diff options
Diffstat (limited to 'science/rdkit')
| -rw-r--r-- | science/rdkit/Makefile | 68 | ||||
| -rw-r--r-- | science/rdkit/distinfo | 30 | ||||
| -rw-r--r-- | science/rdkit/files/patch-CMakeLists.txt | 27 | ||||
| -rw-r--r-- | science/rdkit/pkg-plist | 25 |
4 files changed, 106 insertions, 44 deletions
diff --git a/science/rdkit/Makefile b/science/rdkit/Makefile index dd2255f3a900..f02115771af1 100644 --- a/science/rdkit/Makefile +++ b/science/rdkit/Makefile @@ -1,12 +1,19 @@ PORTNAME= rdkit DISTVERSIONPREFIX= Release_ -DISTVERSION= 2025_03_1 -PORTREVISION= 2 +DISTVERSION= 2025_09_2 CATEGORIES= science -MASTER_SITES= LOCAL/yuri/:font # unstable, changing font file: https://fonts.google.com/download?family=Comic%20Neue&dummy=/:font -DISTFILES= ComicNeue-Regular.ttf:font +MASTER_SITES= https://github.com/schrodinger/maeparser/archive/:maeparser \ + https://github.com/schrodinger/coordgenlibs/archive/:coordgen \ + https://codeload.github.com/Glysade/chemdraw/tar.gz/refs/tags/:chemdraw \ + https://github.com/Tencent/rapidjson/archive/:rapidjson \ + LOCAL/yuri/:font # unstable, changing font file: https://fonts.google.com/download?family=Comic%20Neue&dummy=/:font +DISTFILES= v${MAEPARSER_VERSION}.tar.gz:maeparser \ + v${COORDGEN_VERSION}.tar.gz:coordgen \ + v${CHEMDRAW_VERSION}:chemdraw \ + v${RAPIDJSON_VERSION}.tar.gz:rapidjson \ + ComicNeue-Regular.ttf:font DIST_SUBDIR= ${PORTNAME}-${PORTVERSION} -EXTRACT_ONLY= ${DISTFILES:C/:.*//:N*.ttf} +EXTRACT_ONLY= ${DISTFILES:C/:.*//:Nv*:N*.ttf} MAINTAINER= yuri@FreeBSD.org COMMENT= Collection of cheminformatics and machine-learning software @@ -16,19 +23,14 @@ WWW= https://www.rdkit.org/ \ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/license.txt -BROKEN_FreeBSD_15_aarch64= clang-17 crashes, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=272652 -BROKEN_FreeBSD_15_amd64= clang-17 crashes, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=272652 -BROKEN_FreeBSD_15_i386= clang-17 crashes, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=272652 +BROKEN_FreeBSD_16_amd64= clang crashes, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=272652 BUILD_DEPENDS= catch>0:devel/catch \ - flex:textproc/flex \ - rapidjson>=0:devel/rapidjson -LIB_DEPENDS= libboost_system.so:devel/boost-libs \ - libcoordgen.so:science/coordgenlibs \ - libfreetype.so:print/freetype2 \ - libmaeparser.so:science/maeparser - -USES= bison:build cmake:testing compiler:c++11-lang eigen:3 gnome python + flex:textproc/flex +LIB_DEPENDS= libboost_thread.so:devel/boost-libs \ + libfreetype.so:print/freetype2 + +USES= bison:build cmake:testing compiler:c++11-lang eigen:3 gnome pkgconfig python USE_GNOME= cairo USE_LDCONFIG= yes @@ -37,6 +39,11 @@ GH_TUPLE= rareylab:RingDecomposerLib:v1.1.3_rdkit:RingDecomposerLib/External/Rin