third_party/freebsd_python_fix.patch \ - ${WRKSRC}/tensorflow/compiler/mlir/quantization/tensorflow/BUILD - @${REINPLACE_CMD} "s#%%BAZEL_DIR%%#${WRKDIR}#" ${WRKDIR}/bazelrc @${REINPLACE_CMD} "s#%%BAZEL_DIST%%#${WRKDIR}#" ${WRKDIR}/bazelrc - @${REINPLACE_CMD} "s#%%MLIR_LLVM_PATCH%%#/${WRKSRC}/bazel/bazel_llvm-raw_utils_bazel_configure.bzl#" \ - ${WRKSRC}/tensorflow/compiler/mlir/hlo/WORKSPACE - - # use system pybind11, but use sed to fix includes, too many to maintain with patches - @${FIND} ${WRKSRC} -type f -name '*.cc' | ${XARGS} ${REINPLACE_CMD} "s#include\/pybind11#pybind11#" - # copy the toolchain over @${CP} -R ${PATCHDIR}/freebsd \ @@ -137,21 +122,10 @@ post-patch: @${REINPLACE_CMD} "s#%%PATH%%#${PATH}#" ${WRKDIR}/bazelrc - @${REINPLACE_CMD} "s#%%PYTHON%%#${PYTHON_CMD}#" ${WRKSRC}/.bazelrc - - @${REINPLACE_CMD} \ - -e "s#%%LOCALBASE%%#${LOCALBASE}#" \ - -e "s#%%LLVM_PREFIX%%#${LLVM_PREFIX}#g" \ - -e "s#%%LLVM_VERSION%%#${LLVM_VERSION}#g" \ + @${REINPLACE_CMD} -e "s#%%LOCALBASE%%#${LOCALBASE}#" \ ${WRKDIR}/bazelrc \ - ${WRKSRC}/third_party/absl/system.absl.strings.BUILD \ ${WRKSRC}/freebsd/cc_toolchain_config.bzl \ - ${WRKSRC}/.bazelrc \ - ${WRKSRC}/tensorflow/tools/proto_text/BUILD \ - ${WRKSRC}/tensorflow/BUILD \ - ${WRKSRC}/tensorflow/core/BUILD \ - ${WRKSRC}/third_party/systemlibs/protobuf.BUILD - + ${WRKSRC}/.bazelrc do-configure: @cd ${WRKSRC} && ${SETENV} \ @@ -175,14 +149,14 @@ do-configure: PREFIX="${LOCALBASE}" \ TF_SYSTEM_LIBS="absl_py astor_archive astunparse_archive boringssl com_github_googlecloudplatform_google_cloud_cpp com_github_grpc_grpc \ com_google_absl com_google_protobuf curl cython dill_archive double_conversion functools32_archive gast_archive \ - gif hwloc icu jsoncpp_git libjpeg_turbo lmdb nasm nsync opt_einsum_archive org_sqlite pasta png pybind11 six_archive snappy \ + gif hwloc icu jsoncpp_git libjpeg_turbo nasm nsync opt_einsum_archive org_sqlite pasta png pybind11 six_archive snappy \ tblib_archive termcolor_archive typing_extensions_archive wrapt zlib" \ ./configure do-build: @cd ${WRKSRC} && \ bazel --bazelrc="${WRKDIR}/bazelrc" ${BAZEL_BOOT} build --jobs ${TF_JOBS_NUMBER} ${BAZEL_COPT} --host_copt="-I${LOCALBASE}/include" \ - --host_linkopt="-L${LOCALBASE}/lib -lexecinfo" --linkopt="-L${LOCALBASE}/lib -lexecinfo" --copt="-I${LOCALBASE}/include" \ + --host_linkopt="-L${LOCALBASE}/lib -lexecinfo" ${BAZEL_LINKOPT} --copt="-I${LOCALBASE}/include" \ --verbose_failures -s \ --distdir=${WRKDIR}/bazel-dist \ //tensorflow:libtensorflow_framework.so \ @@ -191,7 +165,6 @@ do-build: //tensorflow:install_headers \ //tensorflow/tools/pip_package:build_pip_package - @cd ${WRKSRC} && ${SETENV} TMPDIR=${WRKDIR} \ bazel-bin/tensorflow/tools/pip_package/build_pip_package \ ${WRKDIR}/whl @@ -224,10 +197,8 @@ do-install: @${FIND} ${WRKSRC}/bazel-bin/tensorflow/ -depth 1 -name "*.so*" | ${XARGS} -I{} \ ${INSTALL_LIB} {} ${STAGEDIR}/${LOCALBASE}/lib/ - @${FIND} ${STAGEDIR}/${LOCALBASE}/lib -name "*.so*" | ${XARGS} ${STRIP_CMD} - post-install: # autoplist: thousands of files, all under ${PYTHON_SITELIBDIR} @cd ${STAGEDIR}${PREFIX} && \ - ${FIND} ${PYTHON_SITELIBDIR:C|^${LOCALBASE}/||} -type f -or -type l | grep -v "egg-info/" >> ${TMPPLIST} + ${FIND} ${PYTHON_SITELIBDIR:C|^${LOCALBASE}/||} -type f -or -type l | ${GREP} -v "egg-info/" >> ${TMPPLIST} .include <bsd.port.mk> diff --git a/science/py-tensorflow/Makefile.MASTER_SITES b/science/py-tensorflow/Makefile.MASTER_SITES index 35742be9ba95..5657bdd6a5a9 100644 --- a/science/py-tensorflow/Makefile.MASTER_SITES +++ b/science/py-tensorflow/Makefile.MASTER_SITES @@ -1,56 +1,63 @@ -DISTFILES+= platforms-0.0.2.tar.gz:platforms \ - apple_support.0.12.1.tar.gz:apple \ - bazel-skylib-1.0.3.tar.gz:skylib \ - dfc67056200b674accd08d8f9a21e328098c07e2.tar.gz:toolchain \ +DISTFILES+= platforms-0.0.6.tar.gz:platforms \ + apple_support.1.1.0.tar.gz:apple \ + bazel-skylib-1.3.0.tar.gz:skylib \ + 8c717f8258cd5f6c7a45b97d974292755852b658.tar.gz:toolchain \ v0.1.1.zip:buildrules \ - rules_apple.0.33.0.tar.gz:applerules \ + rules_apple.1.0.1.tar.gz:applerules \ 081771d4a0e9d7d3aa0eed2ef389fa4700dfb23e.tar.gz:rulescc \ 308b05b2419edb5c8ee0471b67a40403df940149.tar.gz:closure \ - rules_docker-v0.10.0.tar.gz:docker \ + 0.7.1.tar.gz:rulesforeigncc \ 7cf3cefd652008d0a64a419c34c13bdca6c8f178.zip:java \ - rules_pkg-0.2.5.tar.gz:pkg \ + 4.3.zip:jvm \ + rules_pkg-0.7.1.tar.gz:pkg \ 11bf7c25e666dd7ddacbcd4d4c4a9de7a25175f8.tar.gz:protolib \ rules_python-0.0.1.tar.gz:pythonrules \ - rules_swift.0.25.0.tar.gz:swift \ - 790d7a083520398268d92d0bd61cf85dfa32ee98.tar.gz:dlpack \ + rules_swift.1.0.0.tar.gz:swift \ + 9351cf542ab478499294864ff3acfdab5c8c5f3d.tar.gz:dlpack \ + f7547e29ccaed7b64ef4f7495ecfff1c9f6f3d03.tar.gz:benchmark \ 0d859a811870d10f53a594927d0d0b97573ad06d.tar.gz:farmhash \ e844ffd17118c1e17d94e1ba4354c075a4577b88.zip:gemmlowp \ - fd3d9af80465e4383162e4a7c5e2f406e82dd968.tar.gz:highwayhash \ - 506cfa4bffd060c06ec338ce50ea3468daa6c814.tar.gz:re2 \ - e6c1b8dc8a8b00ee74e7268aac8b18d7260ab1ce.zip:ruy \ + c13d28517a4db259d738ea4886b1f00352a3cc33.tar.gz:highwayhash \ + a276a8c738735a0fe45a6ee590fe2df69bcf4502.tar.gz:re2 \ + 3286a34cc8de6149ac6844107dfdffac91531e72.zip:ruy \ 835a7d7b1ee3bc83e575e302a985c66ec4b65249.tar.gz:sobol \ openmp-10.0.1.src.tar.xz:llvmorg \ - 36dbc057604f00aacfc0288ddad57e3b21cfc1b8.tar.gz:kiss \ - v2.6.tar.gz:onednn \ + 131.1.0.tar.gz:kiss \ + v2.7.3.tar.gz:onednn \ + 43d81c6883ade82052920bd367c61f9e52f09954.zip:openxla \ v1.0.tar.gz:ooura \ - 5916273f79a21551890fd3d56fc5375a78d1598d.zip:cpuinfo \ - d5e37adf1406cf899d7d9ec1d317c47506ccb970.tar.gz:cpuinfo2 \ - 093ed77f7d50f75b376f40a71ea86e08cedb8b80.tar.gz:runtime \ - eigen-008ff3483a8c5604639e1c4d204eae30ad737af6.tar.gz:eigen \ - 11b2812d64e49bab9b6c489f79067fc94e69db9f.zip:xnnpack \ + 2c4932ed6f6204f1656e245838f4f5eae69d2e29.tar.gz:pybindabseil \ + 72cbbf1fbc830e487e3012862b7b720001b70672.tar.gz:pybindbazel \ + 80f3440cd8fee124e077e2e47a8a17b78b451363.zip:pybindprotobuf \ + fa1c679da8d19e1d87f20175ae1ec10995cd3dd3.zip:cpuinfo \ + 7d879c8b161085a4374ea481b93a52adb19c0529.tar.gz:runtime \ + eigen-b0f877f8e01e90a5b0f3a79d46ea234899f8b499.tar.gz:eigen \ + b9d4073a6913891ce9cbd8965c8d506075d2a45a.zip:xnnpack \ b8374f80e42010941bda6c85b0e3f1a1bd77a1e0.zip:pthread \ 4dfe081cf6bcd15db339cf2680b9281b8451eeb3.zip:fp16 \ 63058eff77e11aa15bf531df5dd34395ec3017c8.zip:fxdiv \ - 1cb299165c859533e22f2ed05eb2abd5071544df.tar.gz:llvm \ - 541b1ded4abadcc38e8178680b0677f65594ea6f.zip:apis \ - v1.12.0.tar.gz:flatbuffer \ - 1200fe90bb174a6224a525ee60148671a786a71f.tar.gz:neon + dc275fd03254d67d29cc70a5a0569acf24d2280d.tar.gz:llvm \ + 6b3fdcea8bc5398be4e7e9930c693f0ea09316a0.tar.gz:apis \ + v23.1.21.tar.gz:flatbuffer \ + a15b489e1222b2087007546b4912e21293ea86ff.tar.gz:neon -MASTER_SITES+= https://github.com/bazelbuild/platforms/releases/download/0.0.2/:platforms \ - https://github.com/bazelbuild/apple_support/releases/download/0.12.1/:apple \ - https://github.com/bazelbuild/bazel-skylib/releases/download/1.0.3/:skylib \ +MASTER_SITES+= https://github.com/bazelbuild/platforms/releases/download/0.0.6/:platforms \ + https://github.com/bazelbuild/apple_support/releases/download/1.1.0/:apple \ + https://github.com/bazelbuild/bazel-skylib/releases/download/1.3.0/:skylib \ https://github.com/bazelbuild/bazel-toolchains/archive/:toolchain \ https://github.com/bazelbuild/rules_android/archive/:buildrules \ - https://github.com/bazelbuild/rules_apple/releases/download/0.33.0/:applerules \ + https://github.com/bazelbuild/rules_apple/releases/download/1.0.1/:applerules \ https://github.com/bazelbuild/rules_cc/archive/:rulescc \ https://github.com/bazelbuild/rules_closure/archive/:closure \ - https://github.com/bazelbuild/rules_docker/releases/download/v0.10.0/:docker \ + https://github.com/bazelbuild/rules_foreign_cc/archive/:rulesforeigncc \ https://github.com/bazelbuild/rules_java/archive/:java \ - https://github.com/bazelbuild/rules_pkg/releases/download/0.2.5/:pkg \ + https://github.com/bazelbuild/rules_jvm_external/archive/:jvm \ + https://github.com/bazelbuild/rules_pkg/releases/download/0.7.1/:pkg \ https://github.com/bazelbuild/rules_proto/archive/:protolib \ https://github.com/bazelbuild/rules_python/releases/download/0.0.1/:pythonrules \ - https://github.com/bazelbuild/rules_swift/releases/download/0.25.0/:swift \ + https://github.com/bazelbuild/rules_swift/releases/download/1.0.0/:swift \ https://github.com/dmlc/dlpack/archive/:dlpack \ + https://github.com/google/benchmark/archive/:benchmark \ https://github.com/google/farmhash/archive/:farmhash \ https://github.com/google/gemmlowp/archive/:gemmlowp \ https://github.com/google/highwayhash/archive/:highwayhash \ @@ -58,18 +65,21 @@ MASTER_SITES+= https://github.com/bazelbuild/platforms/releases/download/0.0.2/: https://github.com/google/ruy/archive/:ruy \ https://github.com/joe-kuo/sobol_data/archive/:sobol \ https://github.com/llvm/llvm-project/releases/download/llvmorg-10.0.1/:llvmorg \ - https://github.com/mborgerding/kissfft/archive/:kiss \ + https://github.com/mborgerding/kissfft/archive/refs/tags/:kiss \ https://github.com/oneapi-src/oneDNN/archive/refs/tags/:onednn \ + https://github.com/openxla/stablehlo/archive/:openxla \ https://github.com/petewarden/OouraFFT/archive/:ooura \ + https://github.com/pybind/pybind11_abseil/archive/:pybindabseil \ + https://github.com/pybind/pybind11_bazel/archive/:pybindbazel \ + https://github.com/pybind/pybind11_protobuf/archive/:pybindprotobuf \ https://github.com/pytorch/cpuinfo/archive/:cpuinfo \ - https://github.com/pytorch/cpuinfo/archive/:cpuinfo2 \ https://github.com/tensorflow/runtime/archive/:runtime \ - https://gitlab.com/libeigen/eigen/-/archive/008ff3483a8c5604639e1c4d204eae30ad737af6/:eigen \ + https://gitlab.com/libeigen/eigen/-/archive/b0f877f8e01e90a5b0f3a79d46ea234899f8b499/:eigen \ https://github.com/google/XNNPACK/archive/:xnnpack \ https://github.com/Maratyszcza/pthreadpool/archive/:pthread \ https://github.com/Maratyszcza/FP16/archive/:fp16 \ https://github.com/Maratyszcza/FXdiv/archive/:fxdiv \ - https://storage.googleapis.com/mirror.tensorflow.org/github.com/llvm/llvm-project/archive/:llvm \ + https://github.com/llvm/llvm-project/archive/:llvm \ https://github.com/googleapis/googleapis/archive/:apis \ https://storage.googleapis.com/mirror.tensorflow.org/github.com/google/flatbuffers/archive/:flatbuffer \ https://github.com/intel/ARM_NEON_2_x86_SSE/archive/:neon diff --git a/science/py-tensorflow/distinfo b/science/py-tensorflow/distinfo index d9d9a2254845..e886c03d0967 100644 --- a/science/py-tensorflow/distinfo +++ b/science/py-tensorflow/distinfo @@ -1,77 +1,91 @@ -TIMESTAMP = 1662651809 -SHA256 (tensorflow/platforms-0.0.2.tar.gz) = 48a2d8d343863989c232843e01afc8a986eb8738766bfd8611420a7db8f6f0c3 -SIZE (tensorflow/platforms-0.0.2.tar.gz) = 5278 -SHA256 (tensorflow/apple_support.0.12.1.tar.gz) = c604b75865c07f45828c7fffd5fdbff81415a9e84a68f71a9c1d8e3b2694e547 -SIZE (tensorflow/apple_support.0.12.1.tar.gz) = 26708 -SHA256 (tensorflow/bazel-skylib-1.0.3.tar.gz) = 1c531376ac7e5a180e0237938a2536de0c54d93f5c278634818e0efc952dd56c -SIZE (tensorflow/bazel-skylib-1.0.3.tar.gz) = 30711 -SHA256 (tensorflow/dfc67056200b674accd08d8f9a21e328098c07e2.tar.gz) = 77c2c3c562907a1114afde7b358bf3d5cc23dc61b3f2fd619bf167af0c9582a3 -SIZE (tensorflow/dfc67056200b674accd08d8f9a21e328098c07e2.tar.gz) = 1056209 +TIMESTAMP = 1731660141 +SHA256 (tensorflow/platforms-0.0.6.tar.gz) = 5308fc1d8865406a49427ba24a9ab53087f17f5266a7aabbfc28823f3916e1ca +SIZE (tensorflow/platforms-0.0.6.tar.gz) = 5537 +SHA256 (tensorflow/apple_support.1.1.0.tar.gz) = ce1042cf936540eaa7b49c4549d7cd9b6b1492acbb6e765840a67a34b8e17a97 +SIZE (tensorflow/apple_support.1.1.0.tar.gz) = 27105 +SHA256 (tensorflow/bazel-skylib-1.3.0.tar.gz) = 74d544d96f4a5bb630d465ca8bbcfe231e3594e5aae57e1edbf17a6eb3ca2506 +SIZE (tensorflow/bazel-skylib-1.3.0.tar.gz) = 36103 +SHA256 (tensorflow/8c717f8258cd5f6c7a45b97d974292755852b658.tar.gz) = 294cdd859e57fcaf101d4301978c408c88683fbc46fbc1a3829da92afbea55fb +SIZE (tensorflow/8c717f8258cd5f6c7a45b97d974292755852b658.tar.gz) = 80728 SHA256 (tensorflow/v0.1.1.zip) = cd06d15dd8bb59926e4d65f9003bfc20f9da4b2519985c27e190cddc8b7a7806 SIZE (tensorflow/v0.1.1.zip) = 14654 -SHA256 (tensorflow/rules_apple.0.33.0.tar.gz) = a5f00fd89eff67291f6cd3efdc8fad30f4727e6ebb90718f3f05bbf3c3dd5ed7 -SIZE (tensorflow/rules_apple.0.33.0.tar.gz) = 2168079 +SHA256 (tensorflow/rules_apple.1.0.1.tar.gz) = 36072d4f3614d309d6a703da0dfe48684ec4c65a89611aeb9590b45af7a3e592 +SIZE (tensorflow/rules_apple.1.0.1.tar.gz) = 2198467 SHA256 (tensorflow/081771d4a0e9d7d3aa0eed2ef389fa4700dfb23e.tar.gz) = ff7876d80cd3f6b8c7a064bd9aa42a78e02096544cca2b22a9cf390a4397a53e SIZE (tensorflow/081771d4a0e9d7d3aa0eed2ef389fa4700dfb23e.tar.gz) = 130803 SHA256 (tensorflow/308b05b2419edb5c8ee0471b67a40403df940149.tar.gz) = 5b00383d08dd71f28503736db0500b6fb4dda47489ff5fc6bed42557c07c6ba9 SIZE (tensorflow/308b05b2419edb5c8ee0471b67a40403df940149.tar.gz) = 464906 -SHA256 (tensorflow/rules_docker-v0.10.0.tar.gz) = 7d453450e1eb70e238eea6b31f4115607ec1200e91afea01c25f9804f37e39c8 -SIZE (tensorflow/rules_docker-v0.10.0.tar.gz) = 549649 +SHA256 (tensorflow/0.7.1.tar.gz) = bcd0c5f46a49b85b384906daae41d277b3dc0ff27c7c752cc51e43048a58ec83 +SIZE (tensorflow/0.7.1.tar.gz) = 215296 SHA256 (tensorflow/7cf3cefd652008d0a64a419c34c13bdca6c8f178.zip) = bc81f1ba47ef5cc68ad32225c3d0e70b8c6f6077663835438da8d5733f917598 SIZE (tensorflow/7cf3cefd652008d0a64a419c34c13bdca6c8f178.zip) = 9422 -SHA256 (tensorflow/rules_pkg-0.2.5.tar.gz) = 352c090cc3d3f9a6b4e676cf42a6047c16824959b438895a76c2989c6d7c246a -SIZE (tensorflow/rules_pkg-0.2.5.tar.gz) = 29857 +SHA256 (tensorflow/4.3.zip) = 6274687f6fc5783b589f56a2f1ed60de3ce1f99bc4e8f9edef3de43bdf7c6e74 +SIZE (tensorflow/4.3.zip) = 3998031 +SHA256 (tensorflow/rules_pkg-0.7.1.tar.gz) = 451e08a4d78988c06fa3f9306ec813b836b1d076d0f055595444ba4ff22b867f +SIZE (tensorflow/rules_pkg-0.7.1.tar.gz) = 77334 SHA256 (tensorflow/11bf7c25e666dd7ddacbcd4d4c4a9de7a25175f8.tar.gz) = 20b240eba17a36be4b0b22635aca63053913d5c1ee36e16be36499d167a2f533 SIZE (tensorflow/11bf7c25e666dd7ddacbcd4d4c4a9de7a25175f8.tar.gz) = 14304 SHA256 (tensorflow/rules_python-0.0.1.tar.gz) = aa96a691d3a8177f3215b14b0edc9641787abaaa30363a080165d06ab65e1161 SIZE (tensorflow/rules_python-0.0.1.tar.gz) = 2302092 -SHA256 (tensorflow/rules_swift.0.25.0.tar.gz) = 8a49da750560b185804a4bc95c82d3f9cc4c2caf788960b0e21945759155fdd9 -SIZE (tensorflow/rules_swift.0.25.0.tar.gz) = 184783 -SHA256 (tensorflow/790d7a083520398268d92d0bd61cf85dfa32ee98.tar.gz) = 147cc89904375dcd0b0d664a2b72dfadbb02058800ad8cba84516094bc406208 -SIZE (tensorflow/790d7a083520398268d92d0bd61cf85dfa32ee98.tar.gz) = 45837 +SHA256 (tensorflow/rules_swift.1.0.0.tar.gz) = 12057b7aa904467284eee640de5e33853e51d8e31aae50b3fb25d2823d51c6b8 +SIZE (tensorflow/rules_swift.1.0.0.tar.gz) = 199181 +SHA256 (tensorflow/9351cf542ab478499294864ff3acfdab5c8c5f3d.tar.gz) = 7aca112f2809b7e9523e9b47b04a393affeca38247861951f07c42dee10180e2 +SIZE (tensorflow/9351cf542ab478499294864ff3acfdab5c8c5f3d.tar.gz) = 76170 +SHA256 (tensorflow/f7547e29ccaed7b64ef4f7495ecfff1c9f6f3d03.tar.gz) = 552ca3d4d1af4beeb1907980f7096315aa24150d6baf5ac1e5ad90f04846c670 +SIZE (tensorflow/f7547e29ccaed7b64ef4f7495ecfff1c9f6f3d03.tar.gz) = 204856 SHA256 (tensorflow/0d859a811870d10f53a594927d0d0b97573ad06d.tar.gz) = 18392cf0736e1d62ecbb8d695c31496b6507859e8c75541d7ad0ba092dc52115 SIZE (tensorflow/0d859a811870d10f53a594927d0d0b97573ad06d.tar.gz) = 467251 SHA256 (tensorflow/e844ffd17118c1e17d94e1ba4354c075a4577b88.zip) = 522b7a82d920ebd0c4408a5365866a40b81d1c0d60b2369011d315cca03c6476 SIZE (tensorflow/e844ffd17118c1e17d94e1ba4354c075a4577b88.zip) = 940590 -SHA256 (tensorflow/fd3d9af80465e4383162e4a7c5e2f406e82dd968.tar.gz) = 9c3e0e87d581feeb0c18d814d98f170ff23e62967a2bd6855847f0b2fe598a37 -SIZE (tensorflow/fd3d9af80465e4383162e4a7c5e2f406e82dd968.tar.gz) = 138574 -SHA256 (tensorflow/506cfa4bffd060c06ec338ce50ea3468daa6c814.tar.gz) = d070e2ffc5476c496a6a872a6f246bfddce8e7797d6ba605a7c8d72866743bf9 -SIZE (tensorflow/506cfa4bffd060c06ec338ce50ea3468daa6c814.tar.gz) = 316237 -SHA256 (tensorflow/e6c1b8dc8a8b00ee74e7268aac8b18d7260ab1ce.zip) = fa9a0b9041095817bc3533f7b125c3b4044570c0b3ee6c436d2d29dae001c06b -SIZE (tensorflow/e6c1b8dc8a8b00ee74e7268aac8b18d7260ab1ce.zip) = 375516 +SHA256 (tensorflow/c13d28517a4db259d738ea4886b1f00352a3cc33.tar.gz) = c0e2b9931fbcce3bfbcd7999c3c114f404ac0f8b89775a5bbccbcaa501868e58 +SIZE (tensorflow/c13d28517a4db259d738ea4886b1f00352a3cc33.tar.gz) = 160745 +SHA256 (tensorflow/a276a8c738735a0fe45a6ee590fe2df69bcf4502.tar.gz) = b90430b2a9240df4459108b3e291be80ae92c68a47bc06ef2dc419c5724de061 +SIZE (tensorflow/a276a8c738735a0fe45a6ee590fe2df69bcf4502.tar.gz) = 306766 +SHA256 (tensorflow/3286a34cc8de6149ac6844107dfdffac91531e72.zip) = a22c42e80c7bb450db8492728e4742ee66f46d5458c45fe67ce2c9b61240630c +SIZE (tensorflow/3286a34cc8de6149ac6844107dfdffac91531e72.zip) = 381045 SHA256 (tensorflow/835a7d7b1ee3bc83e575e302a985c66ec4b65249.tar.gz) = 583d7b975e506c076fc579d9139530596906b9195b203d42361417e9aad79b73 SIZE (tensorflow/835a7d7b1ee3bc83e575e302a985c66ec4b65249.tar.gz) = 2569603 SHA256 (tensorflow/openmp-10.0.1.src.tar.xz) = d19f728c8e04fb1e94566c8d76aef50ec926cd2f95ef3bf1e0a5de4909b28b44 SIZE (tensorflow/openmp-10.0.1.src.tar.xz) = 955492 -SHA256 (tensorflow/36dbc057604f00aacfc0288ddad57e3b21cfc1b8.tar.gz) = 42b7ef406d5aa2d57a7b3b56fc44e8ad3011581692458a69958a911071efdcf2 -SIZE (tensorflow/36dbc057604f00aacfc0288ddad57e3b21cfc1b8.tar.gz) = 44744 -SHA256 (tensorflow/v2.6.tar.gz) = 9695640f55acd833ddcef4776af15e03446c4655f9296e5074b1b178dd7a4fb2 -SIZE (tensorflow/v2.6.tar.gz) = 5840464 +SHA256 (tensorflow/131.1.0.tar.gz) = 76c1aac87ddb7258f34b08a13f0eebf9e53afa299857568346aa5c82bcafaf1a +SIZE (tensorflow/131.1.0.tar.gz) = 52383 +SHA256 (tensorflow/v2.7.3.tar.gz) = a50993aa6265b799b040fe745e0010502f9f7103cc53a9525d59646aef006633 +SIZE (tensorflow/v2.7.3.tar.gz) = 6410473 +SHA256 (tensorflow/43d81c6883ade82052920bd367c61f9e52f09954.zip) = 57a8a93e51211f990d760631f2bfdbba5257b22dda3d60e35a186bba988a2ace +SIZE (tensorflow/43d81c6883ade82052920bd367c61f9e52f09954.zip) = 27954369 SHA256 (tensorflow/v1.0.tar.gz) = 5f4dabc2ae21e1f537425d58a49cdca1c49ea11db0d6271e2a4b27e9697548eb SIZE (tensorflow/v1.0.tar.gz) = 110531 -SHA256 (tensorflow/5916273f79a21551890fd3d56fc5375a78d1598d.zip) = 2a160c527d3c58085ce260f34f9e2b161adc009b34186a2baf24e74376e89e6d -SIZE (tensorflow/5916273f79a21551890fd3d56fc5375a78d1598d.zip) = 3787933 -SHA256 (tensorflow/d5e37adf1406cf899d7d9ec1d317c47506ccb970.tar.gz) = 3f2dc1970f397a0e59db72f9fca6ff144b216895c1d606f6c94a507c1e53a025 -SIZE (tensorflow/d5e37adf1406cf899d7d9ec1d317c47506ccb970.tar.gz) = 3489028 -SHA256 (tensorflow/093ed77f7d50f75b376f40a71ea86e08cedb8b80.tar.gz) = fce593c95eb508092c4a1752130868b6d2eae0fd4a5363b9d96195fd85b7cfec -SIZE (tensorflow/093ed77f7d50f75b376f40a71ea86e08cedb8b80.tar.gz) = 15323415 -SHA256 (tensorflow/eigen-008ff3483a8c5604639e1c4d204eae30ad737af6.tar.gz) = e1dd31ce174c3d26fbe38388f64b09d2adbd7557a59e90e6f545a288cc1755fc -SIZE (tensorflow/eigen-008ff3483a8c5604639e1c4d204eae30ad737af6.tar.gz) = 2733792 -SHA256 (tensorflow/11b2812d64e49bab9b6c489f79067fc94e69db9f.zip) = 7e9ad45391e5158fd00e816022bda21d54a6180788af7c455c864a78cee252c6 -SIZE (tensorflow/11b2812d64e49bab9b6c489f79067fc94e69db9f.zip) = 17103217 +SHA256 (tensorflow/2c4932ed6f6204f1656e245838f4f5eae69d2e29.tar.gz) = 0223b647b8cc817336a51e787980ebc299c8d5e64c069829bf34b69d72337449 +SIZE (tensorflow/2c4932ed6f6204f1656e245838f4f5eae69d2e29.tar.gz) = 28202 +SHA256 (tensorflow/72cbbf1fbc830e487e3012862b7b720001b70672.tar.gz) = 516c1b3a10d87740d2b7de6f121f8e19dde2c372ecbfe59aef44cd1872c10395 +SIZE (tensorflow/72cbbf1fbc830e487e3012862b7b720001b70672.tar.gz) = 8722 +SHA256 (tensorflow/80f3440cd8fee124e077e2e47a8a17b78b451363.zip) = c7ab64b1ccf9a678694a89035a8c865a693e4e872803778f91f0965c2f281d78 +SIZE (tensorflow/80f3440cd8fee124e077e2e47a8a17b78b451363.zip) = 76830 +SHA256 (tensorflow/fa1c679da8d19e1d87f20175ae1ec10995cd3dd3.zip) = 2bf2b62eb86e2d2eaf862d0b9683a6c467a4d69fb2f7f1dc47c799809148608f +SIZE (tensorflow/fa1c679da8d19e1d87f20175ae1ec10995cd3dd3.zip) = 3848981 +SHA256 (tensorflow/7d879c8b161085a4374ea481b93a52adb19c0529.tar.gz) = cfde5639b7c67c0edfa073b779b977aae744137c2b2fcb25a992f8d57bd033dd +SIZE (tensorflow/7d879c8b161085a4374ea481b93a52adb19c0529.tar.gz) = 15228644 +SHA256 (tensorflow/eigen-b0f877f8e01e90a5b0f3a79d46ea234899f8b499.tar.gz) = bdb1353ba33a5a7a5caadf822057ac1f0254ba2c5e70512dd1ec20cbb64e2f6c +SIZE (tensorflow/eigen-b0f877f8e01e90a5b0f3a79d46ea234899f8b499.tar.gz) = 2833536 +SHA256 (tensorflow/b9d4073a6913891ce9cbd8965c8d506075d2a45a.zip) = c979b62e8b77af60dfd7567f22ade20d5a9d4d0888f8a2d60d155fc0d31b22ab +SIZE (tensorflow/b9d4073a6913891ce9cbd8965c8d506075d2a45a.zip) = 24168206 SHA256 (tensorflow/b8374f80e42010941bda6c85b0e3f1a1bd77a1e0.zip) = b96413b10dd8edaa4f6c0a60c6cf5ef55eebeef78164d5d69294c8173457f0ec SIZE (tensorflow/b8374f80e42010941bda6c85b0e3f1a1bd77a1e0.zip) = 61524 SHA256 (tensorflow/4dfe081cf6bcd15db339cf2680b9281b8451eeb3.zip) = d973501a40c55126b31accc2d9f08d931ec3cc190c0430309a5e341d3c0ce32a SIZE (tensorflow/4dfe081cf6bcd15db339cf2680b9281b8451eeb3.zip) = 91462 SHA256 (tensorflow/63058eff77e11aa15bf531df5dd34395ec3017c8.zip) = 3d7b0e9c4c658a84376a1086126be02f9b7f753caa95e009d9ac38d11da444db SIZE (tensorflow/63058eff77e11aa15bf531df5dd34395ec3017c8.zip) = 16646 -SHA256 (tensorflow/1cb299165c859533e22f2ed05eb2abd5071544df.tar.gz) = 5a19ab6de4b0089fff456c0bc406b37ba5f95c76026e6bec294ec28dc28e4cb9 -SIZE (tensorflow/1cb299165c859533e22f2ed05eb2abd5071544df.tar.gz) = 162307281 -SHA256 (tensorflow/541b1ded4abadcc38e8178680b0677f65594ea6f.zip) = 7ebab01b06c555f4b6514453dc3e1667f810ef91d1d4d2d3aa29bb9fcb40a900 -SIZE (tensorflow/541b1ded4abadcc38e8178680b0677f65594ea6f.zip) = 5498751 -SHA256 (tensorflow/v1.12.0.tar.gz) = 62f2223fb9181d1d6338451375628975775f7522185266cd5296571ac152bc45 -SIZE (tensorflow/v1.12.0.tar.gz) = 1145348 -SHA256 (tensorflow/1200fe90bb174a6224a525ee60148671a786a71f.tar.gz) = 213733991310b904b11b053ac224fee2d4e0179e46b52fe7f8735b8831e04dcc -SIZE (tensorflow/1200fe90bb174a6224a525ee60148671a786a71f.tar.gz) = 100612 -SHA256 (tensorflow/tensorflow-tensorflow-v2.9.1_GH0.tar.gz) = 6eaf86ead73e23988fe192da1db68f4d3828bcdd0f3a9dc195935e339c95dbdc -SIZE (tensorflow/tensorflow-tensorflow-v2.9.1_GH0.tar.gz) = 66654318 +SHA256 (tensorflow/dc275fd03254d67d29cc70a5a0569acf24d2280d.tar.gz) = 3e91127af59a6b07fea7901c80a7b8b9234eced42b0f14abbad5f9f7674dba69 +SIZE (tensorflow/dc275fd03254d67d29cc70a5a0569acf24d2280d.tar.gz) = 182909064 +SHA256 (tensorflow/6b3fdcea8bc5398be4e7e9930c693f0ea09316a0.tar.gz) = 249d83abc5d50bf372c35c49d77f900bff022b2c21eb73aa8da1458b6ac401fc +SIZE (tensorflow/6b3fdcea8bc5398be4e7e9930c693f0ea09316a0.tar.gz) = 6091152 +SHA256 (tensorflow/v23.1.21.tar.gz) = d84cb25686514348e615163b458ae0767001b24b42325f426fd56406fd384238 +SIZE (tensorflow/v23.1.21.tar.gz) = 2181861 +SHA256 (tensorflow/a15b489e1222b2087007546b4912e21293ea86ff.tar.gz) = 019fbc7ec25860070a1d90e12686fc160cfb33e22aa063c80f52b363f1361e9d +SIZE (tensorflow/a15b489e1222b2087007546b4912e21293ea86ff.tar.gz) = 103972 +SHA256 (tensorflow/tensorflow-tensorflow-v2.13.1_GH0.tar.gz) = 89c07aebd4f41fbe0d08cc88aef00305542134f2f16d3b62918dc3c1182f33e2 +SIZE (tensorflow/tensorflow-tensorflow-v2.13.1_GH0.tar.gz) = 70663056 +SHA256 (tensorflow/ba7501696cc.patch) = d06dda3f889d7ffcd9dcec16f7f96e8ac24ffd5f999307fe0ceb623e57c7fa9f +SIZE (tensorflow/ba7501696cc.patch) = 740 +SHA256 (tensorflow/667cf3ed2d7.patch) = dc3cc6c8b9bd6f4978904c1a28df61ab00634cb6cab461690a83c58fde55a0d9 +SIZE (tensorflow/667cf3ed2d7.patch) = 960 diff --git a/science/py-tensorflow/files/bazel/fix-environ.patch b/science/py-tensorflow/files/bazel/fix-environ.patch index 2e38ce60543d..d1437f158055 100644 --- a/science/py-tensorflow/files/bazel/fix-environ.patch +++ b/science/py-tensorflow/files/bazel/fix-environ.patch @@ -1,18 +1,18 @@ ---- a/llvm/lib/Support/Unix/Program.inc 2022-09-06 21:14:28.808580000 +0100 -+++ b/llvm/lib/Support/Unix/Program.inc 2022-09-06 21:16:15.007790000 +0100 +--- a/llvm/lib/Support/Unix/Program.inc 2023-04-28 21:51:01.000000000 +0200 ++++ b/llvm/lib/Support/Unix/Program.inc 2024-07-02 11:12:41.645169000 +0200 @@ -54,10 +54,8 @@ #define USE_NSGETENVIRON 0 #endif -#if !USE_NSGETENVIRON +#if USE_NSGETENVIRON - extern char **environ; + extern char **environ; -#else -#include <crt_externs.h> // _NSGetEnviron #endif #endif -@@ -240,14 +238,6 @@ +@@ -238,14 +236,6 @@ } } @@ -27,16 +27,16 @@ constexpr int maxRetries = 8; int retries = 0; pid_t PID; -@@ -308,11 +298,7 @@ +@@ -312,11 +302,7 @@ - // Execute! - std::string PathStr = std::string(Program); -- if (Envp != nullptr) -- execve(PathStr.c_str(), const_cast<char **>(Argv), -- const_cast<char **>(Envp)); -- else -- execv(PathStr.c_str(), const_cast<char **>(Argv)); -+ execv(PathStr.c_str(), const_cast<char **>(Argv)); - // If the execve() failed, we should exit. Follow Unix protocol and - // return 127 if the executable was not found, and 126 otherwise. - // Use _exit rather than exit so that atexit functions and static + // Execute! + std::string PathStr = std::string(Program); +- if (Envp != nullptr) +- execve(PathStr.c_str(), const_cast<char **>(Argv), +- const_cast<char **>(Envp)); +- else +- execv(PathStr.c_str(), const_cast<char **>(Argv)); ++ execv(PathStr.c_str(), const_cast<char **>(Argv)); + // If the execve() failed, we should exit. Follow Unix protocol and + // return 127 if the executable was not found, and 126 otherwise. + // Use _exit rather than exit so that atexit functions and static diff --git a/science/py-tensorflow/files/bazel/fix-pybind11_protobuf.patch b/science/py-tensorflow/files/bazel/fix-pybind11_protobuf.patch new file mode 100644 index 000000000000..80d30bf25333 --- /dev/null +++ b/science/py-tensorflow/files/bazel/fix-pybind11_protobuf.patch @@ -0,0 +1,116 @@ +diff --git a/pybind11_protobuf/BUILD b/pybind11_protobuf/BUILD +index b62eb91..1856ad3 100644 +--- a/pybind11_protobuf/BUILD ++++ b/pybind11_protobuf/BUILD +@@ -61,9 +61,11 @@ pybind_library( + "@com_google_absl//absl/container:flat_hash_map", + "@com_google_absl//absl/strings", + "@com_google_absl//absl/types:optional", +- "@com_google_protobuf//:proto_api", + "@com_google_protobuf//:protobuf", +- ], ++ ] + select({ ++ ":enable_pyproto_api_setting": ["@com_google_protobuf//:proto_api"], ++ "//conditions:default": [], ++ }), + ) + + pybind_library( +diff --git a/pybind11_protobuf/proto_cast_util.cc b/pybind11_protobuf/proto_cast_util.cc +index 52c57c9..771e688 100644 +--- a/pybind11_protobuf/proto_cast_util.cc ++++ b/pybind11_protobuf/proto_cast_util.cc +@@ -14,9 +14,12 @@ + + #include "google/protobuf/descriptor.pb.h" + #include "google/protobuf/descriptor.h" ++#include "google/protobuf/descriptor_database.h" + #include "google/protobuf/dynamic_message.h" + #include "google/protobuf/message.h" ++#if defined(PYBIND11_PROTOBUF_ENABLE_PYPROTO_API) + #include "python/google/protobuf/proto_api.h" ++#endif + #include "absl/container/flat_hash_map.h" + #include "absl/strings/numbers.h" + #include "absl/strings/str_replace.h" +@@ -35,8 +38,12 @@ using ::google::protobuf::FileDescriptor; + using ::google::protobuf::FileDescriptorProto; + using ::google::protobuf::Message; + using ::google::protobuf::MessageFactory; ++#if defined(PYBIND11_PROTOBUF_ENABLE_PYPROTO_API) + using ::google::protobuf::python::PyProto_API; + using ::google::protobuf::python::PyProtoAPICapsuleName; ++#else ++struct PyProto_API; ++#endif + + namespace pybind11_protobuf { + namespace { +@@ -321,6 +328,7 @@ py::object GlobalState::PyMessageInstance(const Descriptor* descriptor) { + module_name + "?"); + } + ++#if defined(PYBIND11_PROTOBUF_ENABLE_PYPROTO_API) + std::pair<py::object, Message*> GlobalState::PyFastCppProtoMessageInstance( + const Descriptor* descriptor) { + assert(descriptor != nullptr); +@@ -361,6 +369,7 @@ std::pair<py::object, Message*> GlobalState::PyFastCppProtoMessageInstance( + } + return {std::move(result), message}; + } ++#endif + + // Create C++ DescriptorPools based on Python DescriptorPools. + // The Python pool will provide message definitions when they are needed. +@@ -500,6 +509,7 @@ class PythonDescriptorPoolWrapper { + private: + bool CopyToFileDescriptorProto(py::handle py_file_descriptor, + FileDescriptorProto* output) { ++#if defined(PYBIND11_PROTOBUF_ENABLE_PYPROTO_API) + if (GlobalState::instance()->py_proto_api()) { + try { + py::object c_proto = py::reinterpret_steal<py::object>( +@@ -518,6 +528,7 @@ class PythonDescriptorPoolWrapper { + PyErr_Print(); + } + } ++#endif + + py::object wire = py_file_descriptor.attr("serialized_pb"); + const char* bytes = PYBIND11_BYTES_AS_STRING(wire.ptr()); +@@ -561,6 +572,9 @@ void ImportProtoDescriptorModule(const Descriptor* descriptor) { + + const Message* PyProtoGetCppMessagePointer(py::handle src) { + assert(PyGILState_Check()); ++#ifndef PYBIND11_PROTOBUF_ENABLE_PYPROTO_API ++ return nullptr; ++#else + if (!GlobalState::instance()->py_proto_api()) return nullptr; + auto* ptr = + GlobalState::instance()->py_proto_api()->GetMessagePointer(src.ptr()); +@@ -571,6 +585,7 @@ const Message* PyProtoGetCppMessagePointer(py::handle src) { + return nullptr; + } + return ptr; ++#endif + } + + absl::optional<std::string> PyProtoDescriptorName(py::handle py_proto) { +@@ -732,6 +747,9 @@ py::handle GenericPyProtoCast(Message* src, py::return_value_policy policy, + + py::handle GenericFastCppProtoCast(Message* src, py::return_value_policy policy, + py::handle parent, bool is_const) { ++#ifndef PYBIND11_PROTOBUF_ENABLE_PYPROTO_API ++ throw std::logic_error("Not implemented"); ++#else + assert(policy != pybind11::return_value_policy::automatic); + assert(policy != pybind11::return_value_policy::automatic_reference); + assert(src != nullptr); +@@ -802,6 +820,7 @@ py::handle GenericFastCppProtoCast(Message* src, py::return_value_policy policy, + std::string message("pybind11_protobuf unhandled return_value_policy::"); + throw py::cast_error(message + ReturnValuePolicyName(policy)); + } ++#endif + } + + py::handle GenericProtoCast(Message* src, py::return_value_policy policy, diff --git a/science/py-tensorflow/files/bazel/add-default-option.patch b/science/py-tensorflow/files/bazel/fix-xnnpack.patch index ce5c250608fb..7a995bbff74d 100644 --- a/science/py-tensorflow/files/bazel/add-default-option.patch +++ b/science/py-tensorflow/files/bazel/fix-xnnpack.patch @@ -1,6 +1,8 @@ ---- a/build_defs.bzl 2022-08-28 12:18:33.375130000 +0100 -+++ b/build_defs.bzl 2022-08-28 12:21:40.701070000 +0100 -@@ -173,7 +173,7 @@ +diff --git a/build_defs.bzl b/build_defs.bzl +index 01b436eb7..ca4abd54d 100644 +--- a/build_defs.bzl ++++ b/build_defs.bzl +@@ -146,7 +146,7 @@ def xnnpack_cc_library( ":emscripten_wasm": wasm_srcs, ":emscripten_wasmsimd": wasmsimd_srcs, ":emscripten_wasmrelaxedsimd": wasmrelaxedsimd_srcs, @@ -9,7 +11,7 @@ }), copts = [ "-Iinclude", -@@ -210,7 +210,7 @@ +@@ -179,7 +179,7 @@ def xnnpack_cc_library( ":emscripten_wasm": wasm_copts, ":emscripten_wasmsimd": wasmsimd_copts, ":emscripten_wasmrelaxedsimd": wasmrelaxedsimd_copts, @@ -18,7 +20,7 @@ }) + select({ ":windows_x86_64_clang": ["/clang:" + opt for opt in gcc_copts], ":windows_x86_64_mingw": gcc_copts, -@@ -233,7 +233,7 @@ +@@ -202,7 +202,7 @@ def xnnpack_cc_library( ":linux_armv7a": ["-lpthread"], ":linux_arm64": ["-lpthread"], ":android": ["-lm"], @@ -27,11 +29,24 @@ }), textual_hdrs = hdrs, visibility = visibility, -@@ -304,6 +304,7 @@ - ":emscripten_wasm": wasm_deps, +@@ -249,6 +249,7 @@ def xnnpack_aggregate_library( ":emscripten_wasmsimd": wasmsimd_deps, ":emscripten_wasmrelaxedsimd": wasmrelaxedsimd_deps, + ":riscv": riscv_deps, + "//conditions:default": x86_deps, }), - ) + defines = defines, + compatible_with = compatible_with, +diff --git a/src/runtime.c b/src/runtime.c +index 0c4649017..29e74a85b 100644 +--- a/src/runtime.c ++++ b/src/runtime.c +@@ -4,7 +4,7 @@ + // LICENSE file in the root directory of this source tree. + #ifndef __MACH__ +-#define _POSIX_C_SOURCE 199309L ++#define _POSIX_C_SOURCE 199506L + #endif + + #include <assert.h> diff --git a/science/py-tensorflow/files/bazel/fix_cpuinfo.patch b/science/py-tensorflow/files/bazel/fix_cpuinfo.patch deleted file mode 100644 index 1041a2319286..000000000000 --- a/science/py-tensorflow/files/bazel/fix_cpuinfo.patch +++ /dev/null @@ -1,80 +0,0 @@ ---- a/src/mach/topology.c 2022-09-01 12:09:36.036365000 +0100 -+++ b/src/mach/topology.c 2022-09-01 12:09:07.146529000 +0100 -@@ -1,5 +1,4 @@ - #include <string.h> --#include <alloca.h> - #include <errno.h> - - #include <sys/types.h> -@@ -8,38 +7,27 @@ - #include <cpuinfo/log.h> - #include <mach/api.h> - --#include <TargetConditionals.h> - -- - struct cpuinfo_mach_topology cpuinfo_mach_detect_topology(void) { - int cores = 1; - size_t sizeof_cores = sizeof(cores); -- if (sysctlbyname("hw.physicalcpu_max", &cores, &sizeof_cores, NULL, 0) != 0) { -- cpuinfo_log_error("sysctlbyname(\"hw.physicalcpu_max\") failed: %s", strerror(errno)); -+ if (sysctlbyname("hw.ncpu", &cores, &sizeof_cores, NULL, 0) != 0) { -+ cpuinfo_log_error("sysctlbyname(\"hw.ncpu\") failed: %s", strerror(errno)); - } else if (cores <= 0) { -- cpuinfo_log_error("sysctlbyname(\"hw.physicalcpu_max\") returned invalid value %d", cores); -+ cpuinfo_log_error("sysctlbyname(\"hw.ncpu\") returned invalid value %d", cores); - cores = 1; - } - - int threads = 1; - size_t sizeof_threads = sizeof(threads); -- if (sysctlbyname("hw.logicalcpu_max", &threads, &sizeof_threads, NULL, 0) != 0) { -- cpuinfo_log_error("sysctlbyname(\"hw.logicalcpu_max\") failed: %s", strerror(errno)); -+ if (sysctlbyname("hw.ncpu", &threads, &sizeof_threads, NULL, 0) != 0) { -+ cpuinfo_log_error("sysctlbyname(\"ncpu\") failed: %s", strerror(errno)); - } else if (threads <= 0) { -- cpuinfo_log_error("sysctlbyname(\"hw.logicalcpu_max\") returned invalid value %d", threads); -+ cpuinfo_log_error("sysctlbyname(\"ncpu\") returned invalid value %d", threads); - threads = cores; - } - - int packages = 1; --#if !TARGET_OS_IPHONE -- size_t sizeof_packages = sizeof(packages); -- if (sysctlbyname("hw.packages", &packages, &sizeof_packages, NULL, 0) != 0) { -- cpuinfo_log_error("sysctlbyname(\"hw.packages\") failed: %s", strerror(errno)); -- } else if (packages <= 0) { -- cpuinfo_log_error("sysctlbyname(\"hw.packages\") returned invalid value %d", packages); -- packages = 1; -- } --#endif - - cpuinfo_log_debug("mach topology: packages = %d, cores = %d, threads = %d", packages, (int) cores, (int) threads); - struct cpuinfo_mach_topology topology = { -@@ -48,26 +36,5 @@ - .threads = (uint32_t) threads - }; - --#if !TARGET_OS_IPHONE -- size_t cacheconfig_size = 0; -- if (sysctlbyname("hw.cacheconfig", NULL, &cacheconfig_size, NULL, 0) != 0) { -- cpuinfo_log_error("sysctlbyname(\"hw.cacheconfig\") failed: %s", strerror(errno)); -- } else { -- uint64_t* cacheconfig = alloca(cacheconfig_size); -- if (sysctlbyname("hw.cacheconfig", cacheconfig, &cacheconfig_size, NULL, 0) != 0) { -- cpuinfo_log_error("sysctlbyname(\"hw.cacheconfig\") failed: %s", strerror(errno)); -- } else { -- size_t cache_configs = cacheconfig_size / sizeof(uint64_t); -- cpuinfo_log_debug("mach hw.cacheconfig count: %zu", cache_configs); -- if (cache_configs > CPUINFO_MACH_MAX_CACHE_LEVELS) { -- cache_configs = CPUINFO_MACH_MAX_CACHE_LEVELS; -- } -- for (size_t i = 0; i < cache_configs; i++) { -- cpuinfo_log_debug("mach hw.cacheconfig[%zu]: %"PRIu64, i, cacheconfig[i]); -- topology.threads_per_cache[i] = cacheconfig[i]; -- } -- } -- } --#endif - return topology; - } diff --git a/science/py-tensorflow/files/bazel/freebsd_python_fix.patch b/science/py-tensorflow/files/bazel/freebsd_python_fix.patch deleted file mode 100644 index e6bcae9950be..000000000000 --- a/science/py-tensorflow/files/bazel/freebsd_python_fix.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/utils/bazel/configure.bzl 2022-08-27 19:11:41.138993000 +0100 -+++ b/utils/bazel/configure.bzl 2022-08-27 19:12:07.525186000 +0100 -@@ -37,7 +37,7 @@ - overlay_path = bazel_path.get_child("llvm-project-overlay") - script_path = bazel_path.get_child("overlay_directories.py") - -- python_bin = repository_ctx.which("python3") -+ python_bin = repository_ctx.which("%%PYTHON%%") - if not python_bin: - # Windows typically just defines "python" as python3. The script itself - # contains a check to ensure python3. diff --git a/science/py-tensorflow/files/bazel/set-c++17.patch b/science/py-tensorflow/files/bazel/set-c++17.patch deleted file mode 100644 index aef1f6c38467..000000000000 --- a/science/py-tensorflow/files/bazel/set-c++17.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/cc/private/toolchain/freebsd_cc_toolchain_config.bzl 2022-08-28 16:31:59.271838000 +0100 -+++ b/cc/private/toolchain/freebsd_cc_toolchain_config.bzl 2022-08-28 16:32:10.096301000 +0100 -@@ -159,7 +159,7 @@ - ), - flag_set( - actions = all_cpp_compile_actions + [ACTION_NAMES.lto_backend], -- flag_groups = [flag_group(flags = ["-std=c++0x"])], -+ flag_groups = [flag_group(flags = ["-std=c++17"])], - ), - ], - ) diff --git a/science/py-tensorflow/files/bazelrc b/science/py-tensorflow/files/bazelrc index f3a2c1a76cb3..d6488176d91b 100644 --- a/science/py-tensorflow/files/bazelrc +++ b/science/py-tensorflow/files/bazelrc @@ -1,6 +1,5 @@ startup --batch -build --strip=never build --verbose_failures --noshow_loading_progress test --verbose_test_summary --verbose_failures --noshow_loading_progress diff --git a/science/py-tensorflow/files/freebsd/BUILD b/science/py-tensorflow/files/freebsd/BUILD index 4096b1c74d42..116c8428aee9 100644 --- a/science/py-tensorflow/files/freebsd/BUILD +++ b/science/py-tensorflow/files/freebsd/BUILD @@ -50,7 +50,7 @@ cc_toolchain( ) cc_toolchain_config( name = "local_freebsd", - cpu = "k8", + cpu = "freebsd", ) toolchain( diff --git a/science/py-tensorflow/files/freebsd/cc_toolchain_config.bzl b/science/py-tensorflow/files/freebsd/cc_toolchain_config.bzl index ce3def7dfd66..719a537f3f29 100644 --- a/science/py-tensorflow/files/freebsd/cc_toolchain_config.bzl +++ b/science/py-tensorflow/files/freebsd/cc_toolchain_config.bzl @@ -226,17 +226,17 @@ def _impl(ctx): else: features = [supports_dynamic_linker_feature, supports_pic_feature] if (is_bsd): - cxx_builtin_include_directories = ["%%LLVM_PREFIX%%/lib/clang/%%LLVM_VERSION%%.0.0", "%%LLVM_PREFIX%%/lib/clang/%%LLVM_VERSION%%/include", "/usr/include/c++/v1", "/usr/local/include", "/usr/include"] + cxx_builtin_include_directories = ["/usr/lib/clang", "/usr/include/c++/v1", "/usr/local/include", "/usr/include"] else: cxx_builtin_include_directories = [] if is_bsd: tool_paths = [ tool_path(name = "ar", path = "/usr/bin/ar"), - tool_path(name = "cpp", path = "%%LLVM_PREFIX%%/bin/clang-cpp"), + tool_path(name = "cpp", path = "/usr/bin/cpp"), tool_path(name = "dwp", path = "/usr/bin/dwp"), - tool_path(name = "gcc", path = "%%LLVM_PREFIX%%/bin/clang-%%LLVM_VERSION%%"), + tool_path(name = "gcc", path = "/usr/bin/clang"), tool_path(name = "gcov", path = "/usr/bin/gcov"), - tool_path(name = "ld", path = "%%LLVM_PREFIX%%/bin/ld"), + tool_path(name = "ld", path = "/usr/bin/ld"), tool_path(name = "nm", path = "/usr/bin/nm"), tool_path(name = "objcopy", path = "/usr/bin/objcopy"), tool_path(name = "objdump", path = "/usr/bin/objdump"), diff --git a/science/py-tensorflow/files/patch-.bazelrc b/science/py-tensorflow/files/patch-.bazelrc index 49784e41f3b9..fe656d032236 100644 --- a/science/py-tensorflow/files/patch-.bazelrc +++ b/science/py-tensorflow/files/patch-.bazelrc @@ -1,22 +1,22 @@ ---- .bazelrc.orig 2022-05-22 22:28:22 UTC +--- .bazelrc.orig 2023-09-12 16:46:28 UTC +++ .bazelrc -@@ -151,6 +151,19 @@ build --experimental_cc_shared_library - - # Default options should come above this line. +@@ -166,6 +166,19 @@ build:libc++ --linkopt -fuse-ld=lld + build:libc++ --define force_libcpp=enabled + build:libc++ --linkopt -fuse-ld=lld +# Use our custom-configured c++ toolchain. +# Use --cpu as a differentiator. -+build:freebsd --cpu=k8 ++build:freebsd --cpu=freebsd + +# Use the default Bazel C++ toolchain to build the tools used during the +# build. +build:freebsd --crosstool_top=//freebsd:freebsd_clang +build:freebsd --linkopt=-L%%LOCALBASE%%/lib + -+build:freebsd --python_path="%%PYTHON%%" ++build:freebsd --define build_with_onednn_v2=true +build:freebsd --define force_libcpp=enabled +build:freebsd --action_env=CXXFLAGS=-stdlib=libc++ + - # Allow builds using libc++ as a linker library - # This is mostly for OSSFuzz, so we also pass in the flags from environment to clean build file - build:libc++ --action_env=CC + # Android configs. Bazel needs to have --cpu and --fat_apk_cpu both set to the + # target CPU to build transient dependencies correctly. See + # https://docs.bazel.build/versions/master/user-manual.html#flag--fat_apk_cpu diff --git a/science/py-tensorflow/files/patch-WORKSPACE b/science/py-tensorflow/files/patch-WORKSPACE deleted file mode 100644 index d037b0785741..000000000000 --- a/science/py-tensorflow/files/patch-WORKSPACE +++ /dev/null @@ -1,18 +0,0 @@ ---- WORKSPACE.orig 2022-05-22 22:28:22 UTC -+++ WORKSPACE -@@ -1,4 +1,15 @@ - workspace(name = "org_tensorflow") -+register_toolchains("//freebsd:freebsd_py_toolchain") -+ -+load("@bazel_tools//tools/build_defs/repo:http.bzl", "http_archive") -+http_archive( -+ name = "io_bazel_rules_docker", -+ sha256 = "7d453450e1eb70e238eea6b31f4115607ec1200e91afea01c25f9804f37e39c8", -+ strip_prefix = "rules_docker-0.10.0", -+ urls = [ -+ "https://github.com/bazelbuild/rules_docker/releases/download/v0.10.0/rules_docker-v0.10.0.tar.gz", -+ ], -+) - - # Initialize the TensorFlow repository and all dependencies. - # diff --git a/science/py-tensorflow/files/patch-configure b/science/py-tensorflow/files/patch-configure deleted file mode 100644 index bf95a05716ba..000000000000 --- a/science/py-tensorflow/files/patch-configure +++ /dev/null @@ -1,11 +0,0 @@ ---- configure.orig 2022-05-22 22:28:22 UTC -+++ configure -@@ -4,7 +4,7 @@ set -e - set -o pipefail - - if [ -z "$PYTHON_BIN_PATH" ]; then -- PYTHON_BIN_PATH=$(which python3 || which python || true) -+ PYTHON_BIN_PATH=$(which %%PYTHON%% || which python || true) - fi - - # Set all env variables diff --git a/science/py-tensorflow/files/patch-tensorflow_BUILD b/science/py-tensorflow/files/patch-tensorflow_BUILD index 1dfdce1c7da7..f45dad0e6ce2 100644 --- a/science/py-tensorflow/files/patch-tensorflow_BUILD +++ b/science/py-tensorflow/files/patch-tensorflow_BUILD @@ -1,31 +1,12 @@ ---- tensorflow/BUILD.orig 2022-05-23 00:28:22.000000000 +0200 -+++ tensorflow/BUILD 2023-03-30 17:47:04.211287000 +0200 -@@ -938,8 +938,11 @@ +--- tensorflow/BUILD.orig 2023-09-12 16:46:28 UTC ++++ tensorflow/BUILD +@@ -1290,7 +1290,8 @@ tf_cc_shared_library( ], "//tensorflow:windows": [], - "//tensorflow:freebsd": [ -+ "-Wl,--unresolved-symbols=ignore-all", -+ "-Wl,--undefined-version", - "-Wl,--version-script,$(location //tensorflow:tf_framework_version_script.lds)", - "-lexecinfo", -+ "-L/usr/local/lib", - ], - "//conditions:default": [ - "-Wl,--version-script,$(location //tensorflow:tf_framework_version_script.lds)", -@@ -1021,7 +1024,7 @@ - # copybara:uncomment_end - "//conditions:default": [ - "-z defs", -- "-Wl,--version-script,$(location //tensorflow/c:version_script.lds)", -+ "-L/lib,-L/usr/lib,--unresolved-symbols=ignore-all,-Wl,--undefined-version,-Wl,--version-script,$(location //tensorflow/c:version_script.lds)", - ], - }), - per_os_targets = True, -@@ -1054,6 +1057,7 @@ - "//tensorflow:windows": [], "//conditions:default": [ - "-z defs", -+ "-Wl,--undefined-version", +- "-z defs", ++ "-Wl,-z,defs", ++ "-lnsync_cpp", "-Wl,--version-script,$(location //tensorflow:tf_version_script.lds)", ], }), diff --git a/science/py-tensorflow/files/patch-tensorflow_compiler_mlir_hlo_WORKSPACE b/science/py-tensorflow/files/patch-tensorflow_compiler_mlir_hlo_WORKSPACE deleted file mode 100644 index 876a4cd2a5b6..000000000000 --- a/science/py-tensorflow/files/patch-tensorflow_compiler_mlir_hlo_WORKSPACE +++ /dev/null @@ -1,11 +0,0 @@ ---- tensorflow/compiler/mlir/hlo/WORKSPACE.orig 2022-05-22 22:28:22 UTC -+++ tensorflow/compiler/mlir/hlo/WORKSPACE -@@ -34,6 +34,8 @@ http_archive( - name = "llvm-raw", - build_file_content = "# empty", - sha256 = LLVM_SHA256, -+ patch_args = ["-p0"], -+ patches = ["@%%MLIR_LLVM_PATCH%%"], - strip_prefix = "llvm-project-" + LLVM_COMMIT, - urls = ["https://github.com/llvm/llvm-project/archive/{commit}.tar.gz".format(commit = LLVM_COMMIT)], - ) diff --git a/science/py-tensorflow/files/patch-tensorflow_compiler_mlir_lite_python_jax__to__tfl__flatbuffer.cc b/science/py-tensorflow/files/patch-tensorflow_compiler_mlir_lite_python_jax__to__tfl__flatbuffer.cc new file mode 100644 index 000000000000..149f60042f0d --- /dev/null +++ b/science/py-tensorflow/files/patch-tensorflow_compiler_mlir_lite_python_jax__to__tfl__flatbuffer.cc @@ -0,0 +1,11 @@ +--- tensorflow/compiler/mlir/lite/python/jax_to_tfl_flatbuffer.cc.orig 2023-09-12 16:46:28 UTC ++++ tensorflow/compiler/mlir/lite/python/jax_to_tfl_flatbuffer.cc +@@ -60,7 +60,7 @@ class NoOpErrorCollector : public tensorflow::protobuf + // Error collector that simply ignores errors reported. + class NoOpErrorCollector : public tensorflow::protobuf::io::ErrorCollector { + public: +- void AddError(int line, int column, const string& message) override {} ++ void RecordError(int line, int column, absl::string_view message) override {} + }; + + bool LoadHloProto(const std::string& contents, xla::HloProto* hlo_proto) { diff --git a/science/py-tensorflow/files/patch-tensorflow_compiler_mlir_quantization_tensorflow_BUILD b/science/py-tensorflow/files/patch-tensorflow_compiler_mlir_quantization_tensorflow_BUILD deleted file mode 100644 index 50bc0af36e7b..000000000000 --- a/science/py-tensorflow/files/patch-tensorflow_compiler_mlir_quantization_tensorflow_BUILD +++ /dev/null @@ -1,11 +0,0 @@ ---- tensorflow/compiler/mlir/quantization/tensorflow/BUILD.orig 2022-09-06 21:29:53 UTC -+++ tensorflow/compiler/mlir/quantization/tensorflow/BUILD -@@ -32,7 +32,7 @@ genrule( - outs = [ - "passes/quantized_function_library.h", - ], -- cmd = "$(location gen_quantized_function_library) --output_file $(RULEDIR)/passes/quantized_function_library.h --src $(SRCS)", -+ cmd = "%%PYTHON%% $(location gen_quantized_function_library) --output_file $(RULEDIR)/passes/quantized_function_library.h --src $(SRCS)", - exec_tools = ["gen_quantized_function_library"], - ) - diff --git a/science/py-tensorflow/files/patch-tensorflow_compiler_mlir_tensorflow_utils_parse__text__proto.cc b/science/py-tensorflow/files/patch-tensorflow_compiler_mlir_tensorflow_utils_parse__text__proto.cc new file mode 100644 index 000000000000..9e9b3aadad0b --- /dev/null +++ b/science/py-tensorflow/files/patch-tensorflow_compiler_mlir_tensorflow_utils_parse__text__proto.cc @@ -0,0 +1,11 @@ +--- tensorflow/compiler/mlir/tensorflow/utils/parse_text_proto.cc.orig 2023-09-12 16:46:28 UTC ++++ tensorflow/compiler/mlir/tensorflow/utils/parse_text_proto.cc +@@ -28,7 +28,7 @@ class NoOpErrorCollector : public protobuf::io::ErrorC + // Error collector that simply ignores errors reported. + class NoOpErrorCollector : public protobuf::io::ErrorCollector { + public: +- void AddError(int line, int column, const std::string& message) override {} ++ void RecordError(int line, int column, absl::string_view message) override {} + }; + } // namespace + diff --git a/science/py-tensorflow/files/patch-tensorflow_compiler_xla_stream__executor_host_BUILD b/science/py-tensorflow/files/patch-tensorflow_compiler_xla_stream__executor_host_BUILD new file mode 100644 index 000000000000..3e73733f8e2d --- /dev/null +++ b/science/py-tensorflow/files/patch-tensorflow_compiler_xla_stream__executor_host_BUILD @@ -0,0 +1,10 @@ +--- tensorflow/compiler/xla/stream_executor/host/BUILD.orig 2023-09-12 16:46:28 UTC ++++ tensorflow/compiler/xla/stream_executor/host/BUILD +@@ -95,6 +95,7 @@ cc_library( + hdrs = [ + "host_gpu_executor.h", + ], ++ linkopts = ["-labsl_tracing_internal"], + deps = [ + ":host_platform_id", + ":host_stream", diff --git a/science/py-tensorflow/files/patch-tensorflow_core_BUILD b/science/py-tensorflow/files/patch-tensorflow_core_BUILD deleted file mode 100644 index 91f1f88aee8d..000000000000 --- a/science/py-tensorflow/files/patch-tensorflow_core_BUILD +++ /dev/null @@ -1,11 +0,0 @@ ---- tensorflow/core/BUILD.orig 2022-05-22 22:28:22 UTC -+++ tensorflow/core/BUILD -@@ -1284,7 +1284,7 @@ cc_library( - hdrs = [":lib_internal_public_headers"], - copts = tf_copts(), - linkopts = select({ -- "//tensorflow:freebsd": [], -+ "//tensorflow:freebsd": ["-L%%LOCALBASE%%/lib"], - "//tensorflow:windows": [], - "//tensorflow:android": [], - "//conditions:default": [ diff --git a/science/py-tensorflow/files/patch-tensorflow_core_debug_debug__io__utils.cc b/science/py-tensorflow/files/patch-tensorflow_core_debug_debug__io__utils.cc new file mode 100644 index 000000000000..6e492427b425 --- /dev/null +++ b/science/py-tensorflow/files/patch-tensorflow_core_debug_debug__io__utils.cc @@ -0,0 +1,11 @@ +--- tensorflow/core/debug/debug_io_utils.cc.orig 2023-09-12 16:46:28 UTC ++++ tensorflow/core/debug/debug_io_utils.cc +@@ -94,7 +94,7 @@ Event PrepareChunkEventProto(const DebugNodeKey& debug + // Encode the data in JSON. + string json_output; + tensorflow::protobuf::util::JsonPrintOptions json_options; +- json_options.always_print_primitive_fields = true; ++ json_options.always_print_fields_with_no_presence = true; + auto status = tensorflow::protobuf::util::MessageToJsonString( + metadata, &json_output, json_options); + if (status.ok()) { diff --git a/science/py-tensorflow/files/patch-tensorflow_core_ir_importexport_parse__text__proto.cc b/science/py-tensorflow/files/patch-tensorflow_core_ir_importexport_parse__text__proto.cc new file mode 100644 index 000000000000..cb19475b9689 --- /dev/null +++ b/science/py-tensorflow/files/patch-tensorflow_core_ir_importexport_parse__text__proto.cc @@ -0,0 +1,11 @@ +--- tensorflow/core/ir/importexport/parse_text_proto.cc.orig 2023-09-12 16:46:28 UTC ++++ tensorflow/core/ir/importexport/parse_text_proto.cc +@@ -33,7 +33,7 @@ class NoOpErrorCollector : public tensorflow::protobuf + // Error collector that simply ignores errors reported. + class NoOpErrorCollector : public tensorflow::protobuf::io::ErrorCollector { + public: +- void AddError(int line, int column, const std::string& message) override {} ++ void RecordError(int line, int column, absl::string_view message) override {} + }; + } // namespace + diff --git a/science/py-tensorflow/files/patch-tensorflow_core_lib_png_BUILD b/science/py-tensorflow/files/patch-tensorflow_core_lib_png_BUILD deleted file mode 100644 index 76a365c9a661..000000000000 --- a/science/py-tensorflow/files/patch-tensorflow_core_lib_png_BUILD +++ /dev/null @@ -1,10 +0,0 @@ ---- tensorflow/core/lib/png/BUILD.orig 2022-08-28 14:35:19 UTC -+++ tensorflow/core/lib/png/BUILD -@@ -23,6 +23,7 @@ cc_library( - "@com_google_absl//absl/base", - "@zlib", - ], -+ copts = ["-std=c++17"], - ) - - alias( diff --git a/science/py-tensorflow/files/patch-tensorflow_core_platform_BUILD b/science/py-tensorflow/files/patch-tensorflow_core_platform_BUILD deleted file mode 100644 index dc2a75c1daa6..000000000000 --- a/science/py-tensorflow/files/patch-tensorflow_core_platform_BUILD +++ /dev/null @@ -1,10 +0,0 @@ ---- tensorflow/core/platform/BUILD.orig 2022-08-29 08:52:22 UTC -+++ tensorflow/core/platform/BUILD -@@ -680,6 +680,7 @@ cc_library( - ":str_util", - ":stringpiece", - ], -+ copts = ["-std=c++17"], - ) - - cc_library( diff --git a/science/py-tensorflow/files/patch-tensorflow_core_profiler_convert_hlo__to__tools__data.cc b/science/py-tensorflow/files/patch-tensorflow_core_profiler_convert_hlo__to__tools__data.cc new file mode 100644 index 000000000000..ad9c4d7d7886 --- /dev/null +++ b/science/py-tensorflow/files/patch-tensorflow_core_profiler_convert_hlo__to__tools__data.cc @@ -0,0 +1,11 @@ +--- tensorflow/core/profiler/convert/hlo_to_tools_data.cc.orig 2023-09-12 16:46:28 UTC ++++ tensorflow/core/profiler/convert/hlo_to_tools_data.cc +@@ -51,7 +51,7 @@ StatusOr<std::string> ConvertHloProtoToMemoryViewer( + + std::string json_output; + tensorflow::protobuf::util::JsonPrintOptions options; +- options.always_print_primitive_fields = true; ++ options.always_print_fields_with_no_presence = true; + auto encoded_status = tensorflow::protobuf::util::MessageToJsonString( + result_or.value(), &json_output, options); + if (!encoded_status.ok()) { diff --git a/science/py-tensorflow/files/patch-tensorflow_core_profiler_convert_xplane__to__memory__profile.cc b/science/py-tensorflow/files/patch-tensorflow_core_profiler_convert_xplane__to__memory__profile.cc new file mode 100644 index 000000000000..8dc4e9453872 --- /dev/null +++ b/science/py-tensorflow/files/patch-tensorflow_core_profiler_convert_xplane__to__memory__profile.cc @@ -0,0 +1,11 @@ +--- tensorflow/core/profiler/convert/xplane_to_memory_profile.cc.orig 2023-09-12 16:46:28 UTC ++++ tensorflow/core/profiler/convert/xplane_to_memory_profile.cc +@@ -529,7 +529,7 @@ Status ConvertProtoToJson(const Proto& proto_output, s + template <typename Proto> + Status ConvertProtoToJson(const Proto& proto_output, std::string* json_output) { + protobuf::util::JsonPrintOptions json_options; +- json_options.always_print_primitive_fields = true; ++ json_options.always_print_fields_with_no_presence = true; + auto status = protobuf::util::MessageToJsonString(proto_output, json_output, + json_options); + if (!status.ok()) { diff --git a/science/py-tensorflow/files/patch-tensorflow_core_profiler_convert_xplane__to__tools__data.cc b/science/py-tensorflow/files/patch-tensorflow_core_profiler_convert_xplane__to__tools__data.cc new file mode 100644 index 000000000000..985be6cab23c --- /dev/null +++ b/science/py-tensorflow/files/patch-tensorflow_core_profiler_convert_xplane__to__tools__data.cc @@ -0,0 +1,20 @@ +--- tensorflow/core/profiler/convert/xplane_to_tools_data.cc.orig 2023-09-12 16:46:28 UTC ++++ tensorflow/core/profiler/convert/xplane_to_tools_data.cc +@@ -147,7 +147,7 @@ StatusOr<std::string> ConvertMultiXSpacesToPodViewer( + + std::string json_output; + protobuf::util::JsonPrintOptions opts; +- opts.always_print_primitive_fields = true; ++ opts.always_print_fields_with_no_presence = true; + auto encode_status = protobuf::util::MessageToJsonString( + ConvertOpStatsToPodViewer(combined_op_stats), &json_output, opts); + if (!encode_status.ok()) { +@@ -201,7 +201,7 @@ StatusOr<std::string> ConvertMultiXSpacesToOpProfileVi + profile); + std::string json_output; + protobuf::util::JsonPrintOptions opts; +- opts.always_print_primitive_fields = true; ++ opts.always_print_fields_with_no_presence = true; + + auto encode_status = + protobuf::util::MessageToJsonString(profile, &json_output, opts); diff --git a/science/py-tensorflow/files/patch-tensorflow_core_util_proto_proto__utils.cc b/science/py-tensorflow/files/patch-tensorflow_core_util_proto_proto__utils.cc new file mode 100644 index 000000000000..d2977a24c290 --- /dev/null +++ b/science/py-tensorflow/files/patch-tensorflow_core_util_proto_proto__utils.cc @@ -0,0 +1,25 @@ +--- tensorflow/core/util/proto/proto_utils.cc.orig 2023-09-12 16:46:28 UTC ++++ tensorflow/core/util/proto/proto_utils.cc +@@ -101,17 +101,17 @@ StringErrorCollector::StringErrorCollector(string* err + } + } + +-void StringErrorCollector::AddError(int line, int column, +- const string& message) { ++void StringErrorCollector::RecordError(int line, int column, ++ absl::string_view message) { + if (error_text_ != nullptr) { + absl::SubstituteAndAppend(error_text_, "$0($1): $2\n", line + index_offset_, + column + index_offset_, message); + } + } + +-void StringErrorCollector::AddWarning(int line, int column, +- const string& message) { +- AddError(line, column, message); ++void StringErrorCollector::RecordWarning(int line, int column, ++ absl::string_view message) { ++ RecordError(line, column, message); + } + + } // namespace proto_utils diff --git a/science/py-tensorflow/files/patch-tensorflow_core_util_proto_proto__utils.h b/science/py-tensorflow/files/patch-tensorflow_core_util_proto_proto__utils.h new file mode 100644 index 000000000000..049dd023f7fc --- /dev/null +++ b/science/py-tensorflow/files/patch-tensorflow_core_util_proto_proto__utils.h @@ -0,0 +1,18 @@ +--- tensorflow/core/util/proto/proto_utils.h.orig 2023-09-12 16:46:28 UTC ++++ tensorflow/core/util/proto/proto_utils.h +@@ -52,11 +52,11 @@ class StringErrorCollector : public protobuf::io::Erro + StringErrorCollector(const StringErrorCollector&) = delete; + StringErrorCollector& operator=(const StringErrorCollector&) = delete; + +- // Implementation of protobuf::io::ErrorCollector::AddError. +- void AddError(int line, int column, const string& message) override; ++ // Implementation of protobuf::io::ErrorCollector::RecordError. ++ void RecordError(int line, int column, absl::string_view message) override; + +- // Implementation of protobuf::io::ErrorCollector::AddWarning. +- void AddWarning(int line, int column, const string& message) override; ++ // Implementation of protobuf::io::ErrorCollector::RecordWarning. ++ void RecordWarning(int line, int column, absl::string_view message) override; + + private: + string* const error_text_; diff --git a/science/py-tensorflow/files/patch-tensorflow_java_BUILD b/science/py-tensorflow/files/patch-tensorflow_java_BUILD deleted file mode 100644 index 33b7db687b88..000000000000 --- a/science/py-tensorflow/files/patch-tensorflow_java_BUILD +++ /dev/null @@ -1,10 +0,0 @@ ---- tensorflow/java/BUILD.orig 2023-03-30 17:51:23.641040000 +0200 -+++ tensorflow/java/BUILD 2023-03-30 17:51:34.802406000 +0200 -@@ -446,6 +446,7 @@ - "//tensorflow:windows": [], - "//conditions:default": [ - "-z defs", -+ "-Wl,--undefined-version", - "-s", - "-Wl,--version-script,$(location {})".format(LINKER_VERSION_SCRIPT), - ], diff --git a/science/py-tensorflow/files/patch-tensorflow_lite_BUILD b/science/py-tensorflow/files/patch-tensorflow_lite_BUILD deleted file mode 100644 index 8d54d284e506..000000000000 --- a/science/py-tensorflow/files/patch-tensorflow_lite_BUILD +++ /dev/null @@ -1,10 +0,0 @@ ---- tensorflow/lite/BUILD.orig 2023-03-30 18:04:54.206396000 +0200 -+++ tensorflow/lite/BUILD 2023-03-30 18:04:24.422539000 +0200 -@@ -1204,6 +1204,7 @@ - "//tensorflow:windows": [], - "//conditions:default": [ - "-Wl,-z,defs", -+ "-Wl,--undefined-version", - "-Wl,--version-script,$(location //tensorflow/lite:tflite_version_script.lds)", - ], - }), diff --git a/science/py-tensorflow/files/patch-tensorflow_lite_build_def.bzl b/science/py-tensorflow/files/patch-tensorflow_lite_build_def.bzl deleted file mode 100644 index 58d62b5e5dd5..000000000000 --- a/science/py-tensorflow/files/patch-tensorflow_lite_build_def.bzl +++ /dev/null @@ -1,10 +0,0 @@ ---- tensorflow/lite/build_def.bzl.orig 2023-03-30 17:56:40.338369000 +0200 -+++ tensorflow/lite/build_def.bzl 2023-03-30 17:56:50.244995000 +0200 -@@ -172,6 +172,7 @@ - ], - clean_dep("//tensorflow:windows"): [], - "//conditions:default": [ -+ "-Wl,--undefined-version", - "-Wl,--version-script,$(location {})".format(linkscript), - "-Wl,-soname," + name, - ], diff --git a/science/py-tensorflow/files/patch-tensorflow_lite_c_BUILD b/science/py-tensorflow/files/patch-tensorflow_lite_c_BUILD deleted file mode 100644 index c88f9a6c9aa4..000000000000 --- a/science/py-tensorflow/files/patch-tensorflow_lite_c_BUILD +++ /dev/null @@ -1,10 +0,0 @@ ---- tensorflow/lite/c/BUILD.orig 2023-03-30 18:05:35.316884000 +0200 -+++ tensorflow/lite/c/BUILD 2023-03-30 18:05:48.639862000 +0200 -@@ -29,6 +29,7 @@ - "//tensorflow:windows": [], - "//conditions:default": [ - "-z defs", -+ "-Wl,--undefined-version", - "-Wl,--version-script,$(location //tensorflow/lite/c:version_script.lds)", - ], - }), diff --git a/science/py-tensorflow/files/patch-tensorflow_lite_delegates_flex_build_def.bzl b/science/py-tensorflow/files/patch-tensorflow_lite_delegates_flex_build_def.bzl deleted file mode 100644 index 9b207ba77c9d..000000000000 --- a/science/py-tensorflow/files/patch-tensorflow_lite_delegates_flex_build_def.bzl +++ /dev/null @@ -1,10 +0,0 @@ ---- tensorflow/lite/delegates/flex/build_def.bzl.orig 2023-03-30 17:57:26.322444000 +0200 -+++ tensorflow/lite/delegates/flex/build_def.bzl 2023-03-30 17:58:45.005163000 +0200 -@@ -223,6 +223,7 @@ - "//tensorflow:windows": [], - "//conditions:default": [ - "-Wl,-z,defs", -+ "-Wl,--undefined-version", - "-Wl,--version-script,$(location //tensorflow/lite/delegates/flex:version_script.lds)", - ], - }), diff --git a/science/py-tensorflow/files/patch-tensorflow_lite_delegates_hexagon_hexagon_nn_BUILD b/science/py-tensorflow/files/patch-tensorflow_lite_delegates_hexagon_hexagon_nn_BUILD deleted file mode 100644 index 010da725e1f8..000000000000 --- a/science/py-tensorflow/files/patch-tensorflow_lite_delegates_hexagon_hexagon_nn_BUILD +++ /dev/null @@ -1,10 +0,0 @@ ---- tensorflow/lite/delegates/hexagon/hexagon_nn/BUILD.orig 2023-03-30 17:50:25.801299000 +0200 -+++ tensorflow/lite/delegates/hexagon/hexagon_nn/BUILD 2023-03-30 17:50:38.457225000 +0200 -@@ -76,6 +76,7 @@ - name = "libhexagon_interface.so", - linkopts = [ - "-Wl,-soname=libhexagon_interface.so", -+ "-Wl,--undefined-version", - "-z defs", - "-Wl,--version-script,$(location //tensorflow/lite/delegates/hexagon/hexagon_nn:version_scripts.lds)", - ] + select({ diff --git a/science/py-tensorflow/files/patch-tensorflow_python_BUILD b/science/py-tensorflow/files/patch-tensorflow_python_BUILD new file mode 100644 index 000000000000..571aaeb6f5ee --- /dev/null +++ b/science/py-tensorflow/files/patch-tensorflow_python_BUILD @@ -0,0 +1,10 @@ +--- tensorflow/python/BUILD.orig 2023-09-12 16:46:28 UTC ++++ tensorflow/python/BUILD +@@ -5043,7 +5043,6 @@ tf_python_pybind_extension( + features = ["-layering_check"], + deps = [ + ":pywrap_densor_device_headers", +- "//tensorflow/dtensor/proto:layout_proto_cc", + "//tensorflow/python/lib/core:pybind11_lib", + "//tensorflow/python/lib/core:pybind11_status_headers", + "//third_party/python_runtime:headers", # buildcleaner: keep diff --git a/science/py-tensorflow/files/patch-tensorflow_python_framework_BUILD b/science/py-tensorflow/files/patch-tensorflow_python_framework_BUILD new file mode 100644 index 000000000000..6333ffbb7fe6 --- /dev/null +++ b/science/py-tensorflow/files/patch-tensorflow_python_framework_BUILD @@ -0,0 +1,23 @@ +--- tensorflow/python/framework/BUILD.orig 2023-09-12 16:46:28 UTC ++++ tensorflow/python/framework/BUILD +@@ -421,11 +421,11 @@ py_library( + "//tensorflow/core:protos_all_py", + "//tensorflow/core/function/trace_type", + "//tensorflow/python:pywrap_tensorflow", +- "//tensorflow/python/lib/core:_pywrap_bfloat16", + "//tensorflow/python/lib/core:_pywrap_custom_casts", + "//tensorflow/python/lib/core:_pywrap_float8", + "//tensorflow/python/types:doc_typealias", + "//tensorflow/python/util:tf_export", ++ "//tensorflow/tsl/python/lib/core:pywrap_bfloat16", + ], + ) + +@@ -942,6 +942,7 @@ tf_python_pybind_extension( + "//tensorflow/python/util:function_parameter_canonicalizer_hdrs", + "//third_party/python_runtime:headers", # buildcleaner: keep + "@com_google_absl//absl/container:flat_hash_map", ++ "@com_google_absl//absl/strings", + "@pybind11", + ], + ) diff --git a/science/py-tensorflow/files/patch-tensorflow_python_framework_python__api__dispatcher__wrapper.cc b/science/py-tensorflow/files/patch-tensorflow_python_framework_python__api__dispatcher__wrapper.cc new file mode 100644 index 000000000000..7f87215ca928 --- /dev/null +++ b/science/py-tensorflow/files/patch-tensorflow_python_framework_python__api__dispatcher__wrapper.cc @@ -0,0 +1,10 @@ +--- tensorflow/python/framework/python_api_dispatcher_wrapper.cc.orig 2023-09-12 16:46:28 UTC ++++ tensorflow/python/framework/python_api_dispatcher_wrapper.cc +@@ -14,6 +14,7 @@ limitations under the License. + ==============================================================================*/ + // Python bindings for tensorflow/python/framework/python_api_dispatcher.h. + ++#include "absl/strings/str_cat.h" + #include "pybind11/pybind11.h" // from @pybind11 + #include "pybind11/pytypes.h" // from @pybind11 + #include "pybind11/stl.h" // from @pybind11 diff --git a/science/py-tensorflow/files/patch-tensorflow_python_util_BUILD b/science/py-tensorflow/files/patch-tensorflow_python_util_BUILD new file mode 100644 index 000000000000..9c99182fba88 --- /dev/null +++ b/science/py-tensorflow/files/patch-tensorflow_python_util_BUILD @@ -0,0 +1,10 @@ +--- tensorflow/python/util/BUILD.orig 2023-09-12 16:46:28 UTC ++++ tensorflow/python/util/BUILD +@@ -442,6 +442,7 @@ cc_library( + "//tensorflow/python/lib/core:safe_pyobject_ptr", + "//third_party/python_runtime:headers", # buildcleaner: keep + "@com_google_absl//absl/container:flat_hash_set", ++ "@com_google_absl//absl/strings", + "@com_google_absl//absl/types:span", + ], + ) diff --git a/science/py-tensorflow/files/patch-tensorflow_python_util_function__parameter__canonicalizer.cc b/science/py-tensorflow/files/patch-tensorflow_python_util_function__parameter__canonicalizer.cc new file mode 100644 index 000000000000..decd6b668369 --- /dev/null +++ b/science/py-tensorflow/files/patch-tensorflow_python_util_function__parameter__canonicalizer.cc @@ -0,0 +1,10 @@ +--- tensorflow/python/util/function_parameter_canonicalizer.cc.orig 2023-09-12 16:46:28 UTC ++++ tensorflow/python/util/function_parameter_canonicalizer.cc +@@ -16,6 +16,7 @@ limitations under the License. + #include "tensorflow/python/util/function_parameter_canonicalizer.h" + + #include "absl/container/flat_hash_set.h" ++#include "absl/strings/str_cat.h" + #include "tensorflow/core/platform/logging.h" + #include "tensorflow/core/platform/macros.h" + #include "tensorflow/python/lib/core/py_util.h" diff --git a/science/py-tensorflow/files/patch-tensorflow_tensorflow.bzl b/science/py-tensorflow/files/patch-tensorflow_tensorflow.bzl deleted file mode 100644 index a630a8fa1d09..000000000000 --- a/science/py-tensorflow/files/patch-tensorflow_tensorflow.bzl +++ /dev/null @@ -1,26 +0,0 @@ ---- tensorflow/tensorflow.bzl.orig 2023-03-30 17:54:35.641567000 +0200 -+++ tensorflow/tensorflow.bzl 2023-03-30 17:56:12.747346000 +0200 -@@ -2305,6 +2305,7 @@ - ], - clean_dep("//tensorflow:windows"): [], - "//conditions:default": [ -+ "-Wl,--undefined-version", - "-Wl,--version-script", - "$(location %s.lds)" % vscriptname, - ], -@@ -2975,6 +2976,7 @@ - "/ignore:4070", - ] if win_def_file else [], - "//conditions:default": [ -+ "-Wl,--undefined-version", - "-Wl,--version-script", - "$(location %s)" % version_script_file, - ], -@@ -3035,6 +3037,7 @@ - ], - clean_dep("//tensorflow:windows"): [], - "//conditions:default": [ -+ "-Wl,--undefined-version", - "-Wl,--version-script", - "$(location %s)" % version_script_file, - ], diff --git a/science/py-tensorflow/files/patch-tensorflow_tf__framework__version__script.lds b/science/py-tensorflow/files/patch-tensorflow_tf__framework__version__script.lds new file mode 100644 index 000000000000..e20aa6bda712 --- /dev/null +++ b/science/py-tensorflow/files/patch-tensorflow_tf__framework__version__script.lds @@ -0,0 +1,12 @@ +--- tensorflow/tf_framework_version_script.lds.orig 2023-09-12 16:46:28 UTC ++++ tensorflow/tf_framework_version_script.lds +@@ -3,9 +3,6 @@ VERS_1.0 { + local: + jpeg_*; + jinit_*; +- jdiv_round_up; +- jround_up; +- jzero_far; + jcopy_*; + jsimd_*; + hwloc_*; diff --git a/science/py-tensorflow/files/patch-tensorflow_tf_framework_version_script.lds b/science/py-tensorflow/files/patch-tensorflow_tf_framework_version_script.lds deleted file mode 100644 index 890e1456b9ba..000000000000 --- a/science/py-tensorflow/files/patch-tensorflow_tf_framework_version_script.lds +++ /dev/null @@ -1,12 +0,0 @@ ---- tensorflow/tf_framework_version_script.lds.orig 2023-03-30 17:42:11.255357000 +0200 -+++ tensorflow/tf_framework_version_script.lds 2023-03-30 17:42:18.431845000 +0200 -@@ -3,9 +3,6 @@ - local: - jpeg_*; - jinit_*; -- jdiv_round_up; -- jround_up; -- jzero_far; - jcopy_*; - jsimd_*; - hwloc_*; diff --git a/science/py-tensorflow/files/patch-tensorflow_tools_pip__package_build__pip__package.sh b/science/py-tensorflow/files/patch-tensorflow_tools_pip__package_build__pip__package.sh new file mode 100644 index 000000000000..643344bac97f --- /dev/null +++ b/science/py-tensorflow/files/patch-tensorflow_tools_pip__package_build__pip__package.sh @@ -0,0 +1,32 @@ +--- tensorflow/tools/pip_package/build_pip_package.sh.orig 2023-09-12 16:46:28 UTC ++++ tensorflow/tools/pip_package/build_pip_package.sh +@@ -183,9 +183,9 @@ function prepare_src() { + bazel-bin/tensorflow/tools/pip_package/build_pip_package.runfiles/org_tensorflow \ + "${XLA_AOT_RUNTIME_SOURCES}" + # Copy MKL libs over so they can be loaded at runtime +- # TODO(b/271299337): shared libraries that depend on libbfloat16.so.so have ++ # TODO(b/271299337): shared libraries that depend on libbfloat16.so have + # their NEEDED and RUNPATH set corresponding to a dependency on +- # RUNFILES/_solib_local/libtensorflow_Stsl_Spython_Slib_Score_Slibbfloat16.so.so, ++ # RUNFILES/_solib_local/libtensorflow_Stsl_Spython_Slib_Score_Slibbfloat16.so, + # which is a symlink to tensorflow/tsl/python/lib/core/libbfloat16.so in + # the Bazel build tree. We do not export the file in _solib_local (nor + # symlinks in general, I think Python wheels have poor support for them?) +@@ -193,13 +193,13 @@ function prepare_src() { + if is_macos; then + chmod +rw ${TMPDIR}/tensorflow/tsl/python/lib/core/pywrap_bfloat16.so + chmod +rw ${TMPDIR}/tensorflow/python/_pywrap_tensorflow_internal.so +- install_name_tool -change "@loader_path/../../../../../${so_lib_dir}//libtensorflow_Stsl_Spython_Slib_Score_Slibbfloat16.so.so" "@loader_path/libbfloat16.so.so" ${TMPDIR}/tensorflow/tsl/python/lib/core/pywrap_bfloat16.so +- install_name_tool -change "@loader_path/../../${so_lib_dir}//libtensorflow_Stsl_Spython_Slib_Score_Slibbfloat16.so.so" "@loader_path/../tsl/python/lib/core/libbfloat16.so.so" ${TMPDIR}/tensorflow/python/_pywrap_tensorflow_internal.so ++ install_name_tool -change "@loader_path/../../../../../${so_lib_dir}//libtensorflow_Stsl_Spython_Slib_Score_Slibbfloat16.so" "@loader_path/libbfloat16.so" ${TMPDIR}/tensorflow/tsl/python/lib/core/pywrap_bfloat16.so ++ install_name_tool -change "@loader_path/../../${so_lib_dir}//libtensorflow_Stsl_Spython_Slib_Score_Slibbfloat16.so" "@loader_path/../tsl/python/lib/core/libbfloat16.so" ${TMPDIR}/tensorflow/python/_pywrap_tensorflow_internal.so + else + chmod +rw ${TMPDIR}/tensorflow/tsl/python/lib/core/pywrap_bfloat16.so + chmod +rw ${TMPDIR}/tensorflow/python/_pywrap_tensorflow_internal.so +- patchelf --replace-needed libtensorflow_Stsl_Spython_Slib_Score_Slibbfloat16.so.so libbfloat16.so.so ${TMPDIR}/tensorflow/tsl/python/lib/core/pywrap_bfloat16.so +- patchelf --replace-needed libtensorflow_Stsl_Spython_Slib_Score_Slibbfloat16.so.so libbfloat16.so.so ${TMPDIR}/tensorflow/python/_pywrap_tensorflow_internal.so ++ patchelf --replace-needed libtensorflow_Stsl_Spython_Slib_Score_Slibbfloat16.so libbfloat16.so ${TMPDIR}/tensorflow/tsl/python/lib/core/pywrap_bfloat16.so ++ patchelf --replace-needed libtensorflow_Stsl_Spython_Slib_Score_Slibbfloat16.so libbfloat16.so ${TMPDIR}/tensorflow/python/_pywrap_tensorflow_internal.so + patchelf --set-rpath $(patchelf --print-rpath ${TMPDIR}/tensorflow/tsl/python/lib/core/pywrap_bfloat16.so):\$ORIGIN ${TMPDIR}/tensorflow/tsl/python/lib/core/pywrap_bfloat16.so + patchelf --set-rpath $(patchelf --print-rpath ${TMPDIR}/tensorflow/python/_pywrap_tensorflow_internal.so):\$ORIGIN/../tsl/python/lib/core ${TMPDIR}/tensorflow/python/_pywrap_tensorflow_internal.so + patchelf --shrink-rpath ${TMPDIR}/tensorflow/tsl/python/lib/core/pywrap_bfloat16.so diff --git a/science/py-tensorflow/files/patch-tensorflow_tools_pip__package_setup.py b/science/py-tensorflow/files/patch-tensorflow_tools_pip__package_setup.py deleted file mode 100644 index 76ac3facf928..000000000000 --- a/science/py-tensorflow/files/patch-tensorflow_tools_pip__package_setup.py +++ /dev/null @@ -1,34 +0,0 @@ ---- tensorflow/tools/pip_package/setup.py.orig 2022-09-07 19:29:52 UTC -+++ tensorflow/tools/pip_package/setup.py -@@ -77,13 +77,12 @@ REQUIRED_PACKAGES = [ - 'astunparse >= 1.6.0', - # TODO(b/187981032): remove the constraint for 2.0 once the incompatibile - # issue is resolved. -- 'flatbuffers >= 1.12, <2', -+ 'flatbuffers', - # TODO(b/213222745) gast versions above 0.4.0 break TF's tests -- 'gast >= 0.2.1, <= 0.4.0', -+ 'gast', - 'google_pasta >= 0.1.1', - 'h5py >= 2.9.0', -- 'keras_preprocessing >= 1.1.1', # 1.1.0 needs tensorflow==1.7 -- 'libclang >= 13.0.0', -+ 'keras_preprocessing >= 1.1.0', # 1.1.0 needs tensorflow==1.7 - 'numpy >= 1.20', - 'opt_einsum >= 2.3.2', - 'packaging', -@@ -94,13 +93,12 @@ REQUIRED_PACKAGES = [ - # See also: https://github.com/protocolbuffers/protobuf/issues/9954 - # See also: https://github.com/tensorflow/tensorflow/issues/56077 - # This is a temporary patch for now, to patch previous TF releases. -- 'protobuf >= 3.9.2, < 3.20', -+ 'protobuf', - 'setuptools', - 'six >= 1.12.0', - 'termcolor >= 1.1.0', - 'typing_extensions >= 3.6.6', - 'wrapt >= 1.11.0', -- 'tensorflow-io-gcs-filesystem >= 0.23.1', - # grpcio does not build correctly on big-endian machines due to lack of - # BoringSSL support. - # See https://github.com/tensorflow/tensorflow/issues/17882. diff --git a/science/py-tensorflow/files/patch-tensorflow_tools_proto__text_BUILD b/science/py-tensorflow/files/patch-tensorflow_tools_proto__text_BUILD deleted file mode 100644 index 8cdff520c744..000000000000 --- a/science/py-tensorflow/files/patch-tensorflow_tools_proto__text_BUILD +++ /dev/null @@ -1,10 +0,0 @@ ---- tensorflow/tools/proto_text/BUILD.orig 2022-05-22 22:28:22 UTC -+++ tensorflow/tools/proto_text/BUILD -@@ -60,6 +60,7 @@ cc_library( - "-lm", - "-lpthread", - "-lrt", -+ "-L%%LOCALBASE%%/lib", - ], - }), - deps = [ diff --git a/science/py-tensorflow/files/patch-tensorflow_tools_proto__text_gen__proto__text__functions.cc b/science/py-tensorflow/files/patch-tensorflow_tools_proto__text_gen__proto__text__functions.cc new file mode 100644 index 000000000000..ee04155163a4 --- /dev/null +++ b/science/py-tensorflow/files/patch-tensorflow_tools_proto__text_gen__proto__text__functions.cc @@ -0,0 +1,13 @@ +--- tensorflow/tools/proto_text/gen_proto_text_functions.cc.orig 2023-09-12 16:46:28 UTC ++++ tensorflow/tools/proto_text/gen_proto_text_functions.cc +@@ -31,8 +31,8 @@ class CrashOnErrorCollector + public: + ~CrashOnErrorCollector() override {} + +- void AddError(const string& filename, int line, int column, +- const string& message) override { ++ void RecordError(absl::string_view filename, int line, int column, ++ absl::string_view message) override { + LOG(FATAL) << "Unexpected error at " << filename << "@" << line << ":" + << column << " - " << message; + } diff --git a/science/py-tensorflow/files/patch-tensorflow_tsl_platform_default_build__config.bzl b/science/py-tensorflow/files/patch-tensorflow_tsl_platform_default_build__config.bzl new file mode 100644 index 000000000000..2df204c53eae --- /dev/null +++ b/science/py-tensorflow/files/patch-tensorflow_tsl_platform_default_build__config.bzl @@ -0,0 +1,25 @@ +--- tensorflow/tsl/platform/default/build_config.bzl.orig 2023-09-12 16:46:28 UTC ++++ tensorflow/tsl/platform/default/build_config.bzl +@@ -401,13 +401,6 @@ def py_proto_library( + # is not explicitly listed in py_libs. Instead, host system is assumed to + # have grpc installed. + +- genproto_deps = [] +- for dep in deps: +- if dep != "@com_google_protobuf//:protobuf_python": +- genproto_deps.append(dep + "_genproto") +- else: +- genproto_deps.append("@com_google_protobuf//:well_known_types_py_pb2_genproto") +- + proto_gen( + name = name + "_genproto", + srcs = srcs, +@@ -418,7 +411,7 @@ def py_proto_library( + plugin_language = "grpc", + protoc = protoc, + visibility = ["//visibility:public"], +- deps = genproto_deps, ++ deps = [s + "_genproto" for s in deps], + ) + + if default_runtime and not default_runtime in py_libs + deps: diff --git a/science/py-tensorflow/files/patch-tensorflow_tsl_platform_default_human__readable__json.cc b/science/py-tensorflow/files/patch-tensorflow_tsl_platform_default_human__readable__json.cc new file mode 100644 index 000000000000..b25b238f479a --- /dev/null +++ b/science/py-tensorflow/files/patch-tensorflow_tsl_platform_default_human__readable__json.cc @@ -0,0 +1,11 @@ +--- tensorflow/tsl/platform/default/human_readable_json.cc.orig 2023-09-12 16:46:28 UTC ++++ tensorflow/tsl/platform/default/human_readable_json.cc +@@ -27,7 +27,7 @@ Status ProtoToHumanReadableJson(const protobuf::Messag + + protobuf::util::JsonPrintOptions json_options; + json_options.preserve_proto_field_names = true; +- json_options.always_print_primitive_fields = true; ++ json_options.always_print_fields_with_no_presence = true; + auto status = + protobuf::util::MessageToJsonString(proto, result, json_options); + if (!status.ok()) { diff --git a/science/py-tensorflow/files/patch-tensorflow_tsl_python_lib_core_BUILD b/science/py-tensorflow/files/patch-tensorflow_tsl_python_lib_core_BUILD new file mode 100644 index 000000000000..4d6d8c57b038 --- /dev/null +++ b/science/py-tensorflow/files/patch-tensorflow_tsl_python_lib_core_BUILD @@ -0,0 +1,11 @@ +--- tensorflow/tsl/python/lib/core/BUILD.orig 2023-09-12 16:46:28 UTC ++++ tensorflow/tsl/python/lib/core/BUILD +@@ -50,7 +50,7 @@ cc_shared_library( + roots = [":bfloat16_lib"], + # TODO(tlongeri): If this is not explicitly specified, dependent DLLs will expect "bfloat16.so" + # and we will generate "bfloat16.so.dll", for some reason +- shared_lib_name = if_windows("bfloat16.so", None), ++ shared_lib_name = if_windows("bfloat16.so", "libbfloat16.so"), + static_deps = [ + # TODO(ddunleavy): If cc_shared_library is ever not a noop in g3, change + # this to be more specific. diff --git a/science/py-tensorflow/files/patch-tensorflow_workspace2.bzl b/science/py-tensorflow/files/patch-tensorflow_workspace2.bzl index 207894ee3c88..91723987576b 100644 --- a/science/py-tensorflow/files/patch-tensorflow_workspace2.bzl +++ b/science/py-tensorflow/files/patch-tensorflow_workspace2.bzl @@ -1,10 +1,32 @@ ---- tensorflow/workspace2.bzl.orig 2022-05-22 22:28:22 UTC +--- tensorflow/workspace2.bzl.orig 2023-09-12 16:46:28 UTC +++ tensorflow/workspace2.bzl -@@ -137,6 +137,7 @@ def _tf_repositories(): +@@ -145,6 +145,7 @@ def _tf_repositories(): name = "XNNPACK", - sha256 = "7e9ad45391e5158fd00e816022bda21d54a6180788af7c455c864a78cee252c6", - strip_prefix = "XNNPACK-11b2812d64e49bab9b6c489f79067fc94e69db9f", -+ patch_file=["//third_party:add-default-option.patch"], - urls = tf_mirror_urls("https://github.com/google/XNNPACK/archive/11b2812d64e49bab9b6c489f79067fc94e69db9f.zip"), + sha256 = "c979b62e8b77af60dfd7567f22ade20d5a9d4d0888f8a2d60d155fc0d31b22ab", + strip_prefix = "XNNPACK-b9d4073a6913891ce9cbd8965c8d506075d2a45a", ++ patch_file=["//third_party:fix-xnnpack.patch"], + urls = tf_mirror_urls("https://github.com/google/XNNPACK/archive/b9d4073a6913891ce9cbd8965c8d506075d2a45a.zip"), ) # LINT.ThenChange(//tensorflow/lite/tools/cmake/modules/xnnpack.cmake) +@@ -165,9 +166,9 @@ def _tf_repositories(): + + tf_http_archive( + name = "cpuinfo", +- strip_prefix = "cpuinfo-3dc310302210c1891ffcfb12ae67b11a3ad3a150", +- sha256 = "ba668f9f8ea5b4890309b7db1ed2e152aaaf98af6f9a8a63dbe1b75c04e52cb9", +- urls = tf_mirror_urls("https://github.com/pytorch/cpuinfo/archive/3dc310302210c1891ffcfb12ae67b11a3ad3a150.zip"), ++ strip_prefix = "cpuinfo-fa1c679da8d19e1d87f20175ae1ec10995cd3dd3", ++ sha256 = "2bf2b62eb86e2d2eaf862d0b9683a6c467a4d69fb2f7f1dc47c799809148608f", ++ urls = tf_mirror_urls("https://github.com/pytorch/cpuinfo/archive/fa1c679da8d19e1d87f20175ae1ec10995cd3dd3.zip"), + ) + + tf_http_archive( +@@ -875,7 +876,7 @@ def _tf_repositories(): + urls = tf_mirror_urls("https://github.com/pybind/pybind11_protobuf/archive/80f3440cd8fee124e077e2e47a8a17b78b451363.zip"), + sha256 = "c7ab64b1ccf9a678694a89035a8c865a693e4e872803778f91f0965c2f281d78", + strip_prefix = "pybind11_protobuf-80f3440cd8fee124e077e2e47a8a17b78b451363", +- patch_file = ["//third_party/pybind11_protobuf:remove_license.patch"], ++ patch_file = ["//third_party/pybind11_protobuf:remove_license.patch","//third_party:fix-pybind11_protobuf.patch"], + ) + + tf_http_archive( diff --git a/science/py-tensorflow/files/patch-third__party_absl_system.absl.base.BUILD b/science/py-tensorflow/files/patch-third__party_absl_system.absl.base.BUILD new file mode 100644 index 000000000000..c92f6c708ed8 --- /dev/null +++ b/science/py-tensorflow/files/patch-third__party_absl_system.absl.base.BUILD @@ -0,0 +1,18 @@ +--- third_party/absl/system.absl.base.BUILD.orig 2023-09-12 16:46:28 UTC ++++ third_party/absl/system.absl.base.BUILD +@@ -17,7 +17,14 @@ cc_library( + + cc_library( + name = "log_severity", +- linkopts = ["-labsl_log_severity"], ++ linkopts = [ ++ "-labsl_log_severity", ++ "-labsl_log_internal_check_op", ++ "-labsl_log_internal_conditions", ++ "-labsl_log_internal_message", ++ "-labsl_log_internal_nullguard", ++ "-labsl_vlog_config_internal", ++ ], + ) + + cc_library( diff --git a/science/py-tensorflow/files/patch-third__party_absl_system.absl.flags.BUILD b/science/py-tensorflow/files/patch-third__party_absl_system.absl.flags.BUILD new file mode 100644 index 000000000000..1376191228ef --- /dev/null +++ b/science/py-tensorflow/files/patch-third__party_absl_system.absl.flags.BUILD @@ -0,0 +1,10 @@ +--- third_party/absl/system.absl.flags.BUILD.orig 2023-09-12 16:46:28 UTC ++++ third_party/absl/system.absl.flags.BUILD +@@ -97,7 +97,6 @@ cc_library( + + cc_library( + name = "flag", +- linkopts = ["-labsl_flags"], + deps = [ + ":config", + ":flag_internal", diff --git a/science/py-tensorflow/files/patch-third__party_absl_system.absl.functional.BUILD b/science/py-tensorflow/files/patch-third__party_absl_system.absl.functional.BUILD new file mode 100644 index 000000000000..2946aa0a5e86 --- /dev/null +++ b/science/py-tensorflow/files/patch-third__party_absl_system.absl.functional.BUILD @@ -0,0 +1,13 @@ +--- third_party/absl/system.absl.functional.BUILD.orig 2023-09-12 16:46:28 UTC ++++ third_party/absl/system.absl.functional.BUILD +@@ -3,6 +3,10 @@ cc_library( + package(default_visibility = ["//visibility:public"]) + + cc_library( ++ name = "any_invocable", ++) ++ ++cc_library( + name = "bind_front", + ) + diff --git a/science/py-tensorflow/files/patch-third__party_absl_system.absl.log.BUILD b/science/py-tensorflow/files/patch-third__party_absl_system.absl.log.BUILD new file mode 100644 index 000000000000..b148e8424213 --- /dev/null +++ b/science/py-tensorflow/files/patch-third__party_absl_system.absl.log.BUILD @@ -0,0 +1,13 @@ +--- third_party/absl/system.absl.log.BUILD.orig 2024-06-26 12:02:28 UTC ++++ third_party/absl/system.absl.log.BUILD +@@ -0,0 +1,10 @@ ++load("@rules_cc//cc:defs.bzl", "cc_library") ++ ++package(default_visibility = ["//visibility:public"]) ++ ++[cc_library( ++ name = n, ++) for n in [ ++ "log", ++ "check", ++]] diff --git a/science/py-tensorflow/files/patch-third__party_absl_system.absl.strings.BUILD b/science/py-tensorflow/files/patch-third__party_absl_system.absl.strings.BUILD index 5db2e76aff4b..dca3d2c50183 100644 --- a/science/py-tensorflow/files/patch-third__party_absl_system.absl.strings.BUILD +++ b/science/py-tensorflow/files/patch-third__party_absl_system.absl.strings.BUILD @@ -1,15 +1,6 @@ ---- third_party/absl/system.absl.strings.BUILD.orig 2022-05-22 22:28:22 UTC +--- third_party/absl/system.absl.strings.BUILD.orig 2023-09-12 16:46:28 UTC +++ third_party/absl/system.absl.strings.BUILD -@@ -4,7 +4,7 @@ package(default_visibility = ["//visibility:public"]) - - cc_library( - name = "strings", -- linkopts = ["-labsl_strings"], -+ linkopts = ["-L%%LOCALBASE%%/lib", "-labsl_strings"], - deps = [ - ":internal", - "//absl/base", -@@ -26,7 +26,13 @@ cc_library( +@@ -26,7 +26,11 @@ cc_library( cc_library( name = "cord", @@ -17,10 +8,8 @@ + linkopts = [ + "-labsl_cord", + "-labsl_cord_internal", -+ "-labsl_cordz_functions", -+ "-labsl_cordz_handle", -+ "-labsl_cordz_info", -+ "-labsl_cordz_sample_token",], ++ "-labsl_cordz_info" ++ ], deps = [ ":str_format", "//absl/container:compressed_tuple", diff --git a/science/py-tensorflow/files/patch-third__party_absl_system.absl.synchronization.BUILD b/science/py-tensorflow/files/patch-third__party_absl_system.absl.synchronization.BUILD new file mode 100644 index 000000000000..fbd76f00be15 --- /dev/null +++ b/science/py-tensorflow/files/patch-third__party_absl_system.absl.synchronization.BUILD @@ -0,0 +1,31 @@ +--- third_party/absl/system.absl.synchronization.BUILD.orig 2023-09-12 16:46:28 UTC ++++ third_party/absl/system.absl.synchronization.BUILD +@@ -17,13 +17,28 @@ cc_library( + ) + + cc_library( ++ name = "kernel_timeout_internal", ++ visibility = [ ++ ], ++ deps = [ ++ "//absl/base", ++ "//absl/base:config", ++ "//absl/base:core_headers", ++ "//absl/base:raw_logging_internal", ++ "//absl/time", ++ ], ++) ++ ++cc_library( + name = "synchronization", + linkopts = [ + "-labsl_synchronization", ++ "-labsl_kernel_timeout_internal", + "-pthread", + ], + deps = [ + ":graphcycles_internal", ++ ":kernel_timeout_internal", + "//absl/base", + "//absl/base:atomic_hook", + "//absl/base:dynamic_annotations", diff --git a/science/py-tensorflow/files/patch-third__party_absl_workspace.bzl b/science/py-tensorflow/files/patch-third__party_absl_workspace.bzl new file mode 100644 index 000000000000..199a88686264 --- /dev/null +++ b/science/py-tensorflow/files/patch-third__party_absl_workspace.bzl @@ -0,0 +1,10 @@ +--- third_party/absl/workspace.bzl.orig 2023-09-12 16:46:28 UTC ++++ third_party/absl/workspace.bzl +@@ -20,6 +20,7 @@ def repo(): + "flags", + "functional", + "hash", ++ "log", + "memory", + "meta", + "numeric", diff --git a/science/py-tensorflow/files/patch-third__party_cpuinfo_cpuinfo.BUILD b/science/py-tensorflow/files/patch-third__party_cpuinfo_cpuinfo.BUILD deleted file mode 100644 index 738e8bc2abd8..000000000000 --- a/science/py-tensorflow/files/patch-third__party_cpuinfo_cpuinfo.BUILD +++ /dev/null @@ -1,51 +0,0 @@ ---- third_party/cpuinfo/cpuinfo.BUILD.orig 2022-05-22 22:28:22 UTC -+++ third_party/cpuinfo/cpuinfo.BUILD -@@ -100,35 +100,7 @@ EMSCRIPTEN_SRCS = [ - cc_library( - name = "cpuinfo_impl", - srcs = select({ -- ":linux_x86_64": COMMON_SRCS + X86_SRCS + LINUX_SRCS + LINUX_X86_SRCS, -- ":linux_arm": COMMON_SRCS + ARM_SRCS + LINUX_SRCS + LINUX_ARM32_SRCS, -- ":linux_armhf": COMMON_SRCS + ARM_SRCS + LINUX_SRCS + LINUX_ARM32_SRCS, -- ":linux_armv7a": COMMON_SRCS + ARM_SRCS + LINUX_SRCS + LINUX_ARM32_SRCS, -- ":linux_armeabi": COMMON_SRCS + ARM_SRCS + LINUX_SRCS + LINUX_ARM32_SRCS, -- ":linux_aarch64": COMMON_SRCS + ARM_SRCS + LINUX_SRCS + LINUX_ARM64_SRCS, -- ":linux_mips64": COMMON_SRCS + LINUX_SRCS, -- ":linux_riscv64": COMMON_SRCS + LINUX_SRCS, -- ":linux_s390x": COMMON_SRCS + LINUX_SRCS, -- ":macos_x86_64": COMMON_SRCS + X86_SRCS + MACH_SRCS + MACH_X86_SRCS, -- ":macos_arm64": COMMON_SRCS + MACH_SRCS + MACH_ARM_SRCS, -- ":windows_x86_64": COMMON_SRCS + X86_SRCS + WINDOWS_X86_SRCS, -- ":android_armv7": COMMON_SRCS + ARM_SRCS + LINUX_SRCS + LINUX_ARM32_SRCS + ANDROID_ARM_SRCS, -- ":android_arm64": COMMON_SRCS + ARM_SRCS + LINUX_SRCS + LINUX_ARM64_SRCS + ANDROID_ARM_SRCS, -- ":android_x86": COMMON_SRCS + X86_SRCS + LINUX_SRCS + LINUX_X86_SRCS, -- ":android_x86_64": COMMON_SRCS + X86_SRCS + LINUX_SRCS + LINUX_X86_SRCS, -- ":ios_x86_64": COMMON_SRCS + X86_SRCS + MACH_SRCS + MACH_X86_SRCS, -- ":ios_x86": COMMON_SRCS + X86_SRCS + MACH_SRCS + MACH_X86_SRCS, -- ":ios_armv7": COMMON_SRCS + MACH_SRCS + MACH_ARM_SRCS, -- ":ios_arm64": COMMON_SRCS + MACH_SRCS + MACH_ARM_SRCS, -- ":ios_arm64e": COMMON_SRCS + MACH_SRCS + MACH_ARM_SRCS, -- ":ios_sim_arm64": COMMON_SRCS + MACH_SRCS + MACH_ARM_SRCS, -- ":watchos_x86_64": COMMON_SRCS + X86_SRCS + MACH_SRCS + MACH_X86_SRCS, -- ":watchos_x86": COMMON_SRCS + X86_SRCS + MACH_SRCS + MACH_X86_SRCS, -- ":watchos_armv7k": COMMON_SRCS + MACH_SRCS + MACH_ARM_SRCS, -- ":watchos_arm64_32": COMMON_SRCS + MACH_SRCS + MACH_ARM_SRCS, -- ":tvos_x86_64": COMMON_SRCS + X86_SRCS + MACH_SRCS + MACH_X86_SRCS, -- ":tvos_arm64": COMMON_SRCS + MACH_SRCS + MACH_ARM_SRCS, -- ":emscripten_wasm": COMMON_SRCS + EMSCRIPTEN_SRCS, -+ "//conditions:default": COMMON_SRCS + X86_SRCS + MACH_SRCS + MACH_X86_SRCS, - }), - copts = select({ - ":windows_x86_64": [], -@@ -187,6 +159,11 @@ cc_library( - ) - - ############################# Build configurations ############################# -+ -+config_setting( -+ name = "default", -+ values = {"cpu": "k8"}, -+) - - config_setting( - name = "linux_x86_64", diff --git a/science/py-tensorflow/files/patch-third__party_cpuinfo_workspace.bzl b/science/py-tensorflow/files/patch-third__party_cpuinfo_workspace.bzl deleted file mode 100644 index aa701dbd58a5..000000000000 --- a/science/py-tensorflow/files/patch-third__party_cpuinfo_workspace.bzl +++ /dev/null @@ -1,9 +0,0 @@ ---- third_party/cpuinfo/workspace.bzl.orig 2022-08-29 16:23:14 UTC -+++ third_party/cpuinfo/workspace.bzl -@@ -8,5 +8,6 @@ def repo(): - strip_prefix = "cpuinfo-5916273f79a21551890fd3d56fc5375a78d1598d", - sha256 = "2a160c527d3c58085ce260f34f9e2b161adc009b34186a2baf24e74376e89e6d", - urls = tf_mirror_urls("https://github.com/pytorch/cpuinfo/archive/5916273f79a21551890fd3d56fc5375a78d1598d.zip"), -+ patch_file = ["//third_party:fix_cpuinfo.patch"], - build_file = "//third_party/cpuinfo:cpuinfo.BUILD", - ) diff --git a/science/py-tensorflow/files/patch-third__party_llvm_macos__build__fix.patch b/science/py-tensorflow/files/patch-third__party_llvm_macos__build__fix.patch deleted file mode 100644 index 772ba624a877..000000000000 --- a/science/py-tensorflow/files/patch-third__party_llvm_macos__build__fix.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- third_party/llvm/macos_build_fix.patch.orig 2022-09-06 16:15:49 UTC -+++ third_party/llvm/macos_build_fix.patch -@@ -38,7 +38,7 @@ index ff64df694048..c9c35b01711c 100644 - - "@bazel_tools//src/conditions:darwin_arm64": native_arch_defines("AArch64", "arm64-apple-darwin"), - - "@bazel_tools//src/conditions:darwin_x86_64": native_arch_defines("X86", "x86_64-unknown-darwin"), - + "//llvm:macos_arm64": native_arch_defines("AArch64", "arm64-apple-darwin"), --+ "@bazel_tools//src/conditions:darwin": native_arch_defines("X86", "x86_64-unknown-darwin"), -++ "@bazel_tools//src/conditions:freebsd": native_arch_defines("X86", "x86_64-unknown-freebsd13.0"), - "@bazel_tools//src/conditions:linux_aarch64": native_arch_defines("AArch64", "aarch64-unknown-linux-gnu"), - "//conditions:default": native_arch_defines("X86", "x86_64-unknown-linux-gnu"), - }) + [ diff --git a/science/py-tensorflow/files/patch-third__party_llvm_workspace.bzl b/science/py-tensorflow/files/patch-third__party_llvm_workspace.bzl index e43914b13105..418755c58645 100644 --- a/science/py-tensorflow/files/patch-third__party_llvm_workspace.bzl +++ b/science/py-tensorflow/files/patch-third__party_llvm_workspace.bzl @@ -1,10 +1,10 @@ ---- third_party/llvm/workspace.bzl.orig 2022-05-22 22:28:22 UTC +--- third_party/llvm/workspace.bzl.orig 2023-09-12 16:46:28 UTC +++ third_party/llvm/workspace.bzl -@@ -16,6 +16,6 @@ def repo(name): - "https://github.com/llvm/llvm-project/archive/{commit}.tar.gz".format(commit = LLVM_COMMIT), +@@ -21,6 +21,7 @@ def repo(name): + "//third_party/llvm:build.patch", + "//third_party/llvm:mathextras.patch", + "//third_party/llvm:zstd.patch", ++ "//third_party:fix-environ.patch" ], - build_file = "//third_party/llvm:llvm.BUILD", -- patch_file = ["//third_party/llvm:macos_build_fix.patch"], -+ patch_file = ["//third_party/llvm:macos_build_fix.patch", "//third_party:freebsd_python_fix.patch", "//third_party:fix-environ.patch"], link_files = {"//third_party/llvm:run_lit.sh": "mlir/run_lit.sh"}, ) diff --git a/science/py-tensorflow/files/patch-third__party_py_BUILD.tpl b/science/py-tensorflow/files/patch-third__party_py_BUILD.tpl deleted file mode 100644 index 664828c179f7..000000000000 --- a/science/py-tensorflow/files/patch-third__party_py_BUILD.tpl +++ /dev/null @@ -1,17 +0,0 @@ ---- third_party/py/BUILD.tpl.orig 2022-09-07 10:53:01 UTC -+++ third_party/py/BUILD.tpl -@@ -9,12 +9,14 @@ load("@bazel_tools//tools/python:toolchain.bzl", "py_r - py_runtime( - name = "py2_runtime", - interpreter_path = "%{PYTHON_BIN_PATH}", -+ stub_shebang = "#!%{PYTHON_BIN_PATH}", - python_version = "PY2", - ) - - py_runtime( - name = "py3_runtime", - interpreter_path = "%{PYTHON_BIN_PATH}", -+ stub_shebang = "#!%{PYTHON_BIN_PATH}", - python_version = "PY3", - ) - diff --git a/science/py-tensorflow/files/patch-third__party_systemlibs_protobuf.BUILD b/science/py-tensorflow/files/patch-third__party_systemlibs_protobuf.BUILD deleted file mode 100644 index 212f48248ef9..000000000000 --- a/science/py-tensorflow/files/patch-third__party_systemlibs_protobuf.BUILD +++ /dev/null @@ -1,25 +0,0 @@ ---- third_party/systemlibs/protobuf.BUILD.orig 2022-09-01 05:13:59 UTC -+++ third_party/systemlibs/protobuf.BUILD -@@ -61,19 +61,19 @@ genrule( - - cc_library( - name = "protobuf", -- linkopts = ["-lprotobuf"], -+ linkopts = ["-L%%LOCALBASE%%/lib", "-lprotobuf"], - visibility = ["//visibility:public"], - ) - - cc_library( - name = "protobuf_headers", -- linkopts = ["-lprotobuf"], -+ linkopts = ["-L%%LOCALBASE%%/lib", "-lprotobuf"], - visibility = ["//visibility:public"], - ) - - cc_library( - name = "protoc_lib", -- linkopts = ["-lprotoc"], -+ linkopts = ["-L%%LOCALBASE%%/lib", "-lprotoc"], - visibility = ["//visibility:public"], - ) - diff --git a/science/py-tensorflow/pkg-plist b/science/py-tensorflow/pkg-plist index a7dbf5fad401..d4ba73bc2b25 100644 --- a/science/py-tensorflow/pkg-plist +++ b/science/py-tensorflow/pkg-plist @@ -8,6 +8,7 @@ include/tensorflow/c/eager/dlpack.h include/tensorflow/c/ops.h include/tensorflow/c/tensor_interface.h include/tensorflow/c/tf_attrtype.h +include/tensorflow/c/tf_buffer.h include/tensorflow/c/tf_datatype.h include/tensorflow/c/tf_file_statistics.h include/tensorflow/c/tf_status.h @@ -94,9 +95,27 @@ include/tensorflow/compiler/xla/array.h include/tensorflow/compiler/xla/array2d.h include/tensorflow/compiler/xla/array3d.h include/tensorflow/compiler/xla/array4d.h +include/tensorflow/compiler/xla/autotune_results.pb.h include/tensorflow/compiler/xla/comparison_util.h include/tensorflow/compiler/xla/debug_options_flags.h include/tensorflow/compiler/xla/debug_options_parsers.h +include/tensorflow/compiler/xla/hlo/ir/dfs_hlo_visitor.h +include/tensorflow/compiler/xla/hlo/ir/dfs_hlo_visitor_with_default.h +include/tensorflow/compiler/xla/hlo/ir/dynamic_parameter_binding.h +include/tensorflow/compiler/xla/hlo/ir/hlo_casting_utils.h +include/tensorflow/compiler/xla/hlo/ir/hlo_clone_context.h +include/tensorflow/compiler/xla/hlo/ir/hlo_computation.h +include/tensorflow/compiler/xla/hlo/ir/hlo_domain_metadata.h +include/tensorflow/compiler/xla/hlo/ir/hlo_input_output_alias_config.h +include/tensorflow/compiler/xla/hlo/ir/hlo_instruction.h +include/tensorflow/compiler/xla/hlo/ir/hlo_instructions.h +include/tensorflow/compiler/xla/hlo/ir/hlo_module.h +include/tensorflow/compiler/xla/hlo/ir/hlo_module_metadata.h +include/tensorflow/compiler/xla/hlo/ir/hlo_op_metadata.h +include/tensorflow/compiler/xla/hlo/ir/hlo_opcode.h +include/tensorflow/compiler/xla/hlo/ir/hlo_schedule.h +include/tensorflow/compiler/xla/hlo/ir/hlo_sharding.h +include/tensorflow/compiler/xla/hlo/ir/hlo_sharding_metadata.h include/tensorflow/compiler/xla/index_util.h include/tensorflow/compiler/xla/iterator_util.h include/tensorflow/compiler/xla/layout.h @@ -104,33 +123,20 @@ include/tensorflow/compiler/xla/layout_util.h include/tensorflow/compiler/xla/literal.h include/tensorflow/compiler/xla/literal_util.h include/tensorflow/compiler/xla/map_util.h +include/tensorflow/compiler/xla/mlir/utils/error_util.h include/tensorflow/compiler/xla/overflow_util.h include/tensorflow/compiler/xla/parse_flags_from_env.h include/tensorflow/compiler/xla/permutation_util.h include/tensorflow/compiler/xla/primitive_util.h +include/tensorflow/compiler/xla/printer.h include/tensorflow/compiler/xla/protobuf_util.h +include/tensorflow/compiler/xla/service/compilation_environments.h include/tensorflow/compiler/xla/service/computation_layout.h include/tensorflow/compiler/xla/service/computation_placer.h -include/tensorflow/compiler/xla/service/dfs_hlo_visitor.h -include/tensorflow/compiler/xla/service/dfs_hlo_visitor_with_default.h -include/tensorflow/compiler/xla/service/dynamic_parameter_binding.h include/tensorflow/compiler/xla/service/global_device_id.h include/tensorflow/compiler/xla/service/hlo.pb.h -include/tensorflow/compiler/xla/service/hlo_casting_utils.h -include/tensorflow/compiler/xla/service/hlo_clone_context.h -include/tensorflow/compiler/xla/service/hlo_computation.h -include/tensorflow/compiler/xla/service/hlo_domain_metadata.h -include/tensorflow/compiler/xla/service/hlo_input_output_alias_config.h -include/tensorflow/compiler/xla/service/hlo_instruction.h -include/tensorflow/compiler/xla/service/hlo_instructions.h -include/tensorflow/compiler/xla/service/hlo_module.h include/tensorflow/compiler/xla/service/hlo_module_config.h -include/tensorflow/compiler/xla/service/hlo_module_metadata.h -include/tensorflow/compiler/xla/service/hlo_op_metadata.h -include/tensorflow/compiler/xla/service/hlo_opcode.h -include/tensorflow/compiler/xla/service/hlo_schedule.h -include/tensorflow/compiler/xla/service/hlo_sharding.h -include/tensorflow/compiler/xla/service/hlo_sharding_metadata.h +include/tensorflow/compiler/xla/service/mapped_ptr_container_sorter.h include/tensorflow/compiler/xla/service/name_uniquer.h include/tensorflow/compiler/xla/shape.h include/tensorflow/compiler/xla/shape_layout.h @@ -139,6 +145,57 @@ include/tensorflow/compiler/xla/shape_util.h include/tensorflow/compiler/xla/status.h include/tensorflow/compiler/xla/status_macros.h include/tensorflow/compiler/xla/statusor.h +include/tensorflow/compiler/xla/stream_executor/allocator_stats.h +include/tensorflow/compiler/xla/stream_executor/blas.h +include/tensorflow/compiler/xla/stream_executor/cuda/cuda_activation.h +include/tensorflow/compiler/xla/stream_executor/cuda/cuda_platform_id.h +include/tensorflow/compiler/xla/stream_executor/data_type.h +include/tensorflow/compiler/xla/stream_executor/device_description.h +include/tensorflow/compiler/xla/stream_executor/device_description.pb.h +include/tensorflow/compiler/xla/stream_executor/device_host_allocator.h +include/tensorflow/compiler/xla/stream_executor/device_id_utils.h +include/tensorflow/compiler/xla/stream_executor/device_mem_allocator.h +include/tensorflow/compiler/xla/stream_executor/device_memory.h +include/tensorflow/compiler/xla/stream_executor/device_memory_allocator.h +include/tensorflow/compiler/xla/stream_executor/device_options.h +include/tensorflow/compiler/xla/stream_executor/dnn.h +include/tensorflow/compiler/xla/stream_executor/dnn.pb.h +include/tensorflow/compiler/xla/stream_executor/event.h +include/tensorflow/compiler/xla/stream_executor/executor_cache.h +include/tensorflow/compiler/xla/stream_executor/fft.h +include/tensorflow/compiler/xla/stream_executor/gpu/gpu_activation.h +include/tensorflow/compiler/xla/stream_executor/gpu/gpu_init.h +include/tensorflow/compiler/xla/stream_executor/gpu_launch_dim.h +include/tensorflow/compiler/xla/stream_executor/host/host_platform_id.h +include/tensorflow/compiler/xla/stream_executor/host_or_device_scalar.h +include/tensorflow/compiler/xla/stream_executor/kernel.h +include/tensorflow/compiler/xla/stream_executor/kernel_cache_config.h +include/tensorflow/compiler/xla/stream_executor/kernel_spec.h +include/tensorflow/compiler/xla/stream_executor/launch_dim.h +include/tensorflow/compiler/xla/stream_executor/module_spec.h +include/tensorflow/compiler/xla/stream_executor/multi_platform_manager.h +include/tensorflow/compiler/xla/stream_executor/numeric_options.h +include/tensorflow/compiler/xla/stream_executor/platform.h +include/tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.h +include/tensorflow/compiler/xla/stream_executor/platform/default/initialize.h +include/tensorflow/compiler/xla/stream_executor/platform/dso_loader.h +include/tensorflow/compiler/xla/stream_executor/platform/initialize.h +include/tensorflow/compiler/xla/stream_executor/platform/logging.h +include/tensorflow/compiler/xla/stream_executor/platform/platform.h +include/tensorflow/compiler/xla/stream_executor/platform/port.h +include/tensorflow/compiler/xla/stream_executor/plugin.h +include/tensorflow/compiler/xla/stream_executor/plugin_registry.h +include/tensorflow/compiler/xla/stream_executor/rng.h +include/tensorflow/compiler/xla/stream_executor/rocm/rocm_platform_id.h +include/tensorflow/compiler/xla/stream_executor/scratch_allocator.h +include/tensorflow/compiler/xla/stream_executor/stream.h +include/tensorflow/compiler/xla/stream_executor/stream_executor.h +include/tensorflow/compiler/xla/stream_executor/stream_executor_internal.h +include/tensorflow/compiler/xla/stream_executor/stream_executor_pimpl.h +include/tensorflow/compiler/xla/stream_executor/temporary_device_memory.h +include/tensorflow/compiler/xla/stream_executor/temporary_memory_manager.h +include/tensorflow/compiler/xla/stream_executor/timer.h +include/tensorflow/compiler/xla/stream_executor/trace_listener.h include/tensorflow/compiler/xla/types.h include/tensorflow/compiler/xla/util.h include/tensorflow/compiler/xla/window_util.h @@ -146,6 +203,7 @@ include/tensorflow/compiler/xla/xla.pb.h include/tensorflow/compiler/xla/xla_data.pb.h include/tensorflow/core/common_runtime/all_to_all.h include/tensorflow/core/common_runtime/allocator_retry.h +include/tensorflow/core/common_runtime/arg_ret_placement.h include/tensorflow/core/common_runtime/base_collective_executor.h include/tensorflow/core/common_runtime/bfc_allocator.h include/tensorflow/core/common_runtime/buf_rendezvous.h @@ -157,7 +215,6 @@ include/tensorflow/core/common_runtime/collective_util.h include/tensorflow/core/common_runtime/colocation_graph.h include/tensorflow/core/common_runtime/composite_device.h include/tensorflow/core/common_runtime/constant_folding.h -include/tensorflow/core/common_runtime/control_flow_deps_to_chains.h include/tensorflow/core/common_runtime/copy_tensor.h include/tensorflow/core/common_runtime/costmodel_manager.h include/tensorflow/core/common_runtime/debugger_state_interface.h @@ -166,7 +223,6 @@ include/tensorflow/core/common_runtime/device/device_event_mgr.h include/tensorflow/core/common_runtime/device/device_host_allocator.h include/tensorflow/core/common_runtime/device/device_id.h include/tensorflow/core/common_runtime/device/device_id_manager.h -include/tensorflow/core/common_runtime/device/device_id_utils.h include/tensorflow/core/common_runtime/device/device_mem_allocator.h include/tensorflow/core/common_runtime/device_factory.h include/tensorflow/core/common_runtime/device_mgr.h @@ -183,12 +239,10 @@ include/tensorflow/core/common_runtime/function_optimization_registry.h include/tensorflow/core/common_runtime/function_utils.h include/tensorflow/core/common_runtime/gpu/gpu_bfc_allocator.h include/tensorflow/core/common_runtime/gpu/gpu_cudamalloc_allocator.h -include/tensorflow/core/common_runtime/gpu/gpu_cudamallocasync_allocator.h include/tensorflow/core/common_runtime/gpu/gpu_debug_allocator.h include/tensorflow/core/common_runtime/gpu/gpu_device.h include/tensorflow/core/common_runtime/gpu/gpu_id.h include/tensorflow/core/common_runtime/gpu/gpu_id_manager.h -include/tensorflow/core/common_runtime/gpu/gpu_init.h include/tensorflow/core/common_runtime/gpu/gpu_managed_allocator.h include/tensorflow/core/common_runtime/gpu/gpu_process_state.h include/tensorflow/core/common_runtime/gpu/gpu_util.h @@ -204,6 +258,7 @@ include/tensorflow/core/common_runtime/hierarchical_tree_broadcaster.h include/tensorflow/core/common_runtime/inline_function_utils.h include/tensorflow/core/common_runtime/input_colocation_exemption_registry.h include/tensorflow/core/common_runtime/inspecting_placer.h +include/tensorflow/core/common_runtime/int32_fulltype.h include/tensorflow/core/common_runtime/isolate_placer_inspection_required_ops_pass.h include/tensorflow/core/common_runtime/local_device.h include/tensorflow/core/common_runtime/local_executor_params.h @@ -216,9 +271,9 @@ include/tensorflow/core/common_runtime/lower_while_op.h include/tensorflow/core/common_runtime/memory_types.h include/tensorflow/core/common_runtime/mkl_cpu_allocator.h include/tensorflow/core/common_runtime/mkl_layout_pass.h -include/tensorflow/core/common_runtime/mkl_tfconversion_pass.h include/tensorflow/core/common_runtime/node_file_writer.h include/tensorflow/core/common_runtime/optimization_registry.h +include/tensorflow/core/common_runtime/optimized_function_graph_info.h include/tensorflow/core/common_runtime/partitioning_utils.h include/tensorflow/core/common_runtime/permuter.h include/tensorflow/core/common_runtime/placer.h @@ -271,6 +326,7 @@ include/tensorflow/core/framework/common_shape_fns.h include/tensorflow/core/framework/control_flow.h include/tensorflow/core/framework/cost_graph.pb.h include/tensorflow/core/framework/dataset.h +include/tensorflow/core/framework/dataset.pb.h include/tensorflow/core/framework/dataset_metadata.pb.h include/tensorflow/core/framework/dataset_options.pb.h include/tensorflow/core/framework/dataset_stateful_op_allowlist.h @@ -285,6 +341,7 @@ include/tensorflow/core/framework/function.h include/tensorflow/core/framework/function.pb.h include/tensorflow/core/framework/function_handle_cache.h include/tensorflow/core/framework/graph.pb.h +include/tensorflow/core/framework/graph_debug_info.pb.h include/tensorflow/core/framework/graph_def_util.h include/tensorflow/core/framework/graph_to_functiondef.h include/tensorflow/core/framework/graph_transfer_info.pb.h @@ -315,12 +372,13 @@ include/tensorflow/core/framework/op_kernel.h include/tensorflow/core/framework/op_requires.h include/tensorflow/core/framework/op_segment.h include/tensorflow/core/framework/ops_util.h +include/tensorflow/core/framework/optimized_function_graph.pb.h include/tensorflow/core/framework/partial_tensor_shape.h include/tensorflow/core/framework/queue_interface.h -include/tensorflow/core/framework/reader_base.h include/tensorflow/core/framework/reader_base.pb.h include/tensorflow/core/framework/reader_interface.h include/tensorflow/core/framework/reader_op_kernel.h +include/tensorflow/core/framework/ref_var.h include/tensorflow/core/framework/register_types.h include/tensorflow/core/framework/register_types_traits.h include/tensorflow/core/framework/registration/options.h @@ -377,7 +435,6 @@ include/tensorflow/core/graph/graph.h include/tensorflow/core/graph/graph_def_builder.h include/tensorflow/core/graph/graph_node_util.h include/tensorflow/core/graph/graph_partition.h -include/tensorflow/core/graph/mkl_graph_util.h include/tensorflow/core/graph/node_builder.h include/tensorflow/core/graph/optimizer_cse.h include/tensorflow/core/graph/subgraph.h @@ -434,6 +491,7 @@ include/tensorflow/core/grappler/optimizers/scoped_allocator_optimizer.h include/tensorflow/core/grappler/optimizers/shape_optimizer.h include/tensorflow/core/grappler/optimizers/static_schedule.h include/tensorflow/core/grappler/optimizers/tfg_optimizer_hook.h +include/tensorflow/core/grappler/optimizers/tfg_passes_builder.h include/tensorflow/core/grappler/utils.h include/tensorflow/core/grappler/utils/canonicalizer.h include/tensorflow/core/grappler/utils/colocation.h @@ -457,10 +515,10 @@ include/tensorflow/core/ir/dialect.h.inc include/tensorflow/core/ir/importexport/convert_attributes.h include/tensorflow/core/ir/importexport/convert_tensor.h include/tensorflow/core/ir/importexport/convert_types.h -include/tensorflow/core/ir/importexport/export.h include/tensorflow/core/ir/importexport/functiondef_export.h