%bcond_with mpich
%bcond_with mpi
%bcond_without bundled_sundials
Name: bionetgen
Version: 2.8.4
Release: 3%{?dist}
Summary: Software for rule-based modeling of biochemical systems
# Bionetgen binary file is compiled against bundled muparser (MIT) and sundials-2.6.0 (BSD) libraries
License: GPLv3 and BSD and MIT
URL: https://github.com/RuleWorld/bionetgen
Source0: https://github.com/RuleWorld/bionetgen/archive/BioNetGen-%{version}/bionetgen-BioNetGen-%{version}.tar.gz
Patch0: %{name}-fix_linker.patch
Patch1: %{name}-fix_cmake_minimum.patch
Patch2: bionetgen-cmake-c99.patch
%if 0%{without bundled_sundials}
BuildRequires: sundials-devel
%endif
BuildRequires: cmake
BuildRequires: gcc-c++
BuildRequires: gcc
BuildRequires: gcc-gfortran
BuildRequires: make
BuildRequires: perl-interpreter
BuildRequires: perl(Carp)
BuildRequires: perl(Class::Struct)
BuildRequires: perl(Config)
BuildRequires: perl(constant)
BuildRequires: perl(Cwd)
BuildRequires: perl(Data::Dumper)
BuildRequires: perl(Exporter)
BuildRequires: perl(File::Basename)
BuildRequires: perl(File::Spec)
BuildRequires: perl(File::Spec::Win32)
BuildRequires: perl(FindBin)
BuildRequires: perl(Getopt::Long)
BuildRequires: perl(IO::Handle)
BuildRequires: perl(IO::Select)
BuildRequires: perl(IPC::Open3)
BuildRequires: perl(lib)
BuildRequires: perl(List::Util)
BuildRequires: perl(POSIX)
BuildRequires: perl(Scalar::Util)
BuildRequires: perl(strict)
BuildRequires: perl(Symbol)
BuildRequires: perl(vars)
BuildRequires: perl(warnings)
Requires: bionetgen-perl = %{version}-%{release}
# BioNetGen does not namespace its perl modules
%global __provides_exclude perl\\(.*BNG.*|Cache|CartesianProduct|Compartment.*|Component.*|Console|EnergyPattern|Expression|Function|HNauty|Map|ModelWrapper|Molecule*|Observable|Param*|PatternGraph|Population*|RateLaw|RefineRule|Rxn*|SBMLMultiAux|Species*|Visualization*|XML::*|XMLReader\\)
%global __requires_exclude perl\\(.*BNG.*|Cache|CartesianProduct|Compartment.*|Component.*|Console|EnergyPattern|Expression|Function|HNauty|Map|ModelWrapper|Molecule*|Observable|Param*|PatternGraph|Population*|RateLaw|RefineRule|Rxn*|SBMLMultiAux|Species*|Visualization*|XML::*|XMLReader\\)
%description
BioNetGen is software for the specification and simulation of
rule-based models of biochemical systems, including signal
transduction, metabolic, and genetic regulatory networks. The
BioNetGen language has recently been extended to include explicit
representation of compartments. A review of methods for rule-based
modeling is available in Science Signaling (Sci. STKE, 18 July 2006,
Issue 344, p. re6).
BioNetGen is presently a mixture of Perl and C++. Network generation
is currently implemented in Perl, the network simulator is C++, and a
new language parser is being developed with ANTLR.
#########
%if 0%{with mpi}
%package openmpi
Summary: Software for rule-based modeling of biochemical systems (OpenMPI)
BuildRequires: muParser-devel
%if 0%{without bundled_sundials}
BuildRequires: sundials-openmpi-devel >= 3.2.1
%endif
BuildRequires: openmpi-devel
Requires: bionetgen-perl = %{version}-%{release}
%description openmpi
BioNetGen is software for the specification and simulation of
rule-based models of biochemical systems, including signal
transduction, metabolic, and genetic regulatory networks. The
BioNetGen language has recently been extended to include explicit
representation of compartments. A review of methods for rule-based
modeling is available in Science Signaling (Sci. STKE, 18 July 2006,
Issue 344, p. re6).
