git: ba44d373cd83 - main - science/rdkit: update 2023_09_6 → 2024_03_6

Reply: Dima Panov : "Re:_git:_ba44d373cd83_-_main_-_science/rdkit:_updat e 2023_09_6 → 2024_03_6"
Go to: [ bottom of page ] [ top of archives ] [ this month ]
From: Yuri Victorovich <yuri_at_FreeBSD.org>
Date: Sat, 31 Aug 2024 07:16:19 UTC
The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=ba44d373cd83b7e0a4af2dbf12a4d1bcfa6187b5

commit ba44d373cd83b7e0a4af2dbf12a4d1bcfa6187b5
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2024-08-31 03:42:20 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2024-08-31 07:16:12 +0000

    science/rdkit: update 2023_09_6 → 2024_03_6
    
    Reported by:    portscout
---
 science/rdkit/Makefile  |  17 ++++++--
 science/rdkit/distinfo  |  14 +++----
 science/rdkit/pkg-plist | 107 ++++++++++++++----------------------------------
 3 files changed, 50 insertions(+), 88 deletions(-)

diff --git a/science/rdkit/Makefile b/science/rdkit/Makefile
index 2aa61a3a6f1c..3d0230c5ffec 100644
--- a/science/rdkit/Makefile
+++ b/science/rdkit/Makefile
@@ -1,10 +1,11 @@
 PORTNAME=	rdkit
 DISTVERSIONPREFIX=	Release_
-DISTVERSION=	2023_09_6
+DISTVERSION=	2024_03_6
 CATEGORIES=	science
 MASTER_SITES=	https://fonts.google.com/download?family=Comic%20Neue&dummy=/:font
-DISTFILES=	Comic_Neue.zip:font
+DISTFILES=	ComicNeue-Regular.ttf:font
 DIST_SUBDIR=	${PORTNAME}-${PORTVERSION}
+EXTRACT_ONLY=	${DISTFILES:C/:.*//:N*.ttf}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Collection of cheminformatics and machine-learning software
@@ -25,7 +26,7 @@ LIB_DEPENDS=	libboost_system.so:devel/boost-libs \
 		libfreetype.so:print/freetype2 \
 		libmaeparser.so:science/maeparser
 
-USES=		bison:build cmake compiler:c++11-lang eigen:3 python
+USES=		bison:build cmake:testing compiler:c++11-lang eigen:3 python
 USE_GITHUB=	yes
 GH_TUPLE=	rareylab:RingDecomposerLib:v1.1.3_rdkit:RingDecomposerLib/External/RingFamilies/RingDecomposerLib
 USE_LDCONFIG=	yes
@@ -42,6 +43,12 @@ CXXFLAGS+=	-D_GNU_SOURCE
 DATADIR=	${PREFIX}/share/RDKit
 DOCSDIR=	${PREFIX}/share/doc/RDKit
 
+#		RDBASE=${STAGEDIR}${PREFIX}
+TEST_ENV=	${MAKE_ENV} \
+		RDBASE=${WRKSRC} \
+		PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} \
+		LD_LIBRARY_PATH=${STAGEDIR}${PREFIX}/lib
+
 PLIST_SUB=	SHLIB_VER=${PORTVERSION}
 
 OPTIONS_DEFINE=		DOCS PGSQL PYTHON
@@ -76,9 +83,11 @@ PLIST_SUB+=	LITTLE_ENDIAN="@comment "
 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 && unzip ${DISTDIR}/${DIST_SUBDIR}/Comic_Neue.zip
+	@cd ${WRKSRC}/Data/Fonts && ${CP} ${DISTDIR}/${DIST_SUBDIR}/ComicNeue-Regular.ttf .
 
 post-install-PGSQL-on:
 	@${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/postgresql/rdkit.so
 
