git: d8e71b111189 - main - science/rdkit: update 2024_09_4 → 2025_03_1

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From: Yuri Victorovich <yuri_at_FreeBSD.org>
Date: Tue, 15 Apr 2025 21:20:12 UTC
The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=d8e71b111189f0fadf0a5448419d46d9dfcad23d

commit d8e71b111189f0fadf0a5448419d46d9dfcad23d
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2025-04-15 21:19:48 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2025-04-15 21:20:10 +0000

    science/rdkit: update 2024_09_4 → 2025_03_1
---
 science/rdkit/Makefile                             | 15 ++++++++-----
 science/rdkit/distinfo                             | 20 +++++++++--------
 science/rdkit/files/patch-CMakeLists.txt           | 25 +++++++++++++++++++---
 .../files/patch-Code_RDGeneral_CMakeLists.txt      | 14 ++++++++++++
 science/rdkit/pkg-plist                            | 19 +++++++++++++---
 5 files changed, 73 insertions(+), 20 deletions(-)

diff --git a/science/rdkit/Makefile b/science/rdkit/Makefile
index c76a5341ccb3..ce633602a1ba 100644
--- a/science/rdkit/Makefile
+++ b/science/rdkit/Makefile
@@ -1,7 +1,6 @@
 PORTNAME=	rdkit
 DISTVERSIONPREFIX=	Release_
-DISTVERSION=	2024_09_4
-PORTREVISION=	1
+DISTVERSION=	2025_03_1
 CATEGORIES=	science
 MASTER_SITES=	LOCAL/yuri/:font # unstable, changing font file: https://fonts.google.com/download?family=Comic%20Neue&dummy=/:font
 DISTFILES=	ComicNeue-Regular.ttf:font
@@ -28,12 +27,16 @@ LIB_DEPENDS=	libboost_system.so:devel/boost-libs \
 		libfreetype.so:print/freetype2 \
 		libmaeparser.so:science/maeparser
 
-USES=		bison:build cmake:testing compiler:c++11-lang eigen:3 python
+USES=		bison:build cmake:testing compiler:c++11-lang eigen:3 gnome python
+USE_GNOME=	cairo
+USE_LDCONFIG=	yes
+
 USE_GITHUB=	yes
 GH_TUPLE=	rareylab:RingDecomposerLib:v1.1.3_rdkit:RingDecomposerLib/External/RingFamilies/RingDecomposerLib
-GH_TUPLE+=	ncbi:pubchem-align3d:daefab3:align3d/External/pubchem_shape/pubchem-align3d
-USE_LDCONFIG=	yes
+GH_TUPLE+=	ncbi:pubchem-align3d:daefab3:align3d/External/pubchem_shape/pubchem-align3d \
+		aantron:better-enums:520d8ee:better_enums/better_enums
 
+CMAKE_ON=	RDK_BUILD_CAIRO_SUPPORT
 CMAKE_OFF=	RDK_INSTALL_INTREE RDK_USE_FLEXBISON \
 		RDK_INSTALL_STATIC_LIBS RDK_SWIG_STATIC RDK_PGSQL_STATIC \
 		RDK_OPTIMIZE_NATIVE \
@@ -42,6 +45,7 @@ CMAKE_ARGS=	-DCATCH_DIR=${LOCALBASE}/include/catch2
 
 CFLAGS+=	-D_GNU_SOURCE
 CXXFLAGS+=	-D_GNU_SOURCE
+		#-I${WRKSRC}/better_enums
 
 DATADIR=	${PREFIX}/share/RDKit
 DOCSDIR=	${PREFIX}/share/doc/RDKit
@@ -87,6 +91,7 @@ post-extract:
 	@${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-install-PGSQL-on:
 	@${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/postgresql/rdkit.so
diff --git a/science/rdkit/distinfo b/science/rdkit/distinfo
index bf713ecd6c60..fe4d068e756e 100644
--- a/science/rdkit/distinfo
+++ b/science/rdkit/distinfo
@@ -1,9 +1,11 @@
-TIMESTAMP = 1734855089
-SHA256 (rdkit-2024.09.4/ComicNeue-Regular.ttf) = 4f0f67d826565ed55f91ca6512e5562d0f2a39030fc7208519354438bc783ff6
-SIZE (rdkit-2024.09.4/ComicNeue-Regular.ttf) = 21915
-SHA256 (rdkit-2024.09.4/rdkit-rdkit-Release_2024_09_4_GH0.tar.gz) = a5e8da75aae7e88f3a50d8577f9027c971187492a93a15085f797fe6fef74ad2
-SIZE (rdkit-2024.09.4/rdkit-rdkit-Release_2024_09_4_GH0.tar.gz) = 82055856
-SHA256 (rdkit-2024.09.4/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 944b5816712a48bbf88aa25d4300ce11871ddf6e971218eac08f90ed2192f715
-SIZE (rdkit-2024.09.4/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 137931
-SHA256 (rdkit-2024.09.4/ncbi-pubchem-align3d-daefab3_GH0.tar.gz) = d7814a00a39f6a798bc1611d0f7bbd1abc91d754309527a9038a0dad42d848c0
-SIZE (rdkit-2024.09.4/ncbi-pubchem-align3d-daefab3_GH0.tar.gz) = 112376
+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
diff --git a/science/rdkit/files/patch-CMakeLists.txt b/science/rdkit/files/patch-CMakeLists.txt
index ae2118c6df4d..2145ea31191e 100644
--- a/science/rdkit/files/patch-CMakeLists.txt
+++ b/science/rdkit/files/patch-CMakeLists.txt
@@ -1,6 +1,6 @@
---- CMakeLists.txt.orig	2024-12-20 08:56:08 UTC
+--- CMakeLists.txt.orig	2025-03-31 18:11:10 UTC
 +++ CMakeLists.txt
-@@ -76,12 +76,12 @@ if(NOT MSVC)
+@@ -78,12 +78,12 @@ if(NOT MSVC)
  
