From fd294731b472df4466e809fcaf3236474da66fb3 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Fri, 5 Jan 2024 07:43:38 -0500 Subject: [PATCH 001/109] Assert that the .dist-info directory contains a license file --- snakemake.spec | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/snakemake.spec b/snakemake.spec index 46fd73f..618f5ed 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -122,7 +122,7 @@ PYTHONPATH="${PWD}" %make_build -C docs latexpdf SPHINXOPTS='%{?_smp_mflags}' %install %pyproject_install -%pyproject_save_files snakemake +%pyproject_save_files -l snakemake # We wait until %%install to generate the man page so that we can use the # proper script entry point. The generated man page is not perfect, but it is From d9cab37bc6011aeffe5803bd252988871eb3e128 Mon Sep 17 00:00:00 2001 From: Packit Date: Fri, 22 Dec 2023 03:29:29 +0000 Subject: [PATCH 002/109] [packit] 8.1.2 upstream release - Resolves rhbz#2255578 Upstream tag: v8.1.2 Upstream commit: 41959557 --- .gitignore | 1 + README.packit | 2 +- snakemake.spec | 97 ++++++++++++++++++++++++++++++-------------------- sources | 2 +- 4 files changed, 61 insertions(+), 41 deletions(-) diff --git a/.gitignore b/.gitignore index 7635a3f..b382443 100644 --- a/.gitignore +++ b/.gitignore @@ -29,3 +29,4 @@ /snakemake-7.32.2.tar.gz /snakemake-7.32.3.tar.gz /snakemake-7.32.4.tar.gz +/snakemake-8.1.2.tar.gz diff --git a/README.packit b/README.packit index 786c2a0..8c508a5 100644 --- a/README.packit +++ b/README.packit @@ -1,3 +1,3 @@ This repository is maintained by packit. https://packit.dev/ -The file was generated using packit 0.80.0.post8+gf2b5fcbc. +The file was generated using packit 0.88.0. diff --git a/snakemake.spec b/snakemake.spec index 618f5ed..261af2d 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -1,4 +1,25 @@ -%bcond tests 1 +# Work around a series of circular test dependencies: +# +# ⬐───╮ +# snakemake → python-snakemake-interface-executor-plugins⬎ +# ￪￪ │ ⬑────────────────────python-snakemake-executor-plugin-cluster-generic +# ││ ↳python-snakemake-interface-storage-plugins────────────────╮ +# ││ ￬ │ +# │╰────────────────────────python-snakemake-storage-plugin-http│ +# ╰─────────────────────────python-snakemake-storage-plugin-s3🠔─╯ +# +# A good build order is: +# +# 1. BOOTSTRAP: python-snakemake-interface-executor-plugins, +# python-snakemake-interface-storage-plugins +# 2. BOOTSTRAP: snakemake +# 3. python-snakemake-executor-plugin-cluster-generic, +# python-snakemake-storage-plugin-http, +# python-snakemake-storage-plugin-s3 +# 4. snakemake, python-snakemake-interface-executor-plugins, +# python-snakemake-interface-storage-plugins +%bcond bootstrap 1 +%bcond tests %{without bootstrap} # Sphinx-generated HTML documentation is not suitable for packaging; see # https://bugzilla.redhat.com/show_bug.cgi?id=2006555 for discussion. %bcond doc_pdf 1 @@ -12,7 +33,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 7.32.4 +Version: 8.1.2 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses @@ -25,7 +46,7 @@ Summary: Workflow management system to create reproducible and scalable d # files as well. License: MIT AND Unlicense URL: https://snakemake.readthedocs.io/en/stable/index.html -Source0: https://github.com/snakemake/snakemake/archive/v%{version}/snakemake-%{version}.tar.gz +Source: https://github.com/snakemake/snakemake/archive/v%{version}/snakemake-%{version}.tar.gz BuildArch: noarch @@ -41,19 +62,24 @@ BuildRequires: vim-filesystem Requires: vim-filesystem Provides: vim-snakemake = %{version}-%{release} +# These extras were removed upstream in Snakemake 8.0.0. Retain the Obsoletes +# until F40 reaches EOL so we have a clean upgrade path. +Obsoletes: snakemake+azure < 8.1.0-1 +Obsoletes: snakemake+google-cloud < 8.1.0-1 %if %{with tests} # See test-environment.yml for a listing of test dependencies, along with a lot # of other cruft. BuildRequires: %{py3_dist boto3} -BuildRequires: %{py3_dist configargparse} -# For tests/test_google_lifesciences.py; but it would need a network connection -#BuildRequires: %%{py3_dist google-api-python-client} -#BuildRequires: %%{py3_dist google-cloud-storage} BuildRequires: %{py3_dist pandas} BuildRequires: %{py3_dist pytest} -BuildRequires: %{py3_dist requests-mock} +BuildRequires: %{py3_dist snakemake-executor-plugin-cluster-generic} +BuildRequires: %{py3_dist snakemake-storage-plugin-s3} %endif +# For import-testing snakemake.gui +BuildRequires: %{py3_dist flask} +# For import-testing snakemake.executors.google_lifesciences_helper: +BuildRequires: %{py3_dist google-cloud-storage} %description %_description @@ -77,7 +103,7 @@ BuildRequires: /usr/bin/rsvg-convert # No metapackage for “pep” extra because the following are not packaged: # - python3-eido # - python3-peppy -%pyproject_extras_subpkg -n snakemake reports messaging google-cloud azure +%pyproject_extras_subpkg -n snakemake reports messaging %prep %autosetup -n snakemake-%{version} -p1 @@ -89,8 +115,10 @@ sed -r -i '1{/^#!