%global  checkout   22272

%global  date       20150528

%bcond_without perl

%bcond_without ruby

%bcond_without octave

%bcond_without check

%bcond_without r

%bcond_without python3

%bcond_without python2

%ifarch %{mono_arches}

%bcond_without mono

%else

%bcond_with mono

%endif

%ifarch s390 s390x %{arm} aarch64 ppc64 ppc64le

%bcond_with java

%else

%bcond_without java

%endif

# those have special requirements, the rest follows main package name

%global octpkg  SBML

%global perlpkg LibSBML

%global rubypkg SBML

%global rpkg    libSBML

%if %{with octave}

# Exclude .oct files from provides

%global __provides_exclude_from ^%{octpkglibdir}/.*\\.oct$

%endif

# Use the same directory of the main package for subpackage licence and docs

%global _docdir_fmt %{name}

Name:           libsbml

Version:        5.11.5

#Release:        1%{?dist}

Release:        0.3.%{date}svn%{checkout}%{?dist}

Summary:        Systems Biology Markup Language library

License:        LGPLv2+

URL:            http://sbml.org/Software/libSBML

## Source archive from svn #22272; obtained by:

## svn checkout http://svn.code.sf.net/p/sbml/code/trunk/libsbml sbml-code

## tar -czvf  libsbml-svn22272.tar.gz sbml-code

Source0:        libsbml-svn%{checkout}.tar.gz

#Source0:        http://downloads.sourceforge.net/project/sbml/libsbml/%%{version}/stable/libSBML-%%{version}-core-src.zip

Source1:        http://sourceforge.net/projects/sbml/files/libsbml/5.11.4/experimental/source/render-5.11.4-beta-1.zip

## Unbundle minizip

Patch0:         libsbml-use-system-minizip-cmake.patch

## Fix library installation paths

Patch1:         libsbml-fix_install_libpaths.patch

BuildRequires:  cmake, clang

BuildRequires:  zlib-devel

BuildRequires:  bzip2-devel

BuildRequires:  libxml2-devel >= 2.6.16

BuildRequires:  expat-devel

BuildRequires:  check-devel

BuildRequires:  minizip-devel

BuildRequires:  swig

BuildRequires:  hostname

%description

LibSBML is an open-source programming library designed to

read, write, manipulate, translate, and validate SBML files and data

streams.  It is not an application itself (though it does come with

example programs), but rather a library you can embed in other

applications.

LibSBML %{version} understands SBML Level 3 Version 1 and older,

as well as the draft SBML Level 2 Layout proposal by Gauges, Rost,

Sahle and Wegner.  It’s written in ISO C and C++ but can also be

used from C#, Java, MATLAB, Octave, PERL, Python, and Ruby.

%package        devel

Summary:        Development files for %{name}

Requires:       %{name}%{?_isa} = %{version}-%{release}

%description    devel

This package contains libraries and header files for developing

applications that use libSBML.

%if %{with python2}

%package -n python-%{name}

BuildRequires:  python2-devel

Summary:        Python 2 bindings for libSBML

Requires:       %{name}%{?_isa} = %{version}-%{release}

%description -n python-%{name}

This package contains %{summary}.

This is the version for Python 2.

%endif

%if %{with python3}

%package -n python3-%{name}

BuildRequires:  python3-devel

Summary:        Python 3 bindings for libSBML

Requires:       %{name}%{?_isa} = %{version}-%{release}

%description -n python3-%{name}

This package contains %{summary}.

This is the version for Python 3.

%endif

%if %{with perl}

%package -n perl-%{perlpkg}

BuildRequires:  perl(Test::More)

BuildRequires:  perl(ExtUtils::MakeMaker)

Requires:       perl(:MODULE_COMPAT_%(eval "`%{__perl} -V:version`"; echo $version))

Summary:        PERL bindings for libSBML

Requires:       %{name}%{?_isa} = %{version}-%{release}

%description -n perl-%{perlpkg}

This package contains %{summary}.

%endif

%if %{with ruby}

%package -n ruby-%{rubypkg}

BuildRequires:  ruby-devel

Requires:       ruby(release)

Requires:       %{name}%{?_isa} = %{version}-%{release}

Provides:       ruby(%{rubypkg}) = %{version}

Summary:        Ruby bindings for libSBML

%description -n ruby-%{rubypkg}

This package contains %{summary}.

%endif

%if %{with java}

%package -n java-%{name}

BuildRequires:  java-devel

Requires:       java-headless

Requires:       jpackage-utils

Requires:       %{name}%{?_isa} = %{version}-%{release}

Summary:        Java bindings for libSBML

%description -n java-%{name}

This package contains %{summary}.

