%{!?python_sitelib: %define python_sitelib %(%{__python} -c "from distutils.sysconfig import get_python_lib; print get_python_lib()")}
%{!?python_sitearch: %define python_sitearch %(%{__python} -c "from distutils.sysconfig import get_python_lib; print get_python_lib(1)")}
Name: python-biopython
Version: 1.66
Release: 1%{?dist}
Summary: Python tools for computational molecular biology
Source0: http://biopython.org/DIST/biopython-%{version}.tar.gz
License: MIT
Url: http://www.biopython.org/
Group: Development/Libraries
BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
BuildRequires: python-devel
BuildRequires: flex-static
BuildRequires: python-reportlab
BuildRequires: numpy
BuildRequires: MySQL-python
BuildRequires: python-psycopg2
Requires: python-reportlab
Requires: numpy
Requires: MySQL-python
Requires: python-psycopg2
Requires: wise2
%description
A set of freely available Python tools for computational molecular
biology.
%prep
%setup -q -n biopython-%{version}
# remove all execute bits from documentation and fix line endings
find Scripts -type f -exec chmod -x {} 2>/dev/null ';'
find Doc -type f -exec chmod -x {} 2>/dev/null ';'
find Doc -type f -exec sed -i 's/\r//' {} 2>/dev/null ';'
# remove execute bits from Python modules
find Bio -type f -exec chmod -x {} 2>/dev/null ';'
# remove she-bang lines in .py files to keep rpmlint happy
find Bio -type f -name "*.py" -exec sed -i '/^#![ ]*\/usr\/bin\/.*$/ d' {} 2>/dev/null ';'
%build
env CFLAGS="$RPM_OPT_FLAGS" %{__python} setup.py build
%install
rm -rf $RPM_BUILD_ROOT
%{__python} setup.py install -O1 --skip-build --root=$RPM_BUILD_ROOT --install-data=%{_datadir}/python-biopython
## disable tests for the moment
%check
%{?_with_check:%{__python} setup.py test --no-gui || :}
%clean
rm -rf $RPM_BUILD_ROOT
%files
%defattr(-,root,root,-)
%doc Doc Scripts
%doc CONTRIB DEPRECATED LICENSE NEWS README
%if 0%{?fedora} >= 9
%{python_sitearch}/*egg-info
%endif
%dir %{python_sitearch}/Bio
%{python_sitearch}/Bio/*
%dir %{python_sitearch}/BioSQL
%{python_sitearch}/BioSQL/*
%changelog
* Tue Dec 08 2015 Luis Bazan <lbazan@fedoraproject.org> - 1.66-1
- new upstream version
* Thu Jun 18 2015 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.65-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild
* Thu Jan 08 2015 Luis Bazan <lbazan@fedoraproject.org> - 1.65-1
- New upstream version
* Sun Aug 17 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.64-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild
* Tue Jun 10 2014 Luis Bazan <lbazan@fedoraproject.org> - 1.64-1
- New Upstream Version
* Sat Jun 07 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.60-4
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild
* Sun Aug 04 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.60-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild
* Thu Feb 14 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.60-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild
* Sat Nov 17 2012 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.60-1
- Update to latest upstream (#835434)
- Drop flex-related patch, no longer needed
* Sat Jul 21 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.59-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild
* Fri Mar 9 2012 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.59-1
- Update to latest upstream (1.59) (#797872)
* Sat Jan 14 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.58-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild
* Tue Sep 20 2011 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.58-1
- Update to upstream 1.58
* Tue Feb 08 2011 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.55-0.2.b
- Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild
* Fri Aug 20 2010 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.55-0.1.b
- Update to 1.55 beta
- BuildRequires: flex-static, libraries are now split out
* Wed Jul 21 2010 David Malcolm <dmalcolm@redhat.com> - 1.54-2
- Rebuilt for https://fedoraproject.org/wiki/Features/Python_2.7/MassRebuild
* Fri May 21 2010 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.54-1
- Update to upstream 1.54
* Tue Apr 6 2010 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.54-0.1.b
- Update to 1.54 beta
* Tue Dec 15 2009 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.53-1
- Update to upstream 1.53
* Thu Oct 15 2009 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.52-1
- Update to latest upstream (1.52)
* Tue Aug 18 2009 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.51-1
- Update to upstream 1.51
- Drop mx {Build}Requires, no longer used upstream
- Remove Martel modules, no longer distributed upstream
- Add flex to BuildRequires, patch setup to build
Bio.PDB.mmCIF.MMCIFlex as per upstream:
http://bugzilla.open-bio.org/show_bug.cgi?id=2619
* Sun Jul 26 2009 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.49-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_12_Mass_Rebuild
* Thu Feb 26 2009 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.49-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_11_Mass_Rebuild
* Mon Dec 1 2008 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.49-1
- Update to latest upstream (1.49) uses numpy and new API for psycopg2
- [Build]Requires python-numeric -> numpy
- [Build]Requires python-psycopg -> python-psycopg2
- Remove interactive question hack, no longer needed
* Sun Nov 30 2008 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.48-3
- Temporarily disable python-psycopg dependency until it is rebuilt
for Python 2.6
* Sat Nov 29 2008 Ignacio Vazquez-Abrams <ivazqueznet+rpm@gmail.com> - 1.48-2
- Rebuild for Python 2.6
* Mon Sep 29 2008 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.48-1
- Update to latest upstream (1.48)
* Fri Jul 4 2008 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.47-1
- Update to latest upstream (1.47)
* Sun Mar 23 2008 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.45-1
- Update to latest upstream (1.45)
* Sat Feb 9 2008 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.44-4
- rebuilt for GCC 4.3 as requested by Fedora Release Engineering
* Thu Dec 13 2007 Alex Lancaster <alexlan[AT]fedoraproject.org> 1.44-3
- Include eggs in file list for F9+
* Sun Oct 28 2007 Alex Lancaster <alexlan[AT]fedoraproject.org> 1.44-2
- Drop patch to setup.py, applied upstream
* Sun Oct 28 2007 Alex Lancaster <alexlan[AT]fedoraproject.org> 1.44-1
- Update to latest upstream (1.44).
* Mon Aug 27 2007 Alex Lancaster <alexlan[AT]fedoraproject.org> 1.43-5
- Used "MIT" as short license name as the "Biopython License
Agreement" is the same as the CMU MIT variant.
* Mon Apr 25 2007 Alex Lancaster <alexlan[AT]fedoraproject.org> 1.43-4
- Add wise2 Requires since the Wise biopython module uses the
command-line behind-the-scenes.
* Mon Apr 17 2007 Alex Lancaster <alexlan[AT]fedoraproject.org> 1.43-3
- Use python_sitearch macro to enable x86_64 builds work.
* Mon Apr 16 2007 Alex Lancaster <alexlan[AT]fedoraproject.org> 1.43-2
- Fix Source0 URL as per suggestion from Parag AN on #235989.
* Mon Apr 02 2007 Alex Lancaster <alexlan[AT]fedoraproject.org> 1.43-1
- Initial Fedora package.