diff options
Diffstat (limited to 'science')
54 files changed, 289 insertions, 129 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/afni/Makefile b/science/afni/Makefile index bd4a59145946..1f79dc95fc41 100644 --- a/science/afni/Makefile +++ b/science/afni/Makefile @@ -1,6 +1,6 @@ PORTNAME= afni DISTVERSIONPREFIX= AFNI_ -DISTVERSION= 25.2.05 +DISTVERSION= 25.2.07 CATEGORIES= science biology graphics perl5 python MAINTAINER= fernape@FreeBSD.org diff --git a/science/afni/distinfo b/science/afni/distinfo index 933eea829f78..04994b71df22 100644 --- a/science/afni/distinfo +++ b/science/afni/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1753208153 -SHA256 (afni-afni-AFNI_25.2.05_GH0.tar.gz) = 7648e71187874d1602afdaa0c776b945c8d236e3a9c6b48439cf0a160d97c4a8 -SIZE (afni-afni-AFNI_25.2.05_GH0.tar.gz) = 53317967 +TIMESTAMP = 1754550205 +SHA256 (afni-afni-AFNI_25.2.07_GH0.tar.gz) = a3e6c9a77afcbb5db2553aa47e36641fe70cd1dea86b2baab74e7f45c66e0331 +SIZE (afni-afni-AFNI_25.2.07_GH0.tar.gz) = 53319926 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/arbor/Makefile b/science/arbor/Makefile index 15368c1b0ac6..d2d6e0cf6ef2 100644 --- a/science/arbor/Makefile +++ b/science/arbor/Makefile @@ -1,7 +1,7 @@ PORTNAME= arbor DISTVERSIONPREFIX= v DISTVERSION= 0.10.1 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/axom/Makefile b/science/axom/Makefile index 35f116e96434..58c94b7ba017 100644 --- a/science/axom/Makefile +++ b/science/axom/Makefile @@ -1,6 +1,7 @@ PORTNAME= axom DISTVERSIONPREFIX= v DISTVERSION= 0.10.1 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/bout++/Makefile b/science/bout++/Makefile index bbdf2813b4cd..43b9accad186 100644 --- a/science/bout++/Makefile +++ b/science/bout++/Makefile @@ -1,7 +1,7 @@ PORTNAME= bout++ DISTVERSIONPREFIX= v DISTVERSION= 5.1.1 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science math # physics MAINTAINER= yuri@FreeBSD.org diff --git a/science/cantera/Makefile b/science/cantera/Makefile index ebaa5cf75809..61a965965fe2 100644 --- a/science/cantera/Makefile +++ b/science/cantera/Makefile @@ -1,7 +1,7 @@ PORTNAME= cantera DISTVERSIONPREFIX= v DISTVERSION= 3.1.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science # chemistry physics MAINTAINER= yuri@FreeBSD.org diff --git a/science/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/chemicalfun/Makefile b/science/chemicalfun/Makefile index 02ab01468d81..9b3afed93586 100644 --- a/science/chemicalfun/Makefile +++ b/science/chemicalfun/Makefile @@ -1,6 +1,6 @@ PORTNAME= chemicalfun DISTVERSION= 0.1.8 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science # chemistry MASTER_SITES= https://bitbucket.org/${BB_ACCOUNT}/${PORTNAME}/get/${BB_COMMIT}${EXTRACT_SUFX}?dummy=/:src DISTFILES= ${PORTNAME}-${DISTVERSION}${EXTRACT_SUFX}:src 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 707410f4fa7a..e4b2b99739a4 100644 --- a/science/csvtk/Makefile +++ b/science/csvtk/Makefile @@ -1,7 +1,7 @@ PORTNAME= csvtk DISTVERSIONPREFIX= v -DISTVERSION= 0.33.0 -PORTREVISION= 4 +DISTVERSION= 0.34.0 +PORTREVISION= 1 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/dynare/Makefile