diff --git a/.gitignore b/.gitignore index 8624a3d..85be4b5 100644 --- a/.gitignore +++ b/.gitignore @@ -5,137 +5,3 @@ /snakemake-6.8.0.tar.gz /snakemake-6.12.3.tar.gz /snakemake-6.13.1.tar.gz -/snakemake-7.8.5.tar.gz -/snakemake-7.9.0.tar.gz -/snakemake-7.11.0.tar.gz -/snakemake-7.12.0.tar.gz -/snakemake-7.12.1.tar.gz -/snakemake-7.13.0.tar.gz -/snakemake-7.17.2.tar.gz -/snakemake-7.18.0.tar.gz -/snakemake-7.18.1.tar.gz -/snakemake-7.18.2.tar.gz -/snakemake-7.19.1.tar.gz -/snakemake-7.20.0.tar.gz -/snakemake-7.21.0.tar.gz -/snakemake-7.22.0.tar.gz -/snakemake-7.24.1.tar.gz -/snakemake-7.25.2.tar.gz -/snakemake-7.25.3.tar.gz -/snakemake-7.26.0.tar.gz -/snakemake-7.30.1.tar.gz -/snakemake-7.31.1.tar.gz -/snakemake-7.32.0.tar.gz -/snakemake-7.32.2.tar.gz -/snakemake-7.32.3.tar.gz -/snakemake-7.32.4.tar.gz -/snakemake-8.1.2.tar.gz -/snakemake-8.2.1.tar.gz -/snakemake-8.2.3.tar.gz -/snakemake-8.4.3.tar.gz -/snakemake-8.4.4.tar.gz -/snakemake-8.4.6.tar.gz -/snakemake-8.4.7.tar.gz -/snakemake-8.4.8.tar.gz -/snakemake-8.4.9.tar.gz -/snakemake-8.4.12.tar.gz -/snakemake-8.5.2.tar.gz -/snakemake-8.5.3.tar.gz -/snakemake-8.5.4.tar.gz -/snakemake-8.5.5.tar.gz -/snakemake-8.6.0.tar.gz -/snakemake-8.7.0.tar.gz -/snakemake-8.8.0.tar.gz -/snakemake-8.9.0.tar.gz -/snakemake-8.10.4.tar.gz -/snakemake-8.10.6.tar.gz -/snakemake-8.10.7.tar.gz -/snakemake-8.10.8.tar.gz -/snakemake-8.11.0.tar.gz -/snakemake-8.11.1.tar.gz -/snakemake-8.11.3.tar.gz -/snakemake-8.11.6.tar.gz -/snakemake-8.12.0.tar.gz -/snakemake-8.13.0.tar.gz -/snakemake-8.14.0.tar.gz -/snakemake-8.15.2.tar.gz -/snakemake-8.16.0.tar.gz -/snakemake-8.17.0.tar.gz -/snakemake-8.18.0.tar.gz -/snakemake-8.18.2.tar.gz -/snakemake-8.30.0.tar.gz -/snakemake-8.30.0-assets.tar.zst -/snakemake-9.3.3.tar.gz -/snakemake-9.3.3-assets.tar.zst -/snakemake-9.3.4.tar.gz -/snakemake-9.3.4-assets.tar.zst -/snakemake-9.4.0.tar.gz -/snakemake-9.4.0-assets.tar.zst -/snakemake-9.5.1.tar.gz -/snakemake-9.5.1-assets.tar.zst -/snakemake-6dee2b55fbfff3bdad33cecdbeb8bd55ff4586bc.tar.gz -/snakemake-6dee2b55fbfff3bdad33cecdbeb8bd55ff4586bc-assets.tar.zst -/snakemake-9.6.1.tar.gz -/snakemake-9.6.1-assets.tar.zst -/snakemake-9.6.2.tar.gz -/snakemake-9.6.2-assets.tar.zst -/snakemake-9.7.1.tar.gz -/snakemake-9.7.1-assets.tar.zst -/snakemake-9.8.0.tar.gz -/snakemake-9.8.0-assets.tar.zst -/snakemake-9.8.1.tar.gz -/snakemake-9.8.1-assets.tar.zst -/snakemake-9.8.2.tar.gz -/snakemake-9.8.2-assets.tar.zst -/snakemake-9.9.0.tar.gz -/snakemake-9.9.0-assets.tar.zst -/snakemake-9.10.0.tar.gz -/snakemake-9.10.0-assets.tar.zst -/snakemake-9.10.1.tar.gz -/snakemake-9.10.1-assets.tar.zst -/snakemake-9.11.0.tar.gz -/snakemake-9.11.0-assets.tar.zst -/snakemake-9.11.2.tar.gz -/snakemake-9.11.2-assets.tar.zst -/snakemake-9.11.3.tar.gz -/snakemake-9.11.3-assets.tar.zst -/snakemake-9.11.4.tar.gz -/snakemake-9.11.4-assets.tar.zst -/snakemake-9.11.5.tar.gz -/snakemake-9.11.5-assets.tar.zst -/snakemake-9.11.6.tar.gz -/snakemake-9.11.6-assets.tar.zst -/snakemake-9.11.7.tar.gz -/snakemake-9.11.7-assets.tar.zst -/snakemake-9.11.8.tar.gz -/snakemake-9.11.8-assets.tar.zst -/snakemake-9.11.9.tar.gz -/snakemake-9.11.9-assets.tar.zst -/snakemake-9.12.0.tar.gz -/snakemake-9.12.0-assets.tar.zst -/snakemake-9.13.0.tar.gz -/snakemake-9.13.0-assets.tar.zst -/snakemake-9.13.1.tar.gz -/snakemake-9.13.1-assets.tar.zst -/snakemake-9.13.2.tar.gz -/snakemake-9.13.2-assets.tar.zst -/snakemake-9.13.3.tar.gz -/snakemake-9.13.3-assets.tar.zst -/snakemake-9.13.4.tar.gz -/snakemake-9.13.4-assets.tar.zst -/snakemake-9.13.5.tar.gz -/snakemake-9.13.5-assets.tar.zst -/snakemake-9.13.6.tar.gz -/snakemake-9.13.6-assets.tar.zst -/snakemake-9.13.7.tar.gz -/snakemake-9.13.7-assets.tar.zst -/snakemake-9.14.2.tar.gz -/snakemake-9.14.2-assets.tar.zst -/snakemake-9.14.3.tar.gz -/snakemake-9.14.3-assets.tar.zst -/snakemake-9.14.4.tar.gz -/snakemake-9.14.4-assets.tar.zst -/snakemake-9.14.5.tar.gz -/snakemake-9.14.5-assets.tar.zst -/snakemake-9.14.6.tar.gz -/snakemake-9.14.6-assets.tar.zst diff --git a/chanegelog b/chanegelog new file mode 100644 index 0000000..bce324f --- /dev/null +++ b/chanegelog @@ -0,0 +1,32 @@ +* 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 diff --git a/changelog b/changelog deleted file mode 100644 index 0b1bd0e..0000000 --- a/changelog +++ /dev/null @@ -1,179 +0,0 @@ -* 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 diff --git a/get_assets b/get_assets deleted file mode 100755 index c69a1cd..0000000 --- a/get_assets +++ /dev/null @@ -1,88 +0,0 @@ -#!