# recommonmark is currently incompatible with commonmark # as included in Fedora # https://github.com/rtfd/recommonmark/issues/24 %global with_docs 0 # Apparently, a prerelease inchi library is breaking our tests %global with_tests 0 %global with_py3 1 %global year 2016 %global month 09 %global extraver 2 %global pkgname Release_%{year}_%{month}_%{extraver} %global rootdir rdkit-%{pkgname} Name: rdkit Version: %{year}.%{month}.%{extraver} Release: 3%{?dist} Summary: Chemical informatics and machine learning toolkit License: BSD URL: http://www.rdkit.org/ Source0: https://github.com/rdkit/rdkit/archive/%{pkgname}.tar.gz BuildRequires: cmake BuildRequires: flex BuildRequires: bison BuildRequires: python2-devel BuildRequires: boost-devel BuildRequires: postgresql-devel BuildRequires: %{_bindir}/pg_config BuildRequires: numpy BuildRequires: inchi-devel BuildRequires: cairo-devel BuildRequires: eigen3-devel BuildRequires: chrpath BuildRequires: swig BuildRequires: java-devel BuildRequires: junit %if 0%{?fedora} && 0%{?with_py3} BuildRequires: python3-devel BuildRequires: boost-python3-devel %endif %if 0%{?with_docs} # Docs build deps BuildRequires: python-sphinx BuildRequires: python2-recommonmark BuildRequires: epydoc BuildRequires: doxygen BuildRequires: pandoc %if 0%{?fedora} BuildRequires: texlive-collection-latexrecommended BuildRequires: texlive-collection-fontsrecommended BuildRequires: tex(titlesec.sty) BuildRequires: tex(framed.sty) BuildRequires: tex(threeparttable.sty) BuildRequires: tex(wrapfig.sty) BuildRequires: tex(upquote.sty) BuildRequires: tex(multirow.sty) BuildRequires: tex(capt-of.sty) BuildRequires: tex(eqparbox.sty) %endif %endif # Needed for tests %if 0%{?with_tests} BuildRequires: pycairo BuildRequires: xorg-x11-fonts-Type1 BuildRequires: python-pandas BuildRequires: python-pillow %if 0%{?fedora} && 0%{?with_py3} BuildRequires: python3-cairocffi BuildRequires: python3-pandas BuildRequires: python3-pillow %endif %endif Patch1: rdkit-2015.03-use_cairo_backend_on_tests.patch Patch2: rdkit-2014.09-do_not_install_sping.patch Patch4: rdkit-2014.09-fix_cmake_files_path.patch Patch7: rdkit-2015.03-dont_install_contrib.patch %description Chemical informatics and machine learning toolkit %package devel Summary: Development files for %{name} Requires: %{name}%{?_isa} = %{version}-%{release} Requires: boost-devel%{?_isa} %description devel The %{name}-devel package contains libraries, build data, and header files for developing applications that use %{name}. %package doc Summary: Documentation for %{name} BuildArch: noarch Requires: %{name} = %{version}-%{release} %description doc Documentation files for %{name}. %package -n python2-rdkit Summary: Python 2 bindings for RDKit libraries %{?python_provide:%python_provide python2-rdkit} Requires: %{name}%{?_isa} = %{version}-%{release} Requires: numpy Requires: pycairo Requires: python-pillow Requires: xorg-x11-fonts-Type1 %description -n python2-rdkit Python 2 bindings for RDKit libraries %if 0%{?fedora} && 0%{?with_py3} %package -n python3-rdkit Summary: Python 3 bindings for RDKit libraries %{?python_provide:%python_provide python3-rdkit} Requires: %{name}%{?