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* [rpms/snakemake] rawhide: Orphaned for 6+ weeks
@ 2026-07-19 0:36 Orphaned Packages Process
0 siblings, 0 replies; only message in thread
From: Orphaned Packages Process @ 2026-07-19 0:36 UTC (permalink / raw)
To: git-commits
A new commit has been pushed.
Repo : rpms/snakemake
Branch : rawhide
Commit : 95a2bd09d0fed54bfe4bd3d2d78e985838fae90e
Author : Orphaned Packages Process <packaging-reports@fedoraproject.org>
Date : 2026-07-18T19:36:33-05:00
Stats : +1/-1162 in 10 file(s)
URL : https://src.fedoraproject.org/rpms/snakemake/c/95a2bd09d0fed54bfe4bd3d2d78e985838fae90e?branch=rawhide
Log:
Orphaned for 6+ weeks
---
diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index 7a076e6..0000000
--- a/.gitignore
+++ /dev/null
@@ -1,163 +0,0 @@
-/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
-/snakemake-9.14.7.tar.gz
-/snakemake-9.14.7-assets.tar.zst
-/snakemake-9.14.8.tar.gz
-/snakemake-9.14.8-assets.tar.zst
-/snakemake-9.15.0.tar.gz
-/snakemake-9.15.0-assets.tar.zst
-/snakemake-9.16.0.tar.gz
-/snakemake-9.16.0-assets.tar.zst
-/snakemake-9.16.2.tar.gz
-/snakemake-9.16.2-assets.tar.zst
-/snakemake-9.16.3.tar.gz
-/snakemake-9.16.3-assets.tar.zst
-/snakemake-9.18.2.tar.gz
-/snakemake-9.18.2-assets.tar.zst
-/snakemake-9.19.0.tar.gz
-/snakemake-9.19.0-assets.tar.zst
-/snakemake-9.20.0.tar.gz
-/snakemake-9.20.0-assets.tar.zst
-/snakemake-9.21.0.tar.gz
-/snakemake-9.21.0-assets.tar.zst
-/snakemake-9.21.1.tar.gz
-/snakemake-9.21.1-assets.tar.zst
diff --git a/4211.patch b/4211.patch
deleted file mode 100644
index 42c54e5..0000000
--- a/4211.patch
+++ /dev/null
@@ -1,44 +0,0 @@
-From 6d13f1135a97f357c96fd42f2ae46d8c0366061e Mon Sep 17 00:00:00 2001
-From: "Benjamin A. Beasley" <code@musicinmybrain.net>
-Date: Mon, 1 Jun 2026 11:33:07 +0100
-Subject: [PATCH] Adapt for dataclasses._MISSING_TYPE replaced with sentinel in
- Python 3.15
-
-See https://github.com/python/cpython/pull/149086 and PEP 661.
----
- src/snakemake/common/argparse.py | 15 ++++++++++++++-
- 1 file changed, 14 insertions(+), 1 deletion(-)
-
-diff --git a/src/snakemake/common/argparse.py b/src/snakemake/common/argparse.py
-index 1801419da1..33a765e1c9 100644
---- a/src/snakemake/common/argparse.py
-+++ b/src/snakemake/common/argparse.py
-@@ -66,6 +66,19 @@ class ArgumentDefaultsHelpFormatter(argparse.HelpFormatter):
- None/dataclasses._MISSING_TYPE/etc.
- """
-
-+ # See https://github.com/python/cpython/pull/149086.