/bin/sh -set -o nounset -set -o errexit - -DIST_GIT="$(cd "$(dirname "$0")"; pwd)" -SPEC="${DIST_GIT}/snakemake.spec" - -WORKDIR="$(mktemp -d)" -trap "rm -rf '${WORKDIR}'" INT TERM EXIT -cd "${WORKDIR}" -# Make sure we have an absolute path to the working directory. -WORKDIR="${PWD}" - -echo "==== Download source archive ====" 1>&2 -SOURCE0="$( - spectool --list-files "${SPEC}" | - awk '$1 == "Source0:" { print $2 }' -)" -TARNAME="$(basename "${SOURCE0}")" -XDIR="$(basename "${TARNAME}" '.tar.gz')" -spectool --get-files "${SPEC}" - -echo "==== Extract source archive ====" 1>&2 -tar -xzf "${TARNAME}" -# Capture modification time from the original source archive, before we touch -# anything; everything in our asset archive will have this mtime for better -# reproducibility. -MTIME="$(stat --format='%Y' "${XDIR}/src/snakemake/assets/")" - -echo "==== Apply patches ====" 1>&2 -spectool --list-files "${SPEC}" | - awk '/^Patch/ && !/modified-assets/ { print $2 }' | - while read -r patchfile - do - set -o nounset - set -o errexit - echo "--> ${patchfile}" 1>&2 - cd "${WORKDIR}/${XDIR}" - patch -p1 < "${DIST_GIT}/$(basename "${patchfile}")" - done - -echo "==== Download assets ====" 1>&2 -PYTHONPATH="${PWD}/${XDIR}/src/snakemake" python3 <<'EOF' -from assets import Assets -Assets.deploy() -EOF - -echo "==== Modify assets ====" 1>&2 -echo "--> Remove array-flat-polyfill (CC0-1.0 code, unused)" 1>&2 -target='src/snakemake/assets/data/vega-lite/vega-lite.js' -echo "To be removed from ${target}:" 1>&2 -grep -E '^[[:blank:]]*Array\.prototype\.flat[[:blank:]]*\|\|' \ - "${XDIR}/${target}" 1>&2 -sed -r -i '/^[[:blank:]]*Array\.prototype\.flat[[:blank:]]*\|\|/d' \ - "${XDIR}/${target}" -echo '--> Search for vestiges of array-flat-polyfill' 1>&2 -if grep -ErinI 'defineProperty\(Array\.prototype,[[:blank:]]*.flat' \ - "${XDIR}/src/snakemake/assets" -then - echo 'MANUAL AUDIT REQUIRED' 1>&2 - exit 1 -fi -# Remove license file and the directory containing it -rm -rv "${XDIR}/src/snakemake/assets/data/array-flat-polyfill" -echo "--> Search for missed CC0-1.0 licenses" 1>&2 -if grep -ErinI '\bCC0\b' "${XDIR}/src/snakemake/assets" -then - echo 'MANUAL AUDIT REQUIRED' 1>&2 - exit 1 -fi - -echo "==== Archive assets ====" 1>&2 -RESULT="${XDIR}-assets.tar.zst" -ls -ld "${XDIR}/src/snakemake/assets/" -# https://www.gnu.org/software/tar/manual/html_section/Reproducibility.html -TZ=UTC LC_ALL=C tar \ - --create \ - --sort=name \ - --format=posix \ - --numeric-owner --owner=0 --group=0 \ - --mode=go+u,go-w \ - --pax-option='delete=atime,delete=ctime' \ - --clamp-mtime --mtime="@${MTIME}" \ - --directory="${XDIR}" \ - src/snakemake/assets/data | - zstdmt --ultra -22 > "${RESULT}" - -mv -v "${RESULT}" "${DIST_GIT}" diff --git a/snakemake-9.1.1-modified-assets.patch b/snakemake-9.1.1-modified-assets.patch deleted file mode 100644 index 6aa4419..0000000 --- a/snakemake-9.1.1-modified-assets.patch +++ /dev/null @@ -1,44 +0,0 @@ -diff -Naur snakemake-9.1.1-original/src/snakemake/assets/__init__.py snakemake-9.1.1/src/snakemake/assets/__init__.py ---- snakemake-9.1.1-original/src/snakemake/assets/__init__.py 2025-03-21 14:49:12.112309938 -0400 -+++ snakemake-9.1.1/src/snakemake/assets/__init__.py 2025-03-21 14:49:56.495171724 -0400 -@@ -379,9 +379,12 @@ - version="0.6.2", - ), - # End copied/derived/adapted code in vega, included in vega/vega.js -+ # Fedora patch: We have removed array-flat-polyfill from the bundle -+ # since its CC0-1.0 code is not-allowed for code; the checksum of the -+ # packaged bundle therefore differs from that of the published one. - "vega-lite/vega-lite.js": Asset( - url="https://cdnjs.cloudflare.com/ajax/libs/vega-lite/{version}/vega-lite.js", -- sha256="6eb7f93121cd9f44cf8640244f87c5e143f87c7a0b6cd113da4a9e41e3adf0aa", -+ sha256="5b9880c2bf7c1daac912ca1e80b384daf2e7dedc3c6b62bc5159ed86d3c51c7b", - version="5.2.0", - ), - "vega-lite/LICENSE": Asset( -@@ -428,13 +431,6 @@ - sha256="c2cfccb812fe482101a8f04597dfc5a9991a6b2748266c47ac91b6a5aae15383", - version="2.1.1", - ), -- "array-flat-polyfill/LICENSE": Asset( -- # Releases are not tagged in git; we use the commit hash -- # corresponding to the 1.0.1 release -- url="https://raw.githubusercontent.com/jonathantneal/array-flat-polyfill/362d855cb6ea2ef12f0676b116c5f9e4233b6f31/LICENSE.md", -- sha256="597756adcb51f243ef4fb386920377f61d012ace0904364e1a8ee9aaec6afc84", -- version="1.0.1", -- ), - "clone/LICENSE": Asset( - url="https://raw.githubusercontent.com/pvorb/clone/refs/tags/v{version}/LICENSE", - sha256="3fb0857ef0133928cf72c88dfc464e931486e88778961eedec25585e2321507f", -diff -Naur snakemake-9.1.1-original/src/snakemake/report/html_reporter/data/packages.py snakemake-9.1.1/src/snakemake/report/html_reporter/data/packages.py ---- snakemake-9.1.1-original/src/snakemake/report/html_reporter/data/packages.py 2025-03-21 14:49:08.721489278 -0400 -+++ snakemake-9.1.1/src/snakemake/report/html_reporter/data/packages.py 2025-03-21 14:49:56.496478714 -0400 -@@ -143,9 +143,6 @@ - "@types-clone": Package( - license_path="@types-clone/LICENSE", - ), -- "array-flat-polyfill": Package( -- license_path="array-flat-polyfill/LICENSE", -- ), - "clone": Package( - license_path="clone/LICENSE", - ), diff --git a/snakemake.rpmlintrc b/snakemake.rpmlintrc deleted file mode 100644 index b0e2093..0000000 --- a/snakemake.rpmlintrc +++ /dev/null @@ -1,12 +0,0 @@ -# It is normal that extras metapackages should not have documentation, or any -# files at all. -addFilter(r"\+\w+.noarch: W: no-documentation") -# Removed in Snakemake 9.6 with no equivalent replacement. -addFilter(r" obsolete-not-provided snakemake\+(messaging)$") -# The -doc subpackage was removed and has no equivalent replacement. -addFilter(r" obsolete-not-provided snakemake-doc$") -# This is, unfortunately, intentional. See the comments in the spec file. -addFilter(r" python-leftover-require python-unversioned-command$") -# The assets bundle needs to be generated with a script, so it has no URL (and -# .tar.zst is perfectly legitimate). -addFilter(r" (invalid-url|inconsistent-file-extension).* snakemake-.*-assets\.tar\.zst") diff --git a/snakemake.spec b/snakemake.spec index 6bb8fdb..c6ab718 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -1,396 +1,7 @@ -# Work around a series of circular test dependencies: -# -# ⬐─python-snakemake-logger-plugin-rich🠔────╮ -# python-snakemake-interface-logger-plugins─╯ -# │￪python-snakemake-interface-scheduler-plugins -# │││￪ python-snakemake-interface-report-plugins -# ￬│￬│ ￬￪ ⬐───╮ -# 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🠔─╯│ -# ╰──────────────────────────python-snakemake-storage-plugin-fs🠔──╯ -# -# A good build order is: -# -# 1. BOOTSTRAP: -# python-snakemake-interface-common -# 2. BOOTSTRAP: -# python-snakemake-interface-executor-plugins -# python-snakemake-interface-logger-plugins -# python-snakemake-interface-report-plugins -# python-snakemake-interface-scheduler-plugins -# python-snakemake-interface-storage-plugins -# 3. BOOTSTRAP: snakemake -# 4. python-snakemake-executor-plugin-cluster-generic -# python-snakemake-logger-plugin-rich -# python-snakemake-storage-plugin-fs -# python-snakemake-storage-plugin-http -# python-snakemake-storage-plugin-s3 -# 5. snakemake -# python-snakemake-interface-executor-plugins -# python-snakemake-interface-logger-plugins -# python-snakemake-interface-report-plugins -# python-snakemake-interface-scheduler-plugins -# python-snakemake-interface-storage-plugins -%bcond bootstrap 0 -%bcond tests %{without bootstrap} -# Run tests that require network access? This only makes sense for local mock -# builds in combination with --enable-network. -%bcond network_tests 0 -# Almost all of the conda tests require network access, but there are also -# other failures that are not straightforward to understand. -%bcond conda_tests 0 -%bcond gcs_tests 1 +%bcond_without tests +%global debug_package %{nil} -Name: snakemake -Version: 9.14.6 -%global srcversion %(echo '%{version}' | cut -d '^' -f 1) -Release: %autorelease -Summary: Workflow management system to create reproducible and scalable data analyses - -# The primary license for Snakemake is MIT; web assets contribute a variety of -# other licenses. -# -# Apache-2.0 AND BSD-2-Clause AND BSD-3-CLause AND ISC AND MIT AND MIT-0: -# - src/snakemake/assets/data/vega/vega.js -# -# BSD-3-Clause AND MIT: -# - src/snakemake/assets/data/vega-lite/vega-lite.js -# -# BSD-3-Clause AND ISC AND MIT: -# - src/snakemake/assets/data/vega-embed/vega-embed.js -# -# MIT: -# - All Snakemake code unless otherwise noted -# - heroicons: It is unclear if anything derived from heroicons is actually -# present in the package, but upstream carries a copy of its license file, so -# we mention the possibility. -# - src/snakemake/assets/data/prop-types/prop-types.min.js -# - src/snakemake/assets/data/tailwindcss/tailwind.css -# -# == License breakdown: src/snakemake/assets/data/vega/vega.js == -# -# The primary license for npm(vega) is BSD-3-Clause. The bundle contains: -# -# Apache-2.0: -# - apache-commons-math, from which an implementation of erfinv is derived -# BSD-2-Clause: -# - npm(esprima), bundled as a copied, derived, or adapted snippet -# BSD-3-Clause: -# - npm(vega) and various npm(vega-*) libraries -# - npm(d3-contour), bundled as a copied, derived, or adapted snippet -# - npm(d3-regression), bundled as a copied, derived, or adapted snippet -# - npm(science), bundled as a copied, derived, or adapted snippet -# - npm(shapefile), bundled as a copied, derived, or adapted snippet -# ISC: -# - various npm(d3-*) libraries -# - npm(delaunator) -# - npm(quickselect) -# - npm(topojson-client) -# ISC AND MIT: -# - npm(d3-geo) (MIT is due to some code being derived from GeographicLib) -# - npm(d3-geo-projection) (MIT is due to some code being derived from -# https://github.com/scijs/integrate-adaptive-simpson) -# MIT: -# - npm(@types/estree) -# - npm(hashlru), bundled as a copied, derived, or adapted snippet -# - npm(regression), bundled as a copied, derived, or adapted snippet -# MIT-0: -# - npm(fabric), bundled as a copied, derived, or adapted snippet -# -# == License breakdown: src/snakemake/assets/data/vega-lite/vega-lite.js == -# -# The primary license for npm(vega-lite) is BSD-3-Clause. The bundle contains: -# -# BSD-3-Clause: -# - npm(vega-lite) and various npm(vega-*) libraries -# MIT: -# - npm(@types/clone) -# - npm(@types/estree) -# - npm(clone) -# - npm(fast-deep-equal) -# - npm(fast-json-stable-stringify) -# - npm(hashlru), bundled as a copied, derived, or adapted snippet -# - npm(json-stringify-pretty-compact) -# -# == License breakdown: src/snakemake/assets/data/vega-embed/vega-embed.js == -# -# The primary license for npm(vega-embed) is BSD-3-Clause. The bundle contains: -# -# BSD-3-Clause: -# - npm(vega-embed) and various npm(vega-*) libraries -# ISC: -# - npm(semver) -# MIT: -# - npm(fast-json-patch) -# - npm(json-stringify-pretty-compact) -License: %{shrink: - Apache-2.0 AND - BSD-2-Clause AND - BSD-3-Clause AND - ISC AND - MIT AND - MIT-0 - } -URL: https://snakemake.readthedocs.io/en/stable/index.html -%global forgeurl https://github.com/snakemake/snakemake -# We could use the PyPI sdist, which already contains the HTML report assets, -# but we would lose at least the vim extensions and changelog, and we would -# have to nontrivially modify the sdist to remove a CC0-1.0-licensed polyfill -# before uploading it to the lookaside cache, so doing so would not be -# meaningfully easier than using the GitHub archive with an additional source -# for the assets. -Source0: %{forgeurl}/archive/v%{version}/snakemake-%{version}.tar.gz -# The assets for HTML reports are normally downloaded in setup.py when creating -# the sdist. We use a script, Source2, executed with no arguments (implicitly -# relying on the spec file in the same directory) to download the assets, -# modify them as necessary, and pack them into an additional source archive. -Source1: snakemake-%{version}-assets.tar.zst -Source2: get_assets - -# Downstream-only: adjust the asset metadata in the sources, including -# checksums, for any adjustments that happened in the get_assets script. -# -# When the get_assets script unpacks and patches Source0 in order to use it to -# download assets, it skips this patch, because we need to first fetch the -# original assets in order to then modify them. The signal for this behavior is -# the substring "modified-assets" in the patch name. -Patch: snakemake-9.1.1-modified-assets.patch - -BuildSystem: pyproject -# Generate BR’s for all supported extras to ensure they do not FTI -BuildOption(generate_buildrequires): -x reports -BuildOption(install): -l snakemake -BuildOption(check): %{shrink: - -e '*.tests*' - %{?!with_gcs_tests:-e 