+# many tests fail, see https://github.com/rdkit/rdkit/issues/7779
+
 .include <bsd.port.mk>
diff --git a/science/rdkit/distinfo b/science/rdkit/distinfo
index f1bd36220762..af1e4cf83c65 100644
--- a/science/rdkit/distinfo
+++ b/science/rdkit/distinfo
@@ -1,7 +1,7 @@
-TIMESTAMP = 1709878620
-SHA256 (rdkit-2023.09.6/Comic_Neue.zip) = ee69c0c8f7ae7777cea33d9df1437815b0c79b12bd5d9ec7ca2877983bb6b980
-SIZE (rdkit-2023.09.6/Comic_Neue.zip) = 180682
-SHA256 (rdkit-2023.09.6/rdkit-rdkit-Release_2023_09_6_GH0.tar.gz) = e8f580db8fe14070d009adafb1f0e5b15c12ebe6c1cf4e99085c0615be3996fc
-SIZE (rdkit-2023.09.6/rdkit-rdkit-Release_2023_09_6_GH0.tar.gz) = 80239558
-SHA256 (rdkit-2023.09.6/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 944b5816712a48bbf88aa25d4300ce11871ddf6e971218eac08f90ed2192f715
-SIZE (rdkit-2023.09.6/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 137931
+TIMESTAMP = 1725065957
+SHA256 (rdkit-2024.03.6/ComicNeue-Regular.ttf) = 8eaa5a108104e41d3f203af0428f2a368bb7217dce74f5b2afd7c97c38c8ca90
+SIZE (rdkit-2024.03.6/ComicNeue-Regular.ttf) = 21915
+SHA256 (rdkit-2024.03.6/rdkit-rdkit-Release_2024_03_6_GH0.tar.gz) = 5002ff97e59d9c08f4faa1c6a2e276a695f6874dfc93e28cbbd62dab4f0b40d7
+SIZE (rdkit-2024.03.6/rdkit-rdkit-Release_2024_03_6_GH0.tar.gz) = 80462644
+SHA256 (rdkit-2024.03.6/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 944b5816712a48bbf88aa25d4300ce11871ddf6e971218eac08f90ed2192f715
+SIZE (rdkit-2024.03.6/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 137931
diff --git a/science/rdkit/pkg-plist b/science/rdkit/pkg-plist
index d0d492982c90..eabbfffc1000 100644
--- a/science/rdkit/pkg-plist
+++ b/science/rdkit/pkg-plist
@@ -1,5 +1,3 @@
-include/rdkit/CIPLabeler/CIPLabeler.h
-include/rdkit/CIPLabeler/TooManyNodesException.h
 include/rdkit/Catalogs/Catalog.h
 include/rdkit/Catalogs/CatalogEntry.h
 include/rdkit/Catalogs/CatalogParams.h
@@ -24,12 +22,19 @@ 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
+include/rdkit/ForceField/AngleConstraint.h
+include/rdkit/ForceField/AngleConstraints.h
 include/rdkit/ForceField/Contrib.h
+include/rdkit/ForceField/DistanceConstraint.h
+include/rdkit/ForceField/DistanceConstraints.h
 include/rdkit/ForceField/ForceField.h
 include/rdkit/ForceField/MMFF/AngleBend.h
 include/rdkit/ForceField/MMFF/AngleConstraint.h
@@ -43,17 +48,21 @@ include/rdkit/ForceField/MMFF/PositionConstraint.h
 include/rdkit/ForceField/MMFF/StretchBend.h
 include/rdkit/ForceField/MMFF/TorsionAngle.h
 include/rdkit/ForceField/MMFF/TorsionConstraint.h
+include/rdkit/ForceField/PositionConstraint.h
+include/rdkit/ForceField/TorsionConstraint.h
 include/rdkit/ForceField/UFF/AngleBend.h
 include/rdkit/ForceField/UFF/AngleConstraint.h
 include/rdkit/ForceField/UFF/BondStretch.h
 include/rdkit/ForceField/UFF/Contribs.h
 include/rdkit/ForceField/UFF/DistanceConstraint.h
 include/rdkit/ForceField/UFF/Inversion.h
+include/rdkit/ForceField/UFF/Inversions.h
 include/rdkit/ForceField/UFF/Nonbonded.h
 include/rdkit/ForceField/UFF/Params.h
 include/rdkit/ForceField/UFF/PositionConstraint.h
 include/rdkit/ForceField/UFF/TorsionAngle.h
 include/rdkit/ForceField/UFF/TorsionConstraint.h
+include/rdkit/ForceField/UFF/Utils.h
 include/rdkit/Geometry/Grid3D.h
 include/rdkit/Geometry/GridUtils.h
 include/rdkit/Geometry/Transform.h
@@ -65,8 +74,11 @@ include/rdkit/Geometry/point.h
 include/rdkit/GraphMol/Abbreviations/Abbreviations.h
 include/rdkit/GraphMol/Atom.h
 include/rdkit/GraphMol/AtomIterators.h
+include/rdkit/GraphMol/Atropisomers.h
 include/rdkit/GraphMol/Bond.h
 include/rdkit/GraphMol/BondIterators.h
+include/rdkit/GraphMol/CIPLabeler/CIPLabeler.h
+include/rdkit/GraphMol/CIPLabeler/TooManyNodesException.h
 include/rdkit/GraphMol/Canon.h
 include/rdkit/GraphMol/ChemReactions/Enumerate/CartesianProduct.h
 include/rdkit/GraphMol/ChemReactions/Enumerate/Enumerate.h
@@ -100,6 +112,7 @@ include/rdkit/GraphMol/Descriptors/BCUT.h
 include/rdkit/GraphMol/Descriptors/ConnectivityDescriptors.h
 include/rdkit/GraphMol/Descriptors/CoulombMat.h
 include/rdkit/GraphMol/Descriptors/Crippen.h
+include/rdkit/GraphMol/Descriptors/DCLV.h
 include/rdkit/GraphMol/Descriptors/Data3Ddescriptors.h
 include/rdkit/GraphMol/Descriptors/EEM.h
 include/rdkit/GraphMol/Descriptors/GETAWAY.h
@@ -125,9 +138,11 @@ include/rdkit/GraphMol/FMCS/Graph.h
 include/rdkit/GraphMol/FileParsers/CDXMLParser.h
 include/rdkit/GraphMol/FileParsers/FileParserUtils.h
 include/rdkit/GraphMol/FileParsers/FileParsers.h
+include/rdkit/GraphMol/FileParsers/FileWriters.h
 include/rdkit/GraphMol/FileParsers/GeneralFileReader.h
 include/rdkit/GraphMol/FileParsers/MolFileStereochem.h
 include/rdkit/GraphMol/FileParsers/MolSupplier.h
+include/rdkit/GraphMol/FileParsers/MolSupplier.v1API.h
