Update to 9.14.6 (close RHBZ#2428070)

These are automatically hardlinked due to
https://fedoraproject.org/wiki/Changes/Hardlink_identical_files_in_packages_by_default,
so we don’t get these warnings anymore.

[skip changelog]

.gitignore

@@ -1,3 +1,141 @@
 /snakemake-6.5.1.tar.gz
 /snakemake-6.5.2.tar.gz
 /snakemake-6.6.0.tar.gz
+/snakemake-6.7.0.tar.gz
+/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

changelog

@@ -0,0 +1,179 @@
+* Fri Dec 22 2023 Benjamin A. Beasley <code@musicinmybrain.net> - 7.32.4-2
+- Fix mis-named “chanegelog” in repo
+
+* Mon Sep 18 2023 Packit <hello@packit.dev> - 7.32.4-1
+- [packit] 7.32.4 upstream release
+
+* Thu Aug 10 2023 Benjamin A. Beasley <code@musicinmybrain.net> - 7.32.3-1
+- Update to 7.32.3
+
+* Thu Aug 10 2023 Packit <hello@packit.dev> - 7.32.2-1
+- [packit] 7.32.2 upstream release
+
+* Thu Aug 10 2023 Ankur Sinha (Ankur Sinha Gmail) <sanjay.ankur@gmail.com> - 7.32.0-8
+- chore(packit): re-add upstream_tag_template
+
+* Thu Aug 10 2023 Ankur Sinha (Ankur Sinha Gmail) <sanjay.ankur@gmail.com> - 7.32.0-7
+- chore(packit): add koji job
+
+* Thu Aug 10 2023 Ankur Sinha (Ankur Sinha Gmail) <sanjay.ankur@gmail.com> - 7.32.0-6
+- chore(packit): limit PRs to rawhide
+
+* Wed Aug 09 2023 Ankur Sinha (Ankur Sinha Gmail) <sanjay.ankur@gmail.com> - 7.32.0-5
+- Revert "chore(packit): define upstream tag template"
+
+* Wed Aug 09 2023 Ankur Sinha (Ankur Sinha Gmail) <sanjay.ankur@gmail.com> - 7.32.0-4
+- chore(packit): define upstream tag template
+
+* Sat Aug 05 2023 Benjamin A. Beasley <code@musicinmybrain.net> - 7.32.0-3
+- Don’t allow packit to report issues upstream
+
+* Fri Aug 04 2023 Ankur Sinha (Ankur Sinha Gmail) <sanjay.ankur@gmail.com> - 7.32.0-2
+- chore: add packit conf
+
+* Fri Aug 04 2023 Benjamin A. Beasley <code@musicinmybrain.net> - 7.32.0-1
+- Update to 7.32.0 (close RHBZ#2229001)
+
+* Wed Aug 02 2023 Benjamin A. Beasley <code@musicinmybrain.net> - 7.31.1-1
+- Update to 7.31.1 (close RHBZ#2224675)
+
+* Sat Jul 22 2023 Fedora Release Engineering <releng@fedoraproject.org> - 7.30.1-4
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild
+
+* Mon Jul 17 2023 Benjamin A. Beasley <code@musicinmybrain.net> - 7.30.1-3
+- Fix FTBFS due to SyntaxWarnings in Python 3.12 (fix RHBZ#2220595)
+
+* Thu Jul 13 2023 Python Maint <python-maint@redhat.com> - 7.30.1-2
+- Rebuilt for Python 3.12
+
+* Thu Jun 29 2023 Benjamin A. Beasley <code@musicinmybrain.net> - 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 <code@musicinmybrain.net> - 7.26.0-6
+- Use new (rpm 4.17.1+) bcond style
+
+* Mon May 22 2023 Benjamin A. Beasley <code@musicinmybrain.net> - 7.26.0-5
+- Install nano syntax highlighting support
+
+* Mon May 22 2023 Benjamin A. Beasley <code@musicinmybrain.net> - 7.26.0-4
+- Install vim syntax highlighting support
+
+* Mon May 22 2023 Benjamin A. Beasley <code@musicinmybrain.net> - 7.26.0-3
+- Install bash completions
+
+* Mon May 22 2023 Benjamin A. Beasley <code@musicinmybrain.net> - 7.26.0-2
+- Add a generated man page
+
+* Mon May 22 2023 Benjamin A. Beasley <code@musicinmybrain.net> - 7.26.0-1
+- Update to 7.26.0 (close RHBZ#2203471)
+
+* Sat May 06 2023 Benjamin A. Beasley <code@musicinmybrain.net> - 7.25.3-1
+- Update to 7.25.3 (close RHBZ#2193279J)
+
+* Sat Apr 29 2023 Benjamin A. Beasley <code@musicinmybrain.net> - 7.25.2-1
+- Update to 7.25.2 (close RHBZ#2178275)
+
+* Sat Mar 11 2023 Benjamin A. Beasley <code@musicinmybrain.net> - 7.24.1-1
+- Update to 7.24.1 (close RHBZ#2171148)
+
+* Mon Feb 13 2023 Benjamin A. Beasley <code@musicinmybrain.net> - 7.22.0-1
