FreeBSD Bugzilla – Attachment 221136 Details for
Bug 252309
science/openbabel: upgrade to 3.1.1
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[patch]
Patch to upgrade OpenBabel to 3.1.1
science_openbabel.diff (text/plain), 15.98 KB, created by
Thierry Thomas
on 2020-12-31 16:24:31 UTC
(
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Description:
Patch to upgrade OpenBabel to 3.1.1
Filename:
MIME Type:
Creator:
Thierry Thomas
Created:
2020-12-31 16:24:31 UTC
Size:
15.98 KB
patch
obsolete
>Index: science/openbabel/Makefile >=================================================================== >--- science/openbabel/Makefile (revision 558294) >+++ science/openbabel/Makefile (working copy) >@@ -2,32 +2,37 @@ > # $FreeBSD$ > > PORTNAME= openbabel >-PORTVERSION= 2.4.1 >-PORTREVISION= 6 >+PORTVERSION= 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 >+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 ${PORTVERSION} nexttime! > >-PLIST_SUB= VERSION="${PORTVERSION}" >- > OPTIONS_DEFINE= CAIRO PYTHON GUI >-OPTIONS_DEFAULT= PYTHON GUI >+OPTIONS_DEFAULT=CAIRO PYTHON GUI > OPTIONS_SUB= yes > > CAIRO_DESC= PNG support via cairo library >-CAIRO_USES= pkgconfig > CAIRO_USE= GNOME=cairo > > PYTHON_USES= python >@@ -44,14 +49,18 @@ > 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> >Index: science/openbabel/distinfo >=================================================================== >--- science/openbabel/distinfo (revision 558294) >+++ science/openbabel/distinfo (working copy) >@@ -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 >Index: science/openbabel/pkg-plist >=================================================================== >--- science/openbabel/pkg-plist (revision 558294) >+++ science/openbabel/pkg-plist (working copy) >@@ -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/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%%/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%%/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 >@@ -200,7 +212,7 @@ > lib/openbabel/%%VERSION%%/plugin_fingerprints.so > lib/openbabel/%%VERSION%%/plugin_forcefields.so > lib/openbabel/%%VERSION%%/plugin_ops.so >-%%CAIRO%%lib/openbabel/%%VERSION%%/png2format.so >+lib/openbabel/%%VERSION%%/png2format.so > lib/openbabel/%%VERSION%%/pngformat.so > lib/openbabel/%%VERSION%%/pointcloudformat.so > lib/openbabel/%%VERSION%%/posformat.so >@@ -211,6 +223,7 @@ > 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 >@@ -227,6 +240,7 @@ > 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 >@@ -233,14 +247,21 @@ > 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/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 @@ > %%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 @@ > %%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 @@ > %%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 @@ > %%DATADIR%%/%%VERSION%%/svgformat.script > %%DATADIR%%/%%VERSION%%/templates.sdf > %%DATADIR%%/%%VERSION%%/torlib.txt >+%%DATADIR%%/%%VERSION%%/torsion.txt > %%DATADIR%%/%%VERSION%%/types.txt
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