/d}' \ snakemake/executors/google_lifesciences_helper.py # Fix calls to unversioned Python interpreter sed -r -i 's@"python"@"%{python3}"@g' tests/test_linting.py -# Now part of Sphinx: -sed -r -i '/sphinxcontrib-napoleon/d' docs/requirements.txt +sed -r -i 's@python -m@"%{python3} -m@g' tests/tests.py +# The sphinxcontrib-napoleon extension is now part of Sphinx. +# The lutra HTML theme is not needed since we do not generate HTML docs. +sed -r -i 's/^(sphinxcontrib-napoleon|lutra)/# &/' docs/requirements.txt # Since pdflatex cannot handle Unicode inputs in general: echo "latex_engine = 'xelatex'" >> docs/conf.py # Copy and rename nano and vim extensions readmes for use in the main @@ -132,18 +160,6 @@ PATH="${PATH-}:%{buildroot}%{_bindir}" \ PYTHONPATH='%{buildroot}%{python3_sitelib}' \ help2man --no-info --name='%{summary}' snakemake \ > %{buildroot}%{_mandir}/man1/snakemake.1 -# No man page for snakemake-bash-completion since it is not intended for manual -# invocation. - -# Generate and install shell completions. -install -d %{buildroot}%{bash_completions_dir} -# Since 7.29.0, snakemake --bash-completion no longer works without a Snakefile -# https://github.com/snakemake/snakemake/issues/2336 -touch Snakefile -PATH="${PATH-}:%{buildroot}%{_bindir}" \ - PYTHONPATH='%{buildroot}%{python3_sitelib}' \ - snakemake --bash-completion \ - > %{buildroot}%{bash_completions_dir}/snakemake.bash # Install nano syntax highlighting install -t '%{buildroot}%{_datadir}/nano' -D -m 0644 -p \ @@ -156,20 +172,26 @@ find '%{buildroot}%{_datadir}/vim/vimfiles' \ -type f -name 'README.*' -print -delete %check -%if %{with tests} -# Lint output “Migrate long run directives into scripts or notebooks …” is -# apparently not expected by upstream -k="${k-}${k+ and }not test_lint[long_run-positive]" -# Needs a network connection -k="${k-}${k+ and }not test_tibanna" -# Requires py-tes. Currently not packaged for Fedora. -k="${k-}${k+ and }not test_tes" -# Require a running slurm instance; maybe this is possible to set up -# temporarily in the offline build environment, but we don’t know how. -k="${k-}${k+ and }not test_slurm_" +# Even if we are running the tests, this is useful; it could turn up import +# errors that would only be revealed by tests we had to disable (e.g. due to +# network access). +# +# ImportError from snakemake.executors.flux (no 'sleep' in +# snakemake_interface_executor_plugins.utils) +# https://github.com/snakemake/snakemake/issues/2598 +# “The flux module is actually supposed to be moved into a plugin and has no +# connection to the rest of the code anymore.” +%pyproject_check_import -e '*.tests*' -e 'snakemake.executors.flux' + +%if %{with tests} +# Needs a network connection: +ignore="${ignore-} --ignore-glob=tests/test_google_lifesciences/*" + +# Needs a network connection (plus, there are some unresolved +# unversioned-python-command issues which we hope are confined to the test +# code): +k="${k-}${k+ and }not test_deploy_sources" -# Needs a network connection (and GCP credentials): -ignore="${ignore-} --ignore=tests/test_google_lifesciences.py" # ______ ERROR collecting tests/test_conda_python_script/test_script.py ______ # import file mismatch: # imported module 'test_script' has this __file__ attribute: @@ -188,9 +210,6 @@ ignore="${ignore-} --ignore-glob=tests/test_conda_python_3_7_script/*" %{_bindir}/snakemake %{_mandir}/man1/snakemake.1* -%{_bindir}/snakemake-bash-completion -%{bash_completions_dir}/snakemake.bash - # 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/ diff --git a/sources b/sources index 41d1ecb..ad1ddc0 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-7.32.4.tar.gz) = 34fef61528b18facab798652c88ed5c698ef02161e023255fdd024b7c7781c4e582cdb04b2740fdff9b6f3600acaec719742984acee57920bb48ef3b5af99d9a +SHA512 (snakemake-8.1.2.tar.gz) = 78934acf36c5dadd037f5f519a387a219c67e5ee7405e834ceb83df016b243bcc35abaa8a5f23ba5258d5f17a7a2944b8b78b172e5ba6120620d820c7029e2a6 From d28443332e6e09f72eb4ace755d87fae338c19ea Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Thu, 18 Jan 2024 23:44:30 -0500 Subject: [PATCH 003/109] Non-bootstrap build --- snakemake.spec | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/snakemake.spec b/snakemake.spec index 261af2d..ac8fc2b 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -18,7 +18,7 @@ # python-snakemake-storage-plugin-s3 # 4. snakemake, python-snakemake-interface-executor-plugins, # python-snakemake-interface-storage-plugins -%bcond bootstrap 1 +%bcond bootstrap 0 %bcond tests %{without bootstrap} # Sphinx-generated HTML documentation is not suitable for packaging; see # https://bugzilla.redhat.com/show_bug.cgi?id=2006555 for discussion. From 14fc53abc4e04e9a443b447463cc69d7412e4f2a Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Fri, 19 Jan 2024 07:58:36 -0500 Subject: [PATCH 004/109] [packit] 8.2.1 upstream release Upstream tag: v8.2.1 Upstream commit: c05cc9e8 --- .gitignore | 1 + README.packit | 2 +- snakemake.spec | 2 +- sources | 2 +- 4 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index b382443..5534294 100644 --- a/.gitignore +++ b/.gitignore @@ -30,3 +30,4 @@ /snakemake-7.32.3.tar.gz /snakemake-7.32.4.tar.gz /snakemake-8.1.2.tar.gz +/snakemake-8.2.1.tar.gz diff --git a/README.packit b/README.packit index 8c508a5..d529207 100644 --- a/README.packit +++ b/README.packit @@ -1,3 +1,3 @@ This repository is maintained by packit. https://packit.dev/ -The file was generated using packit 0.88.0. +The file was generated using packit 0.87.1. diff --git a/snakemake.spec b/snakemake.spec index ac8fc2b..3597781 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -33,7 +33,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.1.2 +Version: 8.2.1 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index ad1ddc0..684641b 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.1.2.tar.gz) = 78934acf36c5dadd037f5f519a387a219c67e5ee7405e834ceb83df016b243bcc35abaa8a5f23ba5258d5f17a7a2944b8b78b172e5ba6120620d820c7029e2a6 +SHA512 (snakemake-8.2.1.tar.gz) = aa53a94a1afac0b253c4b6aaab051431b28904b58e381a4c71d731d4c13320df79a5a1476299e1d4397dba86d2040b2248376c5142871effc5e9347552687b7a From da2ad60d4cb2c20595f95cd7c193592269b642b0 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Sat, 20 Jan 2024 22:42:57 -0500 Subject: [PATCH 005/109] =?UTF-8?q?Don=E2=80=99t=20build=20PDF=20documenta?= =?UTF-8?q?tion?