Name:           python-pysb
Version:        0.1.11
Release:        2%{?dist}
Summary:        Rule-based modeling of biochemical systems as Python programs
License:        BSD
URL:            http://pysb.org/
Source0:        https://pypi.python.org/packages/source/p/pysb/pysb-%{version}.tar.gz
BuildArch:      noarch

BuildRequires:  python2-devel
# For building documentation
#BuildRequires:  dvipng
#BuildRequires:  python-sphinx
#BuildRequires:  tex(latex)
# https://github.com/pysb/pysb/issues/99
Requires:       bionetgen
Requires:       numpy
Requires:       scipy
Requires:       python-matplotlib
Requires:       sympy
Requires:       python-pygraphviz
Patch0:         0001-Mark-run_tutorial_a-executable-same-as-other-example.patch

%description
PySB is a framework for building mathematical models of biochemical
systems as Python programs. PySB abstracts the complex process of
creating equations describing interactions among multiple proteins or
other biomolecules into a simple and intuitive domain specific
programming language, which is internally translated into BioNetGen or
Kappa rules and from there into systems of equations. PySB makes it
straightforward to divide models into modules and to call libraries of
reusable elements (macros) that encode standard biochemical
actions. These features promote model transparency, reuse and
accuracy. PySB also interoperates with standard scientific Python
libraries such as NumPy, SciPy and SymPy enabling model simulation and
analysis.

%if 0
%package doc
Summary:        HTML documentation for %{name}
Group:          Documentation

%description doc
This package contains the HTML documentation for %{name}.
%endif

%prep
%setup -q -n pysb-%{version}
%patch0 -p1
# https://github.com/pysb/pysb/issues/100
sed -i -e "s|/usr/local/share/BioNetGen|%{perl_vendorlib}/BioNetGen|" \
       -e "s|'c:/Program Files/BioNetGen',||" \
    pysb/bng.py
sed -i -s "1 s|/usr/bin/env python|%{__python2}|" pysb/examples/*.py pysb/tools/*.py

%build
python setup.py build

%if 0
# Build documentation
cd doc
python build.py
%endif

%install
python2 setup.py install --skip-build --root %{buildroot}
chmod +x %{buildroot}/%{python_sitelib}/pysb/examples/run_*.py
chmod +x %{buildroot}/%{python_sitelib}/pysb/tools/[a-z]*.py

%files
%license LICENSE.txt
%doc README.rst
%{python_sitelib}/pysb/
%{python_sitelib}/pysb-%{version}-*.egg-info
%{_bindir}/pysb_export

%if 0
%files doc
%doc doc/build/*
%endif

%changelog
* Wed Dec 03 2014 Zbigniew Jędrzejewski-Szmek <zbyszek@in.waw.pl> - 0.1.11-2
- Fix shebangs and permissions on scripts.

* Fri Nov 21 2014 Zbigniew Jędrzejewski-Szmek <zbyszek@in.waw.pl> - 0.1.11-1
- Initial packaging.