BioNetGen is presently a mixture of Perl and C++. Network generation
is currently implemented in Perl, the network simulator is C++, and a
new language parser is being developed with ANTLR.
%package openmpi-devel
Summary: Software for rule-based modeling of biochemical systems (OpenMPI)
%description openmpi-devel
Software for rule-based modeling of biochemical systems (developer files).
%endif
######
#########
%if 0%{with mpich}
%package mpich
Summary: Software for rule-based modeling of biochemical systems (MPICH)
BuildRequires: muParser-devel
%if 0%{without bundled_sundials}
BuildRequires: sundials-mpich-devel >= 3.2.1
%endif
BuildRequires: mpich-devel
Requires: bionetgen-perl = %{version}-%{release}
%description mpich
BioNetGen is software for the specification and simulation of
rule-based models of biochemical systems, including signal
transduction, metabolic, and genetic regulatory networks. The
BioNetGen language has recently been extended to include explicit
representation of compartments. A review of methods for rule-based
modeling is available in Science Signaling (Sci. STKE, 18 July 2006,
Issue 344, p. re6).
BioNetGen is presently a mixture of Perl and C++. Network generation
is currently implemented in Perl, the network simulator is C++, and a
new language parser is being developed with ANTLR.
%package mpich-devel
Summary: Software for rule-based modeling of biochemical systems (MPICH)
%description mpich-devel
Software for rule-based modeling of biochemical systems (developer files).
%endif
######
%package perl
Summary: Perl scripts and Models used by bionetgen
BuildArch: noarch
BuildRequires: perl-generators
BuildRequires: perl(Math::Trig)
BuildRequires: make
Requires: bionetgen = %{version}-%{release}
Requires: perl(:MODULE_COMPAT_%(eval "`%{__perl} -V:version`"; echo $version))
Requires: perl(Math::Trig)
Provides: bundled(XML-TreePP) = 0.41
%description perl
%{summary}.
%prep
%setup -qc
pushd bionetgen-BioNetGen-%{version}
%if 0%{with bundled_sundials}
rm -f bng2/libsource/{gsl-1.9.tar.gz,Mathutils.tar.gz,muparser_v2_2_4.zip}
tar -xvf bng2/libsource/cvode-2.6.0.tar.gz -C bng2/Network3
tar -xvf bng2/libsource/muparser_v2_2_4.tar.gz -C bng2/Network3
%patch0 -p1 -b .backup
%patch1 -p1 -b .backup
%patch2 -p1 -b .c99
rm -f bng2/libsource/*
%endif
popd
%if 0%{with mpi}
cp -a bionetgen-BioNetGen-%{version} openmpi
%endif
%if 0%{with mpich}
cp -a bionetgen-BioNetGen-%{version} mpich
%endif
%build
pushd bionetgen-BioNetGen-%{version}/bng2/Network3
# Compile muparser static library
cd muparser_v2_2_4
%configure --enable-shared=no --enable-static=yes --enable-samples=no
%make_build
cd ../