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Drop and Obsolete the -doc subpackage Building the documentation is becoming too tedious. --- snakemake-7.11.0-docs-no-animated-demo.patch | 16 ----- snakemake.spec | 64 +++----------------- 2 files changed, 10 insertions(+), 70 deletions(-) delete mode 100644 snakemake-7.11.0-docs-no-animated-demo.patch diff --git a/snakemake-7.11.0-docs-no-animated-demo.patch b/snakemake-7.11.0-docs-no-animated-demo.patch deleted file mode 100644 index cef4e57..0000000 --- a/snakemake-7.11.0-docs-no-animated-demo.patch +++ /dev/null @@ -1,16 +0,0 @@ -diff -Naur snakemake-7.11.0-original/docs/snakefiles/rules.rst snakemake-7.11.0/docs/snakefiles/rules.rst ---- snakemake-7.11.0-original/docs/snakefiles/rules.rst 2022-07-27 10:01:28.000000000 -0400 -+++ snakemake-7.11.0/docs/snakefiles/rules.rst 2022-07-27 11:54:32.457308100 -0400 -@@ -970,12 +970,6 @@ - snakemake --cluster ... --jobs 100 --until test.txt - - Then, the notebook rule can easily be executed locally. --An demo of the entire interactive editing process can be found by clicking below: -- --.. image:: images/snakemake-notebook-demo.gif -- :scale: 20% -- :alt: Notebook integration demo -- :align: center - - Finally, it is advisable to combine the ``notebook`` directive with the ``conda`` directive (see :ref:`integrated_package_management`) in order to define a software stack to use. - At least, this software stack should contain jupyter and the language to use (e.g. Python or R). diff --git a/snakemake.spec b/snakemake.spec index 3597781..d6b0a05 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -20,9 +20,6 @@ # python-snakemake-interface-storage-plugins %bcond bootstrap 0 %bcond tests %{without bootstrap} -# Sphinx-generated HTML documentation is not suitable for packaging; see -# https://bugzilla.redhat.com/show_bug.cgi?id=2006555 for discussion. -%bcond doc_pdf 1 %global _description %{expand: The Snakemake workflow management system is a tool to create reproducible and @@ -50,10 +47,6 @@ Source: https://github.com/snakemake/snakemake/archive/v%{version}/snake BuildArch: noarch -# Since we build the docs as a PDF, we can’t include an animated GIF demo. -# Patch out the image reference and the text referring to it. -Patch: snakemake-7.11.0-docs-no-animated-demo.patch - BuildRequires: python3-devel BuildRequires: help2man @@ -66,6 +59,10 @@ Provides: vim-snakemake = %{version}-%{release} # until F40 reaches EOL so we have a clean upgrade path. Obsoletes: snakemake+azure < 8.1.0-1 Obsoletes: snakemake+google-cloud < 8.1.0-1 +# We no longer build Sphinx-generated PDF documentation. Beginning with 8.2.3, +# this would require patching out sphinxawesome-theme from docs/conf.py. It’s +# possible but tedious. +Obsoletes: snakemake-doc < 8.2.1-2 %if %{with tests} # See test-environment.yml for a listing of test dependencies, along with a lot @@ -83,23 +80,6 @@ BuildRequires: %{py3_dist google-cloud-storage} %description %_description -%package doc - -Summary: %{summary} - -BuildArch: noarch - -%if %{with doc_pdf} -BuildRequires: make -BuildRequires: python3-sphinx-latex -BuildRequires: latexmk -BuildRequires: tex-xetex-bin -BuildRequires: /usr/bin/xindy -BuildRequires: /usr/bin/rsvg-convert -%endif - -%description doc %_description - # No metapackage for “pep” extra because the following are not packaged: # - python3-eido # - python3-peppy @@ -116,11 +96,6 @@ sed -r -i '1{/^#!/d}' \ # Fix calls to unversioned Python interpreter sed -r -i 's@"python"@"%{python3}"@g' tests/test_linting.py sed -r -i 's@python -m@"%{python3} -m@g' tests/tests.py -# The sphinxcontrib-napoleon extension is now part of Sphinx. -# The lutra HTML theme is not needed since we do not generate HTML docs. -sed -r -i 's/^(sphinxcontrib-napoleon|lutra)/# &/' docs/requirements.txt -# Since pdflatex cannot handle Unicode inputs in general: -echo "latex_engine = 'xelatex'" >> docs/conf.py # Copy and rename nano and vim extensions readmes for use in the main # documentation directory. for editor in nano vim @@ -130,23 +105,10 @@ done %generate_buildrequires # Generate BR’s for all supported extras to ensure they do not FTI -%pyproject_buildrequires -x reports,messaging,google-cloud,azure %{?with_doc_pdf:docs/requirements.txt} +%pyproject_buildrequires -x reports,messaging,google-cloud,azure %build %pyproject_wheel -%if %{with doc_pdf} -# Cannot use SVG images when building PDF documentation; convert to PDFs -find docs -type f -name '*.svg' | - while read -r fn - do - rsvg-convert --format=pdf \ - --output="$(dirname "${fn}")/$(basename "${fn}" .svg).pdf" "${fn}" - done -find docs/executor_tutorial -type f -exec \ - gawk '/\.svg/ { print FILENAME; nextfile }' '{}' '+' | - xargs -r -t sed -r -i 's/(image::.*)\.svg/\1\.pdf/' -PYTHONPATH="${PWD}" %make_build -C docs latexpdf SPHINXOPTS='%{?_smp_mflags}' -%endif %install %pyproject_install @@ -207,6 +169,11 @@ ignore="${ignore-} --ignore-glob=tests/test_conda_python_3_7_script/*" %endif %files -f %{pyproject_files} +%doc CHANGELOG.md +%doc README.md +%doc README-nano.md +%doc README-vim.md + %{_bindir}/snakemake %{_mandir}/man1/snakemake.1* @@ -219,16 +186,5 @@ ignore="${ignore-} --ignore-glob=tests/test_conda_python_3_7_script/*" %{_datadir}/vim/vimfiles/ftplugin/snakemake/ %{_datadir}/vim/vimfiles/syntax/snakemake.vim -%files doc -%license LICENSE.md -%doc CHANGELOG.md -%doc CODE_OF_CONDUCT.md -%doc README.md -%doc README-nano.md -%doc README-vim.md -%if %{with doc_pdf} -%doc docs/_build/latex/Snakemake.pdf -%endif - %changelog %autochangelog From 7b83604f877952f0b66b2f30f583403cab4537fe Mon Sep 17 00:00:00 2001 From: Packit Date: Sun, 21 Jan 2024 02:04:38 +0000 Subject: [PATCH 006/109] [packit] 8.2.3 upstream release - Resolves rhbz#2259386 Upstream tag: v8.2.3 Upstream commit: 4195a322 --- .gitignore | 1 + README.packit | 2 +- snakemake.spec | 2 +- sources | 2 +- 4 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 5534294..4c79a13 100644 --- a/.gitignore +++ b/.gitignore @@ -31,3 +31,4 @@ /snakemake-7.32.4.tar.gz /snakemake-8.1.2.tar.gz /snakemake-8.2.1.tar.gz +/snakemake-8.2.3.tar.gz diff --git a/README.packit b/README.packit index d529207..115b422 100644 --- a/README.packit +++ b/README.packit @@ -1,3 +1,3 @@ This repository is maintained by packit. https://packit.dev/ -The file was generated using packit 0.87.1. +The file was generated using packit 0.88.0.post1.dev4+gc070191b. diff --git a/snakemake.spec b/snakemake.spec index d6b0a05..765df43 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -30,7 +30,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.2.1 +Version: 8.2.3 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 684641b..2f9789b 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.2.1.tar.gz) = aa53a94a1afac0b253c4b6aaab051431b28904b58e381a4c71d731d4c13320df79a5a1476299e1d4397dba86d2040b2248376c5142871effc5e9347552687b7a +SHA512 (snakemake-8.2.3.tar.gz) = 49a12e3848c4a6ccd77abec204f6dfbc9239dc8203bf7a3d688c3ed3f06da7a5e5861aa2e38b71f83546390cc1e85dbea4e345355e1aec52453db03aeee3e31d From 88fd6314adf2d6092e8a7a011d3a10cd3035b23c Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 27 Jan 2024 03:42:49 +0000 Subject: [PATCH 007/109] Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild From f7239d970ec28f299dccf601bce5f5296f12747b Mon Sep 17 00:00:00 2001 From: Packit Date: Wed, 24 Jan 2024 03:09:19 +0000 Subject: [PATCH 008/109] [packit] 8.4.3 upstream release - Resolves rhbz#2259983 Upstream tag: v8.4.3 Upstream commit: 5a3ff9ef --- .gitignore | 1 + 2670.patch | 22 ++++++++++++++++++++++ README.packit | 2 +- snakemake.spec | 6 +++++- sources | 2 +- 5 files changed, 30 insertions(+), 3 deletions(-) create mode 100644 2670.patch diff --git a/.gitignore b/.gitignore index 4c79a13..0b8e96b 100644 --- a/.gitignore +++ b/.gitignore @@ -32,3 +32,4 @@ /snakemake-8.1.2.tar.gz /snakemake-8.2.1.tar.gz /snakemake-8.2.3.tar.gz +/snakemake-8.4.3.tar.gz diff --git a/2670.patch b/2670.patch new file mode 100644 index 0000000..c6653d8 --- /dev/null +++ b/2670.patch @@ -0,0 +1,22 @@ +From 22a1658069f5b37d2a4585d46fa911428319545b Mon Sep 17 00:00:00 2001 +From: "Benjamin A. Beasley" +Date: Sat, 3 Feb 2024 08:29:54 -0500 +Subject: [PATCH] Fix a SyntaxWarning (non-raw regex pattern string) + +--- + snakemake/ioutils.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/snakemake/ioutils.py b/snakemake/ioutils.py +index a91b607cb..5aad7ea4b 100644 +--- a/snakemake/ioutils.py ++++ b/snakemake/ioutils.py +@@ -12,7 +12,7 @@ + + + class WildcardHandlerBase(ABC): +- fmt_regex = re.compile("\{(?P[^\{][^\{\}]+)\}[^\}]") ++ fmt_regex = re.compile(r"\{(?P[^\{][^\{\}]+)\}[^\}]") + + def __init__(self, func, **namespace): + self.func = func diff --git a/README.packit b/README.packit index 115b422..9a6e969 100644 --- a/README.packit +++ b/README.packit @@ -1,3 +1,3 @@ This repository is maintained by packit. https://packit.dev/ -The file was generated using packit 0.88.0.post1.dev4+gc070191b. +The file was generated using packit 0.90.0.post1.dev3+g3d9551d2. diff --git a/snakemake.spec b/snakemake.spec index 765df43..8dc78da 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -30,7 +30,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.2.3 +Version: 8.4.3 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses @@ -45,6 +45,10 @@ License: MIT AND Unlicense URL: https://snakemake.readthedocs.io/en/stable/index.html Source: https://github.com/snakemake/snakemake/archive/v%{version}/snakemake-%{version}.tar.gz +# Fix a SyntaxWarning (non-raw regex pattern string) +# https://github.com/snakemake/snakemake/pull/2670 +Patch: https://github.com/snakemake/snakemake/pull/2670.patch + BuildArch: noarch BuildRequires: python3-devel diff --git a/sources b/sources index 2f9789b..5a00d82 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.2.3.tar.gz) = 49a12e3848c4a6ccd77abec204f6dfbc9239dc8203bf7a3d688c3ed3f06da7a5e5861aa2e38b71f83546390cc1e85dbea4e345355e1aec52453db03aeee3e31d +SHA512 (snakemake-8.4.3.tar.gz) = 3943d2eb90f95f12f2965457495e5357223704eb6db5133fefe69dfbee689cf639db20a8c49ccb45aa786afb36aa8ce7bb9d4c07d6ace8fa9fe20db4c51586c6 From 760510a64ae9a526935219fe92066170026867ab Mon Sep 17 00:00:00 2001 From: Packit Date: Mon, 5 Feb 2024 18:19:01 +0000 Subject: [PATCH 009/109] [packit] 8.4.4 upstream release - Resolves rhbz#2262847 Upstream tag: v8.4.4 Upstream commit: 805dd0c5 --- .gitignore | 1 + 2670.patch | 22 ---------------------- README.packit | 2 +- snakemake.spec | 6 +----- sources | 2 +- 5 files changed, 4 insertions(+), 29 deletions(-) delete mode 100644 2670.patch diff --git a/.gitignore b/.gitignore index 0b8e96b..5575c1c 100644 --- a/.gitignore +++ b/.gitignore @@ -33,3 +33,4 @@ /snakemake-8.2.1.tar.gz /snakemake-8.2.3.tar.gz /snakemake-8.4.3.tar.gz +/snakemake-8.4.4.tar.gz diff --git a/2670.patch b/2670.patch deleted file mode 100644 index c6653d8..0000000 --- a/2670.patch +++ /dev/null @@ -1,22 +0,0 @@ -From 22a1658069f5b37d2a4585d46fa911428319545b Mon Sep 17 00:00:00 2001 -From: "Benjamin A. Beasley" -Date: Sat, 3 Feb 2024 08:29:54 -0500 -Subject: [PATCH] Fix a SyntaxWarning (non-raw regex pattern string) - ---- - snakemake/ioutils.py | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/snakemake/ioutils.py b/snakemake/ioutils.py -index a91b607cb..5aad7ea4b 100644 ---- a/snakemake/ioutils.py -+++ b/snakemake/ioutils.py -@@ -12,7 +12,7 @@ - - - class WildcardHandlerBase(ABC): -- fmt_regex = re.compile("\{(?P[^\{][^\{\}]+)\}[^\}]") -+ fmt_regex = re.compile(r"\{(?P[^\{][^\{\}]+)\}[^\}]") - - def __init__(self, func, **namespace): - self.func = func diff --git a/README.packit