%if 0%{?rhel} && 0%{?rhel} > 7
%global with_python3 1
%endif
%if 0%{?rhel} && 0%{?rhel} == 7
%global with_python2 1
%endif
%if 0%{?rhel}
%global py2_prefix python
%else
%global py2_prefix python2
%endif
%if 0%{?fedora}
%global with_python3 1
%endif
%if 0%{?python3_version_nodots} == 38
%global with_check 1
%else
%global with_check 1
%endif
%global module biopython
Name: python-biopython
Version: 1.74
Release: 7%{?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
BuildRequires: mysql-connector-%{py2_prefix}
%else
BuildRequires: %{py2_prefix}-numpy
BuildRequires: %{py2_prefix}-mysql
BuildRequires: %{py2_prefix}-mysql-connector
%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
BuildRequires: mysql-connector-python%{python3_pkgversion}
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
BuildRequires: mysql-connector-python%{python3_other_pkgversion}
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}|'
# See https://github.com/biopython/biopython/issues/2128; https://github.com/biopython/biopython/issues/2120
# and https://bugs.python.org/issue24214
%if 0%{?python3_version_nodots} == 38
for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v Affy | grep -v BioSQL | grep -v GenBank | grep -v Location | grep -v SubsMat`; do
%else
for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`; do
%endif
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 Aug 16 2019 Luis M. Segundo <blackfile@fedoraproject.org> - 1.74-1
- Update to 1.74
* Thu Aug 15 2019 Luis Bazan <lbazan@fedoraproject.org> - 1.73-7
- Not recommended to have unversioned Obsoletes
* Fri Jul 26 2019 Fedora Release Engineering <releng@fedoraproject.org> - 1.73-6
- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild
* Mon Jul 15 2019 Antonio Trande <sagitter@fedoraproject.org> - 1.73-5
- Disable failed tests on Python-3.8
* 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.