# Compile mathutils static library
make -j1 -C src/util/mathutils
# Build sundials static libraries
%if %{with bundled_sundials}
SETOPT_FLAGS=$(echo "%{optflags}" | sed -e 's/-Werror=format-security/-Wno-error=format-security/g')
export CFLAGS="$SETOPT_FLAGS"
mkdir -p cvode-2.6.0/build
%define _vpath_builddir cvode-2.6.0/build
%cmake -S cvode-2.6.0 -B cvode-2.6.0/build -DCMAKE_MODULE_LINKER_FLAGS:STRING="%{__global_ldflags}" \
-DCMAKE_INSTALL_PREFIX=%{_prefix} \
-DEXAMPLES_ENABLE=OFF -DEXAMPLES_INSTALL=OFF \
-DBUILD_SHARED_LIBS:BOOL=OFF -DBUILD_STATIC_LIBS:BOOL=ON \
-DMPI_ENABLE:BOOL=OFF \
-DFCMIX_ENABLE:BOOL=ON
%cmake_build
%endif
SETOPT_FLAGS=$(echo "%{optflags}" | sed -e 's/-Werror=format-security/-Wno-error=format-security/g')
export CFLAGS="$SETOPT_FLAGS -I../src/util/mathutils -I../cvode-2.6.0/include -I../muparser_v2_2_4/include"
export CXXFLAGS="$SETOPT_FLAGS -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser"
mkdir -p build
%define _vpath_builddir build
%cmake -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES \
-DBUILD_SHARED_LIBS:BOOL=OFF -DBUILD_STATIC_LIBS:BOOL=ON
%cmake_build
popd
%if 0%{with mpi}
pushd openmpi/bng2/Network3
%{_openmpi_load}
%{_openmpi_unload}
popd
%endif
%if 0%{with mpich}
pushd mpich/bng2/Network3
%{_mpich_load}
%{_mpich_unload}
popd
%endif
%install
pushd bionetgen-BioNetGen-%{version}/bng2/Network3/build
mkdir -vp %{buildroot}%{_bindir}
install -pm 755 run_network %{buildroot}%{_bindir}/
popd
mkdir -vp %{buildroot}%{perl_vendorlib}/BioNetGen
cp -r bionetgen-BioNetGen-%{version}/bng2/Perl2 %{buildroot}%{perl_vendorlib}/BioNetGen/
cp -r bionetgen-BioNetGen-%{version}/bng2/BNG2.pl %{buildroot}%{perl_vendorlib}/BioNetGen/
cp -a bionetgen-BioNetGen-%{version}/bng2/Models2 %{buildroot}%{perl_vendorlib}/BioNetGen/
rm -f %{buildroot}%{perl_vendorlib}/BioNetGen/Models2/bin/run_network_%{_arch}-linux
rm -f %{buildroot}%{perl_vendorlib}/BioNetGen/Models2/run_network
%if 0%{with mpi}
%{_openmpi_load}
%{_openmpi_unload}
%endif
%if 0%{with mpich}
%{_mpich_load}
%{_mpich_unload}
%endif
%check
pushd bionetgen-BioNetGen-%{version}/bng2/Models2
%ifarch %{arm}
install -pm 755 ../Network3/build/run_network -D ./bin/run_network_armv7l-linux
install -pm 755 ../Network3/build/run_network -D ../bin/run_network_armv7l-linux
%else
install -pm 755 ../Network3/build/run_network -D ./bin/run_network_%{_target_cpu}-linux
install -pm 755 ../Network3/build/run_network -D ../bin/run_network_%{_target_cpu}-linux
%endif
echo "Running some tests ..."
../BNG2.pl CaOscillate_Func.bngl CaOscillate_Sat.bngl catalysis.bngl egfr_net.bngl egfr_net_red.bngl egfr_path.bngl energy_example1.bngl fceri_ji.bngl test_continue.bngl
echo "Tests finished."