GH_TUPLE+= ncbi:pubchem-align3d:daefab3:align3d/External/pubchem_shape/pubchem-align3d \ aantron:better-enums:520d8ee:better_enums/better_enums +MAEPARSER_VERSION= 1.3.3 +COORDGEN_VERSION= 3.0.2 +CHEMDRAW_VERSION= 1.0.11 +RAPIDJSON_VERSION= 1.1.0 + CMAKE_ON= RDK_BUILD_CAIRO_SUPPORT CMAKE_OFF= RDK_INSTALL_INTREE RDK_USE_FLEXBISON \ RDK_INSTALL_STATIC_LIBS RDK_SWIG_STATIC RDK_PGSQL_STATIC \ @@ -89,14 +96,39 @@ PLIST_SUB+= LITTLE_ENDIAN="" .endif post-extract: - @${MKDIR} ${WRKSRC}/External/rapidjson-1.1.0 - @cd ${WRKSRC}/External/rapidjson-1.1.0 && ${LN} -s ${LOCALBASE}/include/rapidjson include + #@${MKDIR} ${WRKSRC}/External/rapidjson-1.1.0 + #@cd ${WRKSRC}/External/rapidjson-1.1.0 && ${LN} -s ${LOCALBASE}/include/rapidjson include @cd ${WRKSRC}/Data/Fonts && ${CP} ${DISTDIR}/${DIST_SUBDIR}/ComicNeue-Regular.ttf . @${CP} ${WRKSRC}/better_enums/enum.h ${WRKSRC}/Code/RDGeneral +post-patch: + # replace the URLs for fetched libs with the local file path to the distfiles, so that it can be used without internet access + @${REINPLACE_CMD} \ + -e 's|https://github.com/schrodinger/maeparser/archive/|file://${DISTDIR}/${DIST_SUBDIR}/|g' \ + ${WRKSRC}/External/CoordGen/CMakeLists.txt + @${REINPLACE_CMD} \ + -e 's|https://github.com/schrodinger/coordgenlibs/archive/|file://${DISTDIR}/${DIST_SUBDIR}/|g' \ + ${WRKSRC}/External/CoordGen/CMakeLists.txt + @${REINPLACE_CMD} \ + -e 's|https://codeload.github.com/Glysade/chemdraw/tar.gz/refs/tags/|file://${DISTDIR}/${DIST_SUBDIR}/|g' \ + ${WRKSRC}/External/ChemDraw/CMakeLists.txt + @${REINPLACE_CMD} \ + -e 's|https://github.com/Tencent/rapidjson/archive/|file://${DISTDIR}/${DIST_SUBDIR}/|g' \ + ${WRKSRC}/Code/GraphMol/MolInterchange/CMakeLists.txt + +pre-build: + @${REINPLACE_CMD} \ + -e 's|const SizeType length;|SizeType length;|g' \ + ${WRKSRC}/External/rapidjson/rapidjson-1.1.0/include/rapidjson/document.h + +post-install: + @${RM} -f ${STAGEDIR}${PREFIX}/lib/libexpat.a + post-install-PGSQL-on: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/postgresql/rdkit.so # many tests fail, see https://github.com/rdkit/rdkit/issues/7779 +# tests as of 2025_09_1: 65% tests passed, 24 tests failed out of 68 +# tests as of 2025_09_2: 63% tests passed, 26 tests failed out of 70 .include <bsd.port.mk> diff --git a/science/rdkit/distinfo b/science/rdkit/distinfo index fe4d068e756e..2dd40d607202 100644 --- a/science/rdkit/distinfo +++ b/science/rdkit/distinfo @@ -1,11 +1,19 @@ -TIMESTAMP = 1744735395 -SHA256 (rdkit-2025.03.1/ComicNeue-Regular.ttf) = 4f0f67d826565ed55f91ca6512e5562d0f2a39030fc7208519354438bc783ff6 -SIZE (rdkit-2025.03.1/ComicNeue-Regular.ttf) = 21915 -SHA256 (rdkit-2025.03.1/rdkit-rdkit-Release_2025_03_1_GH0.tar.gz) = 