b/README.packit index 9a6e969..29cc7d8 100644 --- a/README.packit +++ b/README.packit @@ -1,3 +1,3 @@ This repository is maintained by packit. https://packit.dev/ -The file was generated using packit 0.90.0.post1.dev3+g3d9551d2. +The file was generated using packit 0.90.0.post1.dev9+g1f0325d1. diff --git a/snakemake.spec b/snakemake.spec index 8dc78da..cf945f9 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -30,7 +30,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.4.3 +Version: 8.4.4 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses @@ -45,10 +45,6 @@ License: MIT AND Unlicense URL: https://snakemake.readthedocs.io/en/stable/index.html Source: https://github.com/snakemake/snakemake/archive/v%{version}/snakemake-%{version}.tar.gz -# Fix a SyntaxWarning (non-raw regex pattern string) -# https://github.com/snakemake/snakemake/pull/2670 -Patch: https://github.com/snakemake/snakemake/pull/2670.patch - BuildArch: noarch BuildRequires: python3-devel diff --git a/sources b/sources index 5a00d82..3c13e2a 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.4.3.tar.gz) = 3943d2eb90f95f12f2965457495e5357223704eb6db5133fefe69dfbee689cf639db20a8c49ccb45aa786afb36aa8ce7bb9d4c07d6ace8fa9fe20db4c51586c6 +SHA512 (snakemake-8.4.4.tar.gz) = f0281b422b095f58a17b0ae9d4a453fd81a8f046d13a1b617f2a6522dc3e7c90137af423857a1caba9ad4516a344517f53d1d455abfb35bfb0ba484198588268 From 5ec48c585dac92f847fd3828d9a86fb288f9e48c Mon Sep 17 00:00:00 2001 From: Packit Date: Wed, 7 Feb 2024 03:33:29 +0000 Subject: [PATCH 010/109] [packit] 8.4.6 upstream release - Resolves rhbz#2263115 Upstream tag: v8.4.6 Upstream commit: 6f345d31 --- .gitignore | 1 + snakemake.spec | 2 +- sources | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.gitignore b/.gitignore index 5575c1c..7a27d9c 100644 --- a/.gitignore +++ b/.gitignore @@ -34,3 +34,4 @@ /snakemake-8.2.3.tar.gz /snakemake-8.4.3.tar.gz /snakemake-8.4.4.tar.gz +/snakemake-8.4.6.tar.gz diff --git a/snakemake.spec b/snakemake.spec index cf945f9..2a9650e 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -30,7 +30,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.4.4 +Version: 8.4.6 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 3c13e2a..78af703 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.4.4.tar.gz) = f0281b422b095f58a17b0ae9d4a453fd81a8f046d13a1b617f2a6522dc3e7c90137af423857a1caba9ad4516a344517f53d1d455abfb35bfb0ba484198588268 +SHA512 (snakemake-8.4.6.tar.gz) = f65f512066c9cd44ba0e86140cdda323760b4b4165ae4bc0f0bb9b492543f1c71f838b278aa75f63709f63589700119574edc9c6cba683a0d1dd651def0762aa From 6c8408437d061c2036b629a701653d4c88d0d0b4 Mon Sep 17 00:00:00 2001 From: Packit Date: Thu, 8 Feb 2024 17:32:03 +0000 Subject: [PATCH 011/109] [packit] 8.4.7 upstream release - Resolves rhbz#2263390 Upstream tag: v8.4.7 Upstream commit: 42b50a60 --- .gitignore | 1 + snakemake.spec | 2 +- sources | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.gitignore b/.gitignore index 7a27d9c..e74ed0c 100644 --- a/.gitignore +++ b/.gitignore @@ -35,3 +35,4 @@ /snakemake-8.4.3.tar.gz /snakemake-8.4.4.tar.gz /snakemake-8.4.6.tar.gz +/snakemake-8.4.7.tar.gz diff --git a/snakemake.spec b/snakemake.spec index 2a9650e..d92116c 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -30,7 +30,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.4.6 +Version: 8.4.7 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 78af703..b615751 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.4.6.tar.gz) = f65f512066c9cd44ba0e86140cdda323760b4b4165ae4bc0f0bb9b492543f1c71f838b278aa75f63709f63589700119574edc9c6cba683a0d1dd651def0762aa +SHA512 (snakemake-8.4.7.tar.gz) = b73426b4262e8087d1c8b7f95e9c9aa9e7d2eafcec3e892edf2421be7859582e2a53b31ad0fcbcb1fbc17c974ab3ae130c485fb2b4f5bf0713620f17ca96a271 From 802b30a009b07be3f5ee16b6840e226be4233aba Mon Sep 17 00:00:00 2001 From: Packit Date: Fri, 9 Feb 2024 18:30:04 +0000 Subject: [PATCH 012/109] [packit] 8.4.8 upstream release - Resolves rhbz#2263559 Upstream tag: v8.4.8 Upstream commit: 74db8e59 --- .gitignore | 1 + snakemake.spec | 2 +- sources | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.gitignore b/.gitignore index e74ed0c..dbc7ede 100644 --- a/.gitignore +++ b/.gitignore @@ -36,3 +36,4 @@ /snakemake-8.4.4.tar.gz /snakemake-8.4.6.tar.gz /snakemake-8.4.7.tar.gz +/snakemake-8.4.8.tar.gz diff --git a/snakemake.spec b/snakemake.spec index d92116c..b3401f9 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -30,7 +30,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.4.7 +Version: 8.4.8 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index b615751..60b93f0 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.4.7.tar.gz) = b73426b4262e8087d1c8b7f95e9c9aa9e7d2eafcec3e892edf2421be7859582e2a53b31ad0fcbcb1fbc17c974ab3ae130c485fb2b4f5bf0713620f17ca96a271 +SHA512 (snakemake-8.4.8.tar.gz) = c0f4ac8289a0586ff3e81a4358452086bc7672305ee403353eac4e9f60e129ee18d15ea35c824bafb07ace3b079c6704e4038e5e4a7d818ee1ca2f5e5a3cf251 From aa829c6cb5fb44e5597d1a70cc35c66a14ab18bc Mon Sep 17 00:00:00 2001 From: Packit Date: Sun, 18 Feb 2024 23:38:10 +0000 Subject: [PATCH 013/109] [packit] 8.4.9 upstream release - Resolves rhbz#2263559 Upstream tag: v8.4.9 Upstream commit: 8e10bfe5 --- .gitignore | 1 + README.packit | 2 +- snakemake.spec | 2 +- sources | 2 +- 4 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index dbc7ede..91f7020 100644 --- a/.gitignore +++ b/.gitignore @@ -37,3 +37,4 @@ /snakemake-8.4.6.tar.gz /snakemake-8.4.7.tar.gz /snakemake-8.4.8.tar.gz +/snakemake-8.4.9.tar.gz diff --git a/README.packit b/README.packit index 29cc7d8..f592284 100644 --- a/README.packit +++ b/README.packit @@ -1,3 +1,3 @@ This repository is maintained by packit. https://packit.dev/ -The file was generated