'snakemake.executors.google_lifesciences_helper'} - } - -BuildArch: noarch - -BuildRequires: help2man - -# Snakemake uses (unversioned) "python" as the default remote execution -# command. Because remote hosts could be Windows machines, and those are likely -# to lack "python3.exe" (see https://github.com/python/cpython/issues/99185), -# we didn’t try to convince upstream to change this. Instead, we (reluctantly) -# just make sure that our own Snakemake installations are compatible by -# depending on python-unversioned-command. -BuildRequires: python-unversioned-command -Requires: python-unversioned-command - -BuildRequires: vim-filesystem -Requires: vim-filesystem - -# Required for snakemake.script.RScript, snakemake.notebook.RJupyterNotebook -# (Some of the tests in tests/tests_using_conda.py require this.) -BuildRequires: R-core -Recommends: R-core - -Provides: vim-snakemake = %{version}-%{release} - -# Regarding pre-compiled/pre-minified JavaScript, see: -# - https://pagure.io/fesco/issue/3177 -# - https://pagure.io/packaging-committee/pull-request/1370 -# Regarding CSS, see: -# - https://pagure.io/fesco/issue/3269 -# - https://pagure.io/packaging-committee/pull-request/1402 - -# Styles from Pygments are bundled in generated HTML reports (thus the presence -# of a Pygments license file), but the styles come from the system -# python3-pygments package and are not actually bundled in this package. - -# tailwind.css 3.4.16 is src/snakemake/assets/data/tailwindcss/tailwind.css, -# but we do not normally treat CSS frameworks as bundled dependencies, and it -# is not clear how we should name a virtusl Provides if we added one. - -# src/snakemake/assets/data/react/react.production.min.js -Provides: bundled(npm(react)) = 18.2.0 -# src/snakemake/assets/data/react/react-dom.production.min.js -Provides: bundled(npm(react-dom)) = 18.2.0 - -# src/snakemake/assets/data/vega/vega.js -Provides: bundled(npm(vega)) = 5.21.0 -# Bundled in src/snakemake/assets/data/vega/vega.js as dependencies: -# For versions of vega-* packages, see: -# https://github.com/vega/vega/blob/v5.21.0/packages -Provides: bundled(npm(vega-crossfilter)) = 4.0.5 -Provides: bundled(npm(vega-dataflow)) = 5.7.4 -Provides: bundled(npm(vega-encode)) = 4.8.3 -Provides: bundled(npm(vega-event-selector)) = 3.0.0 -Provides: bundled(npm(vega-expression)) = 5.0.0 -Provides: bundled(npm(vega-force)) = 4.0.7 -Provides: bundled(npm(vega-format)) = 1.0.4 -Provides: bundled(npm(vega-functions)) = 5.12.1 -Provides: bundled(npm(vega-geo)) = 4.3.8 -Provides: bundled(npm(vega-hierarchy)) = 4.0.9 -Provides: bundled(npm(vega-label)) = 1.1.0 -Provides: bundled(npm(vega-loader)) = 4.4.1 -Provides: bundled(npm(vega-parser)) = 6.1.4 -Provides: bundled(npm(vega-projection)) = 1.4.5 -Provides: bundled(npm(vega-regression)) = 1.0.9 -Provides: bundled(npm(vega-runtime)) = 6.1.3 -Provides: bundled(npm(vega-scale)) = 7.1.1 -Provides: bundled(npm(vega-scenegraph)) = 4.9.4 -Provides: bundled(npm(vega-statistics)) = 5.3.1 -Provides: bundled(npm(vega-time)) = 2.0.4 -Provides: bundled(npm(vega-transforms)) = 4.9.5 -Provides: bundled(npm(vega-typings)) = 0.22.0 -Provides: bundled(npm(vega-util)) = 1.17.0 -Provides: bundled(npm(vega-view)) = 5.10.1 -Provides: bundled(npm(vega-view-transforms)) = 4.5.8 -Provides: bundled(npm(vega-voronoi)) = 4.1.5 -Provides: bundled(npm(vega-wordcloud)) = 4.1.3 -# For these, see notes in src/snakemake/assets/__init__.py. -Provides: bundled(npm(@types/estree)) = 0.0.50 -Provides: bundled(npm(d3-array)) = 2.12.1 -Provides: bundled(npm(d3-color)) = 2.0.0 -Provides: bundled(npm(d3-delaunay)) = 5.2.0 -Provides: bundled(npm(d3-dispatch)) = 2.0.0 -Provides: bundled(npm(d3-dsv)) = 2.0.0 -Provides: bundled(npm(d3-force)) = 2.1.1 -Provides: bundled(npm(d3-format)) = 2.0.0 -Provides: bundled(npm(d3-geo)) = 2.0.2 -Provides: bundled(npm(d3-geo-projection)) = 3.0.0 -Provides: bundled(npm(d3-hierarchy)) = 2.0.0 -Provides: bundled(npm(d3-interpolate)) = 2.0.1 -Provides: bundled(npm(d3-path)) = 2.0.0 -Provides: bundled(npm(d3-quadtree)) = 2.0.0 -Provides: bundled(npm(d3-scale)) = 3.3.0 -Provides: bundled(npm(d3-shape)) = 2.1.0 -Provides: bundled(npm(d3-time)) = 2.1.1 -Provides: bundled(npm(d3-time-format)) = 3.0.0 -Provides: bundled(npm(d3-timer)) = 2.0.0 -Provides: bundled(npm(delaunator)) = 4.0.1 -Provides: bundled(npm(topojson-client)) = 