## START: Set by rpmautospec ## (rpmautospec version 0.3.5) ## RPMAUTOSPEC: autorelease, autochangelog %define autorelease(e:s:pb:n) %{?-p:0.}%{lua: release_number = 1; 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 # Work around a series of circular test dependencies: # # ⬐───╮ # snakemake → python-snakemake-interface-executor-plugins⬎ # ￪￪ │ ⬑────────────────────python-snakemake-executor-plugin-cluster-generic # ││ ↳python-snakemake-interface-storage-plugins────────────────╮ # ││ ￬ │ # │╰────────────────────────python-snakemake-storage-plugin-http│ # ╰─────────────────────────python-snakemake-storage-plugin-s3🠔─╯ # # A good build order is: # # 1. BOOTSTRAP: python-snakemake-interface-executor-plugins, # python-snakemake-interface-storage-plugins # 2. BOOTSTRAP: snakemake # 3. python-snakemake-executor-plugin-cluster-generic, # python-snakemake-storage-plugin-http, # python-snakemake-storage-plugin-s3 # 4. snakemake, python-snakemake-interface-executor-plugins, # python-snakemake-interface-storage-plugins %bcond bootstrap 0 %bcond tests %{without bootstrap} %global _description %{expand: The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake Version: 8.2.3 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses # The entire project is (SPDX) MIT, except: # - versioneer.py is Unlicense # - snakemake/_version.py says: # This file is released into the public domain. # which would be LicenseRef-Fedora-Public-Domain, except that the comments in # versioneer.py make it clear that Unlicense is intended for the generated # files as well. License: MIT AND Unlicense URL: https://snakemake.readthedocs.io/en/stable/index.html Source: https://github.com/snakemake/snakemake/archive/v%{version}/snakemake-%{version}.tar.gz BuildArch: noarch BuildRequires: python3-devel BuildRequires: help2man BuildRequires: vim-filesystem Requires: vim-filesystem Provides: vim-snakemake = %{version}-%{release} # These extras were removed upstream in Snakemake 8.0.0. Retain the Obsoletes # until F40 reaches EOL so we have a clean upgrade path. Obsoletes: snakemake+azure < 8.1.0-1 Obsoletes: snakemake+google-cloud < 8.1.0-1 # We no longer build Sphinx-generated PDF documentation. Beginning with 8.2.3, # this would require patching out sphinxawesome-theme from docs/conf.py. It’s # possible but tedious. Obsoletes: snakemake-doc < 8.2.1-2 %if %{with tests} # See test-environment.yml for a listing of test dependencies, along with a lot # of other cruft. BuildRequires: %{py3_dist boto3} BuildRequires: %{py3_dist pandas} BuildRequires: %{py3_dist pytest} BuildRequires: %{py3_dist snakemake-executor-plugin-cluster-generic} BuildRequires: %{py3_dist snakemake-storage-plugin-s3} %endif # For import-testing snakemake.gui BuildRequires: %{py3_dist flask} # For import-testing snakemake.executors.google_lifesciences_helper: BuildRequires: %{py3_dist google-cloud-storage} %description %_description # No metapackage for “pep” extra because the following are not packaged: # - python3-eido # - python3-peppy %pyproject_extras_subpkg -n snakemake reports messaging %prep %autosetup -n snakemake-%{version} -p1 %py3_shebang_fix . # Remove shebangs from non-executable scripts. The Python script is executable # in the source tree but will be installed without executable permissions. sed -r -i '1{/^#!