b/science/dynare/Makefile index 0856cc00a8ed..d0babbf623e3 100644 --- a/science/dynare/Makefile +++ b/science/dynare/Makefile @@ -1,6 +1,6 @@ PORTNAME= dynare DISTVERSION= 5.4 -PORTREVISION= 13 +PORTREVISION= 14 CATEGORIES= science # economics MASTER_SITES= https://www.dynare.org/release/source/ diff --git a/science/gramps/Makefile b/science/gramps/Makefile index 4074db4cc44f..f261cd0a1aa4 100644 --- a/science/gramps/Makefile +++ b/science/gramps/Makefile @@ -1,5 +1,5 @@ PORTNAME= gramps -DISTVERSION= 6.0.3 +DISTVERSION= 6.0.4 CATEGORIES= science gnome python MASTER_SITES= PYPI diff --git a/science/gramps/distinfo b/science/gramps/distinfo index 7f082b790a6b..30016e379016 100644 --- a/science/gramps/distinfo +++ b/science/gramps/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1750276417 -SHA256 (gramps-6.0.3.tar.gz) = 079fab79c330c2332e5cc5cd1ec9e953a2b76d9f103aa774b7850d01baf874ee -SIZE (gramps-6.0.3.tar.gz) = 21803163 +TIMESTAMP = 1754945114 +SHA256 (gramps-6.0.4.tar.gz) = ebabb1cfa8dc61859ee0e9c4ad0b54c94ccff2809dd1b0895a38a46b80382692 +SIZE (gramps-6.0.4.tar.gz) = 21963080 diff --git a/science/hypre/Makefile b/science/hypre/Makefile index d5df638850a3..a439de1d4f3c 100644 --- a/science/hypre/Makefile +++ b/science/hypre/Makefile @@ -1,6 +1,7 @@ PORTNAME= hypre DISTVERSIONPREFIX= v DISTVERSION= 2.33.0 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/kalzium/distinfo b/science/kalzium/distinfo index 55a8ed08734d..dc9bdf4527dc 100644 --- a/science/kalzium/distinfo +++ b/science/kalzium/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1751381644 -SHA256 (KDE/release-service/25.04.3/kalzium-25.04.3.tar.xz) = d8d76ae3d123d93fe0ddf33992d7c85292ec5560b76a634f9bf2d731c2fccada -SIZE (KDE/release-service/25.04.3/kalzium-25.04.3.tar.xz) = 22660296 +TIMESTAMP = 1754646547 +SHA256 (KDE/release-service/25.08.0/kalzium-25.08.0.tar.xz) = 8765737e7baeb7fb0d0c16112ce11694ddb90a102e8e6b3e723dae9d595b8529 +SIZE (KDE/release-service/25.08.0/kalzium-25.08.0.tar.xz) = 22650880 diff --git a/science/kalzium/pkg-plist b/science/kalzium/pkg-plist index 6d96ce611615..08dc853471f9 100644 --- a/science/kalzium/pkg-plist +++ b/science/kalzium/pkg-plist @@ -10,6 +10,9 @@ include/libkdeedu/psetables.h include/libkdeedu/science_export.h include/libkdeedu/spectrum.h include/libkdeedu/spectrumparser.h +lib/libcompoundviewer.so +lib/libcompoundviewer.so.5 +lib/libcompoundviewer.so.5.0.0 lib/libscience.so lib/libscience.so.5 lib/libscience.so.5.0.0 @@ -348,6 +351,7 @@ share/icons/hicolor/scalable/apps/kalzium.svgz %%DATADIR%%/icons/hicolor/scalable/actions/statematter.svgz %%DATADIR%%/icons/hicolor/scalable/actions/timeline.svgz %%DATADIR%%/icons/hicolor/scalable/actions/tooltip.svgz +share/knsrcfiles/kalzium.knsrc share/libkdeedu/data/elements.xml share/libkdeedu/data/isotopes.xml share/libkdeedu/data/spectra.xml @@ -383,6 +387,7 @@ share/locale/hi/LC_MESSAGES/kalzium.mo share/locale/hne/LC_MESSAGES/kalzium.mo share/locale/hr/LC_MESSAGES/kalzium.mo share/locale/hu/LC_MESSAGES/kalzium.mo +share/locale/ia/LC_MESSAGES/kalzium.mo share/locale/is/LC_MESSAGES/kalzium.mo