diff options
Diffstat (limited to 'science')
137 files changed, 1510 insertions, 1131 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/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-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 a310bee72cd0..2347581589fd 100644 --- a/science/abinit/Makefile +++ b/science/abinit/Makefile @@ -1,6 +1,5 @@ PORTNAME= abinit -DISTVERSION= 10.2.7 -PORTREVISION= 1 +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 c0481228a28e..bd4a59145946 100644 --- a/science/afni/Makefile +++ b/science/afni/Makefile @@ -1,6 +1,6 @@ PORTNAME= afni DISTVERSIONPREFIX= AFNI_ -DISTVERSION= 25.2.02 +DISTVERSION= 25.2.05 CATEGORIES= science biology graphics perl5 python MAINTAINER= fernape@FreeBSD.org diff --git a/science/afni/distinfo b/science/afni/distinfo index 93c962c51cb9..933eea829f78 100644 --- a/science/afni/distinfo +++ b/science/afni/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1751528740 -SHA256 (afni-afni-AFNI_25.2.02_GH0.tar.gz) = 5f9462da5e779b03a38906495be4ae1228d58daea0ff3c17901dee47fb687305 -SIZE (afni-afni-AFNI_25.2.02_GH0.tar.gz) = 53285129 +TIMESTAMP = 1753208153 +SHA256 (afni-afni-AFNI_25.2.05_GH0.tar.gz) = 7648e71187874d1602afdaa0c776b945c8d236e3a9c6b48439cf0a160d97c4a8 +SIZE (afni-afni-AFNI_25.2.05_GH0.tar.gz) = 53317967 diff --git a/science/afni/pkg-plist b/science/afni/pkg-plist index 3747916c791c..ff89f38c13a6 100644 --- a/science/afni/pkg-plist +++ b/science/afni/pkg-plist @@ -1297,6 +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 5046ef8d6bc2..ff6dce0acfc3 100644 --- a/science/agrum/Makefile +++ b/science/agrum/Makefile @@ -1,5 +1,5 @@ PORTNAME= agrum -DISTVERSION= 2.1.1 +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= d15a377b0f745a6afd15139d780b23056305a851 +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} ${MAKE_ENV} ./act test release agrum -t all +# tests as of 2.2.0: Failed 0 of 1483 tests + .include <bsd.port.mk> diff --git a/science/agrum/distinfo b/science/agrum/distinfo index 13627e87a707..62c51836a6d8 100644 --- a/science/agrum/distinfo +++ b/science/agrum/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1750005327 -SHA256 (agrumery-aGrUM-d15a377b0f745a6afd15139d780b23056305a851_GL0.tar.gz) = 21f6ad004e8ff15d4b41fb6e30f8c60db3631a84d756bd91d3972432710f8048 -SIZE (agrumery-aGrUM-d15a377b0f745a6afd15139d780b23056305a851_GL0.tar.gz) = 28781050 +TIMESTAMP = 1753632410 +SHA256 (agrumery-aGrUM-cf1283f783aa6803bafbd9a3fb4991316c1b52d9_GL0.tar.gz) = 57f7274925f64129c2f3bfcd178f75edd4cb6eaff1d06c30f20c85c41e6ca3d9 +SIZE (agrumery-aGrUM-cf1283f783aa6803bafbd9a3fb4991316c1b52d9_GL0.tar.gz) = 29175753 diff --git a/science/agrum/pkg-plist b/science/agrum/pkg-plist index 123d787ba5bd..9fe1f9999703 100644 --- a/science/agrum/pkg-plist +++ b/science/agrum/pkg-plist @@ -180,6 +180,7 @@ include/agrum/BN/learning/localSearchWithTabuList_tpl.h include/agrum/BN/learning/paramUtils/DAG2BNLearner.h include/agrum/BN/learning/paramUtils/DAG2BNLearner_inl.h include/agrum/BN/learning/paramUtils/DAG2BNLearner_tpl.h +include/agrum/BN/learning/paramUtils/EMApproximationScheme.h include/agrum/BN/learning/paramUtils/paramEstimator.h include/agrum/BN/learning/paramUtils/paramEstimatorML.h include/agrum/BN/learning/paramUtils/paramEstimatorML_inl.h diff --git a/science/cdf/Makefile b/science/cdf/Makefile index 803a95f11b0d..edc94cf929c9 100644 --- a/science/cdf/Makefile +++ b/science/cdf/Makefile @@ -5,7 +5,7 @@ MASTER_SITES= https://spdf.gsfc.nasa.gov/pub/software/cdf/dist/cdf39_1/ DISTNAME= cdf${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/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/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 45c01911b249..a9105577fa35 100644 --- a/science/csvtk/Makefile +++ b/science/csvtk/Makefile @@ -1,7 +1,6 @@ PORTNAME= csvtk DISTVERSIONPREFIX= v -DISTVERSION= 0.33.0 -PORTREVISION= 3 +DISTVERSION= 0.34.0 CATEGORIES= science MAINTAINER= jwb@FreeBSD.org 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/eccodes/pkg-plist b/science/eccodes/pkg-plist index 29dff88bf736..52d540fa23dd 100644 --- a/science/eccodes/pkg-plist +++ b/science/eccodes/pkg-plist @@ -19886,7 +19886,7 @@ 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/%%PERL_VER%%.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 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/molgif/Makefile b/science/molgif/Makefile index 87d06594401f..cec8591a420f 100644 --- a/science/molgif/Makefile +++ b/science/molgif/Makefile @@ -1,6 +1,6 @@ PORTNAME= molgif DISTVERSION= g20180108 -PORTREVISION= 27 +PORTREVISION= 28 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/ncrystal/Makefile b/science/ncrystal/Makefile index fb63deb58062..9cfb8da272b6 100644 --- a/science/ncrystal/Makefile +++ b/science/ncrystal/Makefile @@ -1,6 +1,6 @@ PORTNAME= ncrystal DISTVERSIONPREFIX= v -DISTVERSION= 4.2.0 +DISTVERSION= 4.2.6 CATEGORIES= science # physics MAINTAINER= yuri@FreeBSD.org @@ -24,6 +24,6 @@ CMAKE_TESTING_ON= NCRYSTAL_ENABLE_TESTING \ 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: 52% tests passed, 42 tests failed out of 87 .include <bsd.port.mk> diff --git a/science/ncrystal/distinfo b/science/ncrystal/distinfo index a9c11355be17..1a8eec6572c9 100644 --- a/science/ncrystal/distinfo +++ b/science/ncrystal/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1749700880 -SHA256 (mctools-ncrystal-v4.2.0_GH0.tar.gz) = bc01465f4e7db596ebba34df96ad744eea7cd1d2308fb2ff1ae532d0dbc50725 -SIZE (mctools-ncrystal-v4.2.0_GH0.tar.gz) = 2812384 +TIMESTAMP = 1753507988 +SHA256 (mctools-ncrystal-v4.2.6_GH0.tar.gz) = 4e7926d8bb931cce3546e9406a2a3d9b182b864e94ce34e31b1a6d9475479602 +SIZE (mctools-ncrystal-v4.2.6_GH0.tar.gz) = 2821990 diff --git a/science/openmodelica/Makefile b/science/openmodelica/Makefile index 7b68d78286ef..dafafc57c8da 100644 --- a/science/openmodelica/Makefile +++ b/science/openmodelica/Makefile @@ -18,7 +18,7 @@ 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 diff --git a/science/packmol/Makefile b/science/packmol/Makefile index 258cb4887b23..627188fa12eb 100644 --- a/science/packmol/Makefile +++ b/science/packmol/Makefile @@ -1,6 +1,6 @@ PORTNAME= packmol DISTVERSIONPREFIX= v -DISTVERSION= 21.0.2 +DISTVERSION= 21.0.4 CATEGORIES= science MAINTAINER= eduardo@FreeBSD.org diff --git a/science/packmol/distinfo b/science/packmol/distinfo index a29aecb117ea..1e7f2f2c9e84 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 = 1752317019 +SHA256 (m3g-packmol-v21.0.4_GH0.tar.gz) = ca2398a6f8f2a326f52cda8e45a8818ea430a1b195fd3801d017e1a18f38fde8 +SIZE (m3g-packmol-v21.0.4_GH0.tar.gz) = 630743 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/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-asdf/Makefile b/science/py-asdf/Makefile index 8efabf947d4c..3986edee3d15 100644 --- a/science/py-asdf/Makefile +++ b/science/py-asdf/Makefile @@ -1,5 +1,5 @@ PORTNAME= asdf -PORTVERSION= 4.2.0 +PORTVERSION= 4.3.0 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-asdf/distinfo b/science/py-asdf/distinfo index 6de3b3412bd5..f3a2707208d2 100644 --- a/science/py-asdf/distinfo +++ b/science/py-asdf/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1748831252 -SHA256 (asdf-4.2.0.tar.gz) = cba00a10cde18deb20100e001fe41022f5c0cda02720dda9f716fb2150a46cf7 -SIZE (asdf-4.2.0.tar.gz) = 892353 +TIMESTAMP = 1753265788 +SHA256 (asdf-4.3.0.tar.gz) = 961d75fb1f1c4868b4533f885655b7ea9a3f0d257c65b49d728da53fe6df087d +SIZE (asdf-4.3.0.tar.gz) = 897816 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 7cf8db927729..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 @@ -22,6 +21,7 @@ %%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 diff --git a/science/py-ncrystal/Makefile b/science/py-ncrystal/Makefile index 16b71cb75d5e..ed1e1279b00e 100644 --- a/science/py-ncrystal/Makefile +++ b/science/py-ncrystal/Makefile @@ -1,6 +1,6 @@ PORTNAME= ncrystal DISTVERSIONPREFIX= v -DISTVERSION= 4.2.0 +DISTVERSION= 4.2.6 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 a23e154ff514..aca64d45e427 100644 --- a/science/py-ncrystal/distinfo +++ b/science/py-ncrystal/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1749705869 -SHA256 (mctools-ncrystal-v4.2.0_GH0.tar.gz) = bc01465f4e7db596ebba34df96ad744eea7cd1d2308fb2ff1ae532d0dbc50725 -SIZE (mctools-ncrystal-v4.2.0_GH0.tar.gz) = 2812384 +TIMESTAMP = 1753507607 +SHA256 (mctools-ncrystal-v4.2.6_GH0.tar.gz) = 4e7926d8bb931cce3546e9406a2a3d9b182b864e94ce34e31b1a6d9475479602 +SIZE (mctools-ncrystal-v4.2.6_GH0.tar.gz) = 2821990 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-phonopy/Makefile b/science/py-phonopy/Makefile index bb9438585200..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} @@ -36,6 +36,6 @@ TEST_WRKSRC= ${WRKSRC}/test post-install: @${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-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 e28c1d3cd27c..c55d7b2e49e3 100644 --- a/science/py-qiskit/Makefile +++ b/science/py-qiskit/Makefile @@ -1,6 +1,5 @@ PORTNAME= qiskit -DISTVERSION= 2.0.0 -PORTREVISION= 2 +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-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/rmf/Makefile b/science/rmf/Makefile index 5d09f287b9f7..9a1b1c673a5d 100644 --- a/science/rmf/Makefile +++ b/science/rmf/Makefile @@ -6,7 +6,7 @@ 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/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/tinker/Makefile b/science/tinker/Makefile index c5b9b72ff278..a62f2268609b 100644 --- a/science/tinker/Makefile +++ b/science/tinker/Makefile @@ -1,6 +1,5 @@ PORTNAME= tinker -DISTVERSION= 8.11.3 -PORTREVISION= 1 +DISTVERSION= 25.3 CATEGORIES= science MASTER_SITES= https://dasher.wustl.edu/tinker/downloads/ diff --git a/science/tinker/distinfo b/science/tinker/distinfo index 6c20209908c4..7ca60014bed4 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 = 1753634645 +SHA256 (tinker-25.3.tar.gz) = d536f1d4d0d7d4394b3b3d88a52cf12ed3489312ac2ad9c6ce4d198bd681e36c +SIZE (tinker-25.3.tar.gz) = 80772142 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/votca/Makefile b/science/votca/Makefile index 24ce596890b3..f12745e528a9 100644 --- a/science/votca/Makefile +++ b/science/votca/Makefile @@ -1,21 +1,22 @@ PORTNAME= votca DISTVERSIONPREFIX= v DISTVERSION= 2025 -PORTREVISION= 1 +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 \ |