## START: Set by rpmautospec ## (rpmautospec version 0.7.3) ## RPMAUTOSPEC: autorelease, autochangelog %define autorelease(e:s:pb:n) %{?-p:0.}%{lua: release_number = 4; base_release_number = tonumber(rpm.expand("%{?-b*}%{!?-b:1}")); print(release_number + base_release_number - 1); }%{?-e:.%{-e*}}%{?-s:.%{-s*}}%{!?-n:%{?dist}} ## END: Set by rpmautospec %global with_check 1 %global pypi_name biopython %global module %{pypi_name} Name: python-%{pypi_name} Version: 1.84 Release: %autorelease Summary: Python tools for computational molecular biology Source: %{pypi_source} Patch: %{name}-1.84-replace_deprecated_function.patch # Patch for fixing ValueError thrown when tests are run with NumPy 2.x # Upstream is still working in NumPy 2.x compatibility, though I # couldn't find a fix for that particular issue. # See also: https://github.com/biopython/biopython/pull/4897 Patch: numpy-2.x.patch # 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-3-Clause URL: https://biopython.org/ BuildRequires: gcc BuildRequires: pyproject-rpm-macros %description A set of freely available Python tools for computational molecular biology. %package -n python3-%{module} Summary: Python3 tools for computational molecular biology %py_provides python3-%{module} BuildRequires: python3-devel BuildRequires: python3dist(reportlab) Requires: flex%{?_isa} %description -n python3-%{module} A set of freely available Python3 tools for computational molecular biology. %prep %autosetup -n %{pypi_name}-%{version} -p1 %generate_buildrequires %pyproject_buildrequires -x tests %build %pyproject_wheel %install %pyproject_install %pyproject_save_files Bio BioSQL %if 0%{?with_check} %check pushd Tests for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`; do %{py3_test_envvars} %{python3} run_tests.py --offline --verbose -v ${test} done %endif %files -n python3-%{pypi_name} -f %{pyproject_files} %doc Doc %doc Scripts %changelog ## START: Generated by rpmautospec * Mon Dec 23 2024 Sandro - 1.84-4 - Apply patch for NumPy 2.x * Fri Jul 19 2024 Fedora Release Engineering - 1.84-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild * Thu Jul 04 2024 Antonio Trande - 1.84-2 - Rebuild to increase release number * Thu Jul 04 2024 Antonio Trande - 1.84-1 - Release 1.84 (rhbz#2295434) * Sat Jun 08 2024 Python Maint - 1.83-7 - Rebuilt for Python 3.13 * Fri Apr 19 2024 Sandro - 1.83-6 - Replace deprecated PyEval_CallObject() (RHBZ#2259625) * Sat Apr 13 2024 Benjamin A. Beasley - 1.83-5 - Patch tests for zlib-ng and stop skipping test_bgzf.py * Sat Apr 13 2024 Benjamin A. Beasley - 1.83-4 - Patch for expat 2.6.0 (fix RHBZ#2274533) * Sat Feb 03 2024 Antonio Trande - 1.83-3 - Remove wise2 dependency * Fri Jan 26 2024 Fedora Release Engineering - 1.83-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild * Fri Jan 19 2024 Antonio Trande - 1.83-1 - Release 1.83 | Switch to pyproject macros * Mon Jan 08 2024 Sandro - 1.82-1 - Update to 1.82 (RHBZ#2255629) - Drop patches (merged upstream) - Add `Align_bigbed` to excluded tests (test fails) * Tue Nov 07 2023 Antonio Trande - 1.81-5 - Fix license tag * Fri Jul 21 2023 Fedora Release Engineering - 1.81-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild * Fri Jun 30 2023 Antonio Trande - 1.81-3 - Patched for Python-3.12 * Fri Jun 16 2023 Python Maint - 1.81-2 - Rebuilt for Python 3.12 * Tue Feb 14 2023 Antonio Trande - 1.81-1 - Release 1.81 * Fri Jan 20 2023 Fedora