%if 0%{?rhel} && 0%{?rhel} > 7

%global with_python3 1

%global with_python2 0

%endif

%if 0%{?rhel} && 0%{?rhel} == 7

%global with_python3 0

%global with_python2 1

%endif

%if 0%{?rhel}

%global py2_prefix python

%else

%global py2_prefix python2

%endif

%if 0%{?fedora} && 0%{?fedora} < 30

%global with_python3 1

%global with_python2 1

%endif

%if 0%{?fedora} && 0%{?fedora} >= 30

%global with_python3 1

%global with_python2 0

Obsoletes: python2-%{module}

%endif

%global with_check 1

%global module biopython

Name:             python-biopython

Version:          1.73

Release:          4%{?dist}

Summary:          Python tools for computational molecular biology

Source0:          https://files.pythonhosted.org/packages/source/b/%{module}/%{module}-%{version}.tar.gz

# Starting from biopython-1.69, BioPython is released under the

# "Biopython License Agreement"; it looks like a MIT variant

# rhbz #1440337

License:          MIT and BSD

URL:              https://biopython.org/

BuildRequires:    gcc

%if 0%{?with_python3_other}

BuildRequires:  python%{python3_other_pkgversion}-devel

%endif

%description

A set of freely available Python tools for computational molecular

biology.

%if 0%{?with_python2}

%package -n python2-%{module}

Summary:  Python tools for computational molecular biology

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

# Build required packages

BuildRequires:    python2-devel

BuildRequires:    flex-devel

BuildRequires:    %{py2_prefix}-reportlab

BuildRequires:    %{py2_prefix}-psycopg2

BuildRequires:    %{py2_prefix}-rdflib

BuildRequires:    wise2

%if 0%{?rhel}

BuildRequires:    MySQL-%{py2_prefix}

BuildRequires:    numpy

%else

BuildRequires:    %{py2_prefix}-numpy

BuildRequires:    %{py2_prefix}-mysql

%endif

# Required packages

Requires:         %{py2_prefix}-networkx

Requires:         %{py2_prefix}-reportlab

Requires:         %{py2_prefix}-psycopg2

Requires:         wise2

Requires:         %{py2_prefix}-rdflib

%if 0%{?rhel}

Requires:         MySQL-%{py2_prefix}

Requires:         numpy

Requires:         mysql-connector-%{py2_prefix}

Requires:         graphviz-%{py2_prefix}

%else

Requires:         %{py2_prefix}-numpy

Requires:         %{py2_prefix}-pygraphviz

Requires:         %{py2_prefix}-mysql-connector

Requires:         %{py2_prefix}-mysql

%endif

%description -n python2-%{module}

A set of freely available Python tools for computational molecular

biology.

%endif

%if 0%{?with_python3}

%package -n python%{python3_pkgversion}-%{module}

Summary: Python3 tools for computational molecular biology

%{?python_provide:%python_provide python%{python3_pkgversion}-%{module}}

BuildRequires:    python%{python3_pkgversion}-devel

BuildRequires:    flex-devel

BuildRequires:    python%{python3_pkgversion}-reportlab

BuildRequires:    python%{python3_pkgversion}-numpy

BuildRequires:    python%{python3_pkgversion}-mysql

BuildRequires:    python%{python3_pkgversion}-psycopg2

BuildRequires:    python%{python3_pkgversion}-rdflib

Requires:         python%{python3_pkgversion}-networkx

Requires:         python%{python3_pkgversion}-pygraphviz

Requires:         mysql-connector-python%{python3_pkgversion}

Requires:         python%{python3_pkgversion}-reportlab

Requires:         python%{python3_pkgversion}-numpy

Requires:         python%{python3_pkgversion}-mysql

Requires:         python%{python3_pkgversion}-psycopg2

Requires:         wise2

Requires:         python%{python3_pkgversion}-rdflib

%description -n python%{python3_pkgversion}-%{module}

A set of freely available Python3 tools for computational molecular

biology.

