## https://github.com/prody/ProDy/issues/266
ExcludeArch: ppc64 s390x
%if 0%{?fedora} || 0%{?rhel} > 7
%global with_python3 1
%endif
# Tests need internet connection;
# correctly executed in local.
%global with_check 0
%if 0%{?rhel} && 0%{?rhel} == 7
%global with_python3 0
%{!?python2_shortver: %global python2_shortver %(%{__python2} -c 'import sys; print(str(sys.version_info.major) + "." + str(sys.version_info.minor))')}
%{!?python3_shortver: %global python3_shortver %(%{__python3} -c 'import sys; print(str(sys.version_info.major) + "." + str(sys.version_info.minor))')}
%endif
## Filtering of private libraries
%global _privatelibs ^%{python_sitearch}/prody/.*\\.so$
%global __provides_exclude_from ^(%{_privatelibs})$
%global __requires_exclude_from ^(%{_privatelibs})$
Name: ProDy
Summary: Application for protein structure, dynamics and sequence analysis
Version: 1.10.10
Release: 7%{?dist}
# MIT is the main license for ProDy
# prody/utilities/tnt/* code --> 'Public domain' license
# CEalign module is distributed under BSD license
License: MIT and Public domain and BSD
URL: http://www.csb.pitt.edu/ProDy
Source0: https://files.pythonhosted.org/packages/fe/c8/5c8642fd6630f6fe8d3bbca13c3d5f899732893762fa0d114fe863b90cf1/ProDy-%{version}.tar.gz
BuildRequires: gcc, gcc-c++
%description
ProDy is a free and open-source Python package for protein structure, dynamics,
and sequence analysis. It allows for comparative analysis and modeling of
protein structural dynamics and sequence co-evolution. Fast and flexible ProDy
API is for interactive usage as well as application development. ProDy also
comes with several analysis applications and a graphical user interface for
visual analysis.
- Visit http://www.csb.pitt.edu/ProDy/ -
%if 0%{?rhel}
%package -n python2-%{name}
Summary: Application for protein structure, dynamics and sequence analysis
%{?python_provide:%python_provide python2-%{name}}
Provides: ProDy = 0:%{version}-%{release}
### Pyparsing is used to define the atom selection grammar
### Biopython KDTree package and pairwise2 module are used for distance based
## atom selections and pairwise sequence alignment, respectively.
#
### argparse is used to implement applications and provided for
## compatibility with Python 2.6.
BuildRequires: python2-devel
BuildRequires: python-nose
BuildRequires: python-argparse
BuildRequires: scipy
BuildRequires: python2-biopython
BuildRequires: numpy >= 1:1.10.0
BuildRequires: python-matplotlib
BuildRequires: python-unittest2
BuildRequires: pyparsing
Requires: python-argparse
Requires: pyparsing
Requires: python2-biopython
Requires: ipython, pyparsing
Requires: scipy
Requires: numpy >= 1:1.10.0
## Explicit library require for using plotting functions
Requires: python-matplotlib
%description -n python2-%{name}
This is ProDy Python2 package for protein structure, dynamics,
and sequence analysis. It allows for comparative analysis and modeling of
protein structural dynamics and sequence co-evolution. Fast and flexible ProDy
API is for interactive usage as well as application development. ProDy also
comes with several analysis applications and a graphical user interface for
visual analysis.
- Visit http://www.csb.pitt.edu/ProDy/ -
%endif
%if 0%{?with_python3}
%package -n python3-%{name}
Summary: Application for protein structure, dynamics and sequence analysis
%{?python_provide:%python_provide python3-%{name}}
Provides: ProDy = 0:%{version}-%{release}
BuildRequires: python3-devel
BuildRequires: python3-nose
BuildRequires: python3-urllib3
BuildRequires: python3-scipy
BuildRequires: python3-numpy >= 1:1.10.0
BuildRequires: python3-matplotlib
BuildRequires: python3-biopython
Requires: python3-scipy
Requires: python3-biopython
Requires: python3-ipython
Requires: python3-pyparsing
Requires: python3-numpy >= 1:1.10.0
## Explicit library require for using plotting functions
Requires: python3-matplotlib
%description -n python3-%{name}
This is ProDy Python3 package for protein structure, dynamics,
and sequence analysis. It allows for comparative analysis and modeling of
protein structural dynamics and sequence co-evolution. Fast and flexible ProDy
API is for interactive usage as well as application development. ProDy also
comes with several analysis applications and a graphical user interface for
visual analysis.