Release Engineering - 1.80-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild * Sat Dec 24 2022 Antonio Trande - 1.80-4 - Fix changelog * Sat Dec 24 2022 Antonio Trande - 1.80-3 - Use python3-sqlclient * Mon Dec 19 2022 Elliott Sales de Andrade - 1.80-2 - Use canonical dependency names * Thu Nov 24 2022 Antonio Trande - 1.80-1 - Release 1.80 * Tue Nov 01 2022 Lumir Balhar - 1.79-5 - Change location of pathfix.py * Fri Jul 22 2022 Fedora Release Engineering - 1.79-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild * Tue Jun 14 2022 Python Maint - 1.79-3 - Rebuilt for Python 3.11 * Fri Jan 21 2022 Fedora Release Engineering - 1.79-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild * Tue Aug 31 2021 Antonio Trande - 1.79-1 - Release 1.79 * Fri Jul 23 2021 Fedora Release Engineering - 1.78-9 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild * Fri Jun 04 2021 Python Maint - 1.78-8 - Rebuilt for Python 3.10 * Wed Jan 27 2021 Fedora Release Engineering - 1.78-7 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild * Wed Dec 02 2020 Antonio T - 1.78-6 - Exclude test_motifs with python-3.10 /3 * Wed Dec 02 2020 Antonio T - 1.78-5 - Exclude test_motifs with python-3.10 /2 * Wed Dec 02 2020 Antonio T - 1.78-4 - Exclude test_motifs with python-3.10 * Fri Nov 27 2020 Antonio T - 1.78-3 - Remove __init__.py before testing/2 * Fri Nov 27 2020 Antonio T - 1.78-2 - Remove __init__.py before testing * Fri Sep 04 2020 sagitter - 1.78-1 - Release 1.78 * Sat Aug 22 2020 sagitter - 1.77-8 - Fix Changelog * Sat Aug 22 2020 sagitter - 1.77-7 - Use flex as Requires dependency * Sat Aug 22 2020 sagitter - 1.77-6 - Remove flex as BR dependency * Tue Jul 28 2020 Fedora Release Engineering - 1.77-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild * Wed Jun 24 2020 sagitter - 1.77-4 - BuildRequires python3-setuptools explicitly * Fri May 29 2020 sagitter - 1.77-3 - Remove obsolete Python3.9 patch * Tue May 26 2020 Miro Hrončok - 1.77-2 - Rebuilt for Python 3.9 * Mon May 25 2020 sagitter - 1.77-1 - Release 1.77 * Sun Mar 01 2020 sagitter - 1.76-3 - Patched for Python-3.9 * Thu Jan 30 2020 Fedora Release Engineering - 1.76-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild * Mon Dec 23 2019 Luis Bazan - 1.76-1 - Update to 1.76 * Thu Nov 07 2019 sagitter - 1.75-2 - Exclude pairwise_aligner * Thu Nov 07 2019 sagitter - 1.75-1 - Update to 1.75 * Thu Oct 03 2019 Miro Hrončok - 1.74-9 - Rebuilt for Python 3.8.0rc1 (#1748018) * Sun Aug 25 2019 sagitter - 1.74-8 - Fix version * Sun Aug 25 2019 sagitter - 1.74-7 - Override bad release (see Changelog) * Wed Aug 21 2019 sagitter - 1.74-6 - Fix test command * Wed Aug 21 2019 sagitter - 1.74-5 - Exclude tests using Python 3.8 * Mon Aug 19 2019 Miro Hrončok - 1.74-4 - Rebuilt for Python 3.8 * Fri Aug 16 2019 Luis M. Segundo - 1.74-3 - correct release * Fri Aug 16 2019 Luis M. Segundo - 1.74-2 - correct changelog name * Fri Aug 16 2019 Luis M. Segundo - 1.74-1 - New upstream version * Fri Aug 16 2019 sagitter - 1.73-9 - Reorder Fedora builds * Thu Aug 15 2019 Luis Bazan - 1.73-8 - not recommended to have unversioned Obsoletes * Fri Jul 26 2019 Fedora Release Engineering - 1.73-7 - Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild * Mon Jul 15 2019 sagitter - 1.73-6 - Disable failed tests on Python-3.8 * Fri Jun 14 2019 sagitter - 1.73-5 - Fix URL * Fri Jun 14 2019 sagitter - 1.73-4 - Reorganize Requires packages * Thu