using packit 0.90.0.post1.dev9+g1f0325d1. +The file was generated using packit 0.91.0.post1.dev4+ge6fd4a25. diff --git a/snakemake.spec b/snakemake.spec index b3401f9..f71f33d 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -30,7 +30,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.4.8 +Version: 8.4.9 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 60b93f0..87ef744 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.4.8.tar.gz) = c0f4ac8289a0586ff3e81a4358452086bc7672305ee403353eac4e9f60e129ee18d15ea35c824bafb07ace3b079c6704e4038e5e4a7d818ee1ca2f5e5a3cf251 +SHA512 (snakemake-8.4.9.tar.gz) = 57d870ad0c6b20e61ba09c3d01be5a8c8c268c24fb5c54ba0a21a4cededd8ab3cfc526bee8b7d3831bebc030719f628fd25b7e18f8ea9894c0ae7ce31c51a709 From 78f2e112d1728cbf18fa81787f40cdec2bfff5c2 Mon Sep 17 00:00:00 2001 From: Packit Date: Tue, 20 Feb 2024 04:36:25 +0000 Subject: [PATCH 014/109] [packit] 8.4.12 upstream release - Resolves rhbz#2265048 Upstream tag: v8.4.12 Upstream commit: 0c9f681d --- .gitignore | 1 + README.packit | 2 +- snakemake.spec | 2 +- sources | 2 +- 4 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 91f7020..2bae38b 100644 --- a/.gitignore +++ b/.gitignore @@ -38,3 +38,4 @@ /snakemake-8.4.7.tar.gz /snakemake-8.4.8.tar.gz /snakemake-8.4.9.tar.gz +/snakemake-8.4.12.tar.gz diff --git a/README.packit b/README.packit index f592284..49c122d 100644 --- a/README.packit +++ b/README.packit @@ -1,3 +1,3 @@ This repository is maintained by packit. https://packit.dev/ -The file was generated using packit 0.91.0.post1.dev4+ge6fd4a25. +The file was generated using packit 0.91.0. diff --git a/snakemake.spec b/snakemake.spec index f71f33d..a9c8682 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -30,7 +30,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.4.9 +Version: 8.4.12 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 87ef744..49fdfc6 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.4.9.tar.gz) = 57d870ad0c6b20e61ba09c3d01be5a8c8c268c24fb5c54ba0a21a4cededd8ab3cfc526bee8b7d3831bebc030719f628fd25b7e18f8ea9894c0ae7ce31c51a709 +SHA512 (snakemake-8.4.12.tar.gz) = 2ae64b39834d92412217b94f33d7a44565ee3b93b4c278ad466f880818ef8f742e37ed2a9006e757ed49eee394a6a055053554db22edeafb9efdceb4f011dbf9 From a3fd96ca8c7193c0b7013eba7b95a64ca04f90cf Mon Sep 17 00:00:00 2001 From: Packit Date: Sun, 25 Feb 2024 04:28:36 +0000 Subject: [PATCH 015/109] [packit] 8.5.2 upstream release - Resolves rhbz#2265871 Upstream tag: v8.5.2 Upstream commit: 968a8721 --- .gitignore | 1 + README.packit | 2 +- snakemake.spec | 11 +++++++---- sources | 2 +- 4 files changed, 10 insertions(+), 6 deletions(-) diff --git a/.gitignore b/.gitignore index 2bae38b..5d8ac50 100644 --- a/.gitignore +++ b/.gitignore @@ -39,3 +39,4 @@ /snakemake-8.4.8.tar.gz /snakemake-8.4.9.tar.gz /snakemake-8.4.12.tar.gz +/snakemake-8.5.2.tar.gz diff --git a/README.packit b/README.packit index 49c122d..7553f6b 100644 --- a/README.packit +++ b/README.packit @@ -1,3 +1,3 @@ This repository is maintained by packit. https://packit.dev/ -The file was generated using packit 0.91.0. +The file was generated using packit 0.92.0. diff --git a/snakemake.spec b/snakemake.spec index a9c8682..d2107f0 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -1,6 +1,7 @@ # Work around a series of circular test dependencies: # -# ⬐───╮ +# python-snakemake-interface-report-plugins +# ￬￪ ⬐───╮ # snakemake → python-snakemake-interface-executor-plugins⬎ # ￪￪ │ ⬑────────────────────python-snakemake-executor-plugin-cluster-generic # ││ ↳python-snakemake-interface-storage-plugins────────────────╮ @@ -11,13 +12,15 @@ # A good build order is: # # 1. BOOTSTRAP: python-snakemake-interface-executor-plugins, -# python-snakemake-interface-storage-plugins +# python-snakemake-interface-storage-plugins, +# python-snakemake-interface-report-plugins # 2. BOOTSTRAP: snakemake # 3. python-snakemake-executor-plugin-cluster-generic, # python-snakemake-storage-plugin-http, # python-snakemake-storage-plugin-s3 # 4. snakemake, python-snakemake-interface-executor-plugins, -# python-snakemake-interface-storage-plugins +# python-snakemake-interface-storage-plugins, +# python-snakemake-interface-report-plugins %bcond bootstrap 0 %bcond tests %{without bootstrap} @@ -30,7 +33,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.4.12 +Version: 8.5.2 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 49fdfc6..27ab110 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.4.12.tar.gz) = 2ae64b39834d92412217b94f33d7a44565ee3b93b4c278ad466f880818ef8f742e37ed2a9006e757ed49eee394a6a055053554db22edeafb9efdceb4f011dbf9 +SHA512 (snakemake-8.5.2.tar.gz) = 588d69ac598f97bb752815765a2d81db90aa7fe1b5bebbea1b9277901874c30075f7f15d539f1f21f12d484ebeb01ad011d30c3f677e5961af199e071c8aba07 From cc4908806b68c0a63f4d2c677e456a8925b3d57f Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Mon, 26 Feb 2024 09:34:23 -0500 Subject: [PATCH 016/109] Update to 8.5.3 --- .gitignore | 1 + snakemake.spec | 2 +- sources | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.gitignore b/.gitignore index 5d8ac50..494ecb0 100644 --- a/.gitignore +++ b/.gitignore @@ -40,3 +40,4 @@ /snakemake-8.4.9.tar.gz /snakemake-8.4.12.tar.gz /snakemake-8.5.2.tar.gz +/snakemake-8.5.3.tar.gz diff --git a/snakemake.spec b/snakemake.spec index d2107f0..ce4347f 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -33,7 +33,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.5.2 +Version: 8.5.3 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 27ab110..9a17d8a 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.5.2.tar.gz) = 588d69ac598f97bb752815765a2d81db90aa7fe1b5bebbea1b9277901874c30075f7f15d539f1f21f12d484ebeb01ad011d30c3f677e5961af199e071c8aba07 +SHA512 (snakemake-8.5.3.tar.gz) = bbe53078928bf71abbe6ad1050aae3a080d614324cde980c5d8cce1a31642d37da1581e538e4f80b6f2013b3eaa62739ea6261aafe13b136f86fbbc9c0dec5bb From 55702dd5c4ae1fc135c3a6fac01c4aae409b662e Mon Sep 17 00:00:00 2001 From: Packit Date: Thu, 7 Mar 2024 07:01:04 +0000 Subject: [PATCH 017/109] [packit] 8.5.4 upstream release - Resolves rhbz#2268374 Upstream tag: v8.5.4 Upstream commit: dfd76c3a --- .gitignore | 1 + README.packit | 2 +- snakemake.spec | 2 +- sources | 2 +- 4 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 494ecb0..3fb9cac 100644 --- a/.gitignore +++ b/.gitignore @@ -41,3 +41,4 @@ /snakemake-8.4.12.tar.gz /snakemake-8.5.2.tar.gz /snakemake-8.5.3.tar.gz +/snakemake-8.5.4.tar.gz diff --git a/README.packit b/README.packit index 7553f6b..58aeb5d 100644 --- a/README.packit +++ b/README.packit @@ -1,3 +1,3 @@ This repository is maintained by packit. https://packit.dev/ -The file was generated using packit 0.92.0. +The file was generated using packit 0.93.0.post1.dev3+ge6195b47. diff --git a/snakemake.spec b/snakemake.spec index ce4347f..1933f9d 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -33,7 +33,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.5.3 +Version: 8.5.4 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 9a17d8a..9e1b97d 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.5.3.tar.gz) = bbe53078928bf71abbe6ad1050aae3a080d614324cde980c5d8cce1a31642d37da1581e538e4f80b6f2013b3eaa62739ea6261aafe13b136f86fbbc9c0dec5bb +SHA512 (snakemake-8.5.4.tar.gz) = 23030003cebfb669da20676f8844af8c5102d4643acab3d371e1e543350e6a8c5bf2f16eeafe0ee5c8e8e97bfb2b32fa5383e90c7d8b630dac6017e5aabb976f From 24c4fd9cf9a8a6144c4c94f8a4a06f666763104f Mon Sep 17 00:00:00 2001 From: Packit Date: Fri, 8 Mar 2024 11:48:45 +0000 Subject: [PATCH 018/109] [packit] 8.5.5 upstream release - Resolves rhbz#2268576 Upstream tag: v8.5.5 Upstream commit: e0a6be4f --- .gitignore | 1 + snakemake.spec | 2 +- sources | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.gitignore b/.gitignore index 3fb9cac..8a7ffae 100644 --- a/.gitignore +++ b/.gitignore @@ -42,3 +42,4 @@ /snakemake-8.5.2.tar.gz /snakemake-8.5.3.tar.gz /snakemake-8.5.4.tar.gz +/snakemake-8.5.5.tar.gz diff --git a/snakemake.spec b/snakemake.spec index 1933f9d..e44fefd 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -33,7 +33,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.5.4 +Version: 8.5.5 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 9e1b97d..98303d9 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.5.4.tar.gz) = 23030003cebfb669da20676f8844af8c5102d4643acab3d371e1e543350e6a8c5bf2f16eeafe0ee5c8e8e97bfb2b32fa5383e90c7d8b630dac6017e5aabb976f +SHA512 (snakemake-8.5.5.tar.gz) = 0f075d27d3d94edcb9d333d09b0f080b4065a184b57ddda7779cb38306da4e2bbabfe93e2b8ddeeabc19475873f4bd49cce325ce9377cc7e4cd93fbdfddc8292 From fcd08278dddd15069ad4d782a1f3074915fd3f76 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Mon, 11 Mar 2024 12:05:38 -0400 Subject: [PATCH 019/109] Patch to allow smart_open 7.x --- 2745.patch | 23 +++++++++++++++++++++++ snakemake.spec | 4 ++++ 2 files changed, 27 insertions(+) create mode 100644 2745.patch diff --git a/2745.patch b/2745.patch new file mode 100644 index 0000000..7d980ac --- /dev/null +++ b/2745.patch @@ -0,0 +1,23 @@ +From 9fdb6ed5ba3991e79d10fa28a003d3efb934ab61 Mon Sep 17 00:00:00 2001 +From: "Benjamin A. Beasley" +Date: Mon, 11 Mar 2024 11:50:37 -0400 +Subject: [PATCH] Allow smart_open 7.x + +https://github.com/piskvorky/smart_open/releases/tag/v7.0.1 +--- + setup.cfg | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/setup.cfg b/setup.cfg +index 82a58c8fc..85836f7d8 100644 +--- a/setup.cfg ++++ b/setup.cfg +@@ -50,7 +50,7 @@ install_requires = + pyyaml + requests >=2.8.1,<3.0 + reretry +- smart-open >=3.0,<7.0 ++ smart-open >=3.0,<8.0 + snakemake-interface-executor-plugins >=8.1.3,<9.0 + snakemake-interface-common >=1.17.0,<2.0 + snakemake-interface-storage-plugins >=3.1.0,<4.0 diff --git a/snakemake.spec b/snakemake.spec index e44fefd..08240cf 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -48,6 +48,10 @@ License: MIT AND Unlicense URL: https://snakemake.readthedocs.io/en/stable/index.html Source: https://github.com/snakemake/snakemake/archive/v%{version}/snakemake-%{version}.tar.gz +# feat: Allow smart_open 7.x +# https://github.com/snakemake/snakemake/pull/2745 +Patch: https://github.com/snakemake/snakemake/pull/2745.patch + BuildArch: noarch BuildRequires: python3-devel From 203f05dc9e94870aff0fca129db4f44cb6017a53 Mon Sep 17 00:00:00 2001 From: Packit Date: Mon, 11 Mar 2024 23:08:54 +0000 Subject: [PATCH 020/109] [packit] 8.6.0 upstream release (bootstrap) - Resolves rhbz#2269081 Upstream tag: v8.6.0 Upstream commit: 11e13944 --- .gitignore | 1 + 2745.patch | 6 +++--- README.packit | 2 +- snakemake.spec | 4 ++-- sources | 2 +- 5 files changed, 8 insertions(+), 7 deletions(-) diff --git a/.gitignore b/.gitignore index 8a7ffae..9073ec1 100644 --- a/.gitignore +++ b/.gitignore @@ -43,3 +43,4 @@ /snakemake-8.5.3.tar.gz /snakemake-8.5.4.tar.gz /snakemake-8.5.5.tar.gz +/snakemake-8.6.0.tar.gz diff --git a/2745.patch b/2745.patch index 7d980ac..9797866 100644 --- a/2745.patch +++ b/2745.patch @@ -1,4 +1,4 @@ -From 9fdb6ed5ba3991e79d10fa28a003d3efb934ab61 Mon Sep 17 00:00:00 2001 +From 99a89ff7b5f65997869188b580a58bdef154a17b Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Mon, 11 Mar 2024 11:50:37 -0400 Subject: [PATCH] Allow smart_open 7.x @@ -9,7 +9,7 @@ https://github.com/piskvorky/smart_open/releases/tag/v7.0.1 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg -index 82a58c8fc..85836f7d8 100644 +index c3ffb1190..8b3ec8155 100644 --- a/setup.cfg +++ b/setup.cfg @@ -50,7 +50,7 @@ install_requires = @@ -18,6 +18,6 @@ index 