  if(NOT MSVC)
    if(RDK_OPTIMIZE_POPCNT)
@@ -17,7 +17,26 @@
      endif()
    endif()
  endif()
-@@ -516,12 +516,14 @@ if(NOT RDK_INSTALL_INTREE)
+@@ -166,18 +166,6 @@ 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()
+-
+ 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)
        COMPONENT data
        PATTERN ".svn" EXCLUDE
        )
diff --git a/science/rdkit/files/patch-Code_RDGeneral_CMakeLists.txt b/science/rdkit/files/patch-Code_RDGeneral_CMakeLists.txt
new file mode 100644
index 000000000000..590aeb419ef9
--- /dev/null
+++ b/science/rdkit/files/patch-Code_RDGeneral_CMakeLists.txt
@@ -0,0 +1,14 @@
+--- Code/RDGeneral/CMakeLists.txt.orig	2025-04-15 16:44:12 UTC
++++ Code/RDGeneral/CMakeLists.txt
+@@ -5,11 +5,6 @@ CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/RDConfig.h.
+ CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/RDConfig.h.cmake
+         ${CMAKE_CURRENT_SOURCE_DIR}/RDConfig.h)
+ 
+-FetchContent_MakeAvailable(better_enums)
+-if (NOT EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/enum.h)
+-    file(COPY ${better_enums_SOURCE_DIR}/enum.h DESTINATION ${CMAKE_CURRENT_SOURCE_DIR})
+-endif (NOT EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/enum.h)
+-
+ rdkit_library(RDGeneral
+         Invariant.cpp types.cpp utils.cpp RDGeneralExceptions.cpp RDLog.cpp
+         LocaleSwitcher.cpp versions.cpp SHARED)
diff --git a/science/rdkit/pkg-plist b/science/rdkit/pkg-plist
index 02d0d907d04d..db5a4c43384e 100644
--- a/science/rdkit/pkg-plist
+++ b/science/rdkit/pkg-plist
@@ -22,12 +22,9 @@ include/rdkit/DataStructs/SparseIntVect.h
 include/rdkit/DataStructs/base64.h
 include/rdkit/DistGeom/BoundsMatrix.h
 include/rdkit/DistGeom/ChiralSet.h
-include/rdkit/DistGeom/ChiralViolationContrib.h
 include/rdkit/DistGeom/ChiralViolationContribs.h
 include/rdkit/DistGeom/DistGeomUtils.h
-include/rdkit/DistGeom/DistViolationContrib.h
 include/rdkit/DistGeom/DistViolationContribs.h
-include/rdkit/DistGeom/FourthDimContrib.h
 include/rdkit/DistGeom/FourthDimContribs.h
 include/rdkit/DistGeom/TriangleSmooth.h
 include/rdkit/Features/Feature.h
@@ -100,6 +97,7 @@ include/rdkit/GraphMol/ChemReactions/ReactionUtils.h
 include/rdkit/GraphMol/ChemReactions/SanitizeRxn.h
 include/rdkit/GraphMol/ChemTransforms/ChemTransforms.h
 include/rdkit/GraphMol/ChemTransforms/MolFragmenter.h
+include/rdkit/GraphMol/ChemTransforms/MolFragmenterJSONParser.h
 include/rdkit/GraphMol/Chirality.h
 include/rdkit/GraphMol/Conformer.h
 include/rdkit/GraphMol/CoordGen.h
@@ -199,6 +197,7 @@ include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeature.h
 include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h
 include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h
 include/rdkit/GraphMol/MolDraw2D/MolDraw2D.h
+include/rdkit/GraphMol/MolDraw2D/MolDraw2DCairo.h
 include/rdkit/GraphMol/MolDraw2D/MolDraw2DHelpers.h
 include/rdkit/GraphMol/MolDraw2D/MolDraw2DJS.h
 include/rdkit/GraphMol/MolDraw2D/MolDraw2DSVG.h
@@ -246,6 +245,7 @@ include/rdkit/GraphMol/QueryOps.h
 include/rdkit/GraphMol/RDKitBase.h
 include/rdkit/GraphMol/RDKitQueries.h
