Name: bionetgen
Version: 2.3.0
Release: 4%{?dist}
Summary: Software for rule-based modeling of biochemical systems
License: GPLv3
URL: https://github.com/RuleWorld/bionetgen
Source0: https://github.com/RuleWorld/bionetgen/archive/BioNetGen-%{version}.tar.gz#/bionetgen-BioNetGen-%{version}.tar.gz
Patch0: bionetgen-isnan.patch
BuildRequires: muParser-devel >= 2.2.3-6
BuildRequires: perl-generators
BuildRequires: sundials-devel
BuildRequires: openmpi-devel
BuildRequires: autoconf automake
BuildRequires: libtool
Requires: perl(:MODULE_COMPAT_%(eval "`%{__perl} -V:version`"; echo $version))
Requires: %{name}-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*|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*|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.
%package perl
Summary: Perl scripts used by bionetgen
BuildArch: noarch
Requires: bionetgen = %{version}-%{release}
%description perl
%{summary}.
%prep
%autosetup -n bionetgen-BioNetGen-%{version} -p1
rm bng2/libsource/*
pushd bng2/Network3
sed -i 's/AC_PROG_LIBTOOL/AM_PROG_AR\nLT_INIT/' configure.ac
sed -i 's/cvode-.*//; s/muparser_.*//' configure.ac Makefile.am
sed -i -r 's/(run_network_LDADD =).*/\1 libmathutils.la -lmuparser -lsundials_nvecserial -lsundials_cvode/' src/Makefile.am
%build
pushd bng2/Network3
autoreconf -iv
%_openmpi_load
%configure
%make_build -C src
%install
%make_install -C bng2/Network3/src
mkdir -vp %{buildroot}/%{perl_vendorlib}/BioNetGen
cp -r bng2/Perl2 %{buildroot}/%{perl_vendorlib}/BioNetGen/
cp bng2/BNG2.pl %{buildroot}/%{perl_vendorlib}/BioNetGen/
%files
%license bng2/LICENSE.txt
%doc README.md bng2/CREDITS.txt bng2/CHANGES.txt bng2/README_FIRST.txt
%{_bindir}/run_network
%files perl
%{perl_vendorlib}/BioNetGen
%changelog
* 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 <sagitterATfedoraproject.org> - 2.3.0-1
- Update to 2.3.0
* Wed Mar 08 2017 Antonio Trande <sagitterATfedoraproject.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.