/d}' \ snakemake/executors/jobscript.sh \ snakemake/executors/google_lifesciences_helper.py # Fix calls to unversioned Python interpreter sed -r -i 's@"python"@"%{python3}"@g' tests/test_linting.py sed -r -i 's@python -m@"%{python3} -m@g' tests/tests.py # Copy and rename nano and vim extensions readmes for use in the main # documentation directory. for editor in nano vim do cp -vp "misc/${editor}/README.md" "README-${editor}.md" done %generate_buildrequires # Generate BR’s for all supported extras to ensure they do not FTI %pyproject_buildrequires -x reports,messaging,google-cloud,azure %build %pyproject_wheel %install %pyproject_install %pyproject_save_files -l snakemake # We wait until %%install to generate the man page so that we can use the # proper script entry point. The generated man page is not perfect, but it is # good enough to be useful. install -d %{buildroot}%{_mandir}/man1 PATH="${PATH-}:%{buildroot}%{_bindir}" \ PYTHONPATH='%{buildroot}%{python3_sitelib}' \ help2man --no-info --name='%{summary}' snakemake \ > %{buildroot}%{_mandir}/man1/snakemake.1 # Install nano syntax highlighting install -t '%{buildroot}%{_datadir}/nano' -D -m 0644 -p \ misc/nano/syntax/snakemake.nanorc # Install vim syntax highlighting install -d '%{buildroot}%{_datadir}/vim/vimfiles' cp -vrp misc/vim/* '%{buildroot}%{_datadir}/vim/vimfiles' find '%{buildroot}%{_datadir}/vim/vimfiles' \ -type f -name 'README.*' -print -delete %check # Even if we are running the tests, this is useful; it could turn up import # errors that would only be revealed by tests we had to disable (e.g. due to # network access). # # ImportError from snakemake.executors.flux (no 'sleep' in # snakemake_interface_executor_plugins.utils) # https://github.com/snakemake/snakemake/issues/2598 # “The flux module is actually supposed to be moved into a plugin and has no # connection to the rest of the code anymore.” %pyproject_check_import -e '*.tests*' -e 'snakemake.executors.flux' %if %{with tests} # Needs a network connection: ignore="${ignore-} --ignore-glob=tests/test_google_lifesciences/*" # Needs a network connection (plus, there are some unresolved # unversioned-python-command issues which we hope are confined to the test # code): k="${k-}${k+ and }not test_deploy_sources" # ______ ERROR collecting tests/test_conda_python_script/test_script.py ______ # import file mismatch: # imported module 'test_script' has this __file__ attribute: # /builddir/build/BUILD/snakemake-7.31.1/tests/test_conda_python_3_7_script/test_script.py # which is not the same as the test file we want to collect: # /builddir/build/BUILD/snakemake-7.31.1/tests/test_conda_python_script/test_script.py # HINT: remove __pycache__ / .pyc files and/or use a unique basename for your test file modules # # Plus, this would add an unwanted BuildRequires on %%{py3_dist Pillow}. ignore="${ignore-} --ignore-glob=tests/test_conda_python_3_7_script/*" %pytest -v -k "${k-}" ${ignore-} %endif %files -f %{pyproject_files} %doc