%endif

%if 0%{?with_python3_other}

%package -n python%{python3_other_pkgversion}-%{module}

Summary: Python3 tools for computational molecular biology

%{?python_provide:%python_provide python%{python3_other_pkgversion}-%{module}}

BuildRequires:    python%{python3_other_pkgversion}-devel

BuildRequires:    flex-devel

BuildRequires:    python%{python3_other_pkgversion}-reportlab

BuildRequires:    python%{python3_other_pkgversion}-numpy

BuildRequires:    python%{python3_other_pkgversion}-mysql

BuildRequires:    python%{python3_other_pkgversion}-psycopg2

BuildRequires:    python%{python3_other_pkgversion}-rdflib

Requires:         python%{python3_other_pkgversion}-networkx

Requires:         python%{python3_other_pkgversion}-pygraphviz

Requires:         mysql-connector-python%{python3_other_pkgversion}

Requires:         python%{python3_other_pkgversion}-reportlab

Requires:         python%{python3_other_pkgversion}-numpy

Requires:         python%{python3_other_pkgversion}-mysql

Requires:         python%{python3_other_pkgversion}-psycopg2

Requires:         wise2

Requires:         python%{python3_other_pkgversion}-rdflib

%description -n python%{python3_other_pkgversion}-%{module}

A set of freely available Python3 tools for computational molecular

biology.

%endif # with_python3_other

%package doc

Summary: PDF and HTML documentation of %{module}

BuildArch: noarch

%description doc

PDF/HTML documentation of %{module}.

%prep

%setup -qc

pushd %{module}-%{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 ';'

popd

%if 0%{?with_python2}

cp -a %{module}-%{version} python2

%endif

%if 0%{?with_python3}

cp -a %{module}-%{version} python3

%endif # with_python3

%if 0%{?with_python3_other}

cp -a %{module}-%{version} python%{python3_other_pkgversion}

%endif # with_python3_other

%build

%if 0%{?with_python2}

pushd python2

%py2_build

popd

%endif

%if 0%{?with_python3}

pushd python3

%py3_build

popd

%endif # with_python3

%if 0%{?with_python3_other}

pushd python%{python3_other_pkgversion}

%py3_other_build

popd

%endif # with_python3_other

%install

%if 0%{?with_python3}

pushd python3

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

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

popd

%endif

%if 0%{?with_python3_other}

pushd python%{python3_other_pkgversion}

%{__python3_other} setup.py install -O1 --skip-build --root=$RPM_BUILD_ROOT --install-data=%{_datadir}/python-biopython

find Scripts -name '*.py' | xargs sed -i '1s|^#!/usr/bin/env python|#!%{__python3_other}|'

popd

%endif

%if 0%{?with_python2}

pushd python2

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

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

popd

%endif

##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

%if 0%{?with_python2}

pushd python2

export PYTHONPATH=$RPM_BUILD_ROOT%{python2_sitearch}

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

%endif

# See https://github.com/biopython/biopython/issues/855

# https://github.com/biopython/biopython/issues/1889

%if 0%{?with_python3}

pushd python3/Tests

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

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

echo $LANG

export PYTHONPATH=$RPM_BUILD_ROOT%{python3_sitearch}

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

done

popd

%endif

# See https://github.com/biopython/biopython/issues/855

%if 0%{?with_python3_other}

pushd python%{python3_other_pkgversion}/Tests

find . -name 'run_tests.py' | xargs sed -i '1s|^#!/usr/bin/env python|#!%{__python3_other}|'

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

echo $LANG

export PYTHONPATH=$RPM_BUILD_ROOT%{python3_other_sitearch}

%{__python3_other} run_tests.py --offline -v ${test}

done

popd

%endif # with_python3_other

%endif # with_check

%if 0%{?with_python2}

%files -n python2-%{module}

%doc python2/Scripts

%doc python2/CONTRIB.rst python2/DEPRECATED.rst python2/NEWS.rst python2/README.rst

%license python2/LICENSE.rst

%{python2_sitearch}/*egg-info

%{python2_sitearch}/Bio/

%{python2_sitearch}/BioSQL/

%endif

%if 0%{?with_python3}

%files -n python%{python3_pkgversion}-%{module}

%doc python3/Scripts

%doc python3/CONTRIB.rst python3/DEPRECATED.rst python3/NEWS.rst python3/README.rst

%license python3/LICENSE.rst

%{python3_sitearch}/*egg-info

%{python3_sitearch}/Bio/

%{python3_sitearch}/BioSQL/

%endif

%if 0%{?with_python3_other}

%files -n python%{python3_other_pkgversion}-%{module}

%doc python%{python3_other_pkgversion}/Scripts

%doc python%{python3_other_pkgversion}/CONTRIB.rst python%{python3_other_pkgversion}/DEPRECATED.rst python%{python3_other_pkgversion}/NEWS.rst python%{python3_other_pkgversion}/README.rst