_isa} = %{version}-%{release} Requires: python3-numpy Requires: python3-cairocffi Requires: python3-pillow Requires: xorg-x11-fonts-Type1 %description -n python3-rdkit Python 3 bindings for RDKit libraries %endif %package postgresql Summary: RDKit cartridge for PostgreSQL Requires: %{name}%{?_isa} = %{version}-%{release} Requires: postgresql-server(:MODULE_COMPAT_%{postgresql_major}) %description postgresql PostgreSQL module for RDKit, which implements *mol* datatype to describe molecules and *fp* datatype for fingerprints, basic comparison operations, similarity operation (tanimoto, dice) and index support (using GiST indexing framework). To complete installation of the cartridge in PostgreSQL, please follow the steps detailed in: %{_docdir}/%{name}-postgresql/README # Prepare for a double build according to # https://fedoraproject.org/wiki/Packaging:Python_Appendix#Using_separate_build_directories %prep %setup -c -q -n %{rootdir} mv %{rootdir} python2 pushd python2 %patch1 -p1 %patch2 -p1 %patch4 -p1 %patch7 -p1 rm -rf rdkit/sping # Copy docs to top dir cp -pr license.txt ReleaseNotes.* ../ popd %if 0%{?with_py3} cp -a python2 python3 find python3 -name '*.py' | xargs sed -i '1s|^#!.*|#!%{__python3}|' # fix tests scripts for python3 runtime find python3 -name 'test_list.py' | xargs sed -i 's/"python"/"python3"/g' find python3 -name 'test_list.py' | xargs sed -i "s/'python'/'python3'/g" sed -i.orig 's/python/python3/g' python3/Projects/DbCLI/TestDbCLI.py %endif find python2 -name '*.py' | xargs sed -i '1s|^#!.*|#!%{__python2}|' %build # fix rpmlint "unused-direct-shlib-dependency" export CXXFLAGS="%{optflags} -Wl,--as-needed" # Python 2 build pushd python2 %cmake -D RDK_INSTALL_INTREE=OFF \ -D CMAKE_BUILD_TYPE=RelWithDebInfo \ -D RDK_BUILD_INCHI_SUPPORT:BOOL=ON \ -D RDK_BUILD_THREADSAFE_SSS:BOOL=ON \ -D RDK_BUILD_CAIRO_SUPPORT:BOOL=ON \ -D RDK_BUILD_PGSQL:BOOL=ON \ -D RDK_PGSQL_STATIC:BOOL=OFF \ -D RDK_INSTALL_STATIC_LIBS:BOOL=OFF \ -D RDK_USE_FLEXBISON:BOOL=ON \ -D RDK_TEST_MULTITHREADED:BOOL=ON \ -D PYTHON_EXECUTABLE:FILEPATH=%{__python2} \ %ifnarch %{ix86} x86_64 -D RDK_OPTIMIZE_NATIVE:BOOL=OFF \ %endif . # -D RDK_BUILD_SWIG_WRAPPERS:BOOL=ON \ make %{?_smp_mflags} # PostgreSQL cartridge pushd Code/PgSQL/rdkit chrpath -d librdkit.so popd %if 0%{?fedora} && 0%{with_docs} # Documentation (does not currently build on EPEL) export RDBASE=%{_builddir}/%{rootdir}/python2 pushd rdkit epydoc --config epydoc.config popd pushd Code doxygen doxygen/doxygen.config popd pushd Docs/Book make latexpdf popd %endif popd %if 0%{?fedora} && 0%{?with_py3} # Python 3 build pushd python3 %cmake -D RDK_INSTALL_INTREE=OFF \ -D CMAKE_BUILD_TYPE=RelWithDebInfo \ -D RDK_BUILD_INCHI_SUPPORT:BOOL=ON \ -D RDK_BUILD_THREADSAFE_SSS:BOOL=ON \ -D RDK_BUILD_CAIRO_SUPPORT:BOOL=ON \ -D RDK_BUILD_PGSQL:BOOL=ON \ -D RDK_PGSQL_STATIC:BOOL=OFF \ -D RDK_INSTALL_STATIC_LIBS:BOOL=OFF \ -D RDK_USE_FLEXBISON:BOOL=ON \ -D RDK_TEST_MULTITHREADED:BOOL=ON \ -D PYTHON_EXECUTABLE:FILEPATH=%{__python3} \ %ifnarch %{ix86} x86_64 -D RDK_OPTIMIZE_NATIVE:BOOL=OFF \ %endif . # -D RDK_BUILD_SWIG_WRAPPERS:BOOL=ON \ make %{?