 include/rdkit/GraphMol/FileParsers/MolWriters.h
 include/rdkit/GraphMol/FileParsers/MultithreadedMolSupplier.h
 include/rdkit/GraphMol/FileParsers/MultithreadedSDMolSupplier.h
@@ -151,6 +166,7 @@ include/rdkit/GraphMol/Fingerprints/MorganFingerprints.h
 include/rdkit/GraphMol/Fingerprints/MorganGenerator.h
 include/rdkit/GraphMol/Fingerprints/RDKitFPGenerator.h
 include/rdkit/GraphMol/Fingerprints/TopologicalTorsionGenerator.h
+include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleContribs.h
 include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h
 include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h
 include/rdkit/GraphMol/ForceFieldHelpers/FFConvenience.h
@@ -169,7 +185,7 @@ include/rdkit/GraphMol/GeneralizedSubstruct/XQMol.h
 include/rdkit/GraphMol/GenericGroups/GenericGroups.h
 include/rdkit/GraphMol/GraphMol.h
 include/rdkit/GraphMol/MMPA/MMPA.h
-include/rdkit/GraphMol/MarvinParser/MarvinParser.h
+include/rdkit/GraphMol/MarvinParse/MarvinParser.h
 include/rdkit/GraphMol/MolAlign/AlignMolecules.h
 include/rdkit/GraphMol/MolAlign/O3AAlignMolecules.h
 include/rdkit/GraphMol/MolBundle.h
@@ -287,6 +303,7 @@ include/rdkit/Query/XOrQuery.h
 %%PYTHON%%include/rdkit/RDBoost/Wrap.h
 %%PYTHON%%include/rdkit/RDBoost/boost_numpy.h
 %%PYTHON%%include/rdkit/RDBoost/list_indexing_suite.hpp
+%%PYTHON%%include/rdkit/RDBoost/pyint_api.h
 %%PYTHON%%include/rdkit/RDBoost/python.h
 %%PYTHON%%include/rdkit/RDBoost/python_streambuf.h
 include/rdkit/RDGeneral/BadFileException.h
@@ -587,19 +604,7 @@ lib/libRDKitga.so.1.%%SHLIB_VER%%
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolKey/MolKey.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolKey/__init__.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/__init__.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/charge.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/errors.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/fragment.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/metal.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/normalize.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/rdMolStandardize.so
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/resonance.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/standardize.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/tautomer.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/test_standardizer.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/utils.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/validate.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/validations.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolSurf.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/PandasPatcher.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/PandasTools.py
@@ -636,7 +641,7 @@ lib/libRDKitga.so.1.%%SHLIB_VER%%
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/Subshape/SubshapeBuilder.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/Subshape/SubshapeObjects.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/Subshape/__init__.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/Subshape/testCombined.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/Subshape/demoCombined.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/Suppliers/DbMolSupplier.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/Suppliers/MolSupplier.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/Suppliers/__init__.py
@@ -702,34 +707,26 @@ lib/libRDKitga.so.1.%%SHLIB_VER%%
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Dbase/DbConnection.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Dbase/DbInfo.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Dbase/DbModule.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Dbase/DbReport.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Dbase/DbResultSet.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Dbase/DbUtils.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Dbase/StorageUtils.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Dbase/__init__.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/DistanceGeometry/DistGeom.so
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/DistanceGeometry/__init__.py
+%%PYTHON_SITELIBDIR%%/rdkit/Dbase/StorageUtils.py
+%%PYTHON_SITELIBDIR%%/rdkit/Dbase/__init__.py
+%%PYTHON_SITELIBDIR%%/rdkit/DistanceGeometry/DistGeom.so
+%%PYTHON_SITELIBDIR%%/rdkit/DistanceGeometry/__init__.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ForceField/__init__.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ForceField/rdForceField.so
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Geometry/__init__.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Geometry/rdGeometry.so