share/locale/it/LC_MESSAGES/kalzium.mo share/locale/ja/LC_MESSAGES/kalzium.mo @@ -424,6 +429,21 @@ share/locale/uk/LC_MESSAGES/kalzium.mo share/locale/xh/LC_MESSAGES/kalzium.mo share/locale/zh_CN/LC_MESSAGES/kalzium.mo share/locale/zh_TW/LC_MESSAGES/kalzium.mo +share/man/ca/man1/kalzium.1.gz +share/man/da/man1/kalzium.1.gz +share/man/de/man1/kalzium.1.gz +share/man/es/man1/kalzium.1.gz +share/man/et/man1/kalzium.1.gz +share/man/fr/man1/kalzium.1.gz +share/man/gl/man1/kalzium.1.gz +share/man/it/man1/kalzium.1.gz share/man/man1/kalzium.1.gz +share/man/nl/man1/kalzium.1.gz +share/man/pl/man1/kalzium.1.gz +share/man/pt/man1/kalzium.1.gz +share/man/pt_BR/man1/kalzium.1.gz +share/man/ru/man1/kalzium.1.gz +share/man/sv/man1/kalzium.1.gz +share/man/uk/man1/kalzium.1.gz share/metainfo/org.kde.kalzium.appdata.xml share/qlogging-categories6/kalzium.categories diff --git a/science/mbdyn/Makefile b/science/mbdyn/Makefile index c65f1560bb54..4ac211eda4e6 100644 --- a/science/mbdyn/Makefile +++ b/science/mbdyn/Makefile @@ -1,6 +1,6 @@ PORTNAME= mbdyn DISTVERSION= 1.7.3 -PORTREVISION= 18 +PORTREVISION= 19 CATEGORIES= science MASTER_SITES= https://www.mbdyn.org/userfiles/downloads/ diff --git a/science/mcpl/Makefile b/science/mcpl/Makefile index 7ee2ca520278..25c22bb8a36c 100644 --- a/science/mcpl/Makefile +++ b/science/mcpl/Makefile @@ -11,6 +11,9 @@ WWW= https://mctools.github.io/mcpl/ \ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE +NOT_FOR_ARCHS= armv7 powerpc i386 +NOT_FOR_ARCHS_REASON= MCPL does not support 32 bit platforms + BROKEN_i386= compilation fails, see https://github.com/mctools/mcpl/issues/88 USES= cmake:testing diff --git a/science/molgif/Makefile b/science/molgif/Makefile index cec8591a420f..280dc2503615 100644 --- a/science/molgif/Makefile +++ b/science/molgif/Makefile @@ -1,6 +1,6 @@ PORTNAME= molgif DISTVERSION= g20180108 -PORTREVISION= 28 +PORTREVISION= 29 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/ncrystal/Makefile b/science/ncrystal/Makefile index 9cfb8da272b6..8738797874bd 100644 --- a/science/ncrystal/Makefile +++ b/science/ncrystal/Makefile @@ -1,6 +1,6 @@ PORTNAME= ncrystal DISTVERSIONPREFIX= v -DISTVERSION= 4.2.6 +DISTVERSION= 4.2.8 CATEGORIES= science # physics MAINTAINER= yuri@FreeBSD.org @@ -21,9 +21,6 @@ SHEBANG_FILES= tests/scripts/* CMAKE_TESTING_ON= NCRYSTAL_ENABLE_TESTING \ NCRYSTAL_ENABLE_CORE_TEST -post-install: # workaround for https://github.com/mctools/ncrystal/issues/150 - @${RM} ${STAGEDIR}${PREFIX}/*.sh - -# tests as of 4.2.6: 52% tests passed, 42 tests failed out of 87 +# tests as of 4.2.6: 51% tests passed, 43 tests failed out of 88 (only py_xx tests fail) .include <bsd.port.mk> diff --git a/science/ncrystal/distinfo b/science/ncrystal/distinfo index 1a8eec6572c9..ebf4e8a8d01a 100644 --- a/science/ncrystal/distinfo +++ b/science/ncrystal/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1753507988 -SHA256 (mctools-ncrystal-v4.2.6_GH0.tar.gz) = 4e7926d8bb931cce3546e9406a2a3d9b182b864e94ce34e31b1a6d9475479602 -SIZE (mctools-ncrystal-v4.2.6_GH0.tar.gz) = 2821990 +TIMESTAMP = 1754558330 +SHA256 (mctools-ncrystal-v4.2.8_GH0.tar.gz) = 499e355e8cb534954101241c5af1f3d4f729aa87f4d63734b05570033a5d6dbd +SIZE (mctools-ncrystal-v4.2.8_GH0.tar.gz) = 2822048 diff --git a/science/openmc/Makefile b/science/openmc/Makefile index 9481907cdec7..dd31d577e3d7 100644 --- a/science/openmc/Makefile +++ b/science/openmc/Makefile @@ -1,6 +1,7 @@ PORTNAME= openmc DISTVERSIONPREFIX= v DISTVERSION= 0.15.0 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -12,7 +13,7 @@ WWW= https://openmc.org/ \ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE -BROKEN_FreeBSD_15= compilation fails with clang-19, see https://github.com/openmc-dev/openmc/issues/3183 +BROKEN= compilation fails with clang-19, see https://github.com/openmc-dev/openmc/issues/3183 BUILD_DEPENDS= xtensor>0:math/xtensor LIB_DEPENDS= libfmt.so:devel/libfmt \ diff --git a/science/opensph/Makefile b/science/opensph/Makefile index 84075c2486e7..8550bb4472b0 100644 --- a/science/opensph/Makefile +++ b/science/opensph/Makefile @@ -1,6 +1,6 @@ PORTNAME= OpenSPH DISTVERSION= 0.4.1 -PORTREVISION= 8 +PORTREVISION= 9 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/paje/Makefile b/science/paje/Makefile index 6c6a554a8b5b..0d73a91fe8bf 100644 --- a/science/paje/Makefile +++ b/science/paje/Makefile @@ -1,6 +1,6 @@ PORTNAME= paje PORTVERSION= 1.97 -PORTREVISION= 12 +PORTREVISION= 13 CATEGORIES= science gnustep MASTER_SITES= SF/${PORTNAME}/Releases DISTNAME= Paje_${PORTVERSION} diff --git a/science/py-eccodes/Makefile b/science/py-eccodes/Makefile index 5f7093dce593..044eb813edc2 100644 --- a/science/py-eccodes/Makefile +++ b/science/py-eccodes/Makefile @@ -1,5 +1,5 @@ PORTNAME= eccodes -PORTVERSION= 2.42.0 +PORTVERSION= 2.43.0 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-eccodes/distinfo b/science/py-eccodes/distinfo index 21954c2072d6..e37fc89abc25 100644 --- a/science/py-eccodes/distinfo +++ b/science/py-eccodes/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1750954222 -SHA256 (eccodes-2.42.0.tar.gz) = 0abb2bc6c6f4e83749c4e9c313d5428c62b15dc6c5b47d2807943e3a5ffd5291 -SIZE (eccodes-2.42.0.tar.gz) = 2268756 +TIMESTAMP = 1753796092 +SHA256 (eccodes-2.43.0.tar.gz) = b99c41aaa64b20291452297a3d513e0b08cc96bcedfe364d8f58348159c48faa +SIZE (eccodes-2.43.0.tar.gz) = 2269307 diff --git a/science/py-eccodes/files/patch-setup.py b/science/py-eccodes/files/patch-setup.py new file mode 100644 index 000000000000..8a15aeac70e2 --- /dev/null +++ b/science/py-eccodes/files/patch-setup.py @@ -0,0 +1,10 @@ +--- setup.py.orig 2025-07-25 10:03:25 UTC ++++ setup.py +@@ -90,7 +90,6 @@ install_requires += [ + "attrs", + "cffi", + "findlibs", +- "eccodeslib;platform_system!='Windows'", + ] + + setuptools.setup( diff --git a/science/py-ncrystal/Makefile b/science/py-ncrystal/Makefile index ed1e1279b00e..c6a90d0c973f 100644 --- a/science/py-ncrystal/Makefile +++ b/science/py-ncrystal/Makefile @@ -1,6 +1,6 @@ PORTNAME= ncrystal DISTVERSIONPREFIX= v -DISTVERSION= 4.2.6 +DISTVERSION= 4.2.8 CATEGORIES= science # physics PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-ncrystal/distinfo b/science/py-ncrystal/distinfo index aca64d45e427..335765086002 