# 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 <giallu@gmail.com> - 2016.09.2-3

- BR eigen3-devel to activate build of more descriptors

* Wed Nov 23 2016 Gianluca Sforna <giallu@gmail.com> - 2016.09.2-1

- new upstream release

- clean up spec (no more EL6 builds)

* Mon Nov 21 2016 Dan HorĂ¡k <dan[at]danny.cz> - 2016.09.1-2

- fix non-x86 builds universally

* Fri Nov 11 2016 Gianluca Sforna <giallu@gmail.com> - 2016.09.1-1

- new upstream release

- fix ppc/ppc64 build

- drop upstreamed patches

* Wed Nov  2 2016 Gianluca Sforna <giallu@gmail.com> - 2016.03.5-1

- new upstream release

- fix moldraw headers installation with upstream patch

- drop upstreamed patches

* Mon Oct 10 2016 Pavel Raiskup <praiskup@redhat.com> - 2016.03.2-8

- rebuild for postgresql 9.6.0, add guard for incompatible PG plugin

  installation

* Sun Sep 18 2016 Gianluca Sforna <giallu@gmail.com> - 2016.03.2-7

- fix aarch64 build

* Fri Aug 19 2016 Gianluca Sforna <giallu@gmail.com> - 2016.03.2-6

- fix unused-direct-shlib-dependency rpmlint warning

* Wed Aug 17 2016 Gianluca Sforna <giallu@gmail.com> - 2016.03.2-5

- fix wrong-script-interpreter rpmlint error

* Thu Aug 11 2016 Gianluca Sforna <giallu@gmail.com> - 2016.03.2-4

- skip PgSQL tests not working in the build environment

- fix PgSQL cartridge installation

* Fri Aug  5 2016 Gianluca Sforna <giallu@gmail.com> - 2016.03.2-3

- fix arm build

- use CMAKE to build PgSQL cartridge

* Tue Aug  2 2016 Gianluca Sforna <giallu@gmail.com> - 2016.03.2-2

- fix build on rawhide

* Thu Jul 21 2016 Gianluca Sforna <giallu@gmail.com> - 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 <giallu@gmail.com> - 2016.03.1-1

- new upstream release

* Fri Dec  4 2015 Gianluca Sforna <giallu@gmail.com> - 2015.09.2-2

- Fix tests for python 3 wrappers

* Wed Nov 18 2015 Gianluca Sforna <giallu@gmail.com> - 2015.09.2-1

- new upstream release

* Sun Nov  8 2015 Gianluca Sforna <giallu@gmail.com> - 2015.09.1-1

- new upstream release

* Sat Sep 19 2015 Gianluca Sforna <giallu@gmail.com> - 2015.03.1-3

- more fixes from package review

- activate cairo rendering

- add python3 wrappers

* Mon Jul  6 2015 Gianluca Sforna <giallu@gmail.com> - 2015.03.1-2

- activate threading

- always test in verbose mode

* Thu Apr 30 2015 Gianluca Sforna <giallu@gmail.com> - 2015.03.1-1

* new upstream release

* Mon Dec  8 2014 Gianluca Sforna <giallu@gmail.com> - 2014.09.2-1

- new upstream release

* Wed Oct 29 2014 Gianluca Sforna <giallu@gmail.com> - 2014.09.1-1

- new upstream release

- rebase patches

* Wed Jul 16 2014 Gianluca Sforna <giallu@gmail.com> - 2014.03.1-3

- let base package own _datadir/RDKit

* Tue May 27 2014 Gianluca Sforna <giallu@gmail.com> - 2014.03.1-2

- fix EPEL build by adding python2_* macros

* Mon May 12 2014 Gianluca Sforna <giallu@gmail.com> - 2014.03.1-1

- new upstream release

- disable static build with cmake flag, drop related patch

* Sun Mar 30 2014 Gianluca Sforna <giallu@gmail.com> - 2013.09.2-1

- new upstream release

- more spec fixes from review ticket

* Mon Jan  6 2014 Gianluca Sforna <giallu@gmail.com> - 2013.09.1-2

- move cmake files under %%_libdir/cmake

* Mon Nov 11 2013 Gianluca Sforna <giallu@gmail.com> - 2013.09.1-1

- new upstream release

* Tue Jul 30 2013 Gianluca Sforna <giallu@gmail.com> - 2013.06.1-2

- use %%cmake macro

- fix tests in rawhide

* Sun Jul 28 2013 Gianluca Sforna <giallu@gmail.com> - 2013.06.1-1

- new upstream release

- spec clean up

* Thu May 30 2013 Gianluca Sforna <giallu@gmail.com> - 2013.03.2-1

- new upstream release

- fix shebang on rdkit/Chem/MCS.py

* Wed May 29 2013 Gianluca Sforna <giallu@gmail.com> - 2013.03-2

- spec fixes from package review (#804125)

* Sat Apr 27 2013 Gianluca Sforna <giallu@gmail.com> - 2013.03-1

- new upstream release

* Wed Feb  6 2013 Gianluca Sforna <giallu@gmail.com> - 2012.12-2

- add inchi support

* Tue Jan 22 2013 Gianluca Sforna <giallu@gmail.com> - 2012.12-1

- New upstream release

- BR fonts package

* Sun Oct 21 2012 Gianluca Sforna <giallu@gmail.com> - 2012.09-1

- New upstream release

- add python related requires

* Wed Jul 11 2012 Gianluca Sforna <giallu@gmail.com> - 2012.06-1

- New upstream release

* Fri Apr 13 2012 Gianluca Sforna <giallu@gmail.com> - 2012.03-1

- New upstream release

- Fix some packaging issues as per review (#804125)

* Wed Mar 07 2012 Gianluca Sforna <giallu@gmail.com> - 2011.12-1

- New upstream release

* Mon Dec 05 2011 Gianluca Sforna <giallu@gmail.com> - 2011.09-2.20111202svn1877

- Package a newer snapshot for postgres 9.1 support

- Remove rpath from postgres cartridge

* Fri Nov 25 2011 Gianluca Sforna <giallu@gmail.com> - 2011.09-1

- New upstream release

- rebase patches

- drop upstreamed patch

* Mon Aug 15 2011 Gianluca Sforna <giallu@gmail.com> - 2011.06-2

- Final release

- add SDMOlsupplier patch, fixes loop on tests

* Wed Jul  6 2011 Gianluca Sforna <giallu@gmail.com> - 2011.06-1

- New upstream (beta) release

- rebase patches

* Mon Jun 13 2011 Gianluca Sforna <giallu@gmail.com> - 2011.03-1

- New upstream release

- drop upstreamed patch

* Wed Apr  6 2011 Gianluca Sforna <giallu@gmail.com> - 2010.12-3

- Add draw_refactoring patch

* Fri Jan 14 2011 Gianluca Sforna <giallu@gmail.com> - 2010.12-2

- New upstream release

- filter auto-provides for python extensions

* Thu Dec 30 2010 Gianluca Sforna <giallu@gmail.com> - 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 <giallu@gmail.com> - 2010.09-1

- New upstream release

- Move build in tree to support tests

- build PostgreSQL cartridge

* Tue Sep  7 2010 Gianluca Sforna <giallu gmail com>

- Split subpackages

* Mon Jul  5 2010 Gianluca Sforna <giallu gmail com> - 2010.Q2-1

- Initial package