3.1.0 -# Present in src/snakemake/assets/data/vega/vega.js in the form of copied, -# derived, or adapted snippets. See notes in src/snakemake/assets/__init__.py. -# Implementation of erfinv is based on: -Provides: bundled(apache-commons-math) = 3.6.1 -# Expression parser is based on: -Provides: bundled(esprima) = 2.2.0 -Provides: bundled(fabric) = 2.4.5 -Provides: bundled(npm(d3-contour)) = 1.3.2 -Provides: bundled(npm(d3-regression)) = 1.2.1 -Provides: bundled(npm(hashlru)) = 1.0.4 -Provides: bundled(npm(quickselect)) = 2.0.0 -Provides: bundled(npm(regression)) = 2.0.1 -Provides: bundled(npm(science)) = 1.9.3 -Provides: bundled(npm(shapefile)) = 0.6.2 - -# src/snakemake/assets/data/vega-lite/vega-lite.js -Provides: bundled(npm(vega-lite)) = 5.2.0 -# NOTE: Some of the following virtual Provides are commented out. These are -# correct, and need to be considered when determining the license of -# vega-lite.js, but they do not need to be repeated in the spec file because -# they duplicate virtual Provides from vega.js. -# -# Bundled in src/snakemake/assets/data/vega-lite/vega-lite.js as dependencies: -# See notes in src/snakemake/assets/__init__.py. -Provides: bundled(npm(@types/clone)) = 2.1.1 -Provides: bundled(npm(clone)) = 2.1.2 -Provides: bundled(npm(fast-deep-equal)) = 3.1.3 -Provides: bundled(npm(fast-json-stable-stringify)) = 2.1.0 -Provides: bundled(npm(json-stringify-pretty-compact)) = 3.0.0 -# See notes in src/snakemake/assets/__init__.py, as well as dependencies in -# https://github.com/vega/vega-lite/blob/v5.2.0/package.json, and for versions, -# see https://github.com/vega/vega-lite/blob/v5.2.0/yarn.lock; these correspond -# to those associated with vega 5.2.1. -#Provides: bundled(npm(@types/estree)) = 0.0.50 -#Provides: bundled(npm(vega-event-selector)) = 3.0.0 -#Provides: bundled(npm(vega-expression)) = 5.0.0 -#Provides: bundled(npm(vega-util)) = 1.17.0 -# Present in src/snakemake/assets/data/vega-lite/vega-lite.js in the form of -# copied, derived, or adapted snippets. See notes in -# src/snakemake/assets/__init__.py. -#Provides: bundled(npm(hashlru)) = 1.0.4 - -# src/snakemake/assets/data/vega-embed/vega-embed.js -Provides: bundled(npm(vega-embed)) = 6.20.8 -# NOTE: Some of the following virtual Provides are commented out. These are -# correct, and need to be considered when determining the license of -# vega-embed.js, but they do not need to be repeated in the spec file because -# they duplicate virtual Provides from vega.js and/or vega-lite.js. -# -# Bundled in src/snakemake/assets/data/vega-embed/vega-embed.js as -# dependencies: -# See notes in src/snakemake/assets/__init__.py. -Provides: bundled(npm(fast-json-patch)) = 3.1.0 -#Provides: bundled(npm(json-stringify-pretty-compact)) = 3.0.0 -Provides: bundled(npm(semver)) = 7.3.5 -# See notes in src/snakemake/assets/__init__.py, as well as dependencies in -# https://github.com/vega/vega-embed/blob/v6.20.8/package.json, and for -# versions, see https://github.com/vega/vega-embed/blob/v6.20.8/yarn.lock; -# these correspond to those associated with vega 5.2.1. -Provides: bundled(npm(vega-interpreter)) = 1.0.4 -Provides: bundled(npm(vega-schema-url-parser)) = 2.2.0 -Provides: bundled(npm(vega-themes)) = 2.10.0 -Provides: bundled(npm(vega-tooltip)) = 0.28.0 -#Provides: bundled(npm(vega-util)) = 1.17.0 -# Present in src/snakemake/assets/data/vega-embed/vega-embed.js in the form of -# copied, derived, or adapted snippets. See notes in -# src/snakemake/assets/__init__.py. -#Provides: bundled(npm(hashlru)) = 1.0.4 -# _areEquals() is based on: -#Provides: bundled(npm(fast-deep-equal)) = 3.1.3 - -# It is unclear if anything derived from heroicons is actually present in the -# package, but upstream carries a copy of its license file, so we dutifully add -# the virtual Provides, just in case we have missed something. -Provides: bundled(npm(heroicons)) = 1.0.3 - -# src/snakemake/assets/data/prop-types/prop-types.min.js -Provides: bundled(npm(prop-types)) = 15.7.2 - -# 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 -# Removed in 9.6.0; keep the Obsoletes through Fedora 45. -Obsoletes: snakemake+messaging < 9.6.1-1 - -%if %{with tests} -# For several tests (either apptainer or singularity-ce should work): -BuildRequires: (apptainer or singularity-ce) -%if %{with conda_tests} -# We