Date: Wed, 13 Jan 2021 04:02:26 +0000 (UTC) From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r561438 - head/science/openbabel Message-ID: <202101130402.10D42QYP050109@repo.freebsd.org>
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Author: yuri Date: Wed Jan 13 04:02:26 2021 New Revision: 561438 URL: https://svnweb.freebsd.org/changeset/ports/561438 Log: science/openbabel: Update 2.4.1 -> 3.1.1 Modified: head/science/openbabel/Makefile head/science/openbabel/distinfo head/science/openbabel/pkg-plist Modified: head/science/openbabel/Makefile ============================================================================== --- head/science/openbabel/Makefile Wed Jan 13 03:31:32 2021 (r561437) +++ head/science/openbabel/Makefile Wed Jan 13 04:02:26 2021 (r561438) @@ -2,40 +2,45 @@ # $FreeBSD$ PORTNAME= openbabel -PORTVERSION= 2.4.1 -PORTREVISION= 6 +DISTVERSION= 3.1.1 +DISTVERSIONSUFFIX= -source CATEGORIES= science -MASTER_SITES= SF +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+ -LICENSE_FILE= ${WRKSRC}/COPYING +BUILD_DEPENDS= rapidjson>0:devel/rapidjson +LIB_DEPENDS= libmaeparser.so:science/maeparser \ + libcoordgen.so:science/coordgenlibs \ + libboost_thread.so:devel/boost-libs + CONFLICTS_INSTALL= babel-* -USES= compiler:c++11-lang cmake eigen:3 gnome +USES= cmake compiler:c++11-lang eigen:3 gnome pkgconfig tar:bz2 USE_CXXSTD= gnu++98 USE_GNOME= libxml2 USE_LDCONFIG= yes -PLIST_SUB= VERSION="${PORTVERSION}" +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 ${PORTVERSION} nexttime! -OPTIONS_DEFINE= CAIRO PYTHON GUI -OPTIONS_DEFAULT= PYTHON GUI -OPTIONS_SUB= yes +OPTIONS_DEFINE= CAIRO PYTHON GUI +OPTIONS_DEFAULT= CAIRO PYTHON GUI +OPTIONS_SUB= yes -CAIRO_DESC= PNG support via cairo library -CAIRO_USES= pkgconfig -CAIRO_USE= GNOME=cairo +CAIRO_DESC= PNG support via cairo library +CAIRO_USE= GNOME=cairo -PYTHON_USES= python +PYTHON_USES= python PYTHON_CMAKE_BOOL= PYTHON_BINDINGS -GUI_CMAKE_BOOL= BUILD_GUI -GUI_CMAKE_ON= -DwxWidgets_CONFIG_EXECUTABLE:STRING=${WX_CONFIG} -GUI_USE= WX=3.0 +GUI_CMAKE_BOOL= BUILD_GUI +GUI_CMAKE_ON= -DwxWidgets_CONFIG_EXECUTABLE:STRING=${WX_CONFIG} +GUI_USE= WX=3.0 .include <bsd.port.pre.mk> @@ -44,14 +49,18 @@ CXXFLAGS+= -Wno-narrowing USE_CXXSTD= c++11 .endif -post-patch: +pre-configure: ${REINPLACE_CMD} -e '/pkgconfig/s,$${LIB_INSTALL_DIR},libdata,' \ ${WRKSRC}/CMakeLists.txt - ${REINPLACE_CMD} -e 's,man/man1,../man/man1,' \ - ${WRKSRC}/doc/CMakeLists.txt -post-patch-CAIRO-off: +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 <bsd.port.post.mk> Modified: head/science/openbabel/distinfo ============================================================================== --- head/science/openbabel/distinfo Wed Jan 13 03:31:32 2021 (r561437) +++ head/science/openbabel/distinfo Wed Jan 13 04:02:26 2021 (r561438) @@ -1,3 +1,3 @@ -TIMESTAMP = 1495085400 -SHA256 (openbabel-2.4.1.tar.gz) = 204136582cdfe51d792000b20202de8950218d617fd9c6e18cee36706a376dfc -SIZE (openbabel-2.4.1.tar.gz) = 11618304 +TIMESTAMP = 1609084505 +SHA256 (openbabel-3.1.1-source.tar.bz2) = a6ec8381d59ea32a4b241c8b1fbd799acb52be94ab64cdbd72506fb4e2270e68 +SIZE (openbabel-3.1.1-source.tar.bz2) = 27743669 Modified: head/science/openbabel/pkg-plist ============================================================================== --- head/science/openbabel/pkg-plist Wed Jan 13 03:31:32 2021 (r561437) +++ head/science/openbabel/pkg-plist Wed Jan 13 04:02:26 2021 (r561438) @@ -1,14 +1,14 @@ -bin/babel bin/obabel -bin/obchiral bin/obconformer bin/obdistgen bin/obenergy bin/obfit +bin/obfitall bin/obgen bin/obgrep %%GUI%%bin/obgui bin/obminimize +bin/obmm bin/obprobe bin/obprop bin/obrms @@ -20,96 +20,106 @@ bin/obtautomer bin/obthermo bin/roundtrip include/inchi/inchi_api.h -include/openbabel-2.0/openbabel/alias.h -include/openbabel-2.0/openbabel/atom.h -include/openbabel-2.0/openbabel/atomclass.h -include/openbabel-2.0/openbabel/babelconfig.h -include/openbabel-2.0/openbabel/base.h -include/openbabel-2.0/openbabel/bitvec.h -include/openbabel-2.0/openbabel/bond.h -include/openbabel-2.0/openbabel/bondtyper.h -include/openbabel-2.0/openbabel/builder.h -include/openbabel-2.0/openbabel/canon.h -include/openbabel-2.0/openbabel/chains.h -include/openbabel-2.0/openbabel/chargemodel.h -include/openbabel-2.0/openbabel/chemdrawcdx.h -include/openbabel-2.0/openbabel/chiral.h -include/openbabel-2.0/openbabel/conformersearch.h -include/openbabel-2.0/openbabel/data.h -include/openbabel-2.0/openbabel/data_utilities.h -include/openbabel-2.0/openbabel/descriptor.h -include/openbabel-2.0/openbabel/distgeom.h -include/openbabel-2.0/openbabel/dlhandler.h -include/openbabel-2.0/openbabel/fingerprint.h -include/openbabel-2.0/openbabel/forcefield.h -include/openbabel-2.0/openbabel/format.h -include/openbabel-2.0/openbabel/generic.h -include/openbabel-2.0/openbabel/graphsym.h -include/openbabel-2.0/openbabel/grid.h -include/openbabel-2.0/openbabel/griddata.h -include/openbabel-2.0/openbabel/groupcontrib.h -include/openbabel-2.0/openbabel/inchiformat.h -include/openbabel-2.0/openbabel/internalcoord.h -include/openbabel-2.0/openbabel/isomorphism.h -include/openbabel-2.0/openbabel/json/customwriter.h -include/openbabel-2.0/openbabel/json/json-forwards.h -include/openbabel-2.0/openbabel/json/json.h -include/openbabel-2.0/openbabel/kinetics.h -include/openbabel-2.0/openbabel/lineend.h -include/openbabel-2.0/openbabel/locale.h -include/openbabel-2.0/openbabel/math/align.h -include/openbabel-2.0/openbabel/math/erf.h -include/openbabel-2.0/openbabel/math/matrix3x3.h -include/openbabel-2.0/openbabel/math/spacegroup.h -include/openbabel-2.0/openbabel/math/transform3d.h -include/openbabel-2.0/openbabel/math/vector3.h -include/openbabel-2.0/openbabel/matrix.h -include/openbabel-2.0/openbabel/mcdlutil.h -include/openbabel-2.0/openbabel/mol.h -include/openbabel-2.0/openbabel/molchrg.h -include/openbabel-2.0/openbabel/obconversion.h -include/openbabel-2.0/openbabel/oberror.h -include/openbabel-2.0/openbabel/obiter.h -include/openbabel-2.0/openbabel/obmolecformat.h -include/openbabel-2.0/openbabel/obutil.h -include/openbabel-2.0/openbabel/op.h -include/openbabel-2.0/openbabel/optransform.h -include/openbabel-2.0/openbabel/parsmart.h -include/openbabel-2.0/openbabel/patty.h -include/openbabel-2.0/openbabel/phmodel.h -include/openbabel-2.0/openbabel/plugin.h -include/openbabel-2.0/openbabel/pointgroup.h -include/openbabel-2.0/openbabel/query.h -include/openbabel-2.0/openbabel/rand.h -include/openbabel-2.0/openbabel/reaction.h -include/openbabel-2.0/openbabel/residue.h -include/openbabel-2.0/openbabel/ring.h -include/openbabel-2.0/openbabel/rotamer.h -include/openbabel-2.0/openbabel/rotor.h -include/openbabel-2.0/openbabel/shared_ptr.h -include/openbabel-2.0/openbabel/spectrophore.h -include/openbabel-2.0/openbabel/stereo/bindings.h -include/openbabel-2.0/openbabel/stereo/cistrans.h -include/openbabel-2.0/openbabel/stereo/squareplanar.h -include/openbabel-2.0/openbabel/stereo/stereo.h -include/openbabel-2.0/openbabel/stereo/tetrahedral.h -include/openbabel-2.0/openbabel/stereo/tetranonplanar.h -include/openbabel-2.0/openbabel/stereo/tetraplanar.h -include/openbabel-2.0/openbabel/tautomer.h -include/openbabel-2.0/openbabel/text.h -include/openbabel-2.0/openbabel/tokenst.h -include/openbabel-2.0/openbabel/typer.h -include/openbabel-2.0/openbabel/xml.h -lib/cmake/openbabel2/OpenBabel2Config.cmake -lib/cmake/openbabel2/OpenBabel2ConfigVersion.cmake -lib/cmake/openbabel2/OpenBabel2_EXPORTS-%%CMAKE_BUILD_TYPE%%.cmake -lib/cmake/openbabel2/OpenBabel2_EXPORTS.cmake +include/openbabel3/LBFGS.h +include/openbabel3/LBFGS/LineSearchBacktracking.h +include/openbabel3/LBFGS/LineSearchBracketing.h +include/openbabel3/LBFGS/LineSearchNocedalWright.h +include/openbabel3/LBFGS/Param.h +include/openbabel3/openbabel/alias.h +include/openbabel3/openbabel/atom.h +include/openbabel3/openbabel/babelconfig.h +include/openbabel3/openbabel/base.h +include/openbabel3/openbabel/bitvec.h +include/openbabel3/openbabel/bond.h +include/openbabel3/openbabel/bondtyper.h +include/openbabel3/openbabel/builder.h +include/openbabel3/openbabel/canon.h +include/openbabel3/openbabel/chains.h +include/openbabel3/openbabel/chargemodel.h +include/openbabel3/openbabel/chemdrawcdx.h +include/openbabel3/openbabel/conformersearch.h +include/openbabel3/openbabel/data.h +include/openbabel3/openbabel/data_utilities.h +include/openbabel3/openbabel/depict/asciipainter.h +include/openbabel3/openbabel/depict/cairopainter.h +include/openbabel3/openbabel/depict/commandpainter.h +include/openbabel3/openbabel/depict/depict.h +include/openbabel3/openbabel/depict/painter.h +include/openbabel3/openbabel/depict/svgpainter.h +include/openbabel3/openbabel/descriptor.h +include/openbabel3/openbabel/distgeom.h +include/openbabel3/openbabel/dlhandler.h +include/openbabel3/openbabel/elements.h +include/openbabel3/openbabel/fingerprint.h +include/openbabel3/openbabel/forcefield.h +include/openbabel3/openbabel/format.h +include/openbabel3/openbabel/generic.h +include/openbabel3/openbabel/graphsym.h +include/openbabel3/openbabel/grid.h +include/openbabel3/openbabel/griddata.h +include/openbabel3/openbabel/groupcontrib.h +include/openbabel3/openbabel/inchiformat.h +include/openbabel3/openbabel/internalcoord.h +include/openbabel3/openbabel/isomorphism.h +include/openbabel3/openbabel/json.h +include/openbabel3/openbabel/kekulize.h +include/openbabel3/openbabel/kinetics.h +include/openbabel3/openbabel/lineend.h +include/openbabel3/openbabel/locale.h +include/openbabel3/openbabel/math/align.h +include/openbabel3/openbabel/math/erf.h +include/openbabel3/openbabel/math/matrix3x3.h +include/openbabel3/openbabel/math/spacegroup.h +include/openbabel3/openbabel/math/transform3d.h +include/openbabel3/openbabel/math/vector3.h +include/openbabel3/openbabel/matrix.h +include/openbabel3/openbabel/mcdlutil.h +include/openbabel3/openbabel/mol.h +include/openbabel3/openbabel/molchrg.h +include/openbabel3/openbabel/obconversion.h +include/openbabel3/openbabel/oberror.h +include/openbabel3/openbabel/obfunctions.h +include/openbabel3/openbabel/obiter.h +include/openbabel3/openbabel/obmolecformat.h +include/openbabel3/openbabel/obutil.h +include/openbabel3/openbabel/op.h +include/openbabel3/openbabel/optransform.h +include/openbabel3/openbabel/parsmart.h +include/openbabel3/openbabel/patty.h +include/openbabel3/openbabel/phmodel.h +include/openbabel3/openbabel/plugin.h +include/openbabel3/openbabel/pointgroup.h +include/openbabel3/openbabel/query.h +include/openbabel3/openbabel/reaction.h +include/openbabel3/openbabel/reactionfacade.h +include/openbabel3/openbabel/residue.h +include/openbabel3/openbabel/ring.h +include/openbabel3/openbabel/rotamer.h +include/openbabel3/openbabel/rotor.h +include/openbabel3/openbabel/shared_ptr.h +include/openbabel3/openbabel/spectrophore.h +include/openbabel3/openbabel/stereo/bindings.h +include/openbabel3/openbabel/stereo/cistrans.h +include/openbabel3/openbabel/stereo/squareplanar.h +include/openbabel3/openbabel/stereo/stereo.h +include/openbabel3/openbabel/stereo/tetrahedral.h +include/openbabel3/openbabel/stereo/tetranonplanar.h +include/openbabel3/openbabel/stereo/tetraplanar.h +include/openbabel3/openbabel/tautomer.h +include/openbabel3/openbabel/text.h +include/openbabel3/openbabel/tokenst.h +include/openbabel3/openbabel/typer.h +include/openbabel3/openbabel/xml.h +lib/cmake/openbabel3/OpenBabel3Config.cmake +lib/cmake/openbabel3/OpenBabel3ConfigVersion.cmake +lib/cmake/openbabel3/OpenBabel3_EXPORTS-%%CMAKE_BUILD_TYPE%%.cmake +lib/cmake/openbabel3/OpenBabel3_EXPORTS.cmake lib/libinchi.so lib/libinchi.so.0 lib/libinchi.so.0.4.1 lib/libopenbabel.so -lib/libopenbabel.so.5 -lib/libopenbabel.so.5.0.0 +lib/libopenbabel.so.7 +lib/libopenbabel.so.7.0.0 lib/openbabel/%%VERSION%%/APIInterface.so lib/openbabel/%%VERSION%%/CSRformat.so lib/openbabel/%%VERSION%%/MCDLformat.so @@ -141,6 +151,7 @@ lib/openbabel/%%VERSION%%/chemtoolformat.so lib/openbabel/%%VERSION%%/cifformat.so lib/openbabel/%%VERSION%%/cmlformat.so lib/openbabel/%%VERSION%%/cmlreactformat.so +lib/openbabel/%%VERSION%%/cofformat.so lib/openbabel/%%VERSION%%/confabreport.so lib/openbabel/%%VERSION%%/copyformat.so lib/openbabel/%%VERSION%%/crkformat.so @@ -173,6 +184,7 @@ lib/openbabel/%%VERSION%%/inchiformat.so lib/openbabel/%%VERSION%%/jaguarformat.so lib/openbabel/%%VERSION%%/lmpdatformat.so lib/openbabel/%%VERSION%%/lpmdformat.so +lib/openbabel/%%VERSION%%/maeformat.so lib/openbabel/%%VERSION%%/mdffformat.so lib/openbabel/%%VERSION%%/mdlformat.so lib/openbabel/%%VERSION%%/mmcifformat.so @@ -211,6 +223,7 @@ lib/openbabel/%%VERSION%%/pubchemjsonformat.so lib/openbabel/%%VERSION%%/pwscfformat.so lib/openbabel/%%VERSION%%/qchemformat.so lib/openbabel/%%VERSION%%/reportformat.so +lib/openbabel/%%VERSION%%/rinchiformat.so lib/openbabel/%%VERSION%%/rsmiformat.so lib/openbabel/%%VERSION%%/rxnformat.so lib/openbabel/%%VERSION%%/shelxformat.so @@ -227,20 +240,28 @@ lib/openbabel/%%VERSION%%/turbomoleformat.so lib/openbabel/%%VERSION%%/unichemformat.so lib/openbabel/%%VERSION%%/vaspformat.so lib/openbabel/%%VERSION%%/viewmolformat.so +lib/openbabel/%%VERSION%%/wlnformat.so lib/openbabel/%%VERSION%%/xedformat.so lib/openbabel/%%VERSION%%/xmlformat.so lib/openbabel/%%VERSION%%/xsfformat.so lib/openbabel/%%VERSION%%/xyzformat.so lib/openbabel/%%VERSION%%/yasaraformat.so lib/openbabel/%%VERSION%%/zindoformat.so -%%PYTHON%%%%PYTHON_SITELIBDIR%%/_openbabel.so -%%PYTHON%%%%PYTHON_SITELIBDIR%%/openbabel.py -%%PYTHON%%%%PYTHON_SITELIBDIR%%/pybel.py -libdata/pkgconfig/openbabel-2.0.pc -man/man1/babel.1.gz +%%PYTHON%%%%PYTHON_SITELIBDIR%%/openbabel/__init__.