%endif

%if %{with octave}

%package -n octave-%{octpkg}

BuildRequires:  octave-devel

Requires:       octave(api) = %{octave_api}

Requires(post): octave

Requires(postun): octave

Requires:       %{name}%{?_isa} = %{version}-%{release}

Summary:        Octave bindings for libSBML

%description -n octave-%{octpkg}

This package contains %{summary}.

%endif

%if %{with r}

%package -n R-%{rpkg}

BuildRequires:  R-devel

BuildRequires:  R-core-devel

BuildRequires:  tex(latex)

Requires:       R-core

Summary:        R bindings for libSBML

Requires:       %{name}%{?_isa} = %{version}-%{release}

%description -n R-%{rpkg}

This package contains %{summary}.

%endif

%if %{with mono}

%package sharp

BuildRequires:  mono-core

BuildRequires:  xerces-c-devel, libxml2-devel, expat-devel

Summary:        C# bindings for libSBML

Requires:       mono-core

Requires:       %{name}%{?_isa} = %{version}-%{release}

%description sharp

This package contains %{summary}.

%endif

%if %{with doc}

%package        doc

BuildRequires:  doxygen

BuildRequires:  doxygen-latex

BuildRequires:  graphviz

Summary:        API documentation for %{name}

Requires:       %{name} = %{version}-%{release}

##Granted  exception temporarily

##http://fedoraproject.org/wiki/Packaging:No_Bundled_Libraries

Provides:       bundled(jquery)

BuildArch:      noarch

%description    doc

This package contains %{summary}.

%endif

%prep

%autosetup -n sbml-code -p1

sed -i -r 's/DOXYGEN_MAX_VERSION=1\.8\.8/DOXYGEN_MAX_VERSION=1.8.9/' configure

unzip -n %{SOURCE1}

# https://sourceforge.net/p/sbml/libsbml/391

iconv -f latin1 -t utf8 NEWS.txt > t; touch -r NEWS.txt t; mv t NEWS.txt

# Fix invalid shebang

# https://sourceforge.net/p/sbml/libsbml/390

for i in `find docs/src/filters -type f \( -name "*.py" \)`; do

sed -i -r 's|(#!/usr/bin/env python) +#.*|#!%{__python2}|' $i

done

# Delete bundled minizip

rm -v src/sbml/compress/{crypt.h,ioapi.*,iowin32.*,unzip.*,zip.*}

#grep -e 'This file was automatically generated by SWIG' -r . -l|xargs rm

mkdir build-docs

cp -a $(/bin/ls -1|grep -v build-docs) build-docs/

%build

mkdir build2 build

pushd build2

export LDFLAGS="%{__global_ldflags} -Wl,--as-needed"

%if %{with python2}

# This build is only for Python 2

%cmake -DENABLE_{LAYOUT,QUAL,COMP,FBC,RENDER}=ON \

%if 0%{?fedora} > 22

%ifarch x86_64

       -DCMAKE_CXX_COMPILER:FILEPATH=%{_bindir}/clang++ \

%endif

       -DCSHARP_COMPILER:FILEPATH=%{_bindir}/mcs \

%endif

       -DWITH_PYTHON=ON \

%if %{with check}

       -DWITH_CHECK=ON \

%endif

       -DPYTHON_INCLUDE_DIR:PATH=$(pkg-config --cflags python2|sed s/-I//) \

       -DPYTHON_LIBRARY:FILEPATH=$(pkg-config --libs python2) \

       -DPYTHON_EXECUTABLE:FILEPATH=%{__python2} \

       -DCMAKE_INSTALL_LIBDIR:PATH=%{_libdir} \

       -DWITH_LIBXML:BOOL=ON \

       -DWITH_EXPAT:BOOL=OFF \

       -Wno-dev \

       ..

