%if 0%{?fedora}

%global with_python3 1

%endif

%if 0%{?rhel} && 0%{?rhel} <= 6

%{!?__python2: %global __python2 /usr/bin/python2}

%{!?python2_sitelib: %global python2_sitelib %(%{__python2} -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())")}

%{!?python2_sitearch: %global python2_sitearch %(%{__python2} -c "from distutils.sysconfig import get_python_lib; print(get_python_lib(1))")}

%global with_python3 0

%global python2_version 2.6

%endif

%if 0%{?rhel} && 0%{?rhel} > 6

%global with_python3 0

%endif

%global with_check 1

%global module biopython

Name:             python-biopython

Version:          1.66

Release:          2%{?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

%{?python_provide:%python_provide python2-%{module}}

BuildRequires:    python2-devel

BuildRequires:    flex-devel

BuildRequires:    python-reportlab

BuildRequires:    numpy

BuildRequires:    python-psycopg2

BuildRequires:    wise2

Requires:         python-reportlab

Requires:         numpy

Requires:         python-psycopg2

Requires:         wise2

%if 0%{?fedora}

BuildRequires:    python-mysql

Requires:         python-mysql

%else

BuildRequires:    MySQL-python

Requires:         MySQL-python

%endif

%description

A set of freely available Python tools for computational molecular

biology.

%if 0%{?with_python3}

%package -n python3-%{module}

Summary: Python3 tools for computational molecular biology

%{?python_provide:%python_provide python3-%{module}}

BuildRequires:    python3-devel

BuildRequires:    flex-devel

BuildRequires:    python3-reportlab

BuildRequires:    python3-numpy

BuildRequires:    python3-mysql

BuildRequires:    python3-psycopg2

Requires:         python3-reportlab

Requires:         python3-numpy

Requires:         python3-mysql

Requires:         python3-psycopg2

Requires:         wise2

%description -n python3-%{module}

A set of freely available Python3 tools for computational molecular

biology.

%endif

%package doc

Summary: PDF documentation

BuildArch: noarch

%description doc

PDF documentation of %{module}.

%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 ';'

%if 0%{?with_python3}

rm -rf %{py3dir}

cp -a . %{py3dir}

%endif # with_python3

%build

CFLAGS="$RPM_OPT_FLAGS -Wl,-z,relro -Wl,-z,now" %{__python2} setup.py build

%if 0%{?with_python3}

pushd %{py3dir}

CFLAGS="$RPM_OPT_FLAGS -Wl,-z,relro -Wl,-z,now" %{__python3} setup.py build

popd

%endif # with_python3

%install

%if 0%{?with_python3}

pushd %{py3dir}

%{__python3} setup.py install -O1 --skip-build --root=$RPM_BUILD_ROOT --install-data=%{_datadir}/python-biopython

popd

%endif

%{__python2} setup.py install -O1 --skip-build --root=$RPM_BUILD_ROOT --install-data=%{_datadir}/python-biopython

##DocTest cannot be executed

##https://github.com/biopython/biopython/issues/669

##http://lists.open-bio.org/pipermail/biopython-dev/2014-May/020541.html

%if 0%{?with_check}

%check

pushd Tests

find . -name 'run_tests.py' | xargs sed -i '1s|^#!/usr/bin/env python|#!%{__python2}|'

for test in `ls test_*.py | grep -v Tutorial`; do

%{__python2} run_tests.py --offline -v ${test}

done

popd

##Not all tests are ready for Python3

%if 0%{?with_python3}

pushd %{py3dir}

pushd Tests

find . -name 'run_tests.py' | xargs sed -i '1s|^#!/usr/bin/env python|#!%{__python3}|'

for test in `ls test_*.py | grep -v test_Tutorial | grep -v test_SeqIO | grep -v test_NCBIXML | grep -v test_Phylo`; do

%{__python3} run_tests.py --offline -v ${test}

done

%endif

%endif

%files

%{!?_licensedir:%global license %doc}

%doc Scripts

%doc CONTRIB DEPRECATED NEWS README

%license LICENSE

%{python2_sitearch}/*egg-info

%{python2_sitearch}/Bio/

%{python2_sitearch}/BioSQL/*

%if 0%{?with_python3}

%files -n python3-%{module}

%{!?_licensedir:%global license %doc}

%doc Doc Scripts

%doc CONTRIB DEPRECATED NEWS README

%license LICENSE

%{python3_sitearch}/*egg-info

%{python3_sitearch}/Bio/

%{python3_sitearch}/BioSQL/*

%endif

%files doc

%{!?_licensedir:%global license %doc}

%doc Doc/*.pdf

%license LICENSE

%changelog

* Wed Dec 09 2015 Antonio Trande <sagitter@fedoraproject.org> - 1.66-2

- Built with Python3

- Some cleanups

- Set --cflags

- Fixed MySQL dependencies in Fedora

* 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.

* Wed 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.

* Tue 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.