%files
%license bionetgen-BioNetGen-%{version}/LICENSE
%doc bionetgen-BioNetGen-%{version}/README.md bionetgen-BioNetGen-%{version}/bng2/CREDITS.txt
%doc bionetgen-BioNetGen-%{version}/bng2/CHANGES.txt bionetgen-BioNetGen-%{version}/bng2/VERSION
%{_bindir}/run_network
%files perl
%{perl_vendorlib}/BioNetGen/
%if 0%{with mpi}
%files openmpi
%license bionetgen-BioNetGen-%{version}/LICENSE
%doc bionetgen-BioNetGen-%{version}/README.md bionetgen-BioNetGen-%{version}/bng2/CREDITS.txt
%doc bionetgen-BioNetGen-%{version}/bng2/CHANGES.txt bionetgen-BioNetGen-%{version}/bng2/VERSION
%{_libdir}/openmpi/bin/run_network
%endif
%if 0%{with mpich}
%files mpich
%license bionetgen-BioNetGen-%{version}/LICENSE
%doc bionetgen-BioNetGen-%{version}/README.md bionetgen-BioNetGen-%{version}/bng2/CREDITS.txt
%doc bionetgen-BioNetGen-%{version}/bng2/CHANGES.txt bionetgen-BioNetGen-%{version}/bng2/VERSION
%{_libdir}/mpich/bin/run_network
%endif
%changelog
* Sun Dec 11 2022 Florian Weimer <fweimer@redhat.com> - 2.8.4-3
- Port bundled CVODE CMake script to C99
* Fri Sep 09 2022 Antonio Trande <sagitter@fedoraproject.org> - 2.8.4-2
- Switch to CMake method (rhbz#2124489)
* Mon Aug 08 2022 Antonio Trande <sagitter@fedoraproject.org> - 2.8.4-1
- Release 2.8.4
* Wed Jul 20 2022 Fedora Release Engineering <releng@fedoraproject.org> - 2.8.2-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild
* Mon May 30 2022 Jitka Plesnikova <jplesnik@redhat.com> - 2.8.2-2
- Perl 5.36 rebuild
* Sun May 15 2022 Antonio Trande <sagitter@fedoraproject.org> - 2.8.2-1
- Release 2.8.2
* Wed Jan 19 2022 Fedora Release Engineering <releng@fedoraproject.org> - 2.7.0-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild
* Sat Oct 02 2021 Antonio Trande <sagitter@fedoraproject.org> - 2.7.0-1
- Release 2.7.0
* Wed Jul 21 2021 Fedora Release Engineering <releng@fedoraproject.org> - 2.6.0-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild
* Fri May 21 2021 Jitka Plesnikova <jplesnik@redhat.com> - 2.6.0-2
- Perl 5.34 rebuild
* Thu Apr 29 2021 Antonio Trande <sagitter@fedoraproject.org> - 2.6.0-1
- Release 2.6.0
* Tue Jan 26 2021 Fedora Release Engineering <releng@fedoraproject.org> - 2.5.2-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild
* Sun Dec 06 2020 Antonio Trande <sagitter@fedoraproject.org> - 2.5.2-1
- Release 2.5.2
* Sat Aug 01 2020 Fedora Release Engineering <releng@fedoraproject.org> - 2.5.1-4
- Second attempt - Rebuilt for
https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
* Mon Jul 27 2020 Fedora Release Engineering <releng@fedoraproject.org> - 2.5.1-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
* Mon Jun 22 2020 Jitka Plesnikova <jplesnik@redhat.com> - 2.5.1-2
- Perl 5.32 rebuild
* Fri Jun 05 2020 Antonio Trande <sagitter@fedoraproject.org> - 2.5.1-1
- Release 2.5.1
* Fri Mar 20 2020 Petr Pisar <ppisar@redhat.com> - 2.5.0-7
- Specify dependencies for the tests
* Tue Jan 28 2020 Fedora Release Engineering <releng@fedoraproject.org> - 2.5.0-6
- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
* Wed Jul 24 2019 Fedora Release Engineering <releng@fedoraproject.org> - 2.5.0-5
- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild
* Mon Jul 01 2019 Antonio Trande <sagitter@fedoraproject.org> - 2.5.0-4
- Use devtoolset-8 on EPEL 7
* Mon Jul 01 2019 Antonio Trande <sagitter@fedoraproject.org> - 2.5.0-3
- Rebuild for sundials
* Thu May 30 2019 Jitka Plesnikova <jplesnik@redhat.com> - 2.5.0-2
- Perl 5.30 rebuild