 include/rdkit/GraphMol/RGroupDecomposition/RGroupDecomp.h
+include/rdkit/GraphMol/RGroupDecomposition/RGroupDecompJSONParsers.h
 include/rdkit/GraphMol/RGroupDecomposition/RGroupDecompParams.h
 include/rdkit/GraphMol/ROMol.h
 include/rdkit/GraphMol/RWMol.h
@@ -266,6 +266,7 @@ include/rdkit/GraphMol/ShapeHelpers/ShapeEncoder.h
 include/rdkit/GraphMol/ShapeHelpers/ShapeUtils.h
 include/rdkit/GraphMol/SmilesParse/CanonicalizeStereoGroups.h
 include/rdkit/GraphMol/SmilesParse/SmartsWrite.h
+include/rdkit/GraphMol/SmilesParse/SmilesJSONParsers.h
 include/rdkit/GraphMol/SmilesParse/SmilesParse.h
 include/rdkit/GraphMol/SmilesParse/SmilesParseOps.h
 include/rdkit/GraphMol/SmilesParse/SmilesWrite.h
@@ -283,6 +284,7 @@ include/rdkit/GraphMol/SynthonSpaceSearch/Synthon.h
 include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSet.h
 include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpace.h
 include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpaceFingerprintSearcher.h
+include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpaceRascalSearcher.h
 include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpaceSearcher.h
 include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpaceSubstructureSearcher.h
 include/rdkit/GraphMol/TautomerQuery/TautomerQuery.h
@@ -320,9 +322,11 @@ include/rdkit/Query/XOrQuery.h
 %%PYTHON%%include/rdkit/RDBoost/python.h
 %%PYTHON%%include/rdkit/RDBoost/python_streambuf.h
 include/rdkit/RDGeneral/BadFileException.h
+include/rdkit/RDGeneral/BetterEnums.h
 include/rdkit/RDGeneral/BoostEndInclude.h
 include/rdkit/RDGeneral/BoostStartInclude.h
 include/rdkit/RDGeneral/ConcurrentQueue.h
+include/rdkit/RDGeneral/ControlCHandler.h
 include/rdkit/RDGeneral/Dict.h
 include/rdkit/RDGeneral/Exceptions.h
 include/rdkit/RDGeneral/FileParseException.h
@@ -339,6 +343,7 @@ include/rdkit/RDGeneral/RDValue-taggedunion.h
 include/rdkit/RDGeneral/RDValue.h
 include/rdkit/RDGeneral/Ranking.h
 include/rdkit/RDGeneral/StreamOps.h
+include/rdkit/RDGeneral/enum.h
 include/rdkit/RDGeneral/export.h
 include/rdkit/RDGeneral/hanoiSort.h
 include/rdkit/RDGeneral/hash/detail/float_functions.hpp
@@ -360,6 +365,10 @@ lib/cmake/rdkit/rdkit-config-version.cmake
 lib/cmake/rdkit/rdkit-config.cmake
 lib/cmake/rdkit/rdkit-targets-%%CMAKE_BUILD_TYPE%%.cmake
 lib/cmake/rdkit/rdkit-targets.cmake
+lib/cmake/rdkitpython/rdkitpython-config-version.cmake
+lib/cmake/rdkitpython/rdkitpython-config.cmake
+lib/cmake/rdkitpython/rdkitpython-targets-%%CMAKE_BUILD_TYPE%%.cmake
+lib/cmake/rdkitpython/rdkitpython-targets.cmake
 lib/libRDKitAbbreviations.so
 lib/libRDKitAbbreviations.so.1
 lib/libRDKitAbbreviations.so.1.%%SHLIB_VER%%
@@ -1064,6 +1073,10 @@ lib/libRDKitga.so.1.%%SHLIB_VER%%
 %%DATADIR%%/Contrib/SA_Score/data/zim.100.txt
 %%DATADIR%%/Contrib/SA_Score/fpscores.pkl.gz
 %%DATADIR%%/Contrib/SA_Score/sascorer.py
+%%DATADIR%%/Contrib/efgs/README.md
+%%DATADIR%%/Contrib/efgs/ch33query.sql
+%%DATADIR%%/Contrib/efgs/efgs.py
+%%DATADIR%%/Contrib/efgs/try_efgs.py
 %%DATADIR%%/Contrib/fraggle/atomcontrib.py
 %%DATADIR%%/Contrib/fraggle/cxn_tversky.py
 %%DATADIR%%/Contrib/fraggle/data/ChEMBL_11265_actives.smi