100644 --- a/science/py-ncrystal/distinfo +++ b/science/py-ncrystal/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1753507607 -SHA256 (mctools-ncrystal-v4.2.6_GH0.tar.gz) = 4e7926d8bb931cce3546e9406a2a3d9b182b864e94ce34e31b1a6d9475479602 -SIZE (mctools-ncrystal-v4.2.6_GH0.tar.gz) = 2821990 +TIMESTAMP = 1754559207 +SHA256 (mctools-ncrystal-v4.2.8_GH0.tar.gz) = 499e355e8cb534954101241c5af1f3d4f729aa87f4d63734b05570033a5d6dbd +SIZE (mctools-ncrystal-v4.2.8_GH0.tar.gz) = 2822048 diff --git a/science/py-scikit-sparse/Makefile b/science/py-scikit-sparse/Makefile index ecc38f90c432..e80c63af51fe 100644 --- a/science/py-scikit-sparse/Makefile +++ b/science/py-scikit-sparse/Makefile @@ -1,6 +1,7 @@ PORTNAME= scikit-sparse DISTVERSIONPREFIX= v DISTVERSION= 0.4.16 +PORTREVISION= 1 CATEGORIES= science python #MASTER_SITES= PYPI # missing files under tests/ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/qiskit-aer/Makefile b/science/qiskit-aer/Makefile index ef595842d8e7..9a818aa16f08 100644 --- a/science/qiskit-aer/Makefile +++ b/science/qiskit-aer/Makefile @@ -1,6 +1,6 @@ PORTNAME= qiskit-aer DISTVERSION= 0.16.0.1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science # quantum-computing MAINTAINER= yuri@FreeBSD.org diff --git a/science/seacas/Makefile b/science/seacas/Makefile index dab6f638940e..21b0c9a3d190 100644 --- a/science/seacas/Makefile +++ b/science/seacas/Makefile @@ -1,6 +1,7 @@ PORTNAME= seacas DISTVERSIONPREFIX= v DISTVERSION= 2025-03-13 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/siconos/Makefile b/science/siconos/Makefile index 463c424c080d..587760c82cc4 100644 --- a/science/siconos/Makefile +++ b/science/siconos/Makefile @@ -1,6 +1,6 @@ PORTNAME= siconos DISTVERSION= 4.5.0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/step/distinfo b/science/step/distinfo index d0003f376b70..b2a6ad4575c2 100644 --- a/science/step/distinfo +++ b/science/step/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1751381646 -SHA256 (KDE/release-service/25.04.3/step-25.04.3.tar.xz) = 0aa86e2dd0bebbd9da8b8b77d0da3cd924e25be7084accaf11850d51857fba3e -SIZE (KDE/release-service/25.04.3/step-25.04.3.tar.xz) = 987244 +TIMESTAMP = 1754646550 +SHA256 (KDE/release-service/25.08.0/step-25.08.0.tar.xz) = 994bab4d0750cfdeb3af1f92d6453ee173cd483e392ad170bf5250b23b4ddf3a +SIZE (KDE/release-service/25.08.0/step-25.08.0.tar.xz) = 1004072 diff --git a/science/step/pkg-plist b/science/step/pkg-plist index f0365a2c6bf1..4186212eb37b 100644 --- a/science/step/pkg-plist +++ b/science/step/pkg-plist @@ -133,6 +133,8 @@ share/locale/lt/LC_MESSAGES/step_example_files.mo share/locale/lt/LC_MESSAGES/step_objinfo_files.mo share/locale/lt/LC_MESSAGES/step_qt.qm share/locale/lv/LC_MESSAGES/step.mo +share/locale/lv/LC_MESSAGES/step_example_files.mo +share/locale/lv/LC_MESSAGES/step_objinfo_files.mo share/locale/lv/LC_MESSAGES/step_qt.qm share/locale/mai/LC_MESSAGES/step_qt.qm share/locale/ml/LC_MESSAGES/step.mo @@ -561,6 +563,23 @@ share/mime/packages/org.kde.step.xml %%DATADIR%%/examples/lt/solar.step %%DATADIR%%/examples/lt/springs.step %%DATADIR%%/examples/lt/wave.step +%%DATADIR%%/examples/lv/brownian.step +%%DATADIR%%/examples/lv/doublependulum.step +%%DATADIR%%/examples/lv/eightpendula.step +%%DATADIR%%/examples/lv/first.step +%%DATADIR%%/examples/lv/fourpendula.step +%%DATADIR%%/examples/lv/gas.step +%%DATADIR%%/examples/lv/graph.step +%%DATADIR%%/examples/lv/liquid.step +%%DATADIR%%/examples/lv/lissajous.step +%%DATADIR%%/examples/lv/motor.step +%%DATADIR%%/examples/lv/motor1.step +%%DATADIR%%/examples/lv/note.step +%%DATADIR%%/examples/lv/resonance.step +%%DATADIR%%/examples/lv/softbody.step +%%DATADIR%%/examples/lv/solar.step +%%DATADIR%%/examples/lv/springs.step +%%DATADIR%%/examples/lv/wave.step %%DATADIR%%/examples/ml/brownian.step %%DATADIR%%/examples/ml/doublependulum.step %%DATADIR%%/examples/ml/eightpendula.step @@ -1198,6 +1217,25 @@ share/mime/packages/org.kde.step.xml %%DATADIR%%/objinfo/l10n/lt/spring.html %%DATADIR%%/objinfo/l10n/lt/weightforce.html %%DATADIR%%/objinfo/l10n/lt/world.html +%%DATADIR%%/objinfo/l10n/lv/anchor.html +%%DATADIR%%/objinfo/l10n/lv/box.html +%%DATADIR%%/objinfo/l10n/lv/chargedparticle.html +%%DATADIR%%/objinfo/l10n/lv/coulombforce.html +%%DATADIR%%/objinfo/l10n/lv/disk.html +%%DATADIR%%/objinfo/l10n/lv/gas.html +%%DATADIR%%/objinfo/l10n/lv/gasljforce.html +%%DATADIR%%/objinfo/l10n/lv/gasparticle.html +%%DATADIR%%/objinfo/l10n/lv/gravitationforce.html +%%DATADIR%%/objinfo/l10n/lv/linearmotor.html +%%DATADIR%%/objinfo/l10n/lv/meter.html +%%DATADIR%%/objinfo/l10n/lv/note.html +%%DATADIR%%/objinfo/l10n/lv/particle.html +%%DATADIR%%/objinfo/l10n/lv/pin.html +%%DATADIR%%/objinfo/l10n/lv/polygon.html +%%DATADIR%%/objinfo/l10n/lv/softbody.html +%%DATADIR%%/objinfo/l10n/lv/spring.html +%%DATADIR%%/objinfo/l10n/lv/weightforce.html +%%DATADIR%%/objinfo/l10n/lv/world.html %%DATADIR%%/objinfo/l10n/ml/anchor.html %%DATADIR%%/objinfo/l10n/ml/box.html %%DATADIR%%/objinfo/l10n/ml/chargedparticle.html @@ -1555,6 +1593,11 @@ share/mime/packages/org.kde.step.xml %%DATADIR%%/tutorials/lt/tutorial3.step %%DATADIR%%/tutorials/lt/tutorial4.step %%DATADIR%%/tutorials/lt/tutorial5.step +%%DATADIR%%/tutorials/lv/tutorial1.step +%%DATADIR%%/tutorials/lv/tutorial2.step +%%DATADIR%%/tutorials/lv/tutorial3.step +%%DATADIR%%/tutorials/lv/tutorial4.step +%%DATADIR%%/tutorials/lv/tutorial5.step %%DATADIR%%/tutorials/ml/tutorial1.step %%DATADIR%%/tutorials/ml/tutorial2.step %%DATADIR%%/tutorials/ml/tutorial3.step diff --git a/science/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/trilinos/Makefile b/science/trilinos/Makefile index 6c5576de4913..d2c8f9e9253c 100644 --- a/science/trilinos/Makefile +++ b/science/trilinos/Makefile @@ -1,6 +1,7 @@ PORTNAME= trilinos DISTVERSIONPREFIX= trilinos-release- DISTVERSION= 16-1-0 +PORTREVISION= 1 CATEGORIES= science # physics MAINTAINER= yuri@FreeBSD.org diff --git a/science/vipster/Makefile b/science/vipster/Makefile index e0b096c3b3ea..18acb86d904d 100644 --- a/science/vipster/Makefile +++ b/science/vipster/Makefile @@ -1,6 +1,7 @@ PORTNAME= vipster DISTVERSIONPREFIX= v DISTVERSION= 1.19.1b-109 +PORTREVISION= 1 DISTVERSIONSUFFIX= -gfb4a6ed CATEGORIES= science |