svn commit: r469854 - head/science/rdkit

Yuri Victorovich yuri at FreeBSD.org
Mon May 14 06:42:04 UTC 2018 

Author: yuri
Date: Mon May 14 06:42:03 2018
New Revision: 469854
URL: https://svnweb.freebsd.org/changeset/ports/469854

Log:
  science/rdkit: Update 2017_09_3 -> 2018_03_1
  
  Port changes:
  * Add GH_TUPLE for 2 new bundled dependencies
  * Add BUILD_DEPENDS and post-extract script for the new rapidjson dependency
  
  Reported by:	portscout

Modified:
  head/science/rdkit/Makefile
  head/science/rdkit/distinfo
  head/science/rdkit/pkg-plist

Modified: head/science/rdkit/Makefile
==============================================================================
--- head/science/rdkit/Makefile	Mon May 14 06:04:13 2018	(r469853)
+++ head/science/rdkit/Makefile	Mon May 14 06:42:03 2018	(r469854)
@@ -2,8 +2,7 @@
 
 PORTNAME=	rdkit
 DISTVERSIONPREFIX=	Release_
-DISTVERSION=	2017_09_3
-PORTREVISION=	2
+DISTVERSION=	2018_03_1
 CATEGORIES=	science
 
 MAINTAINER=	yuri at FreeBSD.org
@@ -12,11 +11,14 @@ COMMENT=	Collection of cheminformatics and machine-lea
 LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/license.txt
 
-BUILD_DEPENDS=	flex:textproc/flex
+BUILD_DEPENDS=	flex:textproc/flex \
+		rapidjson>=0:devel/rapidjson
 LIB_DEPENDS=	libboost_system.so:devel/boost-libs
 
 USES=		bison:build cmake:outsource eigen:3 python
 USE_GITHUB=	yes
+GH_TUPLE=	schrodinger:maeparser:8336829:maeparser/External/CoordGen/maeparser \
+		schrodinger:coordgenlibs:ede3191:coordgenlibs/External/CoordGen/coordgenlibs
 USE_LDCONFIG=	yes
 
 CMAKE_OFF=	RDK_INSTALL_INTREE RDK_USE_FLEXBISON \
@@ -41,5 +43,9 @@ PYTHON_RUN_DEPENDS=	${PYNUMPY} \
 			${PYTHON_PKGNAMEPREFIX}reportlab>0:print/py-reportlab@${PY_FLAVOR}
 
 PORTDOCS=	*
+
+post-extract:
+	@${MKDIR} ${WRKSRC}/External/rapidjson-1.1.0
+	@cd ${WRKSRC}/External/rapidjson-1.1.0 && ${LN} -s ${LOCALBASE}/include/rapidjson include
 
 .include <bsd.port.mk>

Modified: head/science/rdkit/distinfo
==============================================================================
--- head/science/rdkit/distinfo	Mon May 14 06:04:13 2018	(r469853)
+++ head/science/rdkit/distinfo	Mon May 14 06:42:03 2018	(r469854)
@@ -1,3 +1,7 @@
-TIMESTAMP = 1521697971
-SHA256 (rdkit-rdkit-Release_2017_09_3_GH0.tar.gz) = 6a4d9e9eb0ca06cbcdc20505f0c6ea0b1167b4dcdf7d1185871ba16ce701a5f4
-SIZE (rdkit-rdkit-Release_2017_09_3_GH0.tar.gz) = 29567648
+TIMESTAMP = 1524726444
+SHA256 (rdkit-rdkit-Release_2018_03_1_GH0.tar.gz) = 9edac0f57c963947b59dfe6f5a84cf3bd2d93ca7111d4d3cf883c9c61756905d
+SIZE (rdkit-rdkit-Release_2018_03_1_GH0.tar.gz) = 30290905
+SHA256 (schrodinger-maeparser-8336829_GH0.tar.gz) = b075902313b95e17057199591b90c801c922d63669e8900dea95bef74d41e600
+SIZE (schrodinger-maeparser-8336829_GH0.tar.gz) = 24974
+SHA256 (schrodinger-coordgenlibs-ede3191_GH0.tar.gz) = 85b1ab66647a523a87bee584533fa81315ea82fde42542aa59e1e08bdf734471
+SIZE (schrodinger-coordgenlibs-ede3191_GH0.tar.gz) = 3721485

