## https://github.com/prody/ProDy/issues/266 ExcludeArch: ppc64 s390x # Tests need internet connection; # correctly executed in local. %global with_check 0 ## Filtering of private libraries %global _privatelibs ^%{python3_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: 2.4.0 Release: 4%{?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://github.com/prody/ProDy/archive/v%{version}/ProDy-%{version}.tar.gz BuildRequires: gcc, gcc-c++ Patch0: ProDy-change_requires.patch %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/ - %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 BuildRequires: python3-setuptools Requires: python3-scipy Requires: python3-biopython Requires: python3-ipython Requires: python3-pyparsing Requires: python3-numpy ## 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/ - %prep %autosetup -p1 # Fix permissions find prody/proteins/ccealign -name '*.h' -exec chmod 0644 '{}' \; find prody/proteins/ccealign -name '*.cpp' -exec chmod 0644 '{}' \; %build %py3_build %install %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 .. %if 0%{?with_check} %check pushd 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 %files -n python3-%{name} %license LICENSE.rst %doc 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 %changelog * Wed Jul 19 2023 Fedora Release Engineering - 2.4.0-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild * Sat Jul 01 2023 Python Maint - 2.4.0-3 - Rebuilt for Python 3.12 * Sun Feb 05 2023 Antonio Trande - 2.4.0-2 - Change required packages version * Sun Feb 05 2023 Antonio Trande - 2.4.0-1 - Release 2.4.0 * Wed Jan 18 2023 Fedora Release Engineering - 2.3.1-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild * Tue Nov 15 2022 Antonio Trande - 2.3.1-1 - Release 2.3.1 * Sun Nov 13 2022 Antonio Trande - 2.3.0-1 - Release 2.3.0 * Wed Jul 20 2022 Fedora Release Engineering - 2.2.0-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild * Tue Jul 19 2022 Zbigniew Jędrzejewski-Szmek - 2.2.0-4 - Rebuilt for pyparsing-3.0.9 * Wed Jun 15 2022 Python Maint - 2.2.0-3 - Rebuilt for Python 3.11 * Wed May 25 2022 Antonio Trande - 2.2.0-2 - Do not restrict to Biopython<=1.76 * Sun May 22 2022 Antonio Trande - 2.2.0-1 - Release 2.2.0 * Fri Apr 29 2022 Antonio Trande - 2.1.2-1 - Release 2.1.2 * Tue Apr 19 2022 Antonio Trande - 2.1.1-1 - Release 2.1.1 * Fri Apr 15 2022 Antonio Trande - 2.1.0-1 - Release 2.1.0 * Thu Feb 17 2022 Antonio Trande - 2.0.2-1 - Release 2.0.2 * Wed Jan 19 2022 Fedora Release Engineering - 2.0.1-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild * Thu Dec 23 2021 Antonio Trande - 2.0.1-1 - Release 2.0.1 - Remove Python instructions * Wed Jul 21 2021 Fedora Release Engineering - 2.0-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild * Fri Jun 04 2021 Python Maint - 2.0-2 - Rebuilt for Python 3.10 * Wed Feb 24 2021 Antonio Trande - 2.0-1 - Release 2.0 * Mon Jan 25 2021 Fedora Release Engineering - 1.11-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild * Sat Dec 26 2020 Antonio Trande - 1.11-1 - Release 1.11 * Sat Aug 01 2020 Fedora Release Engineering - 1.10.10-10 - Second attempt - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild * Mon Jul 27 2020 Fedora Release Engineering - 1.10.10-9 - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild * Wed Jun 24 2020 Antonio Trande - 1.10.10-8 - BuildRequires python3-setuptools explicitly * Tue May 26 2020 Miro Hrončok - 1.10.10-7 - Rebuilt for Python 3.9 * Tue Jan 28 2020 Fedora Release Engineering - 1.10.10-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild * Thu Jan 09 2020 Zbigniew Jędrzejewski-Szmek - 1.10.10-5 - Remove dependency on unittest2 (#1789200) * Thu Oct 03 2019 Miro Hrončok - 1.10.10-4 - Rebuilt for Python 3.8.0rc1 (#1748018) * Mon Aug 19 2019 Miro Hrončok - 1.10.10-3 - Rebuilt for Python 3.8 * Wed Jul 24 2019 Fedora Release Engineering - 1.10.10-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild * Tue Jul 23 2019 Antonio Trande - 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 - 1.10.8-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild * Thu Jan 03 2019 Antonio Trande - 1.10.8-1 - Release 1.10.8 * Thu Aug 23 2018 Antonio Trande - 1.10.6-5 - Build with Python3 on fedora and rhel 8+ * Thu Jul 12 2018 Fedora Release Engineering - 1.10.6-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild * Tue Jun 19 2018 Miro Hrončok - 1.10.6-3 - Rebuilt for Python 3.7 * Fri May 25 2018 Antonio Trande - 1.10.6-2 - Fix numpy epoch * Fri May 18 2018 Antonio Trande - 1.10.6-1 - Release 1.10.6 * Tue May 15 2018 Antonio Trande - 1.10.3-1 - Release 1.10.3 * Thu May 03 2018 Antonio Trande - 1.10.2-1 - Release 1.10.2 * Sat Mar 03 2018 Antonio Trande - 1.9.4-0.1 - Pre-release 1.9.4 * Wed Feb 28 2018 Antonio Trande - 1.9.3-5.final - Release 1.9 final (1.9.3 post-release) * Mon Feb 19 2018 Antonio Trande - 1.9.3-4 - Fix python3 shebang * Wed Feb 07 2018 Fedora Release Engineering - 1.9.3-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild * Wed Jan 10 2018 Iryna Shcherbina - 1.9.3-2 - Remove useless Python 2 build-time requirements for Fedora * Sat Nov 04 2017 Antonio Trande - 1.9.3-1 - Update to 1.9.3 - Obsolete old patch * Wed Aug 02 2017 Fedora Release Engineering - 1.8.2-12 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild * Wed Jul 26 2017 Fedora Release Engineering - 1.8.2-11 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild * Thu May 11 2017 Antonio Trande - 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 - 1.8.2-9 - Rebuild for biopython-1.69 * Fri Feb 17 2017 Antonio Trande - 1.8.2-8 - Fix bug (upstream ticket #363) * Fri Feb 10 2017 Fedora Release Engineering - 1.8.2-7 - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild * Sat Dec 24 2016 Antonio Trande - 1.8.2-6 - Exclude architectures ppc64 s390 (upstream bug #266) * Mon Dec 19 2016 Miro Hrončok - 1.8.2-5 - Rebuild for Python 3.6 * Mon Sep 26 2016 Dominik Mierzejewski - 1.8.2-4 - rebuilt for matplotlib-2.0.0 * Tue Aug 16 2016 Antonio Trande - 1.8.2-3 - Rebuild for Python 3.5.2 * Tue Jul 19 2016 Fedora Release Engineering - 1.8.2-2 - https://fedoraproject.org/wiki/Changes/Automatic_Provides_for_Python_RPM_Packages * Mon Jul 11 2016 Antonio Trande - 1.8.2-1 - Update to 1.8.2 * Sat May 14 2016 Antonio Trande - 1.8.1-1 - Update to 1.8.1 - Drop old patch * Sun Feb 14 2016 Antonio Trande - 1.7.1-6 - Rebuilt after GCC6 update - Test enabled * Sun Feb 14 2016 Antonio Trande - 1.7.1-5 - Python2 package renamed - Test disabled * Wed Feb 03 2016 Fedora Release Engineering - 1.7.1-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild * Thu Dec 10 2015 Antonio Trande - 1.7.1-3 - SPEC file adapted to recent guidelines for Python * Sun Nov 22 2015 Antonio Trande - 1.7.1-2 - Original Python2 'prody' and 'evol' binary files preserved - Skip tests that are slow * Fri Nov 13 2015 Antonio Trande - 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 - 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 - 1.6-2 - Fixed python2_version on EL6 * Fri Sep 25 2015 Antonio Trande - 1.6-1 - Update to 1.6 - Performed tests * Tue Jun 16 2015 Fedora Release Engineering - 1.5.1-8 - Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild * Wed May 13 2015 Antonio Trande - 1.5.1-7 - PPC64 excluded * Mon May 04 2015 Antonio Trande - 1.5.1-6 - Fixed License tag - Python3 disabled because of missing BR package * Mon May 04 2015 Antonio Trande - 1.5.1-5 - Rebuild * Sun May 03 2015 Antonio Trande - 1.5.1-4 - Built with Python3 - Built on EPEL6 * Fri Aug 15 2014 Fedora Release Engineering - 1.5.1-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild * Fri Jun 06 2014 Fedora Release Engineering - 1.5.1-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild * Fri Jan 03 2014 Antonio Trande 1.5.1-1 - Update to 1.5.1 * Mon Nov 25 2013 Antonio Trande 1.4.10-1 - Update to 1.4.10 * Sat Nov 16 2013 Antonio Trande 1.4.9-1 - Update to 1.4.9 - Remove 'cpairwise2.c' file * Wed Nov 06 2013 Antonio Trande 1.4.8-1 - Re-defined required packages for EPEL - Update to 1.4.8 * Thu Oct 24 2013 Antonio Trande 1.4.6-2 - Defined a python2 macro only for Fedora * Wed Oct 23 2013 Antonio Trande 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 1.4.4-3 - Bundled files removed - Add new required packages (pyparsing, python-biopython) * Mon Aug 12 2013 Antonio Trande 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 1.4.4-1 - Initial build