- Visit http://www.csb.pitt.edu/ProDy/ -
%endif
# with_python3
%prep
%setup -qc
# Fix permissions
find %{name}-%{version}/prody/proteins/ccealign -name '*.h' -exec chmod 0644 '{}' \;
find %{name}-%{version}/prody/proteins/ccealign -name '*.cpp' -exec chmod 0644 '{}' \;
%if 0%{?rhel}
cp -a %{name}-%{version} python2
%endif
%if 0%{?with_python3}
mv %{name}-%{version} python3
%endif
# with_python3
%build
# Unversioned commands point to Python3 on Fedora and EPEL8+
# Unversioned commands point to Python2 on Fedora and EPEL7
%if 0%{?rhel}
pushd python2
%py2_build
popd
%endif
%if 0%{?with_python3}
pushd python3
%py3_build
popd
%endif
# with_python3
%install
%if 0%{?with_python3}
pushd python3
%py3_install
mkdir -p $RPM_BUILD_ROOT%{_bindir}
rm -f $RPM_BUILD_ROOT%{_bindir}/*
cd scripts
cp -pr ./prody ./python%{python3_version}-prody
cp -pr ./evol ./python%{python3_version}-evol
# Fix shebangs
sed -i '1s=^#!/usr/bin/\(python\|env python\)[0-9.]*=#!%{__python3}=' \
./prody \
./evol \
./python%{python3_version}-prody \
./python%{python3_version}-evol
for i in prody-%{python3_version}; do
touch -r ./python%{python3_version}-prody $i
install -p $i $RPM_BUILD_ROOT%{_bindir}
install -p ./prody $RPM_BUILD_ROOT%{_bindir}
install -p ./python%{python3_version}-prody $RPM_BUILD_ROOT%{_bindir}
ln -sf %{_bindir}/python%{python3_version}-prody $RPM_BUILD_ROOT%{_bindir}/$i
done
for i in evol-%{python3_version}; do
touch -r ./python%{python3_version}-evol $i
install -p $i $RPM_BUILD_ROOT%{_bindir}
install -p ./evol $RPM_BUILD_ROOT%{_bindir}
install -p ./python%{python3_version}-evol $RPM_BUILD_ROOT%{_bindir}
ln -sf %{_bindir}/python%{python3_version}-evol $RPM_BUILD_ROOT%{_bindir}/$i
done
cd ..
%endif
%if 0%{?rhel}
pushd python2
%py2_install
mkdir -p $RPM_BUILD_ROOT%{_bindir}
cd scripts
cp -pr ./prody ./python%{python2_version}-prody
cp -pr ./evol ./python%{python2_version}-evol
for i in prody prody-%{python2_version}; do
touch -r ./python%{python2_version}-prody $i
install -p $i $RPM_BUILD_ROOT%{_bindir}
install -p ./prody $RPM_BUILD_ROOT%{_bindir}
install -p ./python%{python2_version}-prody $RPM_BUILD_ROOT%{_bindir}
ln -sf %{_bindir}/python%{python2_version}-prody $RPM_BUILD_ROOT%{_bindir}/$i
done
for i in evol evol-%{python2_version}; do
touch -r ./python%{python2_version}-evol $i
install -p $i $RPM_BUILD_ROOT%{_bindir}
install -p ./evol $RPM_BUILD_ROOT%{_bindir}
install -p ./python%{python2_version}-evol $RPM_BUILD_ROOT%{_bindir}
ln -sf %{_bindir}/python%{python2_version}-evol $RPM_BUILD_ROOT%{_bindir}/$i
done
popd
%endif
%if 0%{?with_check}
%check
%if 0%{?rhel}
## Some tests are skipped for missing internet connections on koji
pushd python2/scripts
PYTHONPATH=$RPM_BUILD_ROOT%{python2_sitearch} nosetests --verbosity=2 \
-w $RPM_BUILD_ROOT%{python2_sitearch}/prody/tests --tests prody -a '!slow'
popd
%endif
%if 0%{?with_python3}
pushd python3/scripts
PYTHONPATH=$RPM_BUILD_ROOT%{python3_sitearch} nosetests-%{python3_version} --verbosity=2 \
-w $RPM_BUILD_ROOT%{python3_sitearch}/prody/tests --tests prody -a '!slow'
popd
%endif
%endif
%if 0%{?rhel}
%files -n python2-%{name}
%doc python2/README.rst
%license python2/LICENSE.rst
%{_bindir}/prody
%{_bindir}/prody-%{python2_version}
%{_bindir}/python%{python2_version}-prody
%{_bindir}/evol
%{_bindir}/evol-%{python2_version}
%{_bindir}/python%{python2_version}-evol
%{python2_sitearch}/prody/
%{python2_sitearch}/%{name}-*.egg-info
%endif
%if 0%{?with_python3}
%files -n python3-%{name}
%license python3/LICENSE.rst
%doc python3/README.rst
%{_bindir}/prody
%{_bindir}/prody-%{python3_version}
%{_bindir}/python%{python3_version}-prody
%{_bindir}/evol
%{_bindir}/evol-%{python3_version}