947e5aa004047fbec4bf4ba93b84a50ca7f68e248a0654080d8ca0cdb06e3534 -SIZE (rdkit-2025.03.1/rdkit-rdkit-Release_2025_03_1_GH0.tar.gz) = 82192067 -SHA256 (rdkit-2025.03.1/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 944b5816712a48bbf88aa25d4300ce11871ddf6e971218eac08f90ed2192f715 -SIZE (rdkit-2025.03.1/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 137931 -SHA256 (rdkit-2025.03.1/ncbi-pubchem-align3d-daefab3_GH0.tar.gz) = d7814a00a39f6a798bc1611d0f7bbd1abc91d754309527a9038a0dad42d848c0 -SIZE (rdkit-2025.03.1/ncbi-pubchem-align3d-daefab3_GH0.tar.gz) = 112376 -SHA256 (rdkit-2025.03.1/aantron-better-enums-520d8ee_GH0.tar.gz) = 29ef26e79eb489b3ef71f85f904f3f1173ffefc6c853219bee7520188805eca5 -SIZE (rdkit-2025.03.1/aantron-better-enums-520d8ee_GH0.tar.gz) = 136592 +TIMESTAMP = 1762809861 +SHA256 (rdkit-2025.09.2/v1.3.3.tar.gz) = 78e7571a779ea4952e752ecef57c62fb26463947e29ef7f4b31b11988d88ca07 +SIZE (rdkit-2025.09.2/v1.3.3.tar.gz) = 39896 +SHA256 (rdkit-2025.09.2/v3.0.2.tar.gz) = f67697434f7fec03bca150a6d84ea0e8409f6ec49d5aab43badc5833098ff4e3 +SIZE (rdkit-2025.09.2/v3.0.2.tar.gz) = 166817 +SHA256 (rdkit-2025.09.2/v1.0.11) = 405869fc8b3f73395047bc7c54e1da62ef66c08d48bd71af66e47ec9cbe86814 +SIZE (rdkit-2025.09.2/v1.0.11) = 1043261 +SHA256 (rdkit-2025.09.2/v1.1.0.tar.gz) = bf7ced29704a1e696fbccf2a2b4ea068e7774fa37f6d7dd4039d0787f8bed98e +SIZE (rdkit-2025.09.2/v1.1.0.tar.gz) = 1019402 +SHA256 (rdkit-2025.09.2/ComicNeue-Regular.ttf) = 4f0f67d826565ed55f91ca6512e5562d0f2a39030fc7208519354438bc783ff6 +SIZE (rdkit-2025.09.2/ComicNeue-Regular.ttf) = 21915 +SHA256 (rdkit-2025.09.2/rdkit-rdkit-Release_2025_09_2_GH0.tar.gz) = db3254e88ef17cac7bb8480e6da9d1e69dfe180c21774b11637d8a17b5a98fb9 +SIZE (rdkit-2025.09.2/rdkit-rdkit-Release_2025_09_2_GH0.tar.gz) = 82911180 +SHA256 (rdkit-2025.09.2/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 944b5816712a48bbf88aa25d4300ce11871ddf6e971218eac08f90ed2192f715 +SIZE (rdkit-2025.09.2/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 137931 +SHA256 (rdkit-2025.09.2/ncbi-pubchem-align3d-daefab3_GH0.tar.gz) = d7814a00a39f6a798bc1611d0f7bbd1abc91d754309527a9038a0dad42d848c0 +SIZE (rdkit-2025.09.2/ncbi-pubchem-align3d-daefab3_GH0.tar.gz) = 112376 +SHA256 (rdkit-2025.09.2/aantron-better-enums-520d8ee_GH0.tar.gz) = 29ef26e79eb489b3ef71f85f904f3f1173ffefc6c853219bee7520188805eca5 +SIZE (rdkit-2025.09.2/aantron-better-enums-520d8ee_GH0.tar.gz) = 136592 diff --git a/science/rdkit/files/patch-CMakeLists.txt b/science/rdkit/files/patch-CMakeLists.txt index 2145ea31191e..4d7146e3b2c3 100644 --- a/science/rdkit/files/patch-CMakeLists.txt +++ b/science/rdkit/files/patch-CMakeLists.txt @@ -1,6 +1,6 @@ ---- CMakeLists.txt.orig 2025-03-31 18:11:10 UTC +--- CMakeLists.txt.orig 2025-09-30 06:13:45 UTC +++ CMakeLists.txt -@@ -78,12 +78,12 @@ if(NOT MSVC) +@@ -81,12 +81,12 @@ if(NOT MSVC) if(NOT MSVC) if(RDK_OPTIMIZE_POPCNT) @@ -17,26 +17,23 @@ endif() endif() endif() -@@ -166,18 +166,6 @@ endif() +@@ -179,15 +179,7 @@ endif() FetchContent_MakeAvailable(Catch2) endif() --#include better-enums --find_package(better_enums 0 QUIET) --if(NOT better_enums) -- Include(FetchContent) -- -- FetchContent_Declare( -- better_enums -- GIT_REPOSITORY https://github.com/aantron/better-enums.git -- GIT_TAG c35576bed0295689540b39873126129adfa0b4c8 # 0.11.3 -- ) --endif() +-# make sure we have better_enums +-Include(FetchContent) + +-FetchContent_Declare( +- better_enums +- GIT_REPOSITORY https://github.com/aantron/better-enums.git +- GIT_TAG c35576bed0295689540b39873126129adfa0b4c8 # 0.11.3 +-) - if(RDK_INSTALL_INTREE) set(RDKit_BinDir "${CMAKE_SOURCE_DIR}/bin") set(RDKit_LibDir "${CMAKE_SOURCE_DIR}/lib") -@@ -530,12 +518,14 @@ if(NOT RDK_INSTALL_INTREE) +@@ -535,12 +527,14 @@ if(NOT RDK_INSTALL_INTREE) COMPONENT data PATTERN ".svn" EXCLUDE ) diff --git a/science/rdkit/pkg-plist b/science/rdkit/pkg-plist index db5a4c43384e..3cd23f7e900b 100644 --- a/science/rdkit/pkg-plist +++ b/science/rdkit/pkg-plist @@ -133,6 +133,8 @@ include/rdkit/GraphMol/Descriptors/USRDescriptor.h include/rdkit/GraphMol/Descriptors/WHIM.h include/rdkit/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h include/rdkit/GraphMol/DistGeomHelpers/Embedder.h +include/rdkit/GraphMol/EnumerateStereoisomers/EnumerateStereoisomers.h +include/rdkit/GraphMol/EnumerateStereoisomers/Flippers.h include/rdkit/GraphMol/FMCS/FMCS.h include/rdkit/GraphMol/FMCS/Graph.h include/rdkit/GraphMol/FileParsers/CDXMLParser.h @@ -291,6 +293,8 @@ include/rdkit/GraphMol/TautomerQuery/TautomerQuery.h include/rdkit/GraphMol/Trajectory/Snapshot.h include/rdkit/GraphMol/Trajectory/Trajectory.h include/rdkit/GraphMol/atomic_data.h +include/rdkit/GraphMol/chemdraw.h +include/rdkit/GraphMol/chemdrawreaction.h include/rdkit/GraphMol/details.h include/rdkit/GraphMol/new_canon.h include/rdkit/Numerics/Alignment/AlignPoints.h @@ -381,6 +385,9 @@ lib/libRDKitCIPLabeler.so.1.%%SHLIB_VER%% lib/libRDKitCatalogs.so lib/libRDKitCatalogs.so.1 lib/libRDKitCatalogs.so.1.%%SHLIB_VER%% +lib/libRDKitChemDraw.so +lib/libRDKitChemDraw.so.1 +lib/libRDKitChemDraw.so.1.%%SHLIB_VER%% lib/libRDKitChemReactions.so lib/libRDKitChemReactions.so.1 lib/libRDKitChemReactions.so.1.%%SHLIB_VER%% @@ -411,6 +418,9 @@ lib/libRDKitDistGeometry.so.1.%%SHLIB_VER%% lib/libRDKitEigenSolvers.so lib/libRDKitEigenSolvers.so.1 lib/libRDKitEigenSolvers.so.1.%%SHLIB_VER%% +lib/libRDKitEnumerateStereoisomers.so +lib/libRDKitEnumerateStereoisomers.so.1 +lib/libRDKitEnumerateStereoisomers.so.1.