%{!?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:          1.54

Release:          1%{?dist}

Summary:          Python tools for computational molecular biology

Source0:          http://biopython.org/DIST/biopython-%{version}.tar.gz

Patch0:           python-biopython-1.51-enable-flex.patch

License:          MIT

Url:              http://www.biopython.org/

Group:            Development/Libraries

BuildRoot:        %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)

BuildRequires:    python-devel

BuildRequires:    flex

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}

# enable build of Bio.PDB.mmCIF.MMCIFlex (requires flex)

%patch0 -p0

# 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

* 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.