+- Update to 7.22.0 (close RHBZ#2169240)
+
+* Wed Feb 08 2023 Benjamin A. Beasley <code@musicinmybrain.net> - 7.21.0-1
+- Update to 7.21.0 (close RHBZ#2166983)
+
+* Sun Jan 22 2023 Benjamin A. Beasley <code@musicinmybrain.net> - 7.20.0-1
+- Update to 7.20.0 (close RHBZ#2162603)
+
+* Sat Jan 21 2023 Fedora Release Engineering <releng@fedoraproject.org> - 7.19.1-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild
+
+* Wed Jan 04 2023 Benjamin A. Beasley <code@musicinmybrain.net> - 7.19.1-1
+- Update to 7.19.1 (close RHBZ#2153168)
+
+* Fri Dec 09 2022 Benjamin A. Beasley <code@musicinmybrain.net> - 7.18.2-1
+- Update to 7.8.12 (close RHBZ#2139921)
+
+* Thu Dec 08 2022 Benjamin A. Beasley <code@musicinmybrain.net> - 7.18.1-1
+- Update to 7.18.1
+
+* Tue Nov 01 2022 Benjamin A. Beasley <code@musicinmybrain.net> - 7.18.0-1
+- Update to 7.18.0 (close RHBZ#2138985)
+
+* Tue Nov 01 2022 Benjamin A. Beasley <code@musicinmybrain.net> - 7.17.2-4
+- Remove an obsolete spec file comment
+
+* Tue Nov 01 2022 Benjamin A. Beasley <code@musicinmybrain.net> - 7.17.2-3
+- Confirm the License is SPDX MIT
+
+* Tue Nov 01 2022 Benjamin A. Beasley <code@musicinmybrain.net> - 7.17.2-2
+- Simplify references to the -doc subpackage
+
+* Sun Oct 30 2022 Benjamin A. Beasley <code@musicinmybrain.net> - 7.17.2-1
+- Update to 7.17.2 (close RHBZ#2130414)
+
+* Fri Aug 26 2022 Benjamin A. Beasley <code@musicinmybrain.net> - 7.13.0-1
+- Update to 7.13.0 (close RHBZ#2121550)
+
+* Mon Aug 22 2022 Benjamin A. Beasley <code@musicinmybrain.net> - 7.12.1-2
+- Use rsvg-convert instead of inkscape
+
+* Thu Aug 11 2022 Benjamin A. Beasley <code@musicinmybrain.net> - 7.12.1-1
+- Update to 7.12.1 (close RHBZ#2117565)
+
+* Sun Jul 31 2022 Benjamin A. Beasley <code@musicinmybrain.net> - 7.12.0-1
+- Update to 7.12.0
+
+* Wed Jul 27 2022 Benjamin A. Beasley <code@musicinmybrain.net> - 7.11.0-1
+- Update to 7.11.0
+
+* Sun Jul 24 2022 Benjamin A. Beasley <code@musicinmybrain.net> - 7.9.0-2
+- Build documentation as PDF instead of HTML
+
+* Sun Jul 24 2022 Benjamin A. Beasley <code@musicinmybrain.net> - 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 <releng@fedoraproject.org> - 6.13.1-5
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild
+
+* Thu Jun 16 2022 Python Maint <python-maint@redhat.com> - 6.13.1-4
+- Rebuilt for Python 3.11
+
+* Mon Jan 24 2022 Vanessa_kris <vanessaigwe1@gmail.com> - 6.13.1-3
+- added autochanelog
+
+* Mon Jan 24 2022 Vanessa Christopher <vanessaigwe1@gmail.com> - 6.13.1-2
+- autorelease
+
+* Sun Jan 23 2022 Vanessa Christopher <vanessaigwe1@gmail.com> - 6.13.1-1
+- Version update to v6.13.1
+
+* Sat Jan 22 2022 Fedora Release Engineering <releng@fedoraproject.org> - 6.12.3-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild
+
+* Sat Dec 18 2021 Aniket Pradhan <major AT fedoraproject DOT org> - 6.12.3-1
+- Version update to v6.12.3
+- Use pyproject macros
+
+* Thu Sep 09 2021 Aniket Pradhan <major AT fedoraproject DOT org> - 6.8.0-1
+- Version update to v6.8.0
+
+* Tue Aug 17 2021 Aniket Pradhan <major AT fedoraproject DOT org> - 6.7.0-1
+- Version update to v6.7.0
+
+* Fri Jul 23 2021 Fedora Release Engineering <releng@fedoraproject.org> - 6.6.0-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild
+
+* Sat Jul 17 2021 Aniket Pradhan <major AT fedoraproject DOT org> - 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 <major AT fedoraproject DOT org> - 6.5.2-2
+- Correct the import path of napoleon extension
+- Use pytest macro
+
+* Sat Jul 03 2021 Aniket Pradhan <major AT fedoraproject DOT org> - 6.5.2-1
+- Initial build