need this for test_jupyter_notebook*, even if we are not running tests -# that have conda in their names. When the conda_tests bcond is enabled, this -# is also needed for tests/tests_using_conda.py. -BuildRequires: conda -# For test_conda_pin_file, test_conda_named, test_conda_function -BuildRequires: ripgrep -# For test_script_xsh -BuildRequires: xonsh -%endif -# For test_env_modules: -BuildRequires: environment-modules -# For test_filegraph and test_env_modules, which use dot: -BuildRequires: graphviz -# For test_github_issue1158: -BuildRequires: strace -# For test_benchmark and test_benchmark_jsonl: -BuildRequires: stress-ng - -# 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 pytest-mock} -BuildRequires: %{py3_dist snakemake-executor-plugin-cluster-generic} -BuildRequires: %{py3_dist snakemake-storage-plugin-http} -BuildRequires: %{py3_dist snakemake-storage-plugin-fs} -BuildRequires: %{py3_dist snakemake-storage-plugin-s3} -%endif -# For import-testing snakemake.gui -BuildRequires: %{py3_dist flask} -%if %{with gcs_tests} -# For import-testing snakemake.executors.google_lifesciences_helper: -BuildRequires: %{py3_dist google-cloud-storage} -%endif +%global pypi_name snakemake %global _description %{expand: The Snakemake workflow management system is a tool to create reproducible and @@ -400,200 +11,105 @@ 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: %{pypi_name} +Version: 6.13.1 +Release: %autorelease +Summary: Workflow management system to create reproducible and scalable data analyses + +License: MIT +URL: https://snakemake.readthedocs.io/en/stable/index.html +Source0: https://github.com/%{pypi_name}/%{pypi_name}/archive/v%{version}/%{pypi_name}-%{version}.tar.gz + +BuildArch: noarch + +BuildRequires: python3-devel +BuildRequires: make + +Requires: %{py3_dist smart_open} + +%if %{with tests} +BuildRequires: %{py3_dist pytest} +BuildRequires: %{py3_dist pytest-cov} +BuildRequires: %{py3_dist requests-mock} +BuildRequires: %{py3_dist numpy} +BuildRequires: %{py3_dist pandas} +BuildRequires: %{py3_dist networkx} +BuildRequires: %{py3_dist graphviz} +BuildRequires: %{py3_dist configargparse} +BuildRequires: %{py3_dist boto3} +%endif + +%py_provides %{pypi_name} + +%generate_buildrequires +%pyproject_buildrequires -r + %description %_description +%package -n snakemake-doc -# No metapackage for “pep” extra because the following are not packaged: -# - python3-eido -# - python3-peppy -# Therefore, also no metapakge for “all” extra -%pyproject_extras_subpkg -n snakemake reports +Summary: %{summary} +BuildArch: noarch + +BuildRequires: %{py3_dist sphinx} +BuildRequires: %{py3_dist sphinx-argparse} +BuildRequires: %{py3_dist sphinx_rtd_theme} +BuildRequires: %{py3_dist recommonmark} +BuildRequires: %{py3_dist docutils} +BuildRequires: %{py3_dist configargparse} +BuildRequires: %{py3_dist appdirs} +BuildRequires: %{py3_dist myst-parser} + +%description -n snakemake-doc %_description %prep -%autosetup -n snakemake-%{version} -p1 -%setup -q -T -D -a 1 -c -n snakemake-%{version} +%autosetup -n %{pypi_name}-%{version} -# 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-${editor}.md" -done +rm -rf %{pypi_name}.egg-info +find %{pypi_name}/ -name "*.cpp" -print -delete +find . -type f -name "*.py" -exec sed -i '/^#![ ]*\/usr\/bin\/env.*$/ d' {} 2>/dev/null ';' -# The CDN URL for tailwind.css does not deliver a file with a stable checksum, -# so upstream has not recorded a checksum in src/snakemake/assets/__init__.py. -# A consequence of this is that setup.py will *always* re-download -# tailwind.css, even if it is already present, when building an sdist or -# bdist/wheel. Of course, this is not acceptable in an offline build, so we -# record the actual checksum of the tailwind.css file we are packaging. -cat >> src/snakemake/assets/__init__.py < %{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 -a +%check %if %{with tests} -%if %{without network_tests} -# The following require network access (at least DNS) and pass if it is -# available. -k="${k-}${k+ and }not test_ancient" -k="${k-}${k+ and }not test_dynamic_container" -k="${k-}${k+ and }not test_github_issue78" -k="${k-}${k+ and }not test_issue1083" -k="${k-}${k+ and }not test_issue3361_pass" -k="${k-}${k+ and }not test_keep_local" -k="${k-}${k+ and }not test_modules_prefix" -k="${k-}${k+ and }not test_report_after_run" -k="${k-}${k+ and }not test_retrieve" -k="${k-}${k+ and }not test_shell_exec" +export PYTHONPATH=%{buildroot}%{python3_sitelib} + +# tests/test_tibanna needs a network connection, therefore disabled. +# tests/test_google_lifesciences.py requires the Google Cloud library for python +# tests/test_tes.py requires py-tes. Currently not packaged for Fedora +%pytest\ + --ignore tests/test_google_lifesciences.py\ + --deselect tests/test_tibanna.py\ + --deselect tests/test_tes.py %endif -# These use the s3_storage test fixture, which sets up a server on the local -# loopback interface. For some reason, this does not seem to work in mock, with -# or without network access enabled. It is very likely that this is a quirk of -# the build environment rather than a real issue. -k="${k-}${k+ and }not test_default_storage" -k="${k-}${k+ and }not test_default_storage_local_job" -k="${k-}${k+ and }not test_output_file_cache_storage" -k="${k-}${k+ and }not test_storage" - -# The following requires cwltool, -# https://github.com/common-workflow-language/cwltool, which is not packaged. -k="${k-}${k+ and }not test_cwl_singularity" - -# The following requires polars, which is not packaged. -k="${k-}${k+ and }not test_params_pickling" -k="${k-}${k+ and }not test_validate" - -# The following require the “pep” extra. They might also require network -# access. -k="${k-}${k+ and }not test_modules_peppy" -k="${k-}${k+ and }not test_pep_pathlib" -k="${k-}${k+ and }not test_peppy" - -%if %{without conda_tests} -# All of these try to call conda info --json. We might experiment with making -# conda an unconditional BuildRequires, or with enabling the conda_tests bcond -# and filtering out the tests we cannot run, but we should wait for: -# -# F43FailsToInstall: python3-conda -# https://bugzilla.redhat.com/show_bug.cgi?id=2371696 -k="${k-}${k+ and }not test_jupyter_notebook" -k="${k-}${k+ and }not test_jupyter_notebook_nbconvert" -k="${k-}${k+ and }not test_jupyter_notebook_draft" -%endif - -# Flaky; so far, we have not attempted to understand or report these. -# -# FAILED ../tests/tests.py::test_update_flag - AssertionError: wrong result -# produced for file 'test.txt': -# ------found------ -# foo -# -----expected----- -# foo -# bar -# ----------------- -k="${k-}${k+ and }not test_update_flag" -# FAILED ../tests/tests.py::test_queue_input_dryrun - -# snakemake_interface_common.exceptions.WorkflowError: At least one job did not -# complete successfully. -# (produces no other useful output) - -# Hangs on s390x; we have not attempted to understand or report this, although -# it would be nice to do so. For simplicity, we just skip it on all -# architectures. -k="${k-}${k+ and }not test_github_issue1158" - -# Workaround for Python path issues -cd src/ - -# See discussion in https://github.com/snakemake/snakemake/issues/2961 -# regarding running individual tests explicitly rather than letting pytest -# discover them freely, and see the “Running the full test suite” section in -# docs/project_info/contributing.rst for the list of tests that should be run. -# - tests/test_api.py requires network access and S3 credentials -%pytest -v -k "${k-}" ${ignore-} \ - ../tests/tests.py \ -%if %{with conda_tests} - ../tests/tests_using_conda.py \ -%endif - ../tests/test_expand.py \ - ../tests/test_io.py \ - ../tests/test_schema.py \ - ../tests/test_linting.py \ - ../tests/test_executor_test_suite.py \ - ../tests/test_internals.py -%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 +%{_bindir}/%{pypi_name} +%{_bindir}/%{pypi_name}-bash-completion +%files -n snakemake-doc +%license LICENSE.md +%doc docs/_build/html docs/_build/doctrees %changelog %autochangelog diff --git a/sources b/sources index ac14f3c..972fde1 100644 --- a/sources +++ b/sources @@ -1,2 +1 @@ -SHA512 (snakemake-9.14.6.tar.gz) = 3858d5610271fbf3617e3b88b10b55546ddb2eafffa929a882bf5584c91f85280fa7c5b25bae8951e4feb5aa9568ba51c0979c35b37472d03e1efc239392f1ae -SHA512 (snakemake-9.14.6-assets.tar.zst) = c58043d640c14cdb4057b515ee65d8c8eb76a4abf34d7ebae70cc929023df780ef234dd5a8fa9d76a96bb1aceda8dab1c8f5337d72ff6bb9ae7d6b82c10a16a7 +SHA512 (snakemake-6.13.1.tar.gz) = 545bc08bffa35e1a4b4a4bbfea8c322e01e7a77d7168d56c00e56b48437130c60881398f61e58417cb935e6ad8659bda5298272e20e07e9b39cf754bb8a758ef