%license python%{python3_other_pkgversion}/LICENSE.rst

%{python3_other_sitearch}/*egg-info

%{python3_other_sitearch}/Bio/

%{python3_other_sitearch}/BioSQL/

%endif

%files doc

%doc %{module}-%{version}/Doc

%license %{module}-%{version}/LICENSE.rst

%changelog

* Fri Jun 14 2019 Antonio Trande <sagitter@fedoraproject.org> - 1.73-4

- Reorganize Requires packages for EPEL7

* Thu Jun 13 2019 Antonio Trande <sagitter@fedoraproject.org> - 1.73-3

- Rebuild for python-reportlab-3.5.23

* Sat Feb 02 2019 Fedora Release Engineering <releng@fedoraproject.org> - 1.73-2

- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild

* Thu Jan 03 2019 Antonio Trande <sagitter@fedoraproject.org> - 1.73-1

- Release 1.73

* Sun Sep 30 2018 Antonio Trande <sagitter@fedoraproject.org> - 1.72-3

- Deprecate Python2 on fedora 30+

- Prepare SPEC file for Python3-modules packaging on epel7

* Fri Jul 13 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.72-2

- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild

* Sat Jun 30 2018 Antonio Trande <sagitter@fedoraproject.org> - 1.72-1

- Update to 1.72

* Fri Jun 22 2018 Antonio Trande <sagitter@fedoraproject.org> - 1.71-5

- Enable additional tests (upstream bug #855)

- Enable DSSP test with Python2

- Disable bgzf test with Python3

* Thu Jun 21 2018 Antonio Trande <sagitter@fedoraproject.org> - 1.71-4

- Patched for AlignIO test failure (python-3.7 issue)

* Tue Jun 19 2018 Miro HronĨok <mhroncok@redhat.com> - 1.71-3

- Rebuilt for Python 3.7

* Fri Apr 27 2018 Antonio Trande <sagitter@fedoraproject.org> - 1.71-2

- Conform Python3 builds to coming RHEL major release

* Wed Apr 04 2018 Antonio Trande <sagitter@fedoraproject.org> - 1.71-1

- Update to 1.71 (bz#1563655)

* Thu Feb 22 2018 Antonio Trande <sagitter@fedoraproject.org> - 1.70-11

- Add gcc BR

* Sat Feb 17 2018 Antonio Trande <sagitter@fedoraproject.org> - 1.70-10

- Fix Python2 mysql-connector packages on fedora

* Sat Feb 17 2018 Antonio Trande <sagitter@fedoraproject.org> - 1.70-9

- Fix Python2 required package on rhel

* Fri Feb 16 2018 Antonio Trande <sagitter@fedoraproject.org> - 1.70-8

- Remove %%sum macro

- Use %%py2_prefix

- Required 'numpy' on rhel (without prefix)

* Fri Feb 09 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.70-7

- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild

* Tue Jan 16 2018 Antonio Trande <sagitter@fedoraproject.org> - 1.70-6

- Fix dependencies

* Sun Jan 14 2018 Antonio Trande <sagitter@fedoraproject.org> - 1.70-5

- Use versioned Python packages

* Wed Jan 03 2018 Luis Bazan <lbazan@fedoraproject.org> - 1.70-4

- Fix directory ownership

* Thu Aug 03 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.70-3

- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild

* Thu Jul 27 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.70-2

- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild

* Tue Jul 11 2017 Antonio Trande <sagitter@fedoraproject.org> - 1.70-1

- Update to 1.70 (bz#1440337)

* Wed Apr 12 2017 Antonio Trande <sagitter@fedoraproject.org> - 1.69-1

- Update to 1.69

* Sat Feb 11 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.68-3

- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild

* Mon Dec 19 2016 Miro Hronok <mhroncok@redhat.com> - 1.68-2

- Rebuild for Python 3.6

* Sat Aug 27 2016 Antonio Trande <sagitter@fedoraproject.org> - 1.68-1

- Update to 1.68

- Drop old patch

* Wed Aug 17 2016 Antonio Trande <sagitter@fedoraproject.org> - 1.67-3

- Rebuild for Python 3.5.2

* Tue Jul 19 2016 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.67-2

- https://fedoraproject.org/wiki/Changes/Automatic_Provides_for_Python_RPM_Packages

* Wed Jun 15 2016 Antonio Trande <sagitter@fedoraproject.org> - 1.67-1

- Update to 1.67

* Mon Feb 15 2016 Antonio Trande <sagitter@fedoraproject.org> - 1.66-6

- Typo fixed

* Mon Feb 15 2016 Antonio Trande <sagitter@fedoraproject.org> - 1.66-5

- Created a python2- package

* Thu Feb 04 2016 Fedora Release Engineering <releng@fedoraproject.org> - 1.66-4

- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild

* Wed Dec 09 2015 Antonio Trande <sagitter@fedoraproject.org> - 1.66-3

- SPEC file adapted to recent guidelines for Python

* 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.