get_assets

@@ -0,0 +1,88 @@
+#!/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}"

snakemake-9.1.1-modified-assets.patch

@@ -0,0 +1,44 @@
+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",
+             ),

snakemake.rpmlintrc

@@ -0,0 +1,12 @@
+# 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")

snakemake.spec

@@ -1,7 +1,396 @@
-%bcond_without tests
-%global debug_package %{nil}
+# 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
 
-%global pypi_name snakemake
+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 _description %{expand:
 The Snakemake workflow management system is a tool to create reproducible and
@@ -11,123 +400,200 @@ 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:        6.6.0
-Release:        1%{?dist}
-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:  %{py3_dist setuptools}
-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 filelock}
-BuildRequires:  %{py3_dist datrie}
-BuildRequires:  %{py3_dist ratelimiter}
-BuildRequires:  %{py3_dist pyyaml}
-BuildRequires:  %{py3_dist numpy}
-BuildRequires:  %{py3_dist pandas}
-BuildRequires:  %{py3_dist jsonschema}
-BuildRequires:  %{py3_dist networkx}
-BuildRequires:  %{py3_dist graphviz}
-BuildRequires:  %{py3_dist GitPython}
-BuildRequires:  %{py3_dist configargparse}
-BuildRequires:  %{py3_dist appdirs}
-BuildRequires:  %{py3_dist docutils}
-BuildRequires:  %{py3_dist boto3}
-BuildRequires:  %{py3_dist smart_open}
-BuildRequires:  %{py3_dist tabulate}
-%endif
-
-%py_provides %{pypi_name}
-
 %description %_description
 
-%package -n snakemake-doc
 
-Summary:        %{summary}
+# 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
 
-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}
-
-%description -n snakemake-doc %_description
 
 %prep
-%autosetup -n %{pypi_name}-%{version}
+%autosetup -n snakemake-%{version} -p1
+%setup -q -T -D -a 1 -c -n snakemake-%{version}
 