-+ if hasattr(dataclasses, "MISSING"):
-+ # Python 3.15 and later, with PEP 661
-+ @staticmethod
-+ def _is_missing(value):
-+ return value is dataclasses.MISSING
-+
-+ else:
-+ # Python 3.14 and older, without PEP 661
-+ @staticmethod
-+ def _is_missing(value):
-+ return isinstance(value, dataclasses._MISSING_TYPE)
-+
- def _get_help_string(self, action):
- if (
- (
-@@ -73,7 +86,7 @@ def _get_help_string(self, action):
- or action.nargs in [argparse.OPTIONAL, argparse.ZERO_OR_MORE]
- )
- and action.default not in (None, "", set(), argparse.SUPPRESS)
-- and not isinstance(action.default, dataclasses._MISSING_TYPE)
-+ and not self._is_missing(action.default)
- ):
- if isinstance(action.default, collections.abc.Iterable) and not isinstance(
- action.default, str
diff --git a/README.md b/README.md
deleted file mode 100644
index a7d89f4..0000000
--- a/README.md
+++ /dev/null
@@ -1,3 +0,0 @@
-# snakemake
-
-The snakemake package
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 <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
diff --git a/dead.package b/dead.package
new file mode 100644
index 0000000..5204a84
--- /dev/null
+++ b/dead.package
@@ -0,0 +1 @@
+Orphaned for 6+ weeks
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
deleted file mode 100644
index 9e684bf..0000000
--- a/snakemake.spec
+++ /dev/null
@@ -1,627 +0,0 @@
-# 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
-
-Name: snakemake
-Version: 9.21.1
-Release: %autorelease
-Summary: Workflow management system to create reproducible and scalable data analyses
-# The summary macro is overwritten by extras metapackages, but we want to use
-# the base package’s summary text in the man page.
-%global base_summary %{summary}
-
-# 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
-
-# fix: Adapt for dataclasses._MISSING_TYPE replaced with sentinel in Python 3.15
-# https://github.com/snakemake/snakemake/pull/4211
-# Fixes https://bugzilla.redhat.com/show_bug.cgi?id=2483710.
-Patch: %{forgeurl}/pull/4211.patch
-
-BuildSystem: pyproject
-# Generate BR’s for all supported extras to ensure they do not FTI
-BuildOption(generate_buildrequires): --extras reports
-BuildOption(install): --assert-license snakemake
-BuildOption(check): %{shrink:
- --exclude '*.tests*'
- %{?!with_gcs_tests:--exclude '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
-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.}
-
-%description %_description
-
-
-# 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
-
-
-%prep
-%autosetup -n snakemake-%{version} -p1
-%setup -q -T -D -a 1 -c -n snakemake-%{version}
-
-# Copy and rename nano and vim extensions readmes for use in the main
-# documentation directory.
-for editor in nano vim
-do
- cp --preserve "misc/${editor}/README.md" "README-${editor}.md"
-done
-
-# The CDN URL for tailwind.css does not deliver a file with a stable checksum,
-# so upstream has not recorded a checksum in src/snakemake/assets/__init__.py.
-# A consequence of this is that setup.py will *always* re-download
-# tailwind.css, even if it is already present, when building an sdist or
-# bdist/wheel. Of course, this is not acceptable in an offline build, so we
-# record the actual checksum of the tailwind.css file we are packaging.
-cat >> src/snakemake/assets/__init__.py <<EOF
-
-# Fedora patch: Upstream does not record a checksum for tailwind.css because
-# they report that the CDN URL may serve trivially different copies. Since we
-# package a copy of the file, we record the checksum of the actual packaged
-# file.
-Assets.spec["tailwindcss/tailwind.css"].sha256 = "$(
- sha256sum --binary src/snakemake/assets/data/tailwindcss/tailwind.css |
- awk '{print $1}'
-)"
-EOF
-
-# Downstream-only: remove the upper bound on the version of sqlmodel. Given the
-# 0.0.x version, we understand why upstream has pinned this to a precise
-# release, as any update may be breaking. However, Snakemake’s exposure to the
-# sqlmodel API is small, it’s likely that breakage will be rare in practice,
-# and it’s too tedious to keep updating the version bound, either
-# downstream-only or via repeated upstream PR’s. We might re-evaluate this once
-# sqlmodel reaches 0.1.0.
-%pyproject_patch_dependency sqlmodel:drop_upper
-
-# Downstream-only: remove the upper bound on the version of packaging.