%%SHLIB_VER%% lib/libRDKitFMCS.so lib/libRDKitFMCS.so.1 lib/libRDKitFMCS.so.1.%%SHLIB_VER%% @@ -498,6 +508,12 @@ lib/libRDKitPubChemShape.so.1.%%SHLIB_VER%% %%PYTHON%%lib/libRDKitRDBoost.so %%PYTHON%%lib/libRDKitRDBoost.so.1 %%PYTHON%%lib/libRDKitRDBoost.so.1.%%SHLIB_VER%% +lib/libRDKitRDChemDrawLib.so +lib/libRDKitRDChemDrawLib.so.1 +lib/libRDKitRDChemDrawLib.so.1.%%SHLIB_VER%% +lib/libRDKitRDChemDrawReactionLib.so +lib/libRDKitRDChemDrawReactionLib.so.1 +lib/libRDKitRDChemDrawReactionLib.so.1.%%SHLIB_VER%% lib/libRDKitRDGeneral.so lib/libRDKitRDGeneral.so.1 lib/libRDKitRDGeneral.so.1.%%SHLIB_VER%% @@ -552,12 +568,18 @@ lib/libRDKitTautomerQuery.so.1.%%SHLIB_VER%% lib/libRDKitTrajectory.so lib/libRDKitTrajectory.so.1 lib/libRDKitTrajectory.so.1.%%SHLIB_VER%% +lib/libRDKitcoordgen.so +lib/libRDKitcoordgen.so.1 +lib/libRDKitcoordgen.so.1.%%SHLIB_VER%% lib/libRDKitga.so lib/libRDKitga.so.1 lib/libRDKitga.so.1.%%SHLIB_VER%% %%LITTLE_ENDIAN%%lib/libRDKithc.so %%LITTLE_ENDIAN%%lib/libRDKithc.so.1 %%LITTLE_ENDIAN%%lib/libRDKithc.so.1.%%SHLIB_VER%% +lib/libRDKitmaeparser.so +lib/libRDKitmaeparser.so.1 +lib/libRDKitmaeparser.so.1.%%SHLIB_VER%% %%PGSQL%%lib/postgresql/rdkit.so %%PYTHON%%lib/libRDKitpubchem_align3d.so %%PYTHON%%lib/libRDKitpubchem_align3d.so.1 @@ -688,12 +710,14 @@ lib/libRDKitga.so.1.%%SHLIB_VER%% %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/nbtests/rdkit-structure-renderer.ipynb %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdAbbreviations.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdCIPLabeler.so +%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdChemDraw.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdChemReactions.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdChemicalFeatures.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdCoordGen.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdDepictor.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdDeprotect.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdDistGeom.so +%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdEnumerateStereoisomers.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdFMCS.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdFingerprintGenerator.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdForceFieldHelpers.so @@ -1176,6 +1200,7 @@ lib/libRDKitga.so.1.%%SHLIB_VER%% %%PYTHON%%%%DATADIR%%/Scripts/create_deb_packages.sh %%PYTHON%%%%DATADIR%%/Scripts/gen_rdkit_stubs/__init__.py %%PYTHON%%%%DATADIR%%/Scripts/gen_rdkit_stubs/__main__.py +%%PYTHON%%%%DATADIR%%/Scripts/gen_rdkit_stubs/patch/rdkit/Chem/inchi.pyi.diff %%PYTHON%%%%DATADIR%%/Scripts/gen_rdkit_stubs/worker.py %%PYTHON%%%%DATADIR%%/Scripts/patch_rdkit_docstrings/__init__.py %%PYTHON%%%%DATADIR%%/Scripts/patch_rdkit_docstrings/__main__.py |