CHANGELOG.md %doc README.md %doc README-nano.md %doc README-vim.md %{_bindir}/snakemake %{_mandir}/man1/snakemake.1* # This is not owned by the filesystem package, and there is no nano-filesystem # subpackage, so we co-own the directory to avoid depending on nano. %dir %{_datadir}/nano/ %{_datadir}/nano/snakemake.nanorc %{_datadir}/vim/vimfiles/ftdetect/snakemake.vim %{_datadir}/vim/vimfiles/ftplugin/snakemake/ %{_datadir}/vim/vimfiles/syntax/snakemake.vim %changelog * Sun Jan 21 2024 Packit - 8.2.3-1 - [packit] 8.2.3 upstream release - Resolves rhbz#2259386 * Sun Jan 21 2024 Benjamin A. Beasley - 8.2.1-2 - Don’t build PDF documentation - Drop and Obsolete the -doc subpackage * Fri Jan 19 2024 Benjamin A. Beasley - 8.2.1-1 - [packit] 8.2.1 upstream release * Fri Jan 19 2024 Benjamin A. Beasley - 8.1.2-2 - Non-bootstrap build * Sun Jan 14 2024 Packit - 8.1.2-1 - [packit] 8.1.2 upstream release - Resolves rhbz#2255578 * Fri Jan 05 2024 Benjamin A. Beasley - 7.32.4-3 - Assert that the .dist-info directory contains a license file * Fri Dec 22 2023 Benjamin A. Beasley - 7.32.4-2 - Fix mis-named “chanegelog” in repo * Mon Sep 18 2023 Packit - 7.32.4-1 - [packit] 7.32.4 upstream release * Thu Aug 10 2023 Benjamin A. Beasley - 7.32.3-1 - Update to 7.32.3 * Thu Aug 10 2023 Packit - 7.32.2-1 - [packit] 7.32.2 upstream release * Thu Aug 10 2023 Ankur Sinha (Ankur Sinha Gmail) - 7.32.0-8 - chore(packit): re-add upstream_tag_template * Thu Aug 10 2023 Ankur Sinha (Ankur Sinha Gmail) - 7.32.0-7 - chore(packit): add koji job * Thu Aug 10 2023 Ankur Sinha (Ankur Sinha Gmail) - 7.32.0-6 - chore(packit): limit PRs to rawhide * Wed Aug 09 2023 Ankur Sinha (Ankur Sinha Gmail) - 7.32.0-5 - Revert "chore(packit): define upstream tag template" * Wed Aug 09 2023 Ankur Sinha (Ankur Sinha Gmail) - 7.32.0-4 - chore(packit): define upstream tag template * Sat Aug 05 2023 Benjamin A. Beasley - 7.32.0-3 - Don’t allow packit to report issues upstream * Fri Aug 04 2023 Ankur Sinha (Ankur Sinha Gmail) - 7.32.0-2 - chore: add packit conf * Fri Aug 04 2023 Benjamin A. Beasley - 7.32.0-1 - Update to 7.32.0 (close RHBZ#2229001) * Wed Aug 02 2023 Benjamin A. Beasley - 7.31.1-1 - Update to 7.31.1 (close RHBZ#2224675) * Sat Jul 22 2023 Fedora Release Engineering - 7.30.1-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild * Mon Jul 17 2023 Benjamin A. Beasley - 7.30.1-3 - Fix FTBFS due to SyntaxWarnings in Python 3.12 (fix RHBZ#2220595) * Thu Jul 13 2023 Python Maint - 7.30.1-2 - Rebuilt for Python 3.12 * Thu Jun 29 2023 Benjamin A. Beasley - 7.30.1-1 - Update to 7.30.1 (close RHBZ#2214110) - Adds a metapackage for the new “azure” extra * Thu Jun 29 2023 Benjamin A. Beasley - 7.26.0-6 - Use new (rpm 4.17.1+) bcond style * Mon May 22 2023 Benjamin A. Beasley - 7.26.0-5 - Install nano syntax highlighting support * Mon May 22 2023 Benjamin A. Beasley - 7.26.0-4 - Install vim syntax highlighting support * Mon May 22 2023 Benjamin A. Beasley - 7.26.0-3 - Install bash completions * Mon May 22 2023 Benjamin A. Beasley - 7.26.0-2 - Add a generated man page * Mon May 22 2023 Benjamin A. Beasley - 7.26.0-1 - Update to 7.26.0 (close