drop python2 subpackage (#1648558)
fix running the testsuite with python3 fix line endings for some source files
This commit is contained in:
Dominik 'Rathann' Mierzejewski
parent
6f8313c27e
commit
b8d2a455c4
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@ -0,0 +1,15 @@
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diff -up openbabel-openbabel-2-4-1/scripts/CMakeLists.txt.py3 openbabel-openbabel-2-4-1/scripts/CMakeLists.txt
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--- openbabel-openbabel-2-4-1/scripts/CMakeLists.txt.py3 2019-03-04 11:12:54.369464503 +0100
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+++ openbabel-openbabel-2-4-1/scripts/CMakeLists.txt 2019-03-04 11:59:39.323264995 +0100
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@@ -84,7 +84,10 @@ if (DO_PYTHON_BINDINGS)
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COMMAND ${CMAKE_COMMAND} -E echo " try:" >> ob.py
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COMMAND ${CMAKE_COMMAND} -E echo " import dl" >> ob.py
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COMMAND ${CMAKE_COMMAND} -E echo " except ImportError:" >> ob.py
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- COMMAND ${CMAKE_COMMAND} -E echo " import DLFCN as dl" >> ob.py
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+ COMMAND ${CMAKE_COMMAND} -E echo " try:" >> ob.py
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+ COMMAND ${CMAKE_COMMAND} -E echo " import DLFCN as dl" >> ob.py
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+ COMMAND ${CMAKE_COMMAND} -E echo " except ImportError:" >> ob.py
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+ COMMAND ${CMAKE_COMMAND} -E echo " import ctypes as dl" >> ob.py
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COMMAND ${CMAKE_COMMAND} -E echo " sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)" >> ob.py
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COMMAND cat ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py >> ob.py
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COMMAND ${CMAKE_COMMAND} -E copy ob.py ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py
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@ -0,0 +1,32 @@
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diff -up openbabel-openbabel-2-4-1/test/testpdbformat.py.taberror openbabel-openbabel-2-4-1/test/testpdbformat.py
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--- openbabel-openbabel-2-4-1/test/testpdbformat.py.taberror 2016-10-10 17:56:17.000000000 +0200
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+++ openbabel-openbabel-2-4-1/test/testpdbformat.py 2019-03-04 11:09:24.786801658 +0100
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@@ -24,12 +24,12 @@ class TestPDBFormat(BaseTest):
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def testInsertionCodes(self):
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"""
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- Testing a PDB entry with insertion codes to distinguish residues
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- upon conversion to FASTA.
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+ Testing a PDB entry with insertion codes to distinguish residues
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+ upon conversion to FASTA.
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"""
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self.canFindExecutable("babel")
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- self.entryPDBwithInsertioncodes="""ATOM 406 N VAL L 29 58.041 17.797 48.254 1.00 0.00 N
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+ self.entryPDBwithInsertioncodes="""ATOM 406 N VAL L 29 58.041 17.797 48.254 1.00 0.00 N
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ATOM 407 CA VAL L 29 57.124 18.088 47.170 1.00 0.00 C
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ATOM 408 C VAL L 29 55.739 17.571 47.538 1.00 0.00 C
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ATOM 409 O VAL L 29 55.535 16.362 47.550 1.00 0.00 O
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@@ -100,9 +100,9 @@ ATOM 473 HE1 TYR L 32 48.512
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ATOM 474 HE2 TYR L 32 48.145 19.172 44.648 1.00 0.00 H
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ATOM 475 HH TYR L 32 46.462 17.658 44.280 1.00 0.00 H
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"""
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- output, error = run_exec(self.entryPDBwithInsertioncodes,
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- "babel -ipdb -ofasta")
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- self.assertEqual(output.rstrip().rsplit("\n",1)[1], "VSSSY")
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+ output, error = run_exec(self.entryPDBwithInsertioncodes,
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+ "babel -ipdb -ofasta")
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+ self.assertEqual(output.rstrip().rsplit("\n",1)[1], "VSSSY")
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if __name__ == "__main__":
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testsuite = []
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@ -2,14 +2,13 @@
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%global shortcommit %(c=%{commit}; echo ${c:0:7})
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%{!?perl_vendorarch:%global perl_vendorarch %(eval "`perl -V:installvendorarch`"; echo $installvendorarch)}
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%{!?python2_sitearch:%global python2_sitearch %(%{__python} -c "from distutils.sysconfig import get_python_lib; print get_python_lib(1)")}
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# we don't want to provide private Perl or Python extension libs
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%global __provides_exclude_from ^(%{perl_vendorarch}/auto|%{python2_sitearch}|%{python3_sitearch})/.*\\.so$
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%global __provides_exclude_from ^(%{perl_vendorarch}/auto|%{python3_sitearch})/.*\\.so$
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Name: openbabel
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Version: 2.4.1
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Release: 20%{?dist}
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Release: 21%{?dist}
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Summary: Chemistry software file format converter
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License: GPLv2
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URL: https://openbabel.org/
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@ -35,7 +34,13 @@ Patch9: openbabel-narrowing-conversion.patch
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Patch10: openbabel-fix-libdir-in-pkgconfig.patch
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# Math 4 test is failing on s390x only
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Patch11: openbabel-disable-tests-s390x.patch
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# Fix inconsistent whitespace
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Patch12: openbabel-taberror.patch
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# Fix import of dl module in python3.7
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# https://github.com/openbabel/openbabel/pull/372
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Patch13: openbabel-python-dl.patch
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BuildRequires: cmake
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BuildRequires: dos2unix
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BuildRequires: desktop-file-utils
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BuildRequires: eigen3-devel
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BuildRequires: gcc-c++
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@ -109,15 +114,6 @@ BuildRequires: perl-generators
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%description -n perl-%{name}
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Perl wrapper for the Open Babel library.