-# Upstream added the upper bound in 5ae43aa7ae108b7b87cee524a6015dc3d228dc17 to
-# work around some unspecified “pixi solving caveat.” Whatever was going there
-# (and it doesn’t seem to have been written down), it doesn’t affect us
-# downstream, and we must work with what we have in any case.
-%pyproject_patch_dependency packaging:drop_upper
-
-
-%generate_buildrequires -p
-export SETUPTOOLS_SCM_PRETEND_VERSION='%{version}'
-
-
-%build -p
-export SETUPTOOLS_SCM_PRETEND_VERSION='%{version}'
-
-
-%install -a
-# Fix shebangs (no /usr/env shebangs)
-%py3_shebang_fix %{buildroot}%{python3_sitelib} %{buildroot}%{_bindir}
-
-# Remove shebangs from non-executable scripts. The Python script is executable
-# in the source tree but will be installed without executable permissions.
-sed --regexp-extended --in-place '1{/^#!/d}' \
- %{buildroot}%{python3_sitelib}/snakemake/executors/jobscript.sh \
- %{buildroot}%{python3_sitelib}/snakemake/executors/google_lifesciences_helper.py
-
-# Mark license files in the asset bundle.
-sed --regexp-extended --in-place \
- 's@^.*/(LICEN[CS]E|NOTICE)[^/]*$@%%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 --directory %{buildroot}%{_mandir}/man1
-PATH="${PATH-}:%{buildroot}%{_bindir}" \
- PYTHONPATH='%{buildroot}%{python3_sitelib}' \
- help2man --no-info --name='%{base_summary}' snakemake \
- > %{buildroot}%{_mandir}/man1/snakemake.1
-
-# Install nano syntax highlighting
-install -D --preserve-timestamps --mode=0644 \
- --target='%{buildroot}%{_datadir}/nano' misc/nano/syntax/snakemake.nanorc
-
-# Install vim syntax highlighting
-install --directory '%{buildroot}%{_datadir}/vim/vimfiles'
-cp --verbose --recursive --preserve misc/vim/* \
- '%{buildroot}%{_datadir}/vim/vimfiles'
-find '%{buildroot}%{_datadir}/vim/vimfiles' \
- -type f -name 'README.*' -print -delete
-
-
-%check -a
-%if %{with tests}
-%if %{without network_tests}
-# The following require network access (at least DNS) and pass if it is
-# available.
-k="${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-}${k+ and }not test_module_onerror"
-k="${k-}${k+ and }not test_module_onstart_not_in_main_snakefile"
-k="${k-}${k+ and }not test_module_onstart_onsuccess"
-k="${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-}${k+ and }not test_shell_exec"
-%endif
-
-# These use the s3_storage test fixture, which sets up a server on the local
-# loopback interface. For some reason, this does not seem to work in mock, with
-# or without network access enabled. It is very likely that this is a quirk of
-# the build environment rather than a real issue.
-k="${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-}${k+ and }not test_github_issue1158"
-
-# Workaround for Python path issues
-cd src/
-
-# See discussion in https://github.com/snakemake/snakemake/issues/2961
-# regarding running individual tests explicitly rather than letting pytest
-# discover them freely, and see the “Running the full test suite” section in
-# docs/project_info/contributing.rst for the list of tests that should be run.
-# - tests/test_api.py requires network access and S3 credentials
-%pytest --verbose -k "${k-}" \
- ../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
-
-
-%changelog
-%autochangelog
diff --git a/sources b/sources
deleted file mode 100644
index 7c8d930..0000000
--- a/sources
+++ /dev/null
@@ -1,2 +0,0 @@
-SHA512 (snakemake-9.21.1.tar.gz) = e36559b872f62b7ec3fe35048a1c61bea4e9365e5b19ccb2a69d409f6f3c29f0c1a39d6df36160cd18012d237b1ef974525b812f1acba2ee132f917b505be18a
-SHA512 (snakemake-9.21.1-assets.tar.zst) = 70b737ce86acdf9a3e20c6b44251c5473dc60bcda356dbe5529886ce068bc4a0b38816777d321b2797b97c1a281bdb2ece459aafaf69aec2a0255dfe278aaea7
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