RHBZ#2203471) * Sat May 06 2023 Benjamin A. Beasley - 7.25.3-1 - Update to 7.25.3 (close RHBZ#2193279J) * Sat Apr 29 2023 Benjamin A. Beasley - 7.25.2-1 - Update to 7.25.2 (close RHBZ#2178275) * Sat Mar 11 2023 Benjamin A. Beasley - 7.24.1-1 - Update to 7.24.1 (close RHBZ#2171148) * Mon Feb 13 2023 Benjamin A. Beasley - 7.22.0-1 - Update to 7.22.0 (close RHBZ#2169240) * Wed Feb 08 2023 Benjamin A. Beasley - 7.21.0-1 - Update to 7.21.0 (close RHBZ#2166983) * Sun Jan 22 2023 Benjamin A. Beasley - 7.20.0-1 - Update to 7.20.0 (close RHBZ#2162603) * Sat Jan 21 2023 Fedora Release Engineering - 7.19.1-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild * Wed Jan 04 2023 Benjamin A. Beasley - 7.19.1-1 - Update to 7.19.1 (close RHBZ#2153168) * Fri Dec 09 2022 Benjamin A. Beasley - 7.18.2-1 - Update to 7.8.12 (close RHBZ#2139921) * Thu Dec 08 2022 Benjamin A. Beasley - 7.18.1-1 - Update to 7.18.1 * Tue Nov 01 2022 Benjamin A. Beasley - 7.18.0-1 - Update to 7.18.0 (close RHBZ#2138985) * Tue Nov 01 2022 Benjamin A. Beasley - 7.17.2-4 - Remove an obsolete spec file comment * Tue Nov 01 2022 Benjamin A. Beasley - 7.17.2-3 - Confirm the License is SPDX MIT * Tue Nov 01 2022 Benjamin A. Beasley - 7.17.2-2 - Simplify references to the -doc subpackage * Sun Oct 30 2022 Benjamin A. Beasley - 7.17.2-1 - Update to 7.17.2 (close RHBZ#2130414) * Fri Aug 26 2022 Benjamin A. Beasley - 7.13.0-1 - Update to 7.13.0 (close RHBZ#2121550) * Mon Aug 22 2022 Benjamin A. Beasley - 7.12.1-2 - Use rsvg-convert instead of inkscape * Thu Aug 11 2022 Benjamin A. Beasley - 7.12.1-1 - Update to 7.12.1 (close RHBZ#2117565) * Sun Jul 31 2022 Benjamin A. Beasley - 7.12.0-1 - Update to 7.12.0 * Wed Jul 27 2022 Benjamin A. Beasley - 7.11.0-1 - Update to 7.11.0 * Sun Jul 24 2022 Benjamin A. Beasley - 7.9.0-2 - Build documentation as PDF instead of HTML * Sun Jul 24 2022 Benjamin A. Beasley - 7.9.0-1 - Update to 7.9.0 (close RHBZ#2039280, fix RHBZ#2099173) - Add “extras” metapackages - Generate BuildRequires for documentation * Sat Jul 23 2022 Fedora Release Engineering - 6.13.1-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild * Thu Jun 16 2022 Python Maint - 6.13.1-4 - Rebuilt for Python 3.11 * Mon Jan 24 2022 Vanessa_kris - 6.13.1-3 - added autochanelog * Mon Jan 24 2022 Vanessa Christopher - 6.13.1-2 - autorelease * Sun Jan 23 2022 Vanessa Christopher - 6.13.1-1 - Version update to v6.13.1 * Sat Jan 22 2022 Fedora Release Engineering - 6.12.3-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild * Sat Dec 18 2021 Aniket Pradhan - 6.12.3-1 - Version update to v6.12.3 - Use pyproject macros * Thu Sep 09 2021 Aniket Pradhan - 6.8.0-1 - Version update to v6.8.0 * Tue Aug 17 2021 Aniket Pradhan - 6.7.0-1 - Version update to v6.7.0 * Fri Jul 23 2021 Fedora Release Engineering - 6.6.0-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild * Sat Jul 17 2021 Aniket Pradhan - 6.6.0-1 - Version update to v6.6.0 - Remove patches for documentation as they are no longer needed * Mon Jul 05 2021 Aniket Pradhan - 6.5.2-2 - Correct the import path of napoleon extension - Use pytest macro * Sat Jul 03 2021 Aniket Pradhan - 6.5.2-1 - Initial build