* Tue May 07 2019 Antonio Trande <sagitter@fedoraproject.org> - 2.5.0-1
- Release 2.5.0
* Sat Apr 20 2019 Antonio Trande <sagitter@fedoraproject.org> - 2.4.0-5
- Ready for MPI (disabled)
- Bundle Sundials
* Wed Feb 13 2019 Orion Poplawski <orion@cora.nwra.com> - 2.4.0-4
- Rebuild for openmpi 3.1.3
* Thu Jan 31 2019 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.0-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild
* Fri Nov 09 2018 Antonio Trande <sagitter@fedoraproject.org> - 2.4.0-2
- Filtering of SBMLMultiAux module
* Thu Nov 08 2018 Antonio Trande <sagitter@fedoraproject.org> - 2.4.0-1
- Release 2.4.0
- Drop obsolete patch
- Rebuild on epel7 (rhbz#1647989)
* Thu Jul 12 2018 Fedora Release Engineering <releng@fedoraproject.org> - 2.3.0-9
- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild
* Thu Jun 28 2018 Jitka Plesnikova <jplesnik@redhat.com> - 2.3.0-8
- Perl 5.28 rebuild
* Wed Feb 07 2018 Fedora Release Engineering <releng@fedoraproject.org> - 2.3.0-7
- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild
* Wed Nov 08 2017 Antonio Trande <sagitter@fedoraproject.org> - 2.3.0-6
- Rebuild for sundials-3.0.0
* Wed Aug 02 2017 Fedora Release Engineering <releng@fedoraproject.org> - 2.3.0-5
- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild
* Wed Jul 26 2017 Fedora Release Engineering <releng@fedoraproject.org> - 2.3.0-4
- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild
* Sun Jun 04 2017 Jitka Plesnikova <jplesnik@redhat.com> - 2.3.0-3
- Perl 5.26 rebuild
* Mon May 15 2017 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.3.0-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_27_Mass_Rebuild
* Sun May 07 2017 Antonio Trande <sagitter@fedoraproject.org> - 2.3.0-1
- Update to 2.3.0
* Wed Mar 08 2017 Antonio Trande <sagitter@fedoraproject.org> - 2.2.6-7
- Rebuild for sundials-2.7.0-10
* Fri Feb 10 2017 Fedora Release Engineering <releng@fedoraproject.org> - 2.2.6-6
- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild
* Fri Nov 04 2016 Zbigniew Jędrzejewski-Szmek <zbyszek@in.waw.pl> - 2.2.6-5
- Rebuild for sundials-2.7.0-7
* Tue Oct 25 2016 Zbigniew Jędrzejewski-Szmek <zbyszek@in.waw.pl> - 2.2.6-4
- Rebuild for sundials-2.7.0-6
* Sun Oct 16 2016 Zbigniew Jędrzejewski-Szmek <zbyszek@in.waw.pl> - 2.2.6-3
- Rebuild for libsundials (#1384636)
* Sun May 15 2016 Jitka Plesnikova <jplesnik@redhat.com> - 2.2.6-2
- Perl 5.24 rebuild
* Thu Feb 11 2016 Zbigniew Jędrzejewski-Szmek <zbyszek@bupkis> - 2.2.6-1
- Update to latest version
- Fix gcc6 compilation issue (#1306648)
* Wed Feb 03 2016 Fedora Release Engineering <releng@fedoraproject.org> - 2.2.5-8
- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild
* Wed Jun 17 2015 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.2.5-7
- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild
* Fri Jun 05 2015 Jitka Plesnikova <jplesnik@redhat.com> - 2.2.5-6
- Perl 5.22 rebuild
* Sat May 02 2015 Kalev Lember <kalevlember@gmail.com> - 2.2.5-5
- Rebuilt for GCC 5 C++11 ABI change
* Tue Mar 31 2015 Zbigniew Jędrzejewski-Szmek <zbyszek@in.waw.pl> - 2.2.5-4
- Rebuilt for sundials 2.6.0.
* Thu Feb 26 2015 Zbigniew Jędrzejewski-Szmek <zbyszek@in.waw.pl> - 2.2.5-3
- Rebuilt for https://fedoraproject.org/wiki/Changes/GCC5 (#1195309)
* Sun Nov 30 2014 Zbigniew Jędrzejewski-Szmek <zbyszek@in.waw.pl> - 2.2.5-2
- Drop dependency on compat f77, it is not needed.
* Fri Nov 21 2014 Zbigniew Jędrzejewski-Szmek <zbyszek@in.waw.pl> - 2.2.5-1
- Initial packaging.