Jun 13 2019 sagitter - 1.73-3 - Rebuild for python-reportlab-3.5.23 * Sat Feb 02 2019 Fedora Release Engineering - 1.73-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild * Fri Jan 04 2019 sagitter - 1.73-1 - Release 1.73 * Sun Sep 30 2018 sagitter - 1.72-3 - Deprecate Python2 on fedora 30+ * Fri Jul 13 2018 Fedora Release Engineering - 1.72-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild * Sat Jun 30 2018 sagitter - 1.72-1 - Update to 1.72 * Fri Jun 22 2018 sagitter - 1.71-10 - Enable DSSP test with Python2; disable bgzf test with Python3 * Fri Jun 22 2018 sagitter - 1.71-9 - Enable additional tests (upstream bug #855) * Thu Jun 21 2018 sagitter - 1.71-8 - New patch for fixing Nexus/AlignIO tests (python-3.7.0 issue) * Thu Jun 21 2018 sagitter - 1.71-7 - Include Patch0 * Thu Jun 21 2018 sagitter - 1.71-6 - Enable AlignIO test * Thu Jun 21 2018 sagitter - 1.71-5 - Patched for AlignIO test failure (python-3.7 issue) * Thu Jun 21 2018 sagitter - 1.71-4 - Exclusion of AlignIO test (python-3.7 issue) * Tue Jun 19 2018 Miro Hrončok - 1.71-3 - Rebuilt for Python 3.7 * Fri Apr 27 2018 sagitter - 1.71-2 - Conform Python3 builds to coming RHEL major release * Wed Apr 04 2018 sagitter - 1.71-1 - Update to 1.71 (bz#1563655) * Thu Feb 22 2018 sagitter - 1.70-15 - Add gcc BR * Sat Feb 17 2018 sagitter - 1.70-14 - Fix Python2 mysql-connector packages on fedora * Sat Feb 17 2018 sagitter - 1.70-13 - Fix python2 graphviz on rhel * Sat Feb 17 2018 sagitter - 1.70-12 - Fix Python2 required package on rhel * Fri Feb 16 2018 sagitter - 1.70-11 - Required 'numpy' on rhel (without prefix) * Fri Feb 16 2018 sagitter - 1.70-10 - Use %%%%py2_prefix * Fri Feb 16 2018 sagitter - 1.70-9 - Remove %%%%sum macro * Fri Feb 09 2018 Fedora Release Engineering - 1.70-8 - Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild * Tue Jan 16 2018 sagitter - 1.70-7 - Fix dependencies again * Tue Jan 16 2018 sagitter - 1.70-6 - Fix dependencies * Sun Jan 14 2018 sagitter - 1.70-5 - Use versioned Python packages * Wed Jan 03 2018 Lumir Balhar - 1.70-4 - Fix directory ownership * Thu Aug 03 2017 Fedora Release Engineering - 1.70-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild * Thu Jul 27 2017 Fedora Release Engineering - 1.70-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild * Tue Jul 11 2017 sagitter - 1.70-1 - Update to 1.70 (bz#1440337) * Fri Apr 14 2017 sagitter - 1.69-1 - Update to 1.69 * Sat Feb 11 2017 Fedora Release Engineering - 1.68-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild * Mon Dec 19 2016 Miro Hrončok - 1.68-2 - Rebuild for Python 3.6 * Sat Aug 27 2016 sagitter - 1.68-1 - Update to 1.68 * Wed Aug 17 2016 sagitter - 1.67-3 - Rebuild for Python 3.5.2 * Tue Jul 19 2016 Fedora Release Engineering - 1.67-2 - https://fedoraproject.org/wiki/Changes/Automatic_Provides_for_Python_RPM_ Packages * Wed Jun 15 2016 sagitter - 1.67-1 - Update to 1.67 * Mon Feb 15 2016 sagitter - 1.66-6 - Typo fixed * Mon Feb 15 2016 sagitter - 1.66-5 - Created a python2- package * Thu Feb 04 2016 Fedora Release Engineering - 1.66-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild * Thu Dec 10 2015 sagitter - 1.66-3 - SPEC file adapted to recent guidelines for Python * Wed Dec 09 2015 sagitter - 1.66-2 - Built with Python3 * Tue Dec 08 2015 Luis Bazan - 1.66-1 - new upstream version * Thu Jun 18 2015 Dennis Gilmore - 1.65-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild * Thu Jan 08 2015 lbazan - 1.65-1 - new upstream version * Sun Aug 17 2014 Peter Robinson - 1.64-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild * Wed Jun 11 2014 lbazan - 1.64-1 - new upstream version! * Sat Jun 07 2014 Dennis Gilmore - 1.60-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild * Sun Aug 04 2013 Dennis Gilmore - 1.60-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild * Thu Feb 14 2013 Dennis Gilmore - 1.60-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild * Sat Nov 17 2012 Alex Lancaster - 1.60-1 - Update to latest upstream (#835434). Drop flex-related patch, no longer needed * Sat Jul 21 2012 Dennis Gilmore - 1.59-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild * Fri Mar 09 2012 Alex Lancaster - 1.59-2 - Update to latest upstream (1.59) (#797872) * Fri Mar 09 2012 Alex Lancaster - 1.59-1 - Update to latest upstream (1.59) (#797872) * Sat Jan 14 2012 Dennis Gilmore - 1.58-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild * Wed Sep 21 2011 Alex Lancaster - 1.58-1 - Update to upstream 1.58 * Wed Feb 09 2011 Dennis Gilmore - 1.55-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild * Fri Aug 20 2010 Alex Lancaster - 1.55-1 - Update to 1.55 beta - BuildRequires: flex-static, libraries are now split out * Thu Jul 29 2010 Fedora Release Engineering - 1.54-4 - dist-git conversion * Thu Jul 22 2010 dmalcolm - 1.54-3 - Rebuilt for https://fedoraproject.org/wiki/Features/Python_2.7/MassRebuild * Fri May 21 2010 alexlan - 1.54-2 - Update to upstream final 1.54. * Tue Apr 06 2010 alexlan - 1.54-1 - Update to 1.54 beta * Tue Dec 15 2009 alexlan - 1.53-1 - Update to upstream 1.53 * Wed Nov 25 2009 Bill Nottingham - 1.52-2 - Fix typo that causes a failure to update the common directory. (releng #2781) * Thu Oct 15 2009 alexlan - 1.52-1 - Update to latest upstream (1.52) * Tue Aug 18 2009 alexlan - 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 Jesse Keating - 1.49-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_12_Mass_Rebuild * Thu Feb 26 2009 Jesse Keating - 1.49-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_11_Mass_Rebuild * Mon Dec 01 2008 alexlan - 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 * Mon Dec 01 2008 alexlan - 1.48-3 - Temporarily disable python-psycopg dependency until it is rebuilt for Python 2.6 * Sat Nov 29 2008 Ignacio Vazquez-Abrams - 1.48-2 - Rebuild for Python 2.6 * Mon Sep 29 2008 alexlan - 1.48-1 - Update to latest upstream (1.48) * Sun Jul 06 2008 alexlan - 1.47-1 - Update to latest upstream (1.47) * Sun Mar 23 2008 alexlan - 1.45-1 - Update to latest upstream (1.45) * Sun Feb 10 2008 alexlan - 1.44-4 - rebuilt for GCC 4.3 as requested by Fedora Release Engineering * Fri Dec 14 2007 alexlan - 1.44-3 - Include eggs in file list for F9+ - Actually remove unneeded patch from CVS. * Sun Oct 28 2007 alexlan - 1.44-2 - Drop patch to setup.py, applied upstream * Sun Oct 28 2007 alexlan - 1.44-1 - Update to latest upstream (1.44). * Mon Aug 27 2007 alexlan - 1.43-4 - Used "MIT" as short license name as the "Biopython License Agreement" is the same as the CMU MIT variant. * Wed Apr 25 2007 alexlan - 1.43-3 - Add wise2 Requires since the Wise biopython module uses the command-line behind-the-scenes. * Wed Apr 18 2007 alexlan - 1.43-2 - Use python_sitearch macro to enable x86_64 builds work. * Tue Apr 17 2007 alexlan - 1.43-1 - Initial import. ## END: Generated by rpmautospec