make %{?_smp_mflags}

%endif

pushd ../build

%cmake -DENABLE_{LAYOUT,QUAL,COMP,FBC,RENDER}=ON \

%if 0%{?fedora} > 22

%ifarch x86_64

       -DCMAKE_CXX_COMPILER:FILEPATH=%{_bindir}/clang++ \

%endif

       -DCSHARP_COMPILER:FILEPATH=%{_bindir}/mcs \

%endif

%if %{with python3}

       -DWITH_PYTHON=ON \

       -DPYTHON_INCLUDE_DIR:PATH=$(pkg-config --cflags python3|sed s/-I//) \

       -DPYTHON_LIBRARY:FILEPATH=$(pkg-config --libs python3) \

       -DPYTHON_EXECUTABLE:FILEPATH=%{__python3} \

%endif

%if %{with perl}

       -DWITH_PERL=ON \

%endif

%if %{with ruby}

       -DWITH_RUBY=ON \

%endif

%if %{with java}

       -DWITH_JAVA=ON \

       -DWITH_JAVASCRIPT:BOOL=OFF \

       -DWITH_SWIG:BOOL=ON \

%endif

%if %{with octave}

       -DWITH_OCTAVE=ON \

%endif

%if %{with octave}

       -DWITH_OCTAVE=ON \

%endif

%if %{with r}

       -DWITH_R=ON \

       -DR_INCLUDE_DIRS:PATH=%{_includedir}/R \

%endif

%if %{with mono}

       -DWITH_CSHARP:BOOL=ON \

       -DWITH_XERCES:BOOL=OFF \

       -DWITH_LIBXML:BOOL=ON \

       -DWITH_EXPAT:BOOL=OFF \

       -DWITH_SWIG:BOOL=ON \

%endif

%if %{with check}

       -DWITH_CHECK=ON \

%endif

       -DCMAKE_INSTALL_LIBDIR:PATH=%{_libdir} \

       -DCMAKE_BUILD_TYPE:STRING=Release \

       -DCMAKE_SKIP_RPATH:BOOL=YES \

       -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES \

       -Wno-dev \

       ..

make %{?_smp_mflags}

pushd ../build-docs

%configure --disable-static \

           --with-expat=no \

           --with-libxml=yes \

%if %{with doc}

           --with-doxygen \

%endif

%if %{with python}

           --with-python --with-python-interpreter=%{__python3} \

%endif

           --enable-layout --enable-comp --enable-fbc --enable-qual

%if %{with doc}

cp ../build/src/bindings/python/libsbml-doxygen.py src/bindings/python/

make %{?_smp_mflags} docs

%endif

make %{?_smp_mflags} libsbml.pc

%install

%if %{with python2}

make -C build2 install DESTDIR=%{buildroot}

%endif

make -C build install DESTDIR=%{buildroot}

%if %{with octave}

chmod 0755 %{buildroot}%{octpkglibdir}/*.mex

%endif

%if %{with java}

mkdir -p %{buildroot}%{_libdir}/%{name} %{buildroot}%{_jnidir}

mv %{buildroot}%{_javadir}/libsbmlj.jar %{buildroot}%{_jnidir}/

mv %{buildroot}%{_libdir}/libsbmlj.so %{buildroot}%{_libdir}/%{name}/

%endif

%if %{with r}

mkdir -p %{buildroot}%{_libdir}/R/library

R CMD INSTALL -l %{buildroot}%{_libdir}/R/library build/src/bindings/r/%{rpkg}_%{version}_R_*.tar.gz

rm -rf %{buildroot}%{_libdir}/R/library/%{rpkg}/R.css

%endif

%if %{with doc}

make -C build-docs install-docs DESTDIR=%{buildroot}

mv %{buildroot}%{_pkgdocdir}-%{version} %{buildroot}%{_pkgdocdir}

%endif

make -C build-docs install-pc DESTDIR=%{buildroot}

%if %{with ruby}

install -Dm0644 src/bindings/ruby/README.txt %{buildroot}%{_pkgdocdir}/README-ruby.txt