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%package -n python2-%{name}
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Summary: Python wrapper for the Open Babel library
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Requires: %{name}-libs%{?_isa} = %{version}-%{release}
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BuildRequires: python2-devel
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%{?python_provide:%python_provide python2-%{name}}
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%description -n python2-%{name}
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Python2 wrapper for the Open Babel library.
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%package -n python3-%{name}
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Summary: Python wrapper for the Open Babel library
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Requires: %{name}-libs%{?_isa} = %{version}-%{release}
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@ -150,6 +146,15 @@ Ruby wrapper for the Open Babel library.
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%endif
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%patch9 -p1 -b .nc
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%patch10 -p1
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%patch12 -p1 -b .taberr
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%patch13 -p1 -b .py3dl
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# convert to Unix line endings
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dos2unix -k \
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data/chemdrawcdx.h \
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include/openbabel/{tautomer.h,math/align.h} \
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src/math/align.cpp \
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test/testsmartssym.py \
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convert src/GUI/babel.xpm -transparent white babel.png
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# Remove duplicate html files
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@ -162,19 +167,12 @@ for man in *.1; do
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done
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popd
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mkdir python3
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for f in *; do
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if [ "$f" != "python3" ]; then
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cp -a $f python3/
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fi
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done
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%build
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%cmake \
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-DCMAKE_SKIP_RPATH:BOOL=ON \
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-DBUILD_GUI:BOOL=ON \
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-DPYTHON_BINDINGS:BOOL=ON \
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-DPYTHON_EXECUTABLE=%{__python2} \
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-DPYTHON_EXECUTABLE=%{__python3} \
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-DPERL_BINDINGS:BOOL=ON \
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-DRUBY_BINDINGS:BOOL=ON \
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-DOPENBABEL_USE_SYSTEM_INCHI=true \
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@ -185,32 +183,8 @@ done
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.
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make VERBOSE=1 %{?_smp_mflags}
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BUILD_DIR=$PWD
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pushd python3
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%cmake \
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-DCMAKE_SKIP_RPATH:BOOL=ON \
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-DBUILD_GUI:BOOL=OFF \
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-DPYTHON_BINDINGS:BOOL=ON \
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-DPYTHON_EXECUTABLE=%{__python3} \
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-DPERL_BINDINGS:BOOL=OFF \
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-DRUBY_BINDINGS:BOOL=OFF \
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-DOPENBABEL_USE_SYSTEM_INCHI=true \
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-DENABLE_VERSIONED_FORMATS=false \
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-DRUN_SWIG=true \
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-DENABLE_TESTS:BOOL=OFF \
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-DOPTIMIZE_NATIVE=OFF \
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-DBINDINGS_ONLY:BOOL=ON \
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-DBABEL_SYSTEM_LIBRARY=$BUILD_DIR/%{_lib}/libopenbabel.so \
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.
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make VERBOSE=1 %{?_smp_mflags} bindings_python
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popd
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%install
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make VERBOSE=1 DESTDIR=%{buildroot} install
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pushd python3
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export DESTDIR=%{buildroot}
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%cmake -DCOMPONENT=bindings_python -P cmake_install.cmake
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popd
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rm %{buildroot}%{_libdir}/cmake/openbabel2/*.cmake
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@ -221,8 +195,8 @@ install -Dpm644 babel.png %{buildroot}%{_datadir}/pixmaps/babel.png
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%check
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# rm the built ruby bindings for testsuite to succeed (bug #1191173)
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rm %{_lib}/openbabel.so
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export CTEST_OUTPUT_ON_FAILURE=1
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make test
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export CTEST_OUTPUT_ON_FAILURE=1 PYTHONPATH=%{buildroot}%{python3_sitearch}
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%make_build test
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%endif
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%ldconfig_scriptlets libs
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@ -259,13 +233,6 @@ make test
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%dir %{perl_vendorarch}/*/Chemistry/OpenBabel
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%{perl_vendorarch}/*/Chemistry/OpenBabel/OpenBabel.so
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%files -n python2-%{name}
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%{python2_sitearch}/_openbabel.so
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%{python2_sitearch}/openbabel.py*
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%{python2_sitearch}/pybel.py*
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# Egg-info is not generated in 2.3.2, see upstream bug 837
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#%%{python_sitearch}/openbabel*.egg-info
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%files -n python3-%{name}
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%{python3_sitearch}/_openbabel.so
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%{python3_sitearch}/openbabel.py
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@ -276,6 +243,11 @@ make test
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%{ruby_vendorarchdir}/openbabel.so
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%changelog
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* Fri Mar 01 2019 Dominik Mierzejewski <rpm@greysector.net> - 2.4.1-21
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- drop python2 subpackage (#1648558)
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- fix running the testsuite with python3
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- fix line endings for some source files
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* Fri Feb 01 2019 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-20
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild
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