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/AnalyzeComposite.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/BuildComposite.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Cluster/Butina.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Cluster/ClusterUtils.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Cluster/ClusterVis.py
-%%LITTLE_ENDIAN%%%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Cluster/Clustering.so
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Cluster/Clustering.so
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Cluster/Clusters.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Cluster/Murtagh.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Cluster/Resemblance.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Cluster/Standardize.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Cluster/__init__.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Cluster/murtagh_test.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Composite/AdjustComposite.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Composite/BayesComposite.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Composite/Composite.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Composite/__init__.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/CompositeRun.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Data/DataUtils.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Data/FindQuantBounds.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Data/MLData.py
@@ -739,59 +736,23 @@ lib/libRDKitga.so.1.%%SHLIB_VER%%
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Data/Transforms.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Data/__init__.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Data/cQuantize.so
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/DecTree/BuildQuantTree.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/DecTree/BuildSigTree.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/DecTree/CrossValidate.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/DecTree/DecTree.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/DecTree/Forest.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/DecTree/ID3.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/DecTree/PruneTree.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/DecTree/QuantTree.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/DecTree/SigTree.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/DecTree/Tree.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/DecTree/TreeUtils.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/DecTree/TreeVis.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/DecTree/__init__.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/DecTree/randomtest.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Descriptors/CompoundDescriptors.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Descriptors/Descriptors.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Descriptors/MoleculeDescriptors.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Descriptors/Parser.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Descriptors/__init__.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/EnrichPlot.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/GrowComposite.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/InfoTheory/BitClusterer.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/InfoTheory/BitRank.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/InfoTheory/__init__.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/InfoTheory/entropy.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/InfoTheory/rdInfoTheory.so
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/KNN/CrossValidate.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/KNN/DistFunctions.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/KNN/KNNClassificationModel.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/KNN/KNNModel.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/KNN/KNNRegressionModel.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/KNN/__init__.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/MLUtils/VoteImg.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/MLUtils/__init__.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/MatOps.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/ModelPackage/PackageUtils.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/ModelPackage/Packager.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/ModelPackage/__init__.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/NaiveBayes/ClassificationModel.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/NaiveBayes/CrossValidate.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/NaiveBayes/__init__.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Neural/ActFuncs.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Neural/CrossValidate.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Neural/NetNode.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Neural/Network.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Neural/Trainers.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Neural/__init__.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Neural/architecture.txt