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/openbabel/__pycache__/__init__.cpython-37.opt-1.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/openbabel/__pycache__/__init__.cpython-37.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/openbabel/__pycache__/openbabel.cpython-37.opt-1.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/openbabel/__pycache__/openbabel.cpython-37.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/openbabel/__pycache__/pybel.cpython-37.opt-1.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/openbabel/__pycache__/pybel.cpython-37.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/openbabel/_openbabel.so +%%PYTHON%%%%PYTHON_SITELIBDIR%%/openbabel/openbabel.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/openbabel/pybel.py +libdata/pkgconfig/openbabel-3.pc man/man1/obabel.1.gz man/man1/obchiral.1.gz man/man1/obconformer.1.gz +man/man1/obdistgen.1.gz man/man1/obenergy.1.gz man/man1/obfit.1.gz man/man1/obgen.1.gz @@ -249,14 +270,17 @@ man/man1/obgui.1.gz man/man1/obminimize.1.gz man/man1/obprobe.1.gz man/man1/obprop.1.gz +man/man1/obrms.1.gz man/man1/obrotamer.1.gz man/man1/obrotate.1.gz man/man1/obspectrophore.1.gz +man/man1/obsym.1.gz +man/man1/obtautomer.1.gz +man/man1/obthermo.1.gz man/man1/roundtrip.1.gz %%DATADIR%%/%%VERSION%%/MACCS.txt %%DATADIR%%/%%VERSION%%/SMARTS_InteLigand.txt %%DATADIR%%/%%VERSION%%/UFF.prm -%%DATADIR%%/%%VERSION%%/aromatic.txt %%DATADIR%%/%%VERSION%%/atomization-energies.txt %%DATADIR%%/%%VERSION%%/atomtyp.txt %%DATADIR%%/%%VERSION%%/babel_povray3.inc @@ -268,16 +292,11 @@ man/man1/roundtrip.1.gz %%DATADIR%%/%%VERSION%%/eem2015ha.txt %%DATADIR%%/%%VERSION%%/eem2015hm.txt %%DATADIR%%/%%VERSION%%/eem2015hn.txt -%%DATADIR%%/%%VERSION%%/element.txt %%DATADIR%%/%%VERSION%%/eqeqIonizations.txt -%%DATADIR%%/%%VERSION%%/fragments.txt %%DATADIR%%/%%VERSION%%/gaff.dat %%DATADIR%%/%%VERSION%%/gaff.prm %%DATADIR%%/%%VERSION%%/ghemical.prm -%%DATADIR%%/%%VERSION%%/isotope-small.txt -%%DATADIR%%/%%VERSION%%/isotope.txt %%DATADIR%%/%%VERSION%%/logp.txt -%%DATADIR%%/%%VERSION%%/mpC.txt %%DATADIR%%/%%VERSION%%/mmff94.ff %%DATADIR%%/%%VERSION%%/mmff94s.ff %%DATADIR%%/%%VERSION%%/mmffang.par @@ -294,6 +313,7 @@ man/man1/roundtrip.1.gz %%DATADIR%%/%%VERSION%%/mmffstbn.par %%DATADIR%%/%%VERSION%%/mmfftor.par %%DATADIR%%/%%VERSION%%/mmffvdw.par +%%DATADIR%%/%%VERSION%%/mpC.txt %%DATADIR%%/%%VERSION%%/mr.txt %%DATADIR%%/%%VERSION%%/patterns.txt %%DATADIR%%/%%VERSION%%/phmodel.txt @@ -301,6 +321,9 @@ man/man1/roundtrip.1.gz %%DATADIR%%/%%VERSION%%/psa.txt %%DATADIR%%/%%VERSION%%/qeq.txt %%DATADIR%%/%%VERSION%%/resdata.txt +%%DATADIR%%/%%VERSION%%/rigid-fragments-index.txt +%%DATADIR%%/%%VERSION%%/rigid-fragments.txt +%%DATADIR%%/%%VERSION%%/ring-fragments.txt %%DATADIR%%/%%VERSION%%/ringtyp.txt %%DATADIR%%/%%VERSION%%/space-groups.txt %%DATADIR%%/%%VERSION%%/splash.png @@ -308,4 +331,5 @@ man/man1/roundtrip.1.gz %%DATADIR%%/%%VERSION%%/svgformat.script %%DATADIR%%/%%VERSION%%/templates.sdf %%DATADIR%%/%%VERSION%%/torlib.txt +%%DATADIR%%/%%VERSION%%/torsion.txt %%DATADIR%%/%%VERSION%%/types.txt
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