Modified: head/science/rdkit/pkg-plist
==============================================================================
--- head/science/rdkit/pkg-plist	Mon May 14 06:04:13 2018	(r469853)
+++ head/science/rdkit/pkg-plist	Mon May 14 06:42:03 2018	(r469854)
@@ -83,6 +83,7 @@ include/rdkit/GraphMol/ChemTransforms/ChemTransforms.h
 include/rdkit/GraphMol/ChemTransforms/MolFragmenter.h
 include/rdkit/GraphMol/Chirality.h
 include/rdkit/GraphMol/Conformer.h
+include/rdkit/GraphMol/CoordGen.h
 include/rdkit/GraphMol/Depictor/DepictUtils.h
 include/rdkit/GraphMol/Depictor/EmbeddedFrag.h
 include/rdkit/GraphMol/Depictor/RDDepictor.h
@@ -167,6 +168,8 @@ include/rdkit/GraphMol/MolDrawing/DrawingToCairo.h
 include/rdkit/GraphMol/MolDrawing/DrawingToSVG.h
 include/rdkit/GraphMol/MolDrawing/MolDrawing.h
 include/rdkit/GraphMol/MolHash/MolHash.h
+include/rdkit/GraphMol/MolInterchange/MolInterchange.h
+include/rdkit/GraphMol/MolInterchange/details.h
 include/rdkit/GraphMol/MolOps.h
 include/rdkit/GraphMol/MolPickler.h
 include/rdkit/GraphMol/MolTransforms/MolTransforms.h
@@ -346,6 +349,9 @@ lib/libRDKitMolDraw2D.so.1.%%SHLIB_VER%%
 lib/libRDKitMolHash.so
 lib/libRDKitMolHash.so.1
 lib/libRDKitMolHash.so.1.%%SHLIB_VER%%
+lib/libRDKitMolInterchange.so
+lib/libRDKitMolInterchange.so.1
+lib/libRDKitMolInterchange.so.1.%%SHLIB_VER%%
 lib/libRDKitMolTransforms.so
 lib/libRDKitMolTransforms.so.1
 lib/libRDKitMolTransforms.so.1.%%SHLIB_VER%%
@@ -397,9 +403,15 @@ lib/libRDKitSubstructMatch.so.1.%%SHLIB_VER%%
 lib/libRDKitTrajectory.so
 lib/libRDKitTrajectory.so.1
 lib/libRDKitTrajectory.so.1.%%SHLIB_VER%%
+lib/libRDKitcoordgenlib.so
+lib/libRDKitcoordgenlib.so.1
+lib/libRDKitcoordgenlib.so.1.%%SHLIB_VER%%
 lib/libRDKithc.so
 lib/libRDKithc.so.1
 lib/libRDKithc.so.1.%%SHLIB_VER%%
+lib/libRDKitmaeparser.so
+lib/libRDKitmaeparser.so.1
+lib/libRDKitmaeparser.so.1.%%SHLIB_VER%%
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Avalon/__init__.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/AllChem.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/AtomPairs/Pairs.py
@@ -438,6 +450,7 @@ lib/libRDKithc.so.1.%%SHLIB_VER%%
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/EState/EState_VSA.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/EState/Fingerprinter.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/EState/__init__.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/EnumerateHeterocycles.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/EnumerateStereoisomers.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/FastSDMolSupplier.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/FeatFinderCLI.py
@@ -521,6 +534,7 @@ lib/libRDKithc.so.1.%%SHLIB_VER%%
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/inchi.py
 %%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/rdDistGeom.so
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdFMCS.so
@@ -531,6 +545,7 @@ lib/libRDKithc.so.1.%%SHLIB_VER%%
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdMolChemicalFeatures.so
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdMolDescriptors.so
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdMolHash.so
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdMolInterchange.so
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdMolTransforms.so
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdPartialCharges.so
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdRGroupDecomposition.so
@@ -847,8 +862,20 @@ lib/rdkit-targets.cmake
 %%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
+%%DATADIR%%/Contrib/Fastcluster/clustered.tsv
+%%DATADIR%%/Contrib/Fastcluster/clustered_parse.tsv
+%%DATADIR%%/Contrib/Fastcluster/fastcluster.py
+%%DATADIR%%/Contrib/Fastcluster/fp.tsv
+%%DATADIR%%/Contrib/Fastcluster/testdata/cdk2.sdf
+%%DATADIR%%/Contrib/Fastcluster/testdata/converted.smi
+%%DATADIR%%/Contrib/Fastcluster/testdata/sdf2smi.py
 %%DATADIR%%/Contrib/Glare/README.txt
 %%DATADIR%%/Contrib/Glare/glare.py
+%%DATADIR%%/Contrib/IFG/README
+%%DATADIR%%/Contrib/IFG/ifg.py
 %%DATADIR%%/Contrib/LEF/AddLabels.py
 %%DATADIR%%/Contrib/LEF/ClusterFps.py
 %%DATADIR%%/Contrib/LEF/CreateFps.py
@@ -953,6 +980,7 @@ lib/rdkit-targets.cmake
 %%DATADIR%%/Data/struchk/checkfgs.chk
 %%DATADIR%%/Data/struchk/checkfgs.opt
 %%DATADIR%%/Data/struchk/checkfgs.trn
+%%DATADIR%%/Data/templates.mae
 %%PYTHON%%%%DATADIR%%/Projects/DbCLI/CreateDb.py
 %%PYTHON%%%%DATADIR%%/Projects/DbCLI/SearchDb.py
 %%PYTHON%%%%DATADIR%%/Projects/DbCLI/TestDbCLI.py
@@ -964,4 +992,7 @@ lib/rdkit-targets.cmake
 %%PYTHON%%%%DATADIR%%/Projects/DbCLI/testData/bzr_q1.mol
 %%PYTHON%%%%DATADIR%%/Projects/DbCLI/testData/pubchem.200.sdf
 %%DATADIR%%/README
+%%PYTHON%%%%DATADIR%%/Scripts/FeatFinderCLI.py
+%%PYTHON%%%%DATADIR%%/Scripts/PythonFormat.py
+%%PYTHON%%%%DATADIR%%/Scripts/README.md
 %%DATADIR%%/license.txt

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