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/SLT/Risk.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/SLT/__init__.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Scoring/Scoring.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/Scoring/__init__.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/ScreenComposite.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/__init__.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/ML/files.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Numerics/__init__.py
@@ -821,8 +782,9 @@ lib/libRDKitga.so.1.%%SHLIB_VER%%
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/VLib/Transform.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/VLib/__init__.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/__init__.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/conftest.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/pytest.ini
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/rdBase.so
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/six.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/sping/PDF/__init__.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/sping/PDF/pdfdoc.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/sping/PDF/pdfgen.py
@@ -962,7 +924,6 @@ lib/libRDKitga.so.1.%%SHLIB_VER%%
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/utils/chemdraw.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/utils/chemdraw_qax.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/utils/chemutils.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/utils/comhack.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/utils/fileutils.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/utils/listutils.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/utils/retest.txt
@@ -1015,9 +976,7 @@ lib/libRDKitga.so.1.%%SHLIB_VER%%
 %%DATADIR%%/Contrib/ConformerParser/Wrap/CMakeLists.txt
 %%DATADIR%%/Contrib/ConformerParser/Wrap/rdConformerParser.cpp
 %%DATADIR%%/Contrib/ConformerParser/Wrap/testConformerParser.py
-%%DATADIR%%/Contrib/ConformerParser/Wrap/test_list.py
 %%DATADIR%%/Contrib/ConformerParser/test.cpp
-%%DATADIR%%/Contrib/ConformerParser/test_list.py
 %%DATADIR%%/Contrib/Fastcluster/README.md
 %%DATADIR%%/Contrib/Fastcluster/cdk2.smi
 %%DATADIR%%/Contrib/Fastcluster/centroid.tsv
@@ -1119,7 +1078,6 @@ lib/libRDKitga.so.1.%%SHLIB_VER%%
 %%DATADIR%%/Contrib/mmpa/mol_transform.py
 %%DATADIR%%/Contrib/mmpa/rfrag.py
 %%DATADIR%%/Contrib/mmpa/search_mmp_db.py
-%%DATADIR%%/Contrib/mmpa/test_list.py
 %%DATADIR%%/Contrib/mmpa/test_rfrag.py
 %%DATADIR%%/Contrib/pzc/p_con.html
 %%DATADIR%%/Contrib/pzc/p_con.py
@@ -1130,13 +1088,7 @@ lib/libRDKitga.so.1.%%SHLIB_VER%%
 %%DATADIR%%/Data/DTDs/RD_Model.dtd
 %%DATADIR%%/Data/DTDs/validate.py
 %%DATADIR%%/Data/Fonts/Amadeus.ttf
-%%DATADIR%%/Data/Fonts/ComicNeue-Bold.ttf
-%%DATADIR%%/Data/Fonts/ComicNeue-BoldItalic.ttf
-%%DATADIR%%/Data/Fonts/ComicNeue-Italic.ttf
-%%DATADIR%%/Data/Fonts/ComicNeue-Light.ttf
-%%DATADIR%%/Data/Fonts/ComicNeue-LightItalic.ttf
 %%DATADIR%%/Data/Fonts/ComicNeue-Regular.ttf
-%%DATADIR%%/Data/Fonts/OFL.txt
 %%DATADIR%%/Data/Fonts/Telex-Regular.ttf
 %%DATADIR%%/Data/Fonts/amadeus_font_license.txt
 %%DATADIR%%/Data/Fonts/font_dumper.py
@@ -1168,7 +1120,7 @@ lib/libRDKitga.so.1.%%SHLIB_VER%%
 %%DATADIR%%/Data/struchk/checkfgs.trn
 %%PYTHON%%%%DATADIR%%/Projects/DbCLI/CreateDb.py
 %%PYTHON%%%%DATADIR%%/Projects/DbCLI/SearchDb.py
-%%PYTHON%%%%DATADIR%%/Projects/DbCLI/TestDbCLI.py
+%%PYTHON%%%%DATADIR%%/Projects/DbCLI/UnitTestDbCLI.py
 %%PYTHON%%%%DATADIR%%/Projects/DbCLI/moe_like.dsc
 %%PYTHON%%%%DATADIR%%/Projects/DbCLI/testData/README
 %%PYTHON%%%%DATADIR%%/Projects/DbCLI/testData/bzr.2.smi
@@ -1176,6 +1128,7 @@ lib/libRDKitga.so.1.%%SHLIB_VER%%
 %%PYTHON%%%%DATADIR%%/Projects/DbCLI/testData/bzr.smi
 %%PYTHON%%%%DATADIR%%/Projects/DbCLI/testData/bzr_q1.mol
 %%PYTHON%%%%DATADIR%%/Projects/DbCLI/testData/pubchem.200.sdf
+%%DATADIR%%/Projects/pytest.ini
 %%DATADIR%%/README
 %%PYTHON%%%%DATADIR%%/Scripts/FeatFinderCLI.py
 %%PYTHON%%%%DATADIR%%/Scripts/PythonFormat.py