diff --git a/science/coordgenlibs/Makefile b/science/coordgenlibs/Makefile index eae6ab9be9b8..651a67a4f2c9 100644 --- a/science/coordgenlibs/Makefile +++ b/science/coordgenlibs/Makefile @@ -1,34 +1,34 @@ PORTNAME= coordgenlibs DISTVERSIONPREFIX= v -DISTVERSION= 2.0.3 +DISTVERSION= 3.0.0 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Schrodinger-developed 2D coordinate generation LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${LOCALBASE}/include/boost/dynamic_bitset.hpp:devel/boost-libs LIB_DEPENDS= libmaeparser.so:science/maeparser USES= cmake:testing compiler:c++11-lang localbase:ldflags USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= schrodinger DATADIR= ${LOCALBASE}/share/coordgen CMAKE_ON= COORDGEN_USE_MAEPARSER CMAKE_OFF= COORDGEN_BUILD_TESTS COORDGEN_BUILD_EXAMPLE CMAKE_TESTING_ON= COORDGEN_BUILD_TESTS COORDGEN_BUILD_EXAMPLE post-patch: # see https://github.com/schrodinger/coordgenlibs/issues/64 @${REINPLACE_CMD} 's|return getTempFileProjDir() + suffix;|return "${DATADIR}/templates.mae";|' ${WRKSRC}/sketcherMinimizer.cpp post-install: # see https://github.com/schrodinger/coordgenlibs/issues/64 ${MKDIR} ${STAGEDIR}${DATADIR} ${INSTALL_DATA} ${WRKSRC}/templates.mae ${STAGEDIR}${DATADIR} .include diff --git a/science/coordgenlibs/distinfo b/science/coordgenlibs/distinfo index 522bc2a15217..291d2e594a94 100644 --- a/science/coordgenlibs/distinfo +++ b/science/coordgenlibs/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1623389928 -SHA256 (schrodinger-coordgenlibs-v2.0.3_GH0.tar.gz) = 7db567ba988d9fa92918c174ee7a3ba99ee653ca7eef3bee321a3c4419aff515 -SIZE (schrodinger-coordgenlibs-v2.0.3_GH0.tar.gz) = 162607 +TIMESTAMP = 1631213570 +SHA256 (schrodinger-coordgenlibs-v3.0.0_GH0.tar.gz) = 1efabb1bb98cb7dbaa90339f90783fa6109853db3c63932b07ca394f948068d9 +SIZE (schrodinger-coordgenlibs-v3.0.0_GH0.tar.gz) = 166558 diff --git a/science/coordgenlibs/pkg-plist b/science/coordgenlibs/pkg-plist index a4cf07d1562f..64e692ce624d 100644 --- a/science/coordgenlibs/pkg-plist +++ b/science/coordgenlibs/pkg-plist @@ -1,26 +1,26 @@ include/coordgen/CoordgenConfig.hpp include/coordgen/CoordgenFragmentBuilder.h include/coordgen/CoordgenFragmenter.h include/coordgen/CoordgenMacrocycleBuilder.h include/coordgen/CoordgenMinimizer.h include/coordgen/sketcherMinimizer.h include/coordgen/sketcherMinimizerAtom.h include/coordgen/sketcherMinimizerBendInteraction.h include/coordgen/sketcherMinimizerBond.h include/coordgen/sketcherMinimizerClashInteraction.h include/coordgen/sketcherMinimizerEZConstrainInteraction.h include/coordgen/sketcherMinimizerFragment.h include/coordgen/sketcherMinimizerInteraction.h include/coordgen/sketcherMinimizerMarchingSquares.h include/coordgen/sketcherMinimizerMaths.h include/coordgen/sketcherMinimizerMolecule.h include/coordgen/sketcherMinimizerResidue.h include/coordgen/sketcherMinimizerResidueInteraction.h include/coordgen/sketcherMinimizerRing.h include/coordgen/sketcherMinimizerStretchInteraction.h lib/cmake/coordgen-config-%%CMAKE_BUILD_TYPE%%.cmake lib/cmake/coordgen-config.cmake lib/libcoordgen.so -lib/libcoordgen.so.2 -lib/libcoordgen.so.2.0.3 +lib/libcoordgen.so.3 +lib/libcoordgen.so.3.0.0 %%DATADIR%%/templates.mae diff --git a/science/openbabel/Makefile b/science/openbabel/Makefile index 3b98322f741e..058ccfc5091f 100644 --- a/science/openbabel/Makefile +++ b/science/openbabel/Makefile @@ -1,66 +1,66 @@ # Created by: ijliao PORTNAME= openbabel DISTVERSION= 3.1.1 -PORTREVISION= 1 +PORTREVISION= 2 DISTVERSIONSUFFIX= -source CATEGORIES= science MASTER_SITES= https://github.com/openbabel/openbabel/releases/download/openbabel-${PORTVERSION:C/\./-/g}/ MAINTAINER= yuri@FreeBSD.org COMMENT= Chemical toolbox designed to speak the many languages of chemical data LICENSE= GPLv2+ BUILD_DEPENDS= rapidjson>0:devel/rapidjson LIB_DEPENDS= libmaeparser.so:science/maeparser \ libcoordgen.so:science/coordgenlibs \ libboost_thread.so:devel/boost-libs CONFLICTS_INSTALL= babel-* USES= cmake compiler:c++11-lang eigen:3 gnome pkgconfig tar:bz2 USE_CXXSTD= gnu++98 USE_GNOME= libxml2 USE_LDCONFIG= yes CMAKE_ON= WITH_COORDGEN WITH_JSON OPENBABEL_USE_SYSTEM_RAPIDJSON WITH_MAEPARSER WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION} PLIST_SUB= VERSION=3.1.0 # To be replaced by ${PORTVERSION} nexttime! OPTIONS_DEFINE= CAIRO PYTHON GUI OPTIONS_DEFAULT= CAIRO PYTHON GUI OPTIONS_SUB= yes CAIRO_DESC= PNG support via cairo library CAIRO_USE= GNOME=cairo PYTHON_USES= python PYTHON_CMAKE_BOOL= PYTHON_BINDINGS GUI_CMAKE_BOOL= BUILD_GUI GUI_CMAKE_ON= -DwxWidgets_CONFIG_EXECUTABLE:STRING=${WX_CONFIG} GUI_USE= WX=3.0 .include .if ${CHOSEN_COMPILER_TYPE} == gcc CXXFLAGS+= -Wno-narrowing USE_CXXSTD= c++11 .endif pre-configure: ${REINPLACE_CMD} -e '/pkgconfig/s,$${LIB_INSTALL_DIR},libdata,' \ ${WRKSRC}/CMakeLists.txt pre-configure-CAIRO-off: ${REINPLACE_CMD} -e '/find_package(Cairo)/d' \ ${WRKSRC}/CMakeLists.txt post-install-PYTHON-on: (cd ${STAGEDIR}${PREFIX} && ${PYTHON_CMD} ${PYTHON_LIBDIR}/compileall.py \ -d ${PREFIX} -f ${PYTHONPREFIX_SITELIBDIR:S,${PREFIX}/,,}) (cd ${STAGEDIR}${PREFIX} && ${PYTHON_CMD} -O ${PYTHON_LIBDIR}/compileall.py \ -d ${PREFIX} -f ${PYTHONPREFIX_SITELIBDIR:S,${PREFIX}/,,}) .include diff --git a/science/rdkit/Makefile b/science/rdkit/Makefile index 797effcb2ac1..2868887af376 100644 --- a/science/rdkit/Makefile +++ b/science/rdkit/Makefile @@ -1,77 +1,78 @@ PORTNAME= rdkit DISTVERSIONPREFIX= Release_ DISTVERSION= 2021_03_5 +PORTREVISION= 1 CATEGORIES= science MASTER_SITES= https://fonts.google.com/download?family=Comic%20Neue&dummy=/:font DISTFILES= Comic_Neue.zip:font DIST_SUBDIR= ${PORTNAME}-${PORTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= Collection of cheminformatics and machine-learning software LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/license.txt BUILD_DEPENDS= catch>0:devel/catch \ flex:textproc/flex \ rapidjson>=0:devel/rapidjson LIB_DEPENDS= libboost_system.so:devel/boost-libs \ libcoordgen.so:science/coordgenlibs \ libfreetype.so:print/freetype2 \ libmaeparser.so:science/maeparser USES= bison:build cmake compiler:c++11-lang eigen:3 python:3.7+ USE_GITHUB= yes GH_TUPLE= rareylab:RingDecomposerLib:v1.1.3_rdkit:RingDecomposerLib/External/RingFamilies/RingDecomposerLib USE_LDCONFIG= yes CMAKE_OFF= RDK_INSTALL_INTREE RDK_USE_FLEXBISON \ RDK_INSTALL_STATIC_LIBS RDK_SWIG_STATIC RDK_PGSQL_STATIC \ RDK_OPTIMIZE_NATIVE \ RDK_BUILD_CPP_TESTS CMAKE_ARGS= -DCATCH_DIR=${LOCALBASE}/include/catch2 DATADIR= ${PREFIX}/share/RDKit DOCSDIR= ${PREFIX}/share/doc/RDKit PLIST_SUB= SHLIB_VER=${PORTVERSION} OPTIONS_DEFINE= DOCS PGSQL PYTHON OPTIONS_DEFAULT= PYTHON OPTIONS_SUB= yes DOCS_CMAKE_BOOL= FREEBSD_INSTALL_DOCS DOCS_CMAKE_ON= -DFREEBSD_DOCSDIR:PATH=${DOCSDIR} PGSQL_USES= pgsql PGSQL_DESC= Build the PostgreSQL cartridge PGSQL_CMAKE_BOOL= RDK_BUILD_PGSQL PYTHON_CMAKE_BOOL= RDK_BUILD_PYTHON_WRAPPERS PYTHON_BUILD_DEPENDS= ${PYNUMPY} PYTHON_LIB_DEPENDS= ${PY_BOOST} PYTHON_RUN_DEPENDS= ${PYNUMPY} \ ${PY_PILLOW} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}reportlab>0:print/py-reportlab@${PY_FLAVOR} PORTDOCS= * .include .if ${ARCH} == aarch64 || ${ARCH} == amd64 || ${ARCH:Marm*} || ${ARCH} == i386 || ${ARCH:Mmips*el*} || ${ARCH} == riscv PLIST_SUB+= LITTLE_ENDIAN="" .else PLIST_SUB+= LITTLE_ENDIAN="@comment " .endif post-extract: @${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 post-stage: # https://github.com/rdkit/rdkit/issues/2094 #@${MKDIR} ${STAGEDIR}${PREFIX}/lib/cmake #@${MV} ${STAGEDIR}${PREFIX}/lib/*.cmake ${STAGEDIR}${PREFIX}/lib/cmake .include