%{_bindir}/python%{python3_version}-evol
%{python3_sitearch}/prody/
%{python3_sitearch}/%{name}-*.egg-info
%endif
%changelog
* Tue May 26 2020 Miro Hrončok <mhroncok@redhat.com> - 1.10.10-7
- Rebuilt for Python 3.9
* Tue Jan 28 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.10.10-6
- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
* Thu Jan 09 2020 Zbigniew Jędrzejewski-Szmek <zbyszek@in.waw.pl> - 1.10.10-5
- Remove dependency on unittest2 (#1789200)
* Thu Oct 03 2019 Miro Hrončok <mhroncok@redhat.com> - 1.10.10-4
- Rebuilt for Python 3.8.0rc1 (#1748018)
* Mon Aug 19 2019 Miro Hrončok <mhroncok@redhat.com> - 1.10.10-3
- Rebuilt for Python 3.8
* Wed Jul 24 2019 Fedora Release Engineering <releng@fedoraproject.org> - 1.10.10-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild
* Tue Jul 23 2019 Antonio Trande <sagitterATfedoraproject.org> - 1.10.10-1
- Release 1.10.10
- Unversioned commands point to Python3 on Fedora and EPEL8+
- Unversioned commands point to Python2 on EPEL7
* Thu Jan 31 2019 Fedora Release Engineering <releng@fedoraproject.org> - 1.10.8-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild
* Thu Jan 03 2019 Antonio Trande <sagitterATfedoraproject.org> - 1.10.8-1
- Release 1.10.8
* Thu Aug 23 2018 Antonio Trande <sagitterATfedoraproject.org> - 1.10.6-5
- Build with Python3 on fedora and rhel 8+
* Thu Jul 12 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.10.6-4
- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild
* Tue Jun 19 2018 Miro Hrončok <mhroncok@redhat.com> - 1.10.6-3
- Rebuilt for Python 3.7
* Fri May 25 2018 Antonio Trande <sagitterATfedoraproject.org> - 1.10.6-2
- Fix numpy epoch
* Fri May 18 2018 Antonio Trande <sagitterATfedoraproject.org> - 1.10.6-1
- Release 1.10.6
* Tue May 15 2018 Antonio Trande <sagitterATfedoraproject.org> - 1.10.3-1
- Release 1.10.3
* Thu May 03 2018 Antonio Trande <sagitterATfedoraproject.org> - 1.10.2-1
- Release 1.10.2
* Sat Mar 03 2018 Antonio Trande <sagitterATfedoraproject.org> - 1.9.4-0.1
- Pre-release 1.9.4
* Wed Feb 28 2018 Antonio Trande <sagitterATfedoraproject.org> - 1.9.3-5.final
- Release 1.9 final (1.9.3 post-release)
* Mon Feb 19 2018 Antonio Trande <sagitterATfedoraproject.org> - 1.9.3-4
- Fix python3 shebang
* Wed Feb 07 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.9.3-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild
* Wed Jan 10 2018 Iryna Shcherbina <ishcherb@redhat.com> - 1.9.3-2
- Remove useless Python 2 build-time requirements for Fedora
* Sat Nov 04 2017 Antonio Trande <sagitterATfedoraproject.org> - 1.9.3-1
- Update to 1.9.3
- Obsolete old patch
* Wed Aug 02 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.8.2-12
- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild
* Wed Jul 26 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.8.2-11
- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild
* Thu May 11 2017 Antonio Trande <sagitterATfedoraproject.org> - 1.8.2-10
- Rebuild for ipython-6.0.0
- Drop python2-ProDy for missing python2-ipython on fedora <27
* Fri Apr 14 2017 Antonio Trande <sagitterATfedoraproject.org> - 1.8.2-9
- Rebuild for biopython-1.69
* Fri Feb 17 2017 Antonio Trande <sagitterATfedoraproject.org> - 1.8.2-8
- Fix bug (upstream ticket #363)
* Fri Feb 10 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.8.2-7
- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild
* Sat Dec 24 2016 Antonio Trande <sagitterATfedoraproject.org> - 1.8.2-6
- Exclude architectures ppc64 s390 (upstream bug #266)
* Mon Dec 19 2016 Miro Hrončok <mhroncok@redhat.com> - 1.8.2-5
- Rebuild for Python 3.6
* Mon Sep 26 2016 Dominik Mierzejewski <rpm@greysector.net> - 1.8.2-4
- rebuilt for matplotlib-2.0.0