_smp_mflags} %endif %install # install Python 2 bindings pushd python2 make install DESTDIR=%{buildroot} pushd Code/PgSQL/rdkit # TODO: upstream installation should be fixed install -D librdkit.so %{buildroot}%{_libdir}/pgsql/rdkit.so install -D rdkit.control %{buildroot}%{_datadir}/pgsql/extension/rdkit.control install -D rdkit--3.5.sql %{buildroot}%{_datadir}/pgsql/extension/rdkit--3.5.sql popd popd %if 0%{?fedora} && 0%{?with_py3} # install Python 3 bindings pushd python3 make install DESTDIR=%{buildroot} popd %endif # remove installed doc files rm -r %{buildroot}/%{_datadir}/RDKit # Fix rpmlint warnings FMCS=%{buildroot}%{python2_sitearch}/rdkit/Chem/fmcs/fmcs sed '1{\@^#!%{__python2}@d}' $FMCS.py > $FMCS.new && touch -r $FMCS.py $FMCS.new && mv $FMCS.new $FMCS.py rm $FMCS %if 0%{?fedora} && 0%{?with_py3} FMCS=%{buildroot}%{python3_sitearch}/rdkit/Chem/fmcs/fmcs sed '1{\@^#!%{__python3}@d}' $FMCS.py > $FMCS.new && touch -r $FMCS.py $FMCS.new && mv $FMCS.new $FMCS.py rm $FMCS %endif %check %if 0%{?with_tests} # exclude PostgreSQL tests as they require a running DB instance pushd python2 export RDBASE=%{_builddir}/%{rootdir}/python2 export LD_LIBRARY_PATH=$RDBASE/lib export PYTHONPATH=$RDBASE ARGS="-V -E PgSQL" make test popd %if 0%{?fedora} && 0%{?with_py3} pushd python3 export RDBASE=%{_builddir}/%{rootdir}/python3 export LD_LIBRARY_PATH=$RDBASE/lib export PYTHONPATH=$RDBASE ARGS="-V -E PgSQL" make test popd %endif %endif %post -p /sbin/ldconfig %postun -p /sbin/ldconfig %files %license license.txt %doc ReleaseNotes.* %{_libdir}/lib*.so.* %files devel %{_includedir}/rdkit %{_libdir}/lib*.so %{_libdir}/cmake/*.cmake %files doc %if 0%{?fedora} && 0%{?with_docs} %doc python2/Docs/Book/_build/latex/RDKit.pdf %endif %files -n python2-rdkit %{python2_sitearch}/rdkit %if 0%{?fedora} && 0%{?with_py3} %files -n python3-rdkit %{python3_sitearch}/rdkit %endif %files postgresql %doc python2/Code/PgSQL/rdkit/README %{_libdir}/pgsql/rdkit.so %{_datadir}/pgsql/extension/rdkit--*.sql %{_datadir}/pgsql/extension/rdkit.control %changelog * Sat Nov 26 2016 Gianluca Sforna - 2016.09.2-3 - BR eigen3-devel to activate build of more descriptors * Wed Nov 23 2016 Gianluca Sforna - 2016.09.2-1 - new upstream release - clean up spec (no more EL6 builds) * Mon Nov 21 2016 Dan Horák - 2016.09.1-2 - fix non-x86 builds universally * Fri Nov 11 2016 Gianluca Sforna - 2016.09.1-1 - new upstream release - fix ppc/ppc64 build - drop upstreamed patches * Wed Nov 2 2016 Gianluca Sforna - 2016.03.5-1 - new upstream release - fix moldraw headers installation with upstream patch - drop upstreamed patches * Mon Oct 10 2016 Pavel Raiskup - 2016.03.2-8 - rebuild for postgresql 9.6.0, add guard for incompatible PG plugin installation * Sun Sep 18 2016 Gianluca Sforna - 2016.03.2-7 - fix aarch64 build * Fri Aug 19 2016 Gianluca Sforna - 2016.03.2-6 - fix unused-direct-shlib-dependency rpmlint warning * Wed Aug 17 2016 Gianluca Sforna - 2016.03.2-5 - fix wrong-script-interpreter rpmlint error * Thu Aug 11 2016 Gianluca Sforna - 2016.03.2-4 - skip PgSQL tests not working in the build environment - fix PgSQL cartridge installation * Fri Aug 5 2016 Gianluca Sforna - 2016.03.2-3 - fix arm build - use CMAKE to build PgSQL cartridge * Tue Aug 2 2016 Gianluca Sforna - 2016.03.2-2 - fix build on rawhide * Thu Jul 21 2016 Gianluca Sforna - 2016.03.2-1 - new upstream release - fix documentation build on Fedora 24 - add patch for broken cartridge build * Mon Apr 18 2016 Gianluca Sforna - 2016.03.1-1 - new upstream release * Fri Dec 4 2015 Gianluca Sforna - 2015.09.2-2 - Fix tests for python 