%endif

%if %{with check}

%check

%if %{with python2}

export CK_FORK=no

make -C build2 check CTEST_OUTPUT_ON_FAILURE=TRUE

%endif

#export CK_FORK=no

#make -C build check CTEST_OUTPUT_ON_FAILURE=TRUE

##This test failed on ARM yet

##https://sourceforge.net/p/sbml/libsbml/411/

cd build

%if 0%{?fedora} < 23

%ifarch %{arm}

ctest --force-new-ctest-process -E test_csharp_bindings_full 

%else

ctest --force-new-ctest-process -E test_ruby_binding

%endif #ARM

%else

ctest --force-new-ctest-process

%endif #fedora <23

%endif #with_check

%post -p /sbin/ldconfig

%postun -p /sbin/ldconfig

%files

%license COPYING.txt LICENSE.txt

%doc AUTHORS.txt README* NEWS.txt OLD_NEWS.txt

%{_libdir}/*.so.*

##This directory provides just some txt documentation files

%exclude %{_datadir}/libsbml

%if %{with doc}

%exclude %{_pkgdocdir}/*-api

%endif

%files devel

%{_includedir}/sbml/

%{_libdir}/*.so

%exclude %{_libdir}/libsbml-static.a

%{_libdir}/pkgconfig/%{name}.pc

%if %{with python2}

%license COPYING.txt LICENSE.txt

%files -n python-%{name}

#%%{python2_sitearch}/%%{name}*.egg-info

%{python2_sitearch}/%{name}.pth

%{python2_sitearch}/%{name}

%endif

%if %{with python3}

%files -n python3-%{name}

%license COPYING.txt LICENSE.txt

#%%{python3_sitearch}/%%{name}*.egg-info

%{python3_sitearch}/%{name}.pth

%{python3_sitearch}/%{name}

%endif

%if %{with perl}

%files -n perl-%{perlpkg}

%license COPYING.txt LICENSE.txt

%{perl_vendorarch}/*

%exclude %dir %{perl_vendorarch}/auto/

%endif

%if %{with ruby}

%files -n ruby-%{rubypkg}

%license COPYING.txt LICENSE.txt

%doc %{_pkgdocdir}/README-ruby.txt

%{ruby_vendorarchdir}/*.so

%endif

%if %{with java}

%files -n java-%{name}

%license COPYING.txt LICENSE.txt

%{_jnidir}/libsbmlj.jar

%dir %{_libdir}/%{name}

%{_libdir}/%{name}/libsbmlj.so

%endif

%if %{with octave}

%files -n octave-%{octpkg}

%license COPYING.txt

%{octpkglibdir}/

%endif

%if %{with r}

%files -n R-%{rpkg}

%license COPYING.txt LICENSE.txt

%{_libdir}/R/library/%{rpkg}/

%endif

%if %{with mono}

%files sharp

%license COPYING.txt LICENSE.txt

%{_monodir}/libsbmlcsP/

%endif

%if %{with doc}

%files doc

%{_pkgdocdir}/cpp-api

# Binding docs are here too, as a compromise. Making a separate

# python-libsbml-doc seems overkill, but including them in an arched

# package is not nice.

%{_pkgdocdir}/python-api

%endif

%changelog

* Wed Jun 03 2015 Antonio Trande <sagitterATfedoraproject.org> - 5.11.5-0.3.20150528svn22272

- Exclude 'test_csharp_bindings_full' and 'test_ruby_binding' test in 

* Wed Jun 03 2015 Antonio Trande <sagitterATfedoraproject.org> - 5.11.5-0.2.20150528svn22272

- Exclude 'test_csharp_bindings_full' test in ARM

- Use clang++ in >F22

* Thu May 28 2015 Antonio Trande <sagitterATfedoraproject.org> - 5.11.5-0.1.20150528svn22272

- Update to svn pre-release #22272

- clang++ set as compiler on >F22

- Set C# compiler on >F22

* Thu May 28 2015 Antonio Trande <sagitterATfedoraproject.org> - 5.11.4-1

- Update to 5.11.4

- clang++ set as compiler

* Sat Feb 21 2015 Zbigniew Jędrzejewski-Szmek <zbyszek@in.waw.pl> - 5.11.0-11

- Disable -java and -mono on arch: they crash in tests

* Fri Feb 06 2015 Zbigniew Jędrzejewski-Szmek <zbyszek@in.waw.pl> - 5.11.0-10

- Rename -docs to -doc, run make unparallelized

* Wed Feb 04 2015 Zbigniew Jędrzejewski-Szmek <zbyszek@in.waw.pl> - 5.11.0-9

- Apply upstream patch for arm test failures

* Tue Feb 03 2015 Zbigniew Jędrzejewski-Szmek <zbyszek@in.waw.pl> - 5.11.0-8

- Fix things found in review (macro in comment, R:mono-core, %%doc

  duplication, macro usage)

* Mon Jan 26 2015 Zbigniew Jędrzejewski-Szmek <zbyszek@in.waw.pl> - 5.11.0-7

- Allow newer doxygen

* Fri Jan 09 2015 Zbigniew Jędrzejewski-Szmek <zbyszek@in.waw.pl> - 5.11.0-6

- Enable many many subpackages

* Tue Jan 06 2015 Zbigniew Jędrzejewski-Szmek <zbyszek@in.waw.pl> - 5.11.0-5

- Unbundle minizip

* Wed Dec 17 2014 Zbigniew Jędrzejewski-Szmek <zbyszek@in.waw.pl> - 5.11.0-4

- Do not build on arm

* Sat Dec 13 2014 Zbigniew Jędrzejewski-Szmek <zbyszek@in.waw.pl> - 5.11.0-3

- Convert to hybrid cmake (main part) / make (docs).

* Fri Dec 12 2014 Zbigniew Jędrzejewski-Szmek <zbyszek@in.waw.pl> - 5.11.0-2

- docs subpackage is no arch, remove %%{_isa} from dependency.

* Tue Dec 09 2014 Zbigniew Jędrzejewski-Szmek <zbyszek@in.waw.pl> - 5.11.0-1

- Initial packaging.