include/tensorflow/core/ir/importexport/functiondef_import.h -include/tensorflow/core/ir/importexport/import.h +include/tensorflow/core/ir/importexport/graphdef_export.h +include/tensorflow/core/ir/importexport/graphdef_import.h include/tensorflow/core/ir/importexport/mangling.h include/tensorflow/core/ir/importexport/parse_text_proto.h include/tensorflow/core/ir/interfaces.cc.inc @@ -469,6 +527,8 @@ include/tensorflow/core/ir/interfaces.h.inc include/tensorflow/core/ir/ops.cc.inc include/tensorflow/core/ir/ops.h include/tensorflow/core/ir/ops.h.inc +include/tensorflow/core/ir/tf_op_names.inc +include/tensorflow/core/ir/tf_op_registry.h include/tensorflow/core/ir/tf_op_wrapper.h include/tensorflow/core/ir/types/attributes.cc.inc include/tensorflow/core/ir/types/attributes.h.inc @@ -481,12 +541,12 @@ include/tensorflow/core/ir/types/types.cc.inc include/tensorflow/core/ir/types/types.def include/tensorflow/core/ir/types/types.h.inc include/tensorflow/core/ir/utility.h +include/tensorflow/core/ir/utils/shape_inference_utils.h include/tensorflow/core/kernels/ops_util.h include/tensorflow/core/lib/bfloat16/bfloat16.h include/tensorflow/core/lib/core/arena.h include/tensorflow/core/lib/core/bitmap.h include/tensorflow/core/lib/core/bits.h -include/tensorflow/core/lib/core/blocking_counter.h include/tensorflow/core/lib/core/coding.h include/tensorflow/core/lib/core/error_codes.pb.h include/tensorflow/core/lib/core/errors.h @@ -532,10 +592,6 @@ include/tensorflow/core/lib/io/proto_encode_helper.h include/tensorflow/core/lib/io/random_inputstream.h include/tensorflow/core/lib/io/record_reader.h include/tensorflow/core/lib/io/record_writer.h -include/tensorflow/core/lib/io/snappy/snappy_compression_options.h -include/tensorflow/core/lib/io/snappy/snappy_inputbuffer.h -include/tensorflow/core/lib/io/snappy/snappy_inputstream.h -include/tensorflow/core/lib/io/snappy/snappy_outputbuffer.h include/tensorflow/core/lib/io/table.h include/tensorflow/core/lib/io/table_builder.h include/tensorflow/core/lib/io/table_options.h @@ -545,6 +601,7 @@ include/tensorflow/core/lib/io/zlib_inputstream.h include/tensorflow/core/lib/io/zlib_outputbuffer.h include/tensorflow/core/lib/llvm_rtti/llvm_rtti.h include/tensorflow/core/lib/math/math_util.h +include/tensorflow/core/lib/monitoring/cell_reader.h include/tensorflow/core/lib/monitoring/collected_metrics.h include/tensorflow/core/lib/monitoring/collection_registry.h include/tensorflow/core/lib/monitoring/counter.h @@ -552,12 +609,12 @@ include/tensorflow/core/lib/monitoring/gauge.h include/tensorflow/core/lib/monitoring/metric_def.h include/tensorflow/core/lib/monitoring/percentile_sampler.h include/tensorflow/core/lib/monitoring/sampler.h +include/tensorflow/core/lib/monitoring/test_utils.h include/tensorflow/core/lib/monitoring/timed.h include/tensorflow/core/lib/monitoring/types.h include/tensorflow/core/lib/random/distribution_sampler.h include/tensorflow/core/lib/random/exact_uniform_int.h include/tensorflow/core/lib/random/philox_random.h -include/tensorflow/core/lib/random/philox_random_test_utils.h include/tensorflow/core/lib/random/random.h include/tensorflow/core/lib/random/random_distributions.h include/tensorflow/core/lib/random/random_distributions_utils.h @@ -579,21 +636,6 @@ include/tensorflow/core/platform/bfloat16.h include/tensorflow/core/platform/blocking_counter.h include/tensorflow/core/platform/byte_order.h include/tensorflow/core/platform/casts.h -include/tensorflow/core/platform/cloud/auth_provider.h -include/tensorflow/core/platform/cloud/compute_engine_metadata_client.h -include/tensorflow/core/platform/cloud/compute_engine_zone_provider.h -include/tensorflow/core/platform/cloud/curl_http_request.h -include/tensorflow/core/platform/cloud/expiring_lru_cache.h -include/tensorflow/core/platform/cloud/file_block_cache.h -include/tensorflow/core/platform/cloud/gcs_dns_cache.h -include/tensorflow/core/platform/cloud/gcs_file_system.h -include/tensorflow/core/platform/cloud/gcs_throttle.h -include/tensorflow/core/platform/cloud/google_auth_provider.h -include/tensorflow/core/platform/cloud/http_request.h -include/tensorflow/core/platform/cloud/oauth_client.h -include/tensorflow/core/platform/cloud/ram_file_block_cache.h -include/tensorflow/core/platform/cloud/time_util.h -include/tensorflow/core/platform/cloud/zone_provider.h include/tensorflow/core/platform/coding.h include/tensorflow/core/platform/context.h include/tensorflow/core/platform/cord.h @@ -603,32 +645,19 @@ include/tensorflow/core/platform/crash_analysis.h include/tensorflow/core/platform/ctstring.h include/tensorflow/core/platform/ctstring_internal.h include/tensorflow/core/platform/cuda.h -include/tensorflow/core/platform/cuda_libdevice_path.h -include/tensorflow/core/platform/default/casts.h -include/tensorflow/core/platform/default/context.h -include/tensorflow/core/platform/default/cord.h -include/tensorflow/core/platform/default/dynamic_annotations.h -include/tensorflow/core/platform/default/integral_types.h -include/tensorflow/core/platform/default/logging.h -include/tensorflow/core/platform/default/mutex.h -include/tensorflow/core/platform/default/mutex_data.h -include/tensorflow/core/platform/default/notification.h -include/tensorflow/core/platform/default/posix_file_system.h -include/tensorflow/core/platform/default/stacktrace.h -include/tensorflow/core/platform/default/subprocess.h -include/tensorflow/core/platform/default/tracing_impl.h -include/tensorflow/core/platform/default/unbounded_work_queue.h include/tensorflow/core/platform/demangle.h include/tensorflow/core/platform/denormal.h include/tensorflow/core/platform/dynamic_annotations.h include/tensorflow/core/platform/enable_tf2_utils.h include/tensorflow/core/platform/env.h include/tensorflow/core/platform/env_time.h +include/tensorflow/core/platform/error_payloads.h include/tensorflow/core/platform/errors.h include/tensorflow/core/platform/file_statistics.h include/tensorflow/core/platform/file_system.h include/tensorflow/core/platform/file_system_helper.h include/tensorflow/core/platform/fingerprint.h +include/tensorflow/core/platform/float8.h include/tensorflow/core/platform/hash.h include/tensorflow/core/platform/host_info.h include/tensorflow/core/platform/human_readable_json.h @@ -655,7 +684,6 @@ include/tensorflow/core/platform/profile_utils/clock_cycle_profiler.h include/tensorflow/core/platform/profile_utils/cpu_utils.h include/tensorflow/core/platform/profile_utils/i_cpu_utils_helper.h include/tensorflow/core/platform/protobuf.h -include/tensorflow/core/platform/protobuf_compiler.h include/tensorflow/core/platform/protobuf_internal.h include/tensorflow/core/platform/ram_file_system.h include/tensorflow/core/platform/random.h @@ -677,7 +705,6 @@ include/tensorflow/core/platform/stacktrace_handler.h include/tensorflow/core/platform/status.h include/tensorflow/core/platform/status_matchers.h include/tensorflow/core/platform/statusor.h -include/tensorflow/core/platform/statusor_internals.h include/tensorflow/core/platform/str_util.h include/tensorflow/core/platform/strcat.h include/tensorflow/core/platform/stream_executor.h @@ -698,32 +725,27 @@ include/tensorflow/core/platform/tracing.h include/tensorflow/core/platform/tstring.h include/tensorflow/core/platform/types.h include/tensorflow/core/platform/unbounded_work_queue.h -include/tensorflow/core/profiler/internal/cpu/traceme_recorder.h -include/tensorflow/core/profiler/lib/traceme.h -include/tensorflow/core/profiler/lib/traceme_encode.h include/tensorflow/core/profiler/profiler_options.pb.h include/tensorflow/core/profiler/protobuf/xplane.pb.h -include/tensorflow/core/profiler/utils/math_utils.h -include/tensorflow/core/profiler/utils/time_utils.h include/tensorflow/core/protobuf/bfc_memory_map.pb.h include/tensorflow/core/protobuf/cluster.pb.h include/tensorflow/core/protobuf/composite_tensor_variant.pb.h include/tensorflow/core/protobuf/config.pb.h include/tensorflow/core/protobuf/control_flow.pb.h -include/tensorflow/core/protobuf/coordination_config.pb.h +include/tensorflow/core/protobuf/core_platform_payloads.pb.h include/tensorflow/core/protobuf/data_service.pb.h include/tensorflow/core/protobuf/debug.pb.h include/tensorflow/core/protobuf/debug_event.pb.h include/tensorflow/core/protobuf/device_filters.pb.h include/tensorflow/core/protobuf/device_properties.pb.h -include/tensorflow/core/protobuf/distributed_runtime_payloads.pb.h include/tensorflow/core/protobuf/error_codes.pb.h -include/tensorflow/core/protobuf/graph_debug_info.pb.h +include/tensorflow/core/protobuf/fingerprint.pb.h include/tensorflow/core/protobuf/meta_graph.pb.h include/tensorflow/core/protobuf/named_tensor.pb.h include/tensorflow/core/protobuf/queue_runner.pb.h include/tensorflow/core/protobuf/remote_tensor_handle.pb.h include/tensorflow/core/protobuf/rewriter_config.pb.h +include/tensorflow/core/protobuf/rpc_options.pb.h include/tensorflow/core/protobuf/saved_model.pb.h include/tensorflow/core/protobuf/saved_object_graph.pb.h include/tensorflow/core/protobuf/saver.pb.h @@ -745,22 +767,40 @@ include/tensorflow/core/tpu/ops/tpu_embedding_ops.h include/tensorflow/core/tpu/ops/tpu_embedding_shape_util.h include/tensorflow/core/tpu/tpu_embedding_optimization_parameters_utils.h include/tensorflow/core/tpu/tpu_embedding_output_layout_utils.h -include/tensorflow/core/transforms/cf_sink/cf_sink.h +include/tensorflow/core/transforms/cf_sink/pass.h include/tensorflow/core/transforms/consolidate_attrs/pass.h include/tensorflow/core/transforms/const_dedupe_hoist/pass.h -include/tensorflow/core/transforms/drop_unregistered_attribute/output_shapes.h +include/tensorflow/core/transforms/constant_folding/pass.h +include/tensorflow/core/transforms/cse/pass.h +include/tensorflow/core/transforms/drop_unregistered_attribute/pass.h +include/tensorflow/core/transforms/eliminate_passthrough_iter_args/pass.h +include/tensorflow/core/transforms/func_to_graph/func_to_graph.h +include/tensorflow/core/transforms/func_to_graph/pass.h +include/tensorflow/core/transforms/functional_to_region/impl.h +include/tensorflow/core/transforms/functional_to_region/pass.h +include/tensorflow/core/transforms/graph_compactor/pass.h include/tensorflow/core/transforms/graph_to_func/graph_to_func.h -include/tensorflow/core/transforms/graph_to_func/graph_to_func_pass.h -include/tensorflow/core/transforms/pass_detail.h +include/tensorflow/core/transforms/graph_to_func/pass.h +include/tensorflow/core/transforms/legacy_call/pass.h include/tensorflow/core/transforms/pass_registration.h include/tensorflow/core/transforms/passes.h.inc -include/tensorflow/core/transforms/remapper/remapper_pass.h -include/tensorflow/core/transforms/toposort/toposort_pass.h +include/tensorflow/core/transforms/region_to_functional/impl.h +include/tensorflow/core/transforms/region_to_functional/pass.h +include/tensorflow/core/transforms/remapper/pass.h +include/tensorflow/core/transforms/remapper/pdll/MklPDLLPatterns.h.inc +include/tensorflow/core/transforms/remapper/remapping_helper.h +include/tensorflow/core/transforms/shape_inference/pass.h +include/tensorflow/core/transforms/toposort/pass.h +include/tensorflow/core/transforms/utils/eval_utils.h +include/tensorflow/core/transforms/utils/op_cat_helper.h +include/tensorflow/core/transforms/utils/pdll/PDLLUtils.h.inc +include/tensorflow/core/transforms/utils/pdll/utils.h include/tensorflow/core/transforms/utils/utils.h include/tensorflow/core/util/activation_mode.h include/tensorflow/core/util/batch_util.h include/tensorflow/core/util/bcast.h include/tensorflow/core/util/command_line_flags.h +include/tensorflow/core/util/debug_data_dumper.h include/tensorflow/core/util/debug_events_writer.h include/tensorflow/core/util/determinism.h include/tensorflow/core/util/device_name_utils.h @@ -794,7 +834,8 @@ include/tensorflow/core/util/permutation_input_iterator.h include/tensorflow/core/util/permutation_output_iterator.h include/tensorflow/core/util/port.h include/tensorflow/core/util/presized_cuckoo_map.h -include/tensorflow/core/util/ptr_util.h +include/tensorflow/core/util/quantization/uniform_quant_ops_attr.pb.h +include/tensorflow/core/util/quantization/uniform_quant_ops_params.h include/tensorflow/core/util/ragged_to_dense_util.h include/tensorflow/core/util/ragged_to_dense_util_common.h include/tensorflow/core/util/reffed_status_callback.h @@ -808,9 +849,8 @@ include/tensorflow/core/util/stat_summarizer_options.h include/tensorflow/core/util/stats_calculator.h include/tensorflow/core/util/stream_executor_util.h include/tensorflow/core/util/strided_slice_op.h -include/tensorflow/core/util/tensor_bundle/byte_swap.h -include/tensorflow/core/util/tensor_bundle/naming.h -include/tensorflow/core/util/tensor_bundle/tensor_bundle.h +include/tensorflow/core/util/tensor_bundle/byte_swap_array.h +include/tensorflow/core/util/tensor_bundle/byte_swap_tensor.h include/tensorflow/core/util/tensor_format.h include/tensorflow/core/util/tensor_ops_util.h include/tensorflow/core/util/tensor_slice_reader.h @@ -824,77 +864,234 @@ include/tensorflow/core/util/use_cudnn.h include/tensorflow/core/util/util.h include/tensorflow/core/util/work_sharder.h include/tensorflow/core/util/xla_config_registry.h +include/tensorflow/core/util/zen_util.h include/tensorflow/lite/kernels/shim/op_kernel.h include/tensorflow/lite/kernels/shim/shape.h include/tensorflow/lite/kernels/shim/status_macros.h include/tensorflow/lite/kernels/shim/tensor_view.h include/tensorflow/lite/kernels/shim/tf_op_shim.h include/tensorflow/lite/kernels/shim/tf_tensor_view.h -include/tensorflow/stream_executor/allocator_stats.h -include/tensorflow/stream_executor/blas.h -include/tensorflow/stream_executor/cuda/cuda_dnn.h -include/tensorflow/stream_executor/cuda/cuda_platform_id.h -include/tensorflow/stream_executor/data_type.h -include/tensorflow/stream_executor/device_description.h -include/tensorflow/stream_executor/device_memory.h -include/tensorflow/stream_executor/device_memory_allocator.h -include/tensorflow/stream_executor/device_options.h -include/tensorflow/stream_executor/dnn.h -include/tensorflow/stream_executor/dnn.pb.h -include/tensorflow/stream_executor/event.h -include/tensorflow/stream_executor/executor_cache.h -include/tensorflow/stream_executor/fft.h -include/tensorflow/stream_executor/gpu_launch_dim.h -include/tensorflow/stream_executor/host/host_gpu_executor.h -include/tensorflow/stream_executor/host/host_platform.h -include/tensorflow/stream_executor/host/host_platform_id.h -include/tensorflow/stream_executor/host/host_stream.h -include/tensorflow/stream_executor/host/host_timer.h -include/tensorflow/stream_executor/host_or_device_scalar.h -include/tensorflow/stream_executor/kernel.h -include/tensorflow/stream_executor/kernel_cache_config.h -include/tensorflow/stream_executor/kernel_spec.h -include/tensorflow/stream_executor/launch_dim.h -include/tensorflow/stream_executor/lib/array_slice.h -include/tensorflow/stream_executor/lib/demangle.h -include/tensorflow/stream_executor/lib/env.h -include/tensorflow/stream_executor/lib/error.h -include/tensorflow/stream_executor/lib/human_readable.h -include/tensorflow/stream_executor/lib/initialize.h -include/tensorflow/stream_executor/lib/mathutil.h -include/tensorflow/stream_executor/lib/numbers.h -include/tensorflow/stream_executor/lib/path.h -include/tensorflow/stream_executor/lib/process_state.h -include/tensorflow/stream_executor/lib/stacktrace.h -include/tensorflow/stream_executor/lib/static_threadlocal.h -include/tensorflow/stream_executor/lib/status.h -include/tensorflow/stream_executor/lib/status_macros.h -include/tensorflow/stream_executor/lib/statusor.h -include/tensorflow/stream_executor/lib/thread_options.h -include/tensorflow/stream_executor/lib/threadpool.h -include/tensorflow/stream_executor/module_spec.h -include/tensorflow/stream_executor/multi_platform_manager.h -include/tensorflow/stream_executor/platform.h -include/tensorflow/stream_executor/platform/default/dso_loader.h -include/tensorflow/stream_executor/platform/default/initialize.h -include/tensorflow/stream_executor/platform/dso_loader.h -include/tensorflow/stream_executor/platform/initialize.h -include/tensorflow/stream_executor/platform/logging.h -include/tensorflow/stream_executor/platform/platform.h -include/tensorflow/stream_executor/platform/port.h -include/tensorflow/stream_executor/plugin.h -include/tensorflow/stream_executor/plugin_registry.h -include/tensorflow/stream_executor/rng.h -include/tensorflow/stream_executor/rocm/rocm_platform_id.h -include/tensorflow/stream_executor/scratch_allocator.h -include/tensorflow/stream_executor/stream.h -include/tensorflow/stream_executor/stream_executor.h -include/tensorflow/stream_executor/stream_executor_internal.h -include/tensorflow/stream_executor/stream_executor_pimpl.h -include/tensorflow/stream_executor/temporary_device_memory.h -include/tensorflow/stream_executor/temporary_memory_manager.h -include/tensorflow/stream_executor/timer.h -include/tensorflow/stream_executor/trace_listener.h +include/tensorflow/tsl/c/tsl_status.h +include/tensorflow/tsl/c/tsl_status_helper.h +include/tensorflow/tsl/c/tsl_status_internal.h +include/tensorflow/tsl/framework/allocator.h +include/tensorflow/tsl/framework/allocator_registry.h +include/tensorflow/tsl/framework/allocator_retry.h +include/tensorflow/tsl/framework/bfc_allocator.h +include/tensorflow/tsl/framework/cancellation.h +include/tensorflow/tsl/framework/device_id.h +include/tensorflow/tsl/framework/device_id_manager.h +include/tensorflow/tsl/framework/device_type.h +include/tensorflow/tsl/framework/fixedpoint_types.h +include/tensorflow/tsl/framework/numeric_types.h +include/tensorflow/tsl/framework/shared_counter.h +include/tensorflow/tsl/framework/tracking_allocator.h +include/tensorflow/tsl/framework/type_traits.h +include/tensorflow/tsl/lib/core/bitmap.h +include/tensorflow/tsl/lib/core/bits.h +include/tensorflow/tsl/lib/core/status_test_util.h +include/tensorflow/tsl/lib/gtl/compactptrset.h +include/tensorflow/tsl/lib/gtl/flatmap.h +include/tensorflow/tsl/lib/gtl/flatrep.h +include/tensorflow/tsl/lib/gtl/flatset.h +include/tensorflow/tsl/lib/gtl/inlined_vector.h +include/tensorflow/tsl/lib/gtl/int_type.h +include/tensorflow/tsl/lib/gtl/iterator_range.h +include/tensorflow/tsl/lib/gtl/map_util.h +include/tensorflow/tsl/lib/gtl/subtle/map_traits.h +include/tensorflow/tsl/lib/hash/crc32c.h +include/tensorflow/tsl/lib/histogram/histogram.h +include/tensorflow/tsl/lib/io/block.h +include/tensorflow/tsl/lib/io/block_builder.h +include/tensorflow/tsl/lib/io/buffered_inputstream.h +include/tensorflow/tsl/lib/io/cache.h +include/tensorflow/tsl/lib/io/compression.h +include/tensorflow/tsl/lib/io/format.h +include/tensorflow/tsl/lib/io/inputbuffer.h +include/tensorflow/tsl/lib/io/inputstream_interface.h +include/tensorflow/tsl/lib/io/iterator.h +include/tensorflow/tsl/lib/io/proto_encode_helper.h +include/tensorflow/tsl/lib/io/random_inputstream.h +include/tensorflow/tsl/lib/io/record_reader.h +include/tensorflow/tsl/lib/io/record_writer.h +include/tensorflow/tsl/lib/io/snappy/snappy_compression_options.h +include/tensorflow/tsl/lib/io/snappy/snappy_inputbuffer.h +include/tensorflow/tsl/lib/io/snappy/snappy_inputstream.h +include/tensorflow/tsl/lib/io/snappy/snappy_outputbuffer.h +include/tensorflow/tsl/lib/io/table.h +include/tensorflow/tsl/lib/io/table_builder.h +include/tensorflow/tsl/lib/io/table_options.h +include/tensorflow/tsl/lib/io/two_level_iterator.h +include/tensorflow/tsl/lib/io/zlib_compression_options.h +include/tensorflow/tsl/lib/io/zlib_inputstream.h +include/tensorflow/tsl/lib/io/zlib_outputbuffer.h +include/tensorflow/tsl/lib/math/math_util.h +include/tensorflow/tsl/lib/monitoring/cell_reader.h +include/tensorflow/tsl/lib/monitoring/collected_metrics.h +include/tensorflow/tsl/lib/monitoring/collection_registry.h +include/tensorflow/tsl/lib/monitoring/counter.h +include/tensorflow/tsl/lib/monitoring/gauge.h +include/tensorflow/tsl/lib/monitoring/metric_def.h +include/tensorflow/tsl/lib/monitoring/percentile_sampler.h +include/tensorflow/tsl/lib/monitoring/sampler.h +include/tensorflow/tsl/lib/monitoring/test_utils.h +include/tensorflow/tsl/lib/monitoring/timed.h +include/tensorflow/tsl/lib/monitoring/types.h +include/tensorflow/tsl/lib/random/distribution_sampler.h +include/tensorflow/tsl/lib/random/exact_uniform_int.h +include/tensorflow/tsl/lib/random/philox_random.h +include/tensorflow/tsl/lib/random/philox_random_test_utils.h +include/tensorflow/tsl/lib/random/random_distributions.h +include/tensorflow/tsl/lib/random/random_distributions_utils.h +include/tensorflow/tsl/lib/random/simple_philox.h +include/tensorflow/tsl/lib/random/weighted_picker.h +include/tensorflow/tsl/lib/strings/proto_serialization.h +include/tensorflow/tsl/platform/abi.h +include/tensorflow/tsl/platform/base64.h +include/tensorflow/tsl/platform/bfloat16.h +include/tensorflow/tsl/platform/blocking_counter.h +include/tensorflow/tsl/platform/byte_order.h +include/tensorflow/tsl/platform/casts.h +include/tensorflow/tsl/platform/cloud/auth_provider.h +include/tensorflow/tsl/platform/cloud/compute_engine_metadata_client.h +include/tensorflow/tsl/platform/cloud/compute_engine_zone_provider.h +include/tensorflow/tsl/platform/cloud/curl_http_request.h +include/tensorflow/tsl/platform/cloud/expiring_lru_cache.h +include/tensorflow/tsl/platform/cloud/file_block_cache.h +include/tensorflow/tsl/platform/cloud/gcs_dns_cache.h +include/tensorflow/tsl/platform/cloud/gcs_file_system.h +include/tensorflow/tsl/platform/cloud/gcs_throttle.h +include/tensorflow/tsl/platform/cloud/google_auth_provider.h +include/tensorflow/tsl/platform/cloud/http_request.h +include/tensorflow/tsl/platform/cloud/oauth_client.h +include/tensorflow/tsl/platform/cloud/ram_file_block_cache.h +include/tensorflow/tsl/platform/cloud/time_util.h +include/tensorflow/tsl/platform/cloud/zone_provider.h +include/tensorflow/tsl/platform/coding.h +include/tensorflow/tsl/platform/context.h +include/tensorflow/tsl/platform/cord.h +include/tensorflow/tsl/platform/cpu_info.h +include/tensorflow/tsl/platform/crash_analysis.h +include/tensorflow/tsl/platform/ctstring.h +include/tensorflow/tsl/platform/ctstring_internal.h +include/tensorflow/tsl/platform/cuda_libdevice_path.h +include/tensorflow/tsl/platform/default/casts.h +include/tensorflow/tsl/platform/default/context.h +include/tensorflow/tsl/platform/default/cord.h +include/tensorflow/tsl/platform/default/dso_loader.h +include/tensorflow/tsl/platform/default/dynamic_annotations.h +include/tensorflow/tsl/platform/default/integral_types.h +include/tensorflow/tsl/platform/default/logging.h +include/tensorflow/tsl/platform/default/mutex.h +include/tensorflow/tsl/platform/default/mutex_data.h +include/tensorflow/tsl/platform/default/notification.h +include/tensorflow/tsl/platform/default/posix_file_system.h +include/tensorflow/tsl/platform/default/stacktrace.h +include/tensorflow/tsl/platform/default/status.h +include/tensorflow/tsl/platform/default/subprocess.h +include/tensorflow/tsl/platform/default/tracing_impl.h +include/tensorflow/tsl/platform/default/unbounded_work_queue.h +include/tensorflow/tsl/platform/demangle.h +include/tensorflow/tsl/platform/denormal.h +include/tensorflow/tsl/platform/dso_loader.h +include/tensorflow/tsl/platform/dynamic_annotations.h +include/tensorflow/tsl/platform/env.h +include/tensorflow/tsl/platform/env_time.h +include/tensorflow/tsl/platform/errors.h +include/tensorflow/tsl/platform/file_statistics.h +include/tensorflow/tsl/platform/file_system.h +include/tensorflow/tsl/platform/file_system_helper.h +include/tensorflow/tsl/platform/fingerprint.h +include/tensorflow/tsl/platform/float8.h +include/tensorflow/tsl/platform/hash.h +include/tensorflow/tsl/platform/host_info.h +include/tensorflow/tsl/platform/human_readable_json.h +include/tensorflow/tsl/platform/init_main.h +include/tensorflow/tsl/platform/intrusive_ptr.h +include/tensorflow/tsl/platform/load_library.h +include/tensorflow/tsl/platform/logger.h +include/tensorflow/tsl/platform/logging.h +include/tensorflow/tsl/platform/macros.h +include/tensorflow/tsl/platform/mem.h +include/tensorflow/tsl/platform/mutex.h +include/tensorflow/tsl/platform/net.h +include/tensorflow/tsl/platform/notification.h +include/tensorflow/tsl/platform/null_file_system.h +include/tensorflow/tsl/platform/numa.h +include/tensorflow/tsl/platform/numbers.h +include/tensorflow/tsl/platform/path.h +include/tensorflow/tsl/platform/platform.h +include/tensorflow/tsl/platform/platform_strings_computed.h +include/tensorflow/tsl/platform/prefetch.h +include/tensorflow/tsl/platform/profile_utils/android_armv7a_cpu_utils_helper.h +include/tensorflow/tsl/platform/profile_utils/clock_cycle_profiler.h +include/tensorflow/tsl/platform/profile_utils/cpu_utils.h +include/tensorflow/tsl/platform/profile_utils/i_cpu_utils_helper.h +include/tensorflow/tsl/platform/protobuf.h +include/tensorflow/tsl/platform/protobuf_compiler.h +include/tensorflow/tsl/platform/ram_file_system.h +include/tensorflow/tsl/platform/random.h +include/tensorflow/tsl/platform/raw_coding.h +include/tensorflow/tsl/platform/refcount.h +include/tensorflow/tsl/platform/regexp.h +include/tensorflow/tsl/platform/resource.h +include/tensorflow/tsl/platform/resource_loader.h +include/tensorflow/tsl/platform/retrying_file_system.h +include/tensorflow/tsl/platform/retrying_utils.h +include/tensorflow/tsl/platform/rocm_rocdl_path.h +include/tensorflow/tsl/platform/scanner.h +include/tensorflow/tsl/platform/setround.h +include/tensorflow/tsl/platform/snappy.h +include/tensorflow/tsl/platform/stack_frame.h +include/tensorflow/tsl/platform/stacktrace.h +include/tensorflow/tsl/platform/stacktrace_handler.h +include/tensorflow/tsl/platform/static_threadlocal.h +include/tensorflow/tsl/platform/status.h +include/tensorflow/tsl/platform/status_matchers.h +include/tensorflow/tsl/platform/status_to_from_proto.h +include/tensorflow/tsl/platform/statusor.h +include/tensorflow/tsl/platform/statusor_internals.h +include/tensorflow/tsl/platform/str_util.h +include/tensorflow/tsl/platform/strcat.h +include/tensorflow/tsl/platform/stringpiece.h +include/tensorflow/tsl/platform/stringprintf.h +include/tensorflow/tsl/platform/subprocess.h +include/tensorflow/tsl/platform/tensor_float_32_utils.h +include/tensorflow/tsl/platform/test.h +include/tensorflow/tsl/platform/test_benchmark.h +include/tensorflow/tsl/platform/thread_annotations.h +include/tensorflow/tsl/platform/threadpool.h +include/tensorflow/tsl/platform/threadpool_interface.h +include/tensorflow/tsl/platform/threadpool_options.h +include/tensorflow/tsl/platform/tracing.h +include/tensorflow/tsl/platform/tstring.h +include/tensorflow/tsl/platform/types.h +include/tensorflow/tsl/platform/unbounded_work_queue.h +include/tensorflow/tsl/profiler/backends/cpu/traceme_recorder.h +include/tensorflow/tsl/profiler/lib/traceme.h +include/tensorflow/tsl/profiler/lib/traceme_encode.h +include/tensorflow/tsl/profiler/protobuf/profiler_options.pb.h +include/tensorflow/tsl/profiler/protobuf/xplane.pb.h +include/tensorflow/tsl/profiler/utils/math_utils.h +include/tensorflow/tsl/profiler/utils/time_utils.h +include/tensorflow/tsl/protobuf/autotuning.pb.h +include/tensorflow/tsl/protobuf/bfc_memory_map.pb.h +include/tensorflow/tsl/protobuf/coordination_config.pb.h +include/tensorflow/tsl/protobuf/distributed_runtime_payloads.pb.h +include/tensorflow/tsl/protobuf/dnn.pb.h +include/tensorflow/tsl/protobuf/error_codes.pb.h +include/tensorflow/tsl/protobuf/histogram.pb.h +include/tensorflow/tsl/protobuf/rpc_options.pb.h +include/tensorflow/tsl/protobuf/status.pb.h +include/tensorflow/tsl/protobuf/test_log.pb.h +include/tensorflow/tsl/util/byte_swap_array.h +include/tensorflow/tsl/util/command_line_flags.h +include/tensorflow/tsl/util/determinism.h +include/tensorflow/tsl/util/device_name_utils.h +include/tensorflow/tsl/util/env_var.h +include/tensorflow/tsl/util/stat_summarizer_options.h +include/tensorflow/tsl/util/stats_calculator.h +include/tensorflow/tsl/util/use_cudnn.h lib/libtensorflow.so lib/libtensorflow.so.2 lib/libtensorflow.so.%%TF_PORT_VERSION%% diff --git a/science/py-vedo/Makefile b/science/py-vedo/Makefile index 01c9af75b515..ca0e5d9e8df8 100644 --- a/science/py-vedo/Makefile +++ b/science/py-vedo/Makefile @@ -1,5 +1,6 @@ PORTNAME= vedo DISTVERSION= 2024.5.3 +PORTREVISION= 1 CATEGORIES= science graphics python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/qbox/Makefile b/science/qbox/Makefile index 6eaf55eb80d3..6c76aa7980fe 100644 --- a/science/qbox/Makefile +++ b/science/qbox/Makefile @@ -1,6 +1,7 @@ PORTNAME= qbox DISTVERSIONPREFIX= rel DISTVERSION= 1_78_4 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -16,7 +17,7 @@ LIB_DEPENDS= libblas.so:math/blas \ liblapack.so:math/lapack \ libmpicxx.so:net/mpich \ libscalapack.so:math/scalapack \ - libuuid.so:misc/e2fsprogs-libuuid \ + libuuid.so:misc/libuuid \ libxerces-c.so:textproc/xerces-c3 USES= compiler:c++11-lang gmake iconv:wchar_t localbase:ldflags diff --git a/science/qiskit-aer/Makefile b/science/qiskit-aer/Makefile index ef595842d8e7..9a818aa16f08 100644 --- a/science/qiskit-aer/Makefile +++ b/science/qiskit-aer/Makefile @@ -1,6 +1,6 @@ PORTNAME= qiskit-aer DISTVERSION= 0.16.0.1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science # quantum-computing MAINTAINER= yuri@FreeBSD.org diff --git a/science/qmcpack/Makefile b/science/qmcpack/Makefile index 2906806c19bb..e53ffec135e8 100644 --- a/science/qmcpack/Makefile +++ b/science/qmcpack/Makefile @@ -1,7 +1,7 @@ PORTNAME= qmcpack DISTVERSIONPREFIX= v DISTVERSION= 4.0.0 -PORTREVISION= 1 +PORTREVISION= 3 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/qt6-quick3dphysics/distinfo b/science/qt6-quick3dphysics/distinfo index 8e8b54d5ef29..8e99d6679edf 100644 --- a/science/qt6-quick3dphysics/distinfo +++ b/science/qt6-quick3dphysics/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1743027858 -SHA256 (KDE/Qt/6.8.3/qtquick3dphysics-everywhere-src-6.8.3.tar.xz) = e862233530775dbd9ce914447d23a1e7116e63decf5bf8e5a25899a59e297fac -SIZE (KDE/Qt/6.8.3/qtquick3dphysics-everywhere-src-6.8.3.tar.xz) = 4682552 +TIMESTAMP = 1756197855 +SHA256 (KDE/Qt/6.9.2/qtquick3dphysics-everywhere-src-6.9.2.tar.xz) = 87fc6485638f52cd33dc1a755a11c78fd992e438fe77ef53e0ca57c63505cc8b +SIZE (KDE/Qt/6.9.2/qtquick3dphysics-everywhere-src-6.9.2.tar.xz) = 4668516 diff --git a/science/qt6-quick3dphysics/pkg-plist b/science/qt6-quick3dphysics/pkg-plist index 653fce7b1054..769b63cf2550 100644 --- a/science/qt6-quick3dphysics/pkg-plist +++ b/science/qt6-quick3dphysics/pkg-plist @@ -81,6 +81,22 @@ lib/cmake/Qt6Quick3DPhysicsHelpers/Qt6Quick3DPhysicsHelpersTargets-%%CMAKE_BUILD lib/cmake/Qt6Quick3DPhysicsHelpers/Qt6Quick3DPhysicsHelpersTargets.cmake lib/cmake/Qt6Quick3DPhysicsHelpers/Qt6Quick3DPhysicsHelpersVersionlessAliasTargets.cmake lib/cmake/Qt6Quick3DPhysicsHelpers/Qt6Quick3DPhysicsHelpersVersionlessTargets.cmake +lib/cmake/Qt6Quick3DPhysicsHelpersPrivate/Qt6Quick3DPhysicsHelpersPrivateAdditionalTargetInfo.cmake +lib/cmake/Qt6Quick3DPhysicsHelpersPrivate/Qt6Quick3DPhysicsHelpersPrivateConfig.cmake +lib/cmake/Qt6Quick3DPhysicsHelpersPrivate/Qt6Quick3DPhysicsHelpersPrivateConfigVersion.cmake +lib/cmake/Qt6Quick3DPhysicsHelpersPrivate/Qt6Quick3DPhysicsHelpersPrivateConfigVersionImpl.cmake +lib/cmake/Qt6Quick3DPhysicsHelpersPrivate/Qt6Quick3DPhysicsHelpersPrivateDependencies.cmake +lib/cmake/Qt6Quick3DPhysicsHelpersPrivate/Qt6Quick3DPhysicsHelpersPrivateTargets.cmake +lib/cmake/Qt6Quick3DPhysicsHelpersPrivate/Qt6Quick3DPhysicsHelpersPrivateVersionlessAliasTargets.cmake +lib/cmake/Qt6Quick3DPhysicsHelpersPrivate/Qt6Quick3DPhysicsHelpersPrivateVersionlessTargets.cmake +lib/cmake/Qt6Quick3DPhysicsPrivate/Qt6Quick3DPhysicsPrivateAdditionalTargetInfo.cmake +lib/cmake/Qt6Quick3DPhysicsPrivate/Qt6Quick3DPhysicsPrivateConfig.cmake +lib/cmake/Qt6Quick3DPhysicsPrivate/Qt6Quick3DPhysicsPrivateConfigVersion.cmake +lib/cmake/Qt6Quick3DPhysicsPrivate/Qt6Quick3DPhysicsPrivateConfigVersionImpl.cmake +lib/cmake/Qt6Quick3DPhysicsPrivate/Qt6Quick3DPhysicsPrivateDependencies.cmake +lib/cmake/Qt6Quick3DPhysicsPrivate/Qt6Quick3DPhysicsPrivateTargets.cmake +lib/cmake/Qt6Quick3DPhysicsPrivate/Qt6Quick3DPhysicsPrivateVersionlessAliasTargets.cmake +lib/cmake/Qt6Quick3DPhysicsPrivate/Qt6Quick3DPhysicsPrivateVersionlessTargets.cmake %%QT_BINDIR%%/cooker %%QT_LIBDIR%%/libQt6BundledPhysX.a %%QT_LIBDIR%%/libQt6Quick3DPhysics.prl diff --git a/science/rdkit/Makefile b/science/rdkit/Makefile index ce633602a1ba..d4caaecd8c66 100644 --- a/science/rdkit/Makefile +++ b/science/rdkit/Makefile @@ -1,6 +1,7 @@ PORTNAME= rdkit DISTVERSIONPREFIX= Release_ DISTVERSION= 2025_03_1 +PORTREVISION= 1 CATEGORIES= science MASTER_SITES= LOCAL/yuri/:font # unstable, changing font file: https://fonts.google.com/download?family=Comic%20Neue&dummy=/:font DISTFILES= ComicNeue-Regular.ttf:font diff --git a/science/rmf/Makefile b/science/rmf/Makefile index 28b968a57014..9a1b1c673a5d 100644 --- a/science/rmf/Makefile +++ b/science/rmf/Makefile @@ -1,12 +1,12 @@ PORTNAME= rmf DISTVERSION= 1.7.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science graphics MAINTAINER= yuri@FreeBSD.org COMMENT= Library to support reading and writing of Rich Molecular Format files WWW= https://integrativemodeling.org/rmf/ \ - https://github.com/open-rmf/rmf + https://github.com/salilab/rmf LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/COPYING diff --git a/science/salome-configuration/Makefile b/science/salome-configuration/Makefile index 6afeb92ff2cd..e9e82543ac64 100644 --- a/science/salome-configuration/Makefile +++ b/science/salome-configuration/Makefile @@ -7,6 +7,10 @@ MAINTAINER= yuri@FreeBSD.org COMMENT= Salome Project: Multi-physics simulations: Configuration WWW= https://www.salome-platform.org/ +BROKEN= Unfetchable +DEPRECATED= Fails to fetch +EXPIRATION_DATE=2025-06-30 + FETCH_DEPENDS= git:devel/git GIT_URL= https://git.salome-platform.org/gitpub/tools/configuration.git # all Salome repositories: https://git.salome-platform.org/gitweb/ diff --git a/science/salome-kernel/Makefile b/science/salome-kernel/Makefile index af3fbd5fdcc0..490e715aab60 100644 --- a/science/salome-kernel/Makefile +++ b/science/salome-kernel/Makefile @@ -1,7 +1,7 @@ PORTNAME= salome-kernel DISTVERSIONPREFIX= V DISTVERSION= 9_11_0 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -11,6 +11,9 @@ WWW= https://www.salome-platform.org/ LICENSE= LGPL21 LICENSE_FILE= ${WRKSRC}/COPYING +DEPRECATED= Depends on expired science/salome-configuration +EXPIRATION_DATE=2025-09-30 + FETCH_DEPENDS= git:devel/git PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}omniorb>0:devel/py-omniorb \ diff --git a/science/salome-kernel/pkg-plist b/science/salome-kernel/pkg-plist index d714e8935d5c..a855302486d6 100644 --- a/science/salome-kernel/pkg-plist +++ b/science/salome-kernel/pkg-plist @@ -39,18 +39,18 @@ bin/salome/SALOME_TestComponentPy.py bin/salome/SALOME_Trace.py bin/salome/SALOME_utilities.py bin/salome/SalomeOnDemandTK/__init__.py -bin/salome/SalomeOnDemandTK/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -bin/salome/SalomeOnDemandTK/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -bin/salome/SalomeOnDemandTK/__pycache__/extension_builder%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -bin/salome/SalomeOnDemandTK/__pycache__/extension_builder%%PYTHON_EXT_SUFFIX%%.pyc -bin/salome/SalomeOnDemandTK/__pycache__/extension_query%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -bin/salome/SalomeOnDemandTK/__pycache__/extension_query%%PYTHON_EXT_SUFFIX%%.pyc -bin/salome/SalomeOnDemandTK/__pycache__/extension_remover%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -bin/salome/SalomeOnDemandTK/__pycache__/extension_remover%%PYTHON_EXT_SUFFIX%%.pyc -bin/salome/SalomeOnDemandTK/__pycache__/extension_unpacker%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -bin/salome/SalomeOnDemandTK/__pycache__/extension_unpacker%%PYTHON_EXT_SUFFIX%%.pyc -bin/salome/SalomeOnDemandTK/__pycache__/extension_utilities%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -bin/salome/SalomeOnDemandTK/__pycache__/extension_utilities%%PYTHON_EXT_SUFFIX%%.pyc +bin/salome/SalomeOnDemandTK/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +bin/salome/SalomeOnDemandTK/__pycache__/__init__%%PYTHON_TAG%%.pyc +bin/salome/SalomeOnDemandTK/__pycache__/extension_builder%%PYTHON_TAG%%.opt-1.pyc +bin/salome/SalomeOnDemandTK/__pycache__/extension_builder%%PYTHON_TAG%%.pyc +bin/salome/SalomeOnDemandTK/__pycache__/extension_query%%PYTHON_TAG%%.opt-1.pyc +bin/salome/SalomeOnDemandTK/__pycache__/extension_query%%PYTHON_TAG%%.pyc +bin/salome/SalomeOnDemandTK/__pycache__/extension_remover%%PYTHON_TAG%%.opt-1.pyc +bin/salome/SalomeOnDemandTK/__pycache__/extension_remover%%PYTHON_TAG%%.pyc +bin/salome/SalomeOnDemandTK/__pycache__/extension_unpacker%%PYTHON_TAG%%.opt-1.pyc +bin/salome/SalomeOnDemandTK/__pycache__/extension_unpacker%%PYTHON_TAG%%.pyc +bin/salome/SalomeOnDemandTK/__pycache__/extension_utilities%%PYTHON_TAG%%.opt-1.pyc +bin/salome/SalomeOnDemandTK/__pycache__/extension_utilities%%PYTHON_TAG%%.pyc bin/salome/SalomeOnDemandTK/extension_builder.py bin/salome/SalomeOnDemandTK/extension_query.py bin/salome/SalomeOnDemandTK/extension_remover.py @@ -68,132 +68,132 @@ bin/salome/TestModuleCatalog.py bin/salome/Test_LifeCycleCORBA bin/salome/Utils_Identity.py bin/salome/VERSION -bin/salome/__pycache__/ArgvKeeper%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -bin/salome/__pycache__/ArgvKeeper%%PYTHON_EXT_SUFFIX%%.pyc -bin/salome/__pycache__/IDLparser%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -bin/salome/__pycache__/IDLparser%%PYTHON_EXT_SUFFIX%%.pyc -bin/salome/__pycache__/KernelBasis%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -bin/salome/__pycache__/KernelBasis%%PYTHON_EXT_SUFFIX%%.pyc -bin/salome/__pycache__/KernelContainer%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -bin/salome/__pycache__/KernelContainer%%PYTHON_EXT_SUFFIX%%.pyc -bin/salome/__pycache__/KernelDS%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -bin/salome/__pycache__/KernelDS%%PYTHON_EXT_SUFFIX%%.pyc -bin/salome/__pycache__/KernelLauncher%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -bin/salome/__pycache__/KernelLauncher%%PYTHON_EXT_SUFFIX%%.pyc -bin/salome/__pycache__/KernelLogger%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -bin/salome/__pycache__/KernelLogger%%PYTHON_EXT_SUFFIX%%.pyc -bin/salome/__pycache__/KernelModuleCatalog%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -bin/salome/__pycache__/KernelModuleCatalog%%PYTHON_EXT_SUFFIX%%.pyc -bin/salome/__pycache__/KernelSDS%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -bin/salome/__pycache__/KernelSDS%%PYTHON_EXT_SUFFIX%%.pyc -bin/salome/__pycache__/KernelServices%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -bin/salome/__pycache__/KernelServices%%PYTHON_EXT_SUFFIX%%.pyc -bin/salome/__pycache__/LifeCycleCORBA%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -bin/salome/__pycache__/LifeCycleCORBA%%PYTHON_EXT_SUFFIX%%.pyc -bin/salome/__pycache__/NSparam%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -bin/salome/__pycache__/NSparam%%PYTHON_EXT_SUFFIX%%.pyc -bin/salome/__pycache__/NamingService%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -bin/salome/__pycache__/NamingService%%PYTHON_EXT_SUFFIX%%.pyc -bin/salome/__pycache__/ORBConfigFile%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -bin/salome/__pycache__/ORBConfigFile%%PYTHON_EXT_SUFFIX%%.pyc -bin/salome/__pycache__/PortManager%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -bin/salome/__pycache__/PortManager%%PYTHON_EXT_SUFFIX%%.pyc -bin/salome/__pycache__/SALOME_ComponentPy%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -bin/salome/__pycache__/SALOME_ComponentPy%%PYTHON_EXT_SUFFIX%%.pyc -bin/salome/__pycache__/SALOME_Container%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -bin/salome/__pycache__/SALOME_Container%%PYTHON_EXT_SUFFIX%%.pyc -bin/salome/__pycache__/SALOME_ContainerPy%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -bin/salome/__pycache__/SALOME_ContainerPy%%PYTHON_EXT_SUFFIX%%.pyc 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+%%PYTHON_SITELIBDIR%%/salome/__pycache__/salome_psutil%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/salome/__pycache__/salome_psutil%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/salome/__pycache__/salome_pynode%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/salome/__pycache__/salome_pynode%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/salome/__pycache__/salome_study%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/salome/__pycache__/salome_study%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/salome/__pycache__/salome_test%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/salome/__pycache__/salome_test%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/salome/__pycache__/salome_version%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/salome/__pycache__/salome_version%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/salome/_calcium.so %%PYTHON_SITELIBDIR%%/salome/_libNOTIFICATION.so %%PYTHON_SITELIBDIR%%/salome/_libSALOME_Comm.so @@ -797,39 +797,39 @@ include/salome/version.h %%PYTHON_SITELIBDIR%%/salome/omnipatch.py %%PYTHON_SITELIBDIR%%/salome/pylauncher.py %%PYTHON_SITELIBDIR%%/salome/salome/__init__.py -%%PYTHON_SITELIBDIR%%/salome/salome/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/salome/salome/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/salome/salome/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/salome/salome/__pycache__/__init__%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/salome/salome/kernel/__init__.py -%%PYTHON_SITELIBDIR%%/salome/salome/kernel/__pycache__/datamodeler%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/salome/salome/kernel/__pycache__/datamodeler%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/salome/salome/kernel/__pycache__/deprecation%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/salome/salome/kernel/__pycache__/deprecation%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/salome/salome/kernel/__pycache__/diclookup%%PYTHON_EXT_SUFFIX%%.opt-1.pyc 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+%%PYTHON_SITELIBDIR%%/salome/salome/kernel/__pycache__/studyedit%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/salome/salome/kernel/__pycache__/studyedit%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/salome/salome/kernel/__pycache__/syshelper%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/salome/salome/kernel/__pycache__/syshelper%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/salome/salome/kernel/__pycache__/termcolor%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/salome/salome/kernel/__pycache__/termcolor%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/salome/salome/kernel/__pycache__/testdata%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/salome/salome/kernel/__pycache__/testdata%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/salome/salome/kernel/__pycache__/threadhelper%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/salome/salome/kernel/__pycache__/threadhelper%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/salome/salome/kernel/__pycache__/uiexception%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/salome/salome/kernel/__pycache__/uiexception%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/salome/salome/kernel/__pycache__/unittester%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/salome/salome/kernel/__pycache__/unittester%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/salome/salome/kernel/datamodeler.py %%PYTHON_SITELIBDIR%%/salome/salome/kernel/deprecation.py %%PYTHON_SITELIBDIR%%/salome/salome/kernel/diclookup.py @@ -837,14 +837,14 @@ include/salome/version.h %%PYTHON_SITELIBDIR%%/salome/salome/kernel/logconfig.py %%PYTHON_SITELIBDIR%%/salome/salome/kernel/logger.py %%PYTHON_SITELIBDIR%%/salome/salome/kernel/parametric/__init__.py -%%PYTHON_SITELIBDIR%%/salome/salome/kernel/parametric/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/salome/salome/kernel/parametric/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/salome/salome/kernel/parametric/__pycache__/compo_utils%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/salome/salome/kernel/parametric/__pycache__/compo_utils%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/salome/salome/kernel/parametric/__pycache__/pyscript_utils%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/salome/salome/kernel/parametric/__pycache__/pyscript_utils%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON_SITELIBDIR%%/salome/salome/kernel/parametric/__pycache__/study_exchange_vars%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/salome/salome/kernel/parametric/__pycache__/study_exchange_vars%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/salome/salome/kernel/parametric/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/salome/salome/kernel/parametric/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/salome/salome/kernel/parametric/__pycache__/compo_utils%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/salome/salome/kernel/parametric/__pycache__/compo_utils%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/salome/salome/kernel/parametric/__pycache__/pyscript_utils%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/salome/salome/kernel/parametric/__pycache__/pyscript_utils%%PYTHON_TAG%%.pyc +%%PYTHON_SITELIBDIR%%/salome/salome/kernel/parametric/__pycache__/study_exchange_vars%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/salome/salome/kernel/parametric/__pycache__/study_exchange_vars%%PYTHON_TAG%%.pyc %%PYTHON_SITELIBDIR%%/salome/salome/kernel/parametric/compo_utils.py %%PYTHON_SITELIBDIR%%/salome/salome/kernel/parametric/pyscript_utils.py %%PYTHON_SITELIBDIR%%/salome/salome/kernel/parametric/study_exchange_vars.py diff --git a/science/seacas/Makefile b/science/seacas/Makefile index dab6f638940e..21b0c9a3d190 100644 --- a/science/seacas/Makefile +++ b/science/seacas/Makefile @@ -1,6 +1,7 @@ PORTNAME= seacas DISTVERSIONPREFIX= v DISTVERSION= 2025-03-13 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/siconos/Makefile b/science/siconos/Makefile index 463c424c080d..587760c82cc4 100644 --- a/science/siconos/Makefile +++ b/science/siconos/Makefile @@ -1,6 +1,6 @@ PORTNAME= siconos DISTVERSION= 4.5.0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/simgrid/Makefile b/science/simgrid/Makefile index 4a72765d8d05..5c1bb1e17497 100644 --- a/science/simgrid/Makefile +++ b/science/simgrid/Makefile @@ -1,7 +1,7 @@ PORTNAME= SimGrid DISTVERSIONPREFIX= v DISTVERSION= 3.35 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/smoldyn/Makefile b/science/smoldyn/Makefile index 965707c3adac..55178cea9aca 100644 --- a/science/smoldyn/Makefile +++ b/science/smoldyn/Makefile @@ -1,5 +1,5 @@ PORTNAME= smoldyn -DISTVERSION= 2.74 +DISTVERSION= 2.75 CATEGORIES= science MASTER_SITES= https://www.smoldyn.org/ @@ -32,8 +32,8 @@ PYTHON_CMAKE_BOOL= OPTION_PYTHON PYTHON_USES= python PYTHON_CMAKE_ON= -DPython3_EXECUTABLE=${PYTHON_CMD} PYTHON_BUILD_DEPENDS= ${PY_SETUPTOOLS} -PYTHON_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}biosimulators-utils>0:biology/py-biosimulators-utils@${PY_FLAVOR} -PYTHON_BROKEN= pending biology/py-biosimulators-utils completion +#PYTHON_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}biosimulators-utils>0:biology/py-biosimulators-utils@${PY_FLAVOR} +PYTHON_BROKEN= some python dependencies aren't ported post-extract: # see https://github.com/ssandrews/Smoldyn/issues/127 @${CHMOD} +x ${WRKSRC}/scripts/run_pyscript.py.in diff --git a/science/smoldyn/distinfo b/science/smoldyn/distinfo index 61749de73a7f..5083a957430a 100644 --- a/science/smoldyn/distinfo +++ b/science/smoldyn/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1737604798 -SHA256 (smoldyn-2.74.tgz) = 1abae836ac515092be14e2058af58a25981d7872c3a002fbff67bde0f64fa28a -SIZE (smoldyn-2.74.tgz) = 34348669 +TIMESTAMP = 1755906394 +SHA256 (smoldyn-2.75.tgz) = f7116e207d6ba91d3f709b6839d8054a622383ac6e0c5f81108015d083a2a094 +SIZE (smoldyn-2.75.tgz) = 34008076 diff --git a/science/smoldyn/pkg-plist b/science/smoldyn/pkg-plist index f664bfef6faa..847d17ba0b08 100644 --- a/science/smoldyn/pkg-plist +++ b/science/smoldyn/pkg-plist @@ -6,19 +6,19 @@ lib/libsmoldyn_shared.so lib/libsmoldyn_static.a %%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/__init__.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/__main__.py -%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/__pycache__/smoldyn%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/__pycache__/types%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/__pycache__/utils%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/__pycache__/smoldyn%%PYTHON_TAG%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/__pycache__/types%%PYTHON_TAG%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/__pycache__/utils%%PYTHON_TAG%%.pyc %%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/_smoldyn.cpython-310-darwin.so -%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/_smoldyn%%PYTHON_EXT_SUFFIX%%-darwin.so -%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/_smoldyn%%PYTHON_EXT_SUFFIX%%.so +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/_smoldyn%%PYTHON_TAG%%-darwin.so +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/_smoldyn%%PYTHON_TAG%%.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__init__.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__main__.py -%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__pycache__/_version%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__pycache__/combine%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__pycache__/data_model%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__pycache__/__init__%%PYTHON_TAG%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__pycache__/_version%%PYTHON_TAG%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__pycache__/combine%%PYTHON_TAG%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__pycache__/data_model%%PYTHON_TAG%%.pyc %%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/_version.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/combine.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/data_model.py diff --git a/science/spglib/Makefile b/science/spglib/Makefile index 4615c4db21ff..d12f56544466 100644 --- a/science/spglib/Makefile +++ b/science/spglib/Makefile @@ -1,6 +1,6 @@ PORTNAME= spglib DISTVERSIONPREFIX= v -DISTVERSION= 2.5.0 +DISTVERSION= 2.6.0 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -32,4 +32,6 @@ OPTIONS_SUB= yes FORTRAN_USES= fortran FORTRAN_CMAKE_BOOL= SPGLIB_WITH_Fortran +# tests as of 2.6.0: 100% tests passed, 0 tests failed out of 59 + .include <bsd.port.mk> diff --git a/science/spglib/distinfo b/science/spglib/distinfo index 07218b207bc7..85fbb27635db 100644 --- a/science/spglib/distinfo +++ b/science/spglib/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1720768091 -SHA256 (spglib-spglib-v2.5.0_GH0.tar.gz) = b6026f5e85106c0c9ee57e54b9399890d0f29982e20e96ede0428b3efbe6b914 -SIZE (spglib-spglib-v2.5.0_GH0.tar.gz) = 2926427 +TIMESTAMP = 1753138641 +SHA256 (spglib-spglib-v2.6.0_GH0.tar.gz) = c65af71136c915352eb82444b165ec83289877eb8e46593033f199801b43dbf7 +SIZE (spglib-spglib-v2.6.0_GH0.tar.gz) = 2438640 diff --git a/science/spglib/pkg-plist b/science/spglib/pkg-plist index c3b5f01c8d33..5315006f0e5c 100644 --- a/science/spglib/pkg-plist +++ b/science/spglib/pkg-plist @@ -11,9 +11,9 @@ lib/cmake/Spglib/SpglibTargets_shared.cmake %%FORTRAN%%lib/cmake/Spglib/try_compile.f90 %%FORTRAN%%lib/libspglib_f08.so %%FORTRAN%%lib/libspglib_f08.so.2 -%%FORTRAN%%lib/libspglib_f08.so.2.5.0 +%%FORTRAN%%lib/libspglib_f08.so.2.6.0 lib/libsymspg.so lib/libsymspg.so.2 -lib/libsymspg.so.2.5.0 +lib/libsymspg.so.2.6.0 libdata/pkgconfig/spglib.pc %%FORTRAN%%libdata/pkgconfig/spglib_f08.pc diff --git a/science/spheral/Makefile b/science/spheral/Makefile index 54920fcab65c..7365b12d8edd 100644 --- a/science/spheral/Makefile +++ b/science/spheral/Makefile @@ -1,7 +1,7 @@ PORTNAME= spheral DISTVERSIONPREFIX= v DISTVERSION= 2024.06.1 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science # physics MAINTAINER= yuri@FreeBSD.org diff --git a/science/step/distinfo b/science/step/distinfo index 977665fbfa43..b2a6ad4575c2 100644 --- a/science/step/distinfo +++ b/science/step/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1746557950 -SHA256 (KDE/release-service/25.04.1/step-25.04.1.tar.xz) = bfc136ac296b613812d0c2e6979583b2c2856abc05ec605cf82ad2b4fb4f191d -SIZE (KDE/release-service/25.04.1/step-25.04.1.tar.xz) = 988568 +TIMESTAMP = 1754646550 +SHA256 (KDE/release-service/25.08.0/step-25.08.0.tar.xz) = 994bab4d0750cfdeb3af1f92d6453ee173cd483e392ad170bf5250b23b4ddf3a +SIZE (KDE/release-service/25.08.0/step-25.08.0.tar.xz) = 1004072 diff --git a/science/step/pkg-plist b/science/step/pkg-plist index f0365a2c6bf1..4186212eb37b 100644 --- a/science/step/pkg-plist +++ b/science/step/pkg-plist @@ -133,6 +133,8 @@ share/locale/lt/LC_MESSAGES/step_example_files.mo share/locale/lt/LC_MESSAGES/step_objinfo_files.mo share/locale/lt/LC_MESSAGES/step_qt.qm share/locale/lv/LC_MESSAGES/step.mo +share/locale/lv/LC_MESSAGES/step_example_files.mo +share/locale/lv/LC_MESSAGES/step_objinfo_files.mo share/locale/lv/LC_MESSAGES/step_qt.qm share/locale/mai/LC_MESSAGES/step_qt.qm share/locale/ml/LC_MESSAGES/step.mo @@ -561,6 +563,23 @@ share/mime/packages/org.kde.step.xml %%DATADIR%%/examples/lt/solar.step %%DATADIR%%/examples/lt/springs.step %%DATADIR%%/examples/lt/wave.step +%%DATADIR%%/examples/lv/brownian.step +%%DATADIR%%/examples/lv/doublependulum.step +%%DATADIR%%/examples/lv/eightpendula.step +%%DATADIR%%/examples/lv/first.step +%%DATADIR%%/examples/lv/fourpendula.step +%%DATADIR%%/examples/lv/gas.step +%%DATADIR%%/examples/lv/graph.step +%%DATADIR%%/examples/lv/liquid.step +%%DATADIR%%/examples/lv/lissajous.step +%%DATADIR%%/examples/lv/motor.step +%%DATADIR%%/examples/lv/motor1.step +%%DATADIR%%/examples/lv/note.step +%%DATADIR%%/examples/lv/resonance.step +%%DATADIR%%/examples/lv/softbody.step +%%DATADIR%%/examples/lv/solar.step +%%DATADIR%%/examples/lv/springs.step +%%DATADIR%%/examples/lv/wave.step %%DATADIR%%/examples/ml/brownian.step %%DATADIR%%/examples/ml/doublependulum.step %%DATADIR%%/examples/ml/eightpendula.step @@ -1198,6 +1217,25 @@ share/mime/packages/org.kde.step.xml %%DATADIR%%/objinfo/l10n/lt/spring.html %%DATADIR%%/objinfo/l10n/lt/weightforce.html %%DATADIR%%/objinfo/l10n/lt/world.html +%%DATADIR%%/objinfo/l10n/lv/anchor.html +%%DATADIR%%/objinfo/l10n/lv/box.html +%%DATADIR%%/objinfo/l10n/lv/chargedparticle.html +%%DATADIR%%/objinfo/l10n/lv/coulombforce.html +%%DATADIR%%/objinfo/l10n/lv/disk.html +%%DATADIR%%/objinfo/l10n/lv/gas.html +%%DATADIR%%/objinfo/l10n/lv/gasljforce.html +%%DATADIR%%/objinfo/l10n/lv/gasparticle.html +%%DATADIR%%/objinfo/l10n/lv/gravitationforce.html +%%DATADIR%%/objinfo/l10n/lv/linearmotor.html +%%DATADIR%%/objinfo/l10n/lv/meter.html +%%DATADIR%%/objinfo/l10n/lv/note.html +%%DATADIR%%/objinfo/l10n/lv/particle.html +%%DATADIR%%/objinfo/l10n/lv/pin.html +%%DATADIR%%/objinfo/l10n/lv/polygon.html +%%DATADIR%%/objinfo/l10n/lv/softbody.html +%%DATADIR%%/objinfo/l10n/lv/spring.html +%%DATADIR%%/objinfo/l10n/lv/weightforce.html +%%DATADIR%%/objinfo/l10n/lv/world.html %%DATADIR%%/objinfo/l10n/ml/anchor.html %%DATADIR%%/objinfo/l10n/ml/box.html %%DATADIR%%/objinfo/l10n/ml/chargedparticle.html @@ -1555,6 +1593,11 @@ share/mime/packages/org.kde.step.xml %%DATADIR%%/tutorials/lt/tutorial3.step %%DATADIR%%/tutorials/lt/tutorial4.step %%DATADIR%%/tutorials/lt/tutorial5.step +%%DATADIR%%/tutorials/lv/tutorial1.step +%%DATADIR%%/tutorials/lv/tutorial2.step +%%DATADIR%%/tutorials/lv/tutorial3.step +%%DATADIR%%/tutorials/lv/tutorial4.step +%%DATADIR%%/tutorials/lv/tutorial5.step %%DATADIR%%/tutorials/ml/tutorial1.step %%DATADIR%%/tutorials/ml/tutorial2.step %%DATADIR%%/tutorials/ml/tutorial3.step diff --git a/science/tfel-edf/Makefile b/science/tfel-edf/Makefile index f9c8e00d1607..5115a36f59d8 100644 --- a/science/tfel-edf/Makefile +++ b/science/tfel-edf/Makefile @@ -1,6 +1,6 @@ PORTNAME= tfel DISTVERSION= 3.2.1-1 -PORTREVISION= 7 +PORTREVISION= 8 CATEGORIES= science PKGNAMESUFFIX= -mfront-edf diff --git a/science/tfel/Makefile b/science/tfel/Makefile index 945b3858d928..5fa523762c10 100644 --- a/science/tfel/Makefile +++ b/science/tfel/Makefile @@ -1,6 +1,6 @@ PORTNAME= tfel PORTVERSION= 4.0.0 -PORTREVISION= 6 +PORTREVISION= 7 CATEGORIES= science MASTER_SITES= SF/${PORTNAME}/ PKGNAMESUFFIX= -mfront diff --git a/science/tfel/pkg-plist b/science/tfel/pkg-plist index 9aad35dfce42..1943b5790eed 100644 --- a/science/tfel/pkg-plist +++ b/science/tfel/pkg-plist @@ -982,32 +982,32 @@ lib/libTFELUnicodeSupport.so.%%VER%% lib/libTFELUtilities.so lib/libTFELUtilities.so.%%VER%% %%PYTHON%%%%PYTHON_SITELIBDIR%%/mfront/__init__.py -%%PYTHON%%%%PYTHON_SITELIBDIR%%/mfront/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/mfront/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/mfront/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/mfront/__pycache__/__init__%%PYTHON_TAG%%.pyc %%PYTHON%%%%PYTHON_SITELIBDIR%%/mfront/_mfront.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/mfront/mtest/__init__.py -%%PYTHON%%%%PYTHON_SITELIBDIR%%/mfront/mtest/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/mfront/mtest/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/mfront/mtest/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/mfront/mtest/__pycache__/__init__%%PYTHON_TAG%%.pyc %%PYTHON%%%%PYTHON_SITELIBDIR%%/mfront/umatxx/Behaviour.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/mfront/umatxx/__init__.py -%%PYTHON%%%%PYTHON_SITELIBDIR%%/mfront/umatxx/__pycache__/Behaviour%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/mfront/umatxx/__pycache__/Behaviour%%PYTHON_EXT_SUFFIX%%.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/mfront/umatxx/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/mfront/umatxx/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/mfront/umatxx/__pycache__/Behaviour%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/mfront/umatxx/__pycache__/Behaviour%%PYTHON_TAG%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/mfront/umatxx/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/mfront/umatxx/__pycache__/__init__%%PYTHON_TAG%%.pyc %%PYTHON%%%%PYTHON_SITELIBDIR%%/mtest/__init__.py -%%PYTHON%%%%PYTHON_SITELIBDIR%%/mtest/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/mtest/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/mtest/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/mtest/__pycache__/__init__%%PYTHON_TAG%%.pyc %%PYTHON%%%%PYTHON_SITELIBDIR%%/mtest/_mtest.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/std/__init__.py -%%PYTHON%%%%PYTHON_SITELIBDIR%%/std/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/std/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/std/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/std/__pycache__/__init__%%PYTHON_TAG%%.pyc %%PYTHON%%%%PYTHON_SITELIBDIR%%/std/_stl_map.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/std/_stl_pair.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/std/_stl_tuple.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/std/_stl_vector.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/tfel/__init__.py -%%PYTHON%%%%PYTHON_SITELIBDIR%%/tfel/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/tfel/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/tfel/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/tfel/__pycache__/__init__%%PYTHON_TAG%%.pyc %%PYTHON%%%%PYTHON_SITELIBDIR%%/tfel/_tfel.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/tfel/glossary.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/tfel/material.so diff --git a/science/thermofun/Makefile b/science/thermofun/Makefile index 652e289dbc1c..9dbd9ef9f8b9 100644 --- a/science/thermofun/Makefile +++ b/science/thermofun/Makefile @@ -43,6 +43,6 @@ post-install-PYTHON-on: @${FIND} ${STAGEDIR} -name "*.pyc" -delete @${FIND} ${STAGEDIR} -name __pycache__ -delete # strip binary - @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/thermofun/PyThermoFun${PYTHON_EXT_SUFFIX}.so + @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/thermofun/PyThermoFun${PYTHON_TAG}.so .include <bsd.port.mk> diff --git a/science/thermofun/pkg-plist b/science/thermofun/pkg-plist index deb566488b1f..68b9fb7d44c2 100644 --- a/science/thermofun/pkg-plist +++ b/science/thermofun/pkg-plist @@ -75,5 +75,5 @@ lib/libThermoFun.so %%PYTHON_SITELIBDIR%%/thermofun-0.5.0.dist-info/WHEEL %%PYTHON_SITELIBDIR%%/thermofun-0.5.0.dist-info/direct_url.json %%PYTHON_SITELIBDIR%%/thermofun-0.5.0.dist-info/top_level.txt -%%PYTHON_SITELIBDIR%%/thermofun/PyThermoFun%%PYTHON_EXT_SUFFIX%%.so +%%PYTHON_SITELIBDIR%%/thermofun/PyThermoFun%%PYTHON_TAG%%.so %%PYTHON_SITELIBDIR%%/thermofun/__init__.py diff --git a/science/tinker/Makefile b/science/tinker/Makefile index c5b9b72ff278..2406c4c31a27 100644 --- a/science/tinker/Makefile +++ b/science/tinker/Makefile @@ -1,5 +1,5 @@ PORTNAME= tinker -DISTVERSION= 8.11.3 +DISTVERSION= 25.3 PORTREVISION= 1 CATEGORIES= science MASTER_SITES= https://dasher.wustl.edu/tinker/downloads/ diff --git a/science/tinker/distinfo b/science/tinker/distinfo index 6c20209908c4..6ebb852d7522 100644 --- a/science/tinker/distinfo +++ b/science/tinker/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1719188902 -SHA256 (tinker-8.11.3.tar.gz) = 8dfbc9fb8f26742d91139187657e2c905744b0243538f81b75bc04cdc2606ff7 -SIZE (tinker-8.11.3.tar.gz) = 73256260 +TIMESTAMP = 1755934058 +SHA256 (tinker-25.3.tar.gz) = 84744d00e2936be23be6ed6acbbc251f07e016db53ead079a270280539a42145 +SIZE (tinker-25.3.tar.gz) = 80772560 diff --git a/science/tinker/pkg-plist b/science/tinker/pkg-plist index 286fc0abcadd..b0f9367ade44 100644 --- a/science/tinker/pkg-plist +++ b/science/tinker/pkg-plist @@ -64,6 +64,8 @@ bin/xyzint bin/xyzmol2 bin/xyzpdb %%DATADIR%%/params/0README +%%DATADIR%%/params/amber14sb.prm +%%DATADIR%%/params/amber19sb.prm %%DATADIR%%/params/amber94.prm %%DATADIR%%/params/amber96.prm %%DATADIR%%/params/amber98.prm @@ -82,7 +84,8 @@ bin/xyzpdb %%DATADIR%%/params/basic.prm %%DATADIR%%/params/charmm19.prm %%DATADIR%%/params/charmm22.prm -%%DATADIR%%/params/charmm22cmap.prm +%%DATADIR%%/params/charmm27.prm +%%DATADIR%%/params/charmm36.prm %%DATADIR%%/params/dang.prm %%DATADIR%%/params/hippo19.prm %%DATADIR%%/params/hoch.prm @@ -90,8 +93,9 @@ bin/xyzpdb %%DATADIR%%/params/mm2.prm %%DATADIR%%/params/mm3.prm %%DATADIR%%/params/mm3pro.prm -%%DATADIR%%/params/mmff.prm -%%DATADIR%%/params/oplsaa.prm +%%DATADIR%%/params/mmff94.prm +%%DATADIR%%/params/mmff94s.prm +%%DATADIR%%/params/oplsaa08.prm %%DATADIR%%/params/oplsaal.prm %%DATADIR%%/params/oplsua.prm %%DATADIR%%/params/smoothaa.prm @@ -206,6 +210,10 @@ bin/xyzpdb %%DATADIR%%/test/polyala.key %%DATADIR%%/test/polyala.log %%DATADIR%%/test/polyala.run +%%DATADIR%%/test/pyridine.dat +%%DATADIR%%/test/pyridine.log +%%DATADIR%%/test/pyridine.run +%%DATADIR%%/test/pyridine.xyz %%DATADIR%%/test/salt.cell %%DATADIR%%/test/salt.key %%DATADIR%%/test/salt.log diff --git a/science/trilinos/Makefile b/science/trilinos/Makefile index 6c5576de4913..d2c8f9e9253c 100644 --- a/science/trilinos/Makefile +++ b/science/trilinos/Makefile @@ -1,6 +1,7 @@ PORTNAME= trilinos DISTVERSIONPREFIX= trilinos-release- DISTVERSION= 16-1-0 +PORTREVISION= 1 CATEGORIES= science # physics MAINTAINER= yuri@FreeBSD.org diff --git a/science/vipster/Makefile b/science/vipster/Makefile index e0b096c3b3ea..18acb86d904d 100644 --- a/science/vipster/Makefile +++ b/science/vipster/Makefile @@ -1,6 +1,7 @@ PORTNAME= vipster DISTVERSIONPREFIX= v DISTVERSION= 1.19.1b-109 +PORTREVISION= 1 DISTVERSIONSUFFIX= -gfb4a6ed CATEGORIES= science diff --git a/science/votca/Makefile b/science/votca/Makefile index 38e08f2c7e35..f12745e528a9 100644 --- a/science/votca/Makefile +++ b/science/votca/Makefile @@ -1,20 +1,22 @@ PORTNAME= votca DISTVERSIONPREFIX= v DISTVERSION= 2025 +PORTREVISION= 2 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= CSG and XTP: libraries for atomistic simulations -WWW= https://github.com/votca/votca +WWW= https://www.votca.org/ \ + https://github.com/votca/votca LICENSE= APACHE20 -BROKEN_i386= undefined reference to `__atomic_load' +BROKEN_i386= undefined reference to `__atomic_load' # ' PY_DEPENDS= \ ${PYTHON_PKGNAMEPREFIX}ase>0:science/py-ase@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}lxml>0:devel/py-lxml@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}lxml5>0:devel/py-lxml5@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}xmltodict>0:devel/py-xmltodict@${PY_FLAVOR} \ rdkit>0:science/rdkit BUILD_DEPENDS= bash:shells/bash \ |