-rm -rf %{pypi_name}.egg-info
-find %{pypi_name}/ -name "*.cpp" -print -delete
-find . -type f -name "*.py" -exec sed -i '/^#![  ]*\/usr\/bin\/env.*$/ d' {} 2>/dev/null ';'
+# Copy and rename nano and vim extensions readmes for use in the main
+# documentation directory.
+for editor in nano vim
+do
+  cp -vp "misc/${editor}/README.md" "README-${editor}.md"
+done
 
-# Remove shebang from non-executable script
-sed -i '1d' snakemake/executors/jobscript.sh
+# 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 <<EOF
 
-# Rename subprocess call 'python' to 'python3'
-sed -i 's/python/python3/g' tests/test_linting.py
+# Fedora patch: Upstream does not record a checksum for tailwind.css because
+# they report that the CDN URL may serve trivially different copies. Since we
+# package a copy of the file, we record the checksum of the actual packaged
+# file.
+Assets.spec["tailwindcss/tailwind.css"].sha256 = "$(
+  sha256sum -b src/snakemake/assets/data/tailwindcss/tailwind.css |
+    awk '{print $1}'
+)"
+EOF
 
-%build
-%py3_build
 
-pushd docs/
-mkdir -p _build/doctrees
-mkdir -p _build/html
-make %{?_smp_mflags} html
-popd
+%generate_buildrequires -p
+export SETUPTOOLS_SCM_PRETEND_VERSION='%{srcversion}'
 
-%install
-%py3_install
 
-%check
+%build -p
+export SETUPTOOLS_SCM_PRETEND_VERSION='%{srcversion}'
+
+
+%install -a
+# Fix shebangs (no /usr/env shebangs)
+%py3_shebang_fix %{buildroot}%{python3_sitelib} %{buildroot}%{_bindir}
+
+# 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}' \
+    %{buildroot}%{python3_sitelib}/snakemake/executors/jobscript.sh \
+    %{buildroot}%{python3_sitelib}/snakemake/executors/google_lifesciences_helper.py
+
+# Mark license files in the asset bundle.
+sed -r -i 's@^.*/(LICEN[CS]E|NOTICE)[^/]*$@%%license &@' %{pyproject_files}
+
+# We wait until %%install to generate the man page so that we can use the
+# proper script entry point. The generated man page is not perfect, but it is
+# good enough to be useful.
+install -d %{buildroot}%{_mandir}/man1
+PATH="${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 -a
 %if %{with tests}
-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
+%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"
 %endif
 
-%files
-%doc README.md
-%license LICENSE.md
-%{_bindir}/%{pypi_name}
-%{_bindir}/%{pypi_name}-bash-completion
-%{python3_sitelib}/%{pypi_name}/
-%{python3_sitelib}/%{pypi_name}-%{version}-py%{python3_version}.egg-info/
+# 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
 
-%files -n snakemake-doc
-%license LICENSE.md
-%doc docs/_build/html docs/_build/doctrees
 
 %changelog
-* Sat Jul 17 2021 Aniket Pradhan <major AT fedoraproject DOT org> - 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 <major AT fedoraproject DOT org> - 6.5.2-2
-- Correct the import path of napoleon extension
-- Use pytest macro
-
-* Sat Jul 03 2021 Aniket Pradhan <major AT fedoraproject DOT org> - 6.5.2-1
-- Initial build
+%autochangelog

sources

@@ -1 +1,2 @@
-SHA512 (snakemake-6.6.0.tar.gz) = cab247cc0ff6778b02b03524e9d6f83bed3f647ca2620e6c12ba6e9e3cae6230324e0e66d64dce607a2f98b05a18fe91ef1e308fdd5d1dc77c79acd0b3ee4fce
+SHA512 (snakemake-9.14.6.tar.gz) = 3858d5610271fbf3617e3b88b10b55546ddb2eafffa929a882bf5584c91f85280fa7c5b25bae8951e4feb5aa9568ba51c0979c35b37472d03e1efc239392f1ae
+SHA512 (snakemake-9.14.6-assets.tar.zst) = c58043d640c14cdb4057b515ee65d8c8eb76a4abf34d7ebae70cc929023df780ef234dd5a8fa9d76a96bb1aceda8dab1c8f5337d72ff6bb9ae7d6b82c10a16a7