3 wrappers * Wed Nov 18 2015 Gianluca Sforna - 2015.09.2-1 - new upstream release * Sun Nov 8 2015 Gianluca Sforna - 2015.09.1-1 - new upstream release * Sat Sep 19 2015 Gianluca Sforna - 2015.03.1-3 - more fixes from package review - activate cairo rendering - add python3 wrappers * Mon Jul 6 2015 Gianluca Sforna - 2015.03.1-2 - activate threading - always test in verbose mode * Thu Apr 30 2015 Gianluca Sforna - 2015.03.1-1 * new upstream release * Mon Dec 8 2014 Gianluca Sforna - 2014.09.2-1 - new upstream release * Wed Oct 29 2014 Gianluca Sforna - 2014.09.1-1 - new upstream release - rebase patches * Wed Jul 16 2014 Gianluca Sforna - 2014.03.1-3 - let base package own _datadir/RDKit * Tue May 27 2014 Gianluca Sforna - 2014.03.1-2 - fix EPEL build by adding python2_* macros * Mon May 12 2014 Gianluca Sforna - 2014.03.1-1 - new upstream release - disable static build with cmake flag, drop related patch * Sun Mar 30 2014 Gianluca Sforna - 2013.09.2-1 - new upstream release - more spec fixes from review ticket * Mon Jan 6 2014 Gianluca Sforna - 2013.09.1-2 - move cmake files under %%_libdir/cmake * Mon Nov 11 2013 Gianluca Sforna - 2013.09.1-1 - new upstream release * Tue Jul 30 2013 Gianluca Sforna - 2013.06.1-2 - use %%cmake macro - fix tests in rawhide * Sun Jul 28 2013 Gianluca Sforna - 2013.06.1-1 - new upstream release - spec clean up * Thu May 30 2013 Gianluca Sforna - 2013.03.2-1 - new upstream release - fix shebang on rdkit/Chem/MCS.py * Wed May 29 2013 Gianluca Sforna - 2013.03-2 - spec fixes from package review (#804125) * Sat Apr 27 2013 Gianluca Sforna - 2013.03-1 - new upstream release * Wed Feb 6 2013 Gianluca Sforna - 2012.12-2 - add inchi support * Tue Jan 22 2013 Gianluca Sforna - 2012.12-1 - New upstream release - BR fonts package * Sun Oct 21 2012 Gianluca Sforna - 2012.09-1 - New upstream release - add python related requires * Wed Jul 11 2012 Gianluca Sforna - 2012.06-1 - New upstream release * Fri Apr 13 2012 Gianluca Sforna - 2012.03-1 - New upstream release - Fix some packaging issues as per review (#804125) * Wed Mar 07 2012 Gianluca Sforna - 2011.12-1 - New upstream release * Mon Dec 05 2011 Gianluca Sforna - 2011.09-2.20111202svn1877 - Package a newer snapshot for postgres 9.1 support - Remove rpath from postgres cartridge * Fri Nov 25 2011 Gianluca Sforna - 2011.09-1 - New upstream release - rebase patches - drop upstreamed patch * Mon Aug 15 2011 Gianluca Sforna - 2011.06-2 - Final release - add SDMOlsupplier patch, fixes loop on tests * Wed Jul 6 2011 Gianluca Sforna - 2011.06-1 - New upstream (beta) release - rebase patches * Mon Jun 13 2011 Gianluca Sforna - 2011.03-1 - New upstream release - drop upstreamed patch * Wed Apr 6 2011 Gianluca Sforna - 2010.12-3 - Add draw_refactoring patch * Fri Jan 14 2011 Gianluca Sforna - 2010.12-2 - New upstream release - filter auto-provides for python extensions * Thu Dec 30 2010 Gianluca Sforna - 2010.12-1 - New upstream (beta) release - drop upstream patch - add patches for rpath, static libs - Fix spurious executable bits * Mon Oct 4 2010 Gianluca Sforna - 2010.09-1 - New upstream release - Move build in tree to support tests - build PostgreSQL cartridge * Tue Sep 7 2010 Gianluca Sforna - Split subpackages * Mon Jul 5 2010 Gianluca Sforna - 2010.Q2-1 - Initial package