* Tue Aug 16 2016 Antonio Trande <sagitterATfedoraproject.org> - 1.8.2-3
- Rebuild for Python 3.5.2
* Tue Jul 19 2016 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.8.2-2
- https://fedoraproject.org/wiki/Changes/Automatic_Provides_for_Python_RPM_Packages
* Mon Jul 11 2016 Antonio Trande <sagitterATfedoraproject.org> - 1.8.2-1
- Update to 1.8.2
* Sat May 14 2016 Antonio Trande <sagitterATfedoraproject.org> - 1.8.1-1
- Update to 1.8.1
- Drop old patch
* Sun Feb 14 2016 Antonio Trande <sagitterATfedoraproject.org> - 1.7.1-6
- Rebuilt after GCC6 update
- Test enabled
* Sun Feb 14 2016 Antonio Trande <sagitterATfedoraproject.org> - 1.7.1-5
- Python2 package renamed
- Test disabled
* Wed Feb 03 2016 Fedora Release Engineering <releng@fedoraproject.org> - 1.7.1-4
- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild
* Thu Dec 10 2015 Antonio Trande <sagitterATfedoraproject.org> - 1.7.1-3
- SPEC file adapted to recent guidelines for Python
* Sun Nov 22 2015 Antonio Trande <sagitter@fedoraproject.org> - 1.7.1-2
- Original Python2 'prody' and 'evol' binary files preserved
- Skip tests that are slow
* Fri Nov 13 2015 Antonio Trande <sagitter@fedoraproject.org> - 1.7.1-1
- Update to 1.7.1
- Added scipy as BR package
- Set CFLAGS for hardened builds
* Sun Sep 27 2015 Antonio Trande <sagitter@fedoraproject.org> - 1.6.1-1
- Version changed to 1.6.1
- Some tests excluded on EPEL6
- Tests not entirely ready for Python3
* Sat Sep 26 2015 Antonio Trande <sagitter@fedoraproject.org> - 1.6-2
- Fixed python2_version on EL6
* Fri Sep 25 2015 Antonio Trande <sagitter@fedoraproject.org> - 1.6-1
- Update to 1.6
- Performed tests
* Tue Jun 16 2015 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.5.1-8
- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild
* Wed May 13 2015 Antonio Trande <sagitter@fedoraproject.org> - 1.5.1-7
- PPC64 excluded
* Mon May 04 2015 Antonio Trande <sagitter@fedoraproject.org> - 1.5.1-6
- Fixed License tag
- Python3 disabled because of missing BR package
* Mon May 04 2015 Antonio Trande <sagitter@fedoraproject.org> - 1.5.1-5
- Rebuild
* Sun May 03 2015 Antonio Trande <sagitter@fedoraproject.org> - 1.5.1-4
- Built with Python3
- Built on EPEL6
* Fri Aug 15 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.5.1-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild
* Fri Jun 06 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.5.1-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild
* Fri Jan 03 2014 Antonio Trande <sagitter@fedoraproject.org> 1.5.1-1
- Update to 1.5.1
* Mon Nov 25 2013 Antonio Trande <sagitter@fedoraproject.org> 1.4.10-1
- Update to 1.4.10
* Sat Nov 16 2013 Antonio Trande <sagitter@fedoraproject.org> 1.4.9-1
- Update to 1.4.9
- Remove 'cpairwise2.c' file
* Wed Nov 06 2013 Antonio Trande <sagitter@fedoraproject.org> 1.4.8-1
- Re-defined required packages for EPEL
- Update to 1.4.8
* Thu Oct 24 2013 Antonio Trande <sagitter@fedoraproject.org> 1.4.6-2
- Defined a python2 macro only for Fedora
* Wed Oct 23 2013 Antonio Trande <sagitter@fedoraproject.org> 1.4.6-1
- Update to 1.4.6
- Defined python-argparse required package for EPEL
- Spec file renamed ProDy
- Defined a python2 macro only for Fedora
* Sun Sep 15 2013 Antonio Trande <sagitter@fedoraproject.org> 1.4.4-3
- Bundled files removed
- Add new required packages (pyparsing, python-biopython)
* Mon Aug 12 2013 Antonio Trande <sagitter@fedoraproject.org> 1.4.4-2
- Added python-matplotlib and python-ipython as Requires
- Perform filtering private libraries
- Fix some 'non-executable-script' warnings
- Add a Python shebang
* Mon Aug 12 2013 Antonio Trande <sagitter@fedoraproject.org> 1.4.4-1
- Initial build