82a58c8fc..85836f7d8 100644 reretry - smart-open >=3.0,<7.0 + smart-open >=3.0,<8.0 - snakemake-interface-executor-plugins >=8.1.3,<9.0 + snakemake-interface-executor-plugins >=9.0.0,<10.0 snakemake-interface-common >=1.17.0,<2.0 snakemake-interface-storage-plugins >=3.1.0,<4.0 diff --git a/README.packit b/README.packit index 58aeb5d..38c0a99 100644 --- a/README.packit +++ b/README.packit @@ -1,3 +1,3 @@ This repository is maintained by packit. https://packit.dev/ -The file was generated using packit 0.93.0.post1.dev3+ge6195b47. +The file was generated using packit 0.93.0.post1.dev5+g0048024e. diff --git a/snakemake.spec b/snakemake.spec index 08240cf..2ea2dd5 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -21,7 +21,7 @@ # 4. snakemake, python-snakemake-interface-executor-plugins, # python-snakemake-interface-storage-plugins, # python-snakemake-interface-report-plugins -%bcond bootstrap 0 +%bcond bootstrap 1 %bcond tests %{without bootstrap} %global _description %{expand: @@ -33,7 +33,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.5.5 +Version: 8.6.0 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 98303d9..e9112c0 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.5.5.tar.gz) = 0f075d27d3d94edcb9d333d09b0f080b4065a184b57ddda7779cb38306da4e2bbabfe93e2b8ddeeabc19475873f4bd49cce325ce9377cc7e4cd93fbdfddc8292 +SHA512 (snakemake-8.6.0.tar.gz) = d3c45a35950ec081366d04a72e3709cad52e49f227a1cbb7b36645fee2a721193f066056f0ed04bfdd1e52e0ba63f614916ab432d2880c784cd2d1aac8f2d6bd From e51f8eff33f4248bfbd38743a21aaff29220860d Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Tue, 12 Mar 2024 09:21:02 -0400 Subject: [PATCH 021/109] Non-bootstrap build of snakemake 8.6.0 --- snakemake.spec | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/snakemake.spec b/snakemake.spec index 2ea2dd5..f030c33 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -21,7 +21,7 @@ # 4. snakemake, python-snakemake-interface-executor-plugins, # python-snakemake-interface-storage-plugins, # python-snakemake-interface-report-plugins -%bcond bootstrap 1 +%bcond bootstrap 0 %bcond tests %{without bootstrap} %global _description %{expand: From 55bab12191ddc3909cf8954ad1ff4733f59d4d98 Mon Sep 17 00:00:00 2001 From: Packit Date: Thu, 14 Mar 2024 07:53:19 +0000 Subject: [PATCH 022/109] [packit] 8.7.0 upstream release - Resolves rhbz#2269498 Upstream tag: v8.7.0 Upstream commit: 05ee8126 --- .gitignore | 1 + snakemake.spec | 2 +- sources | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.gitignore b/.gitignore index 9073ec1..3d19e92 100644 --- a/.gitignore +++ b/.gitignore @@ -44,3 +44,4 @@ /snakemake-8.5.4.tar.gz /snakemake-8.5.5.tar.gz /snakemake-8.6.0.tar.gz +/snakemake-8.7.0.tar.gz diff --git a/snakemake.spec b/snakemake.spec index f030c33..db2073a 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -33,7 +33,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.6.0 +Version: 8.7.0 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index e9112c0..bd33809 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.6.0.tar.gz) = d3c45a35950ec081366d04a72e3709cad52e49f227a1cbb7b36645fee2a721193f066056f0ed04bfdd1e52e0ba63f614916ab432d2880c784cd2d1aac8f2d6bd +SHA512 (snakemake-8.7.0.tar.gz) = 08301d227448aadf4177ad27984da7a98407f7d117868f18daee86895cce4f3e2b1b4e6f43aa7dbc6fbb31241cdbc04f05503230bf1b4e568170689fe446e582 From 0b1c405f438e0f111188b22e94ef56c50df37fc5 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Fri, 15 Mar 2024 12:11:13 -0400 Subject: [PATCH 023/109] Update to 8.8.0 --- .gitignore | 1 + 2745.patch | 23 ----------------------- snakemake.spec | 6 +----- sources | 2 +- 4 files changed, 3 insertions(+), 29 deletions(-) delete mode 100644 2745.patch diff --git a/.gitignore b/.gitignore index 3d19e92..663b970 100644 --- a/.gitignore +++ b/.gitignore @@ -45,3 +45,4 @@ /snakemake-8.5.5.tar.gz /snakemake-8.6.0.tar.gz /snakemake-8.7.0.tar.gz +/snakemake-8.8.0.tar.gz diff --git a/2745.patch b/2745.patch deleted file mode 100644 index 9797866..0000000 --- a/2745.patch +++ /dev/null @@ -1,23 +0,0 @@ -From 99a89ff7b5f65997869188b580a58bdef154a17b Mon Sep 17 00:00:00 2001 -From: "Benjamin A. Beasley" -Date: Mon, 11 Mar 2024 11:50:37 -0400 -Subject: [PATCH] Allow smart_open 7.x - -https://github.com/piskvorky/smart_open/releases/tag/v7.0.1 ---- - setup.cfg | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/setup.cfg b/setup.cfg -index c3ffb1190..8b3ec8155 100644 ---- a/setup.cfg -+++ b/setup.cfg -@@ -50,7 +50,7 @@ install_requires = - pyyaml - requests >=2.8.1,<3.0 - reretry -- smart-open >=3.0,<7.0 -+ smart-open >=3.0,<8.0 - snakemake-interface-executor-plugins >=9.0.0,<10.0 - snakemake-interface-common >=1.17.0,<2.0 - snakemake-interface-storage-plugins >=3.1.0,<4.0 diff --git a/snakemake.spec b/snakemake.spec index db2073a..33baa38 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -33,7 +33,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.7.0 +Version: 8.8.0 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses @@ -48,10 +48,6 @@ License: MIT AND Unlicense URL: https://snakemake.readthedocs.io/en/stable/index.html Source: https://github.com/snakemake/snakemake/archive/v%{version}/snakemake-%{version}.tar.gz -# feat: Allow smart_open 7.x -# https://github.com/snakemake/snakemake/pull/2745 -Patch: https://github.com/snakemake/snakemake/pull/2745.patch - BuildArch: noarch BuildRequires: python3-devel diff --git a/sources b/sources index bd33809..bf9dca9 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.7.0.tar.gz) = 08301d227448aadf4177ad27984da7a98407f7d117868f18daee86895cce4f3e2b1b4e6f43aa7dbc6fbb31241cdbc04f05503230bf1b4e568170689fe446e582 +SHA512 (snakemake-8.8.0.tar.gz) = 1c4e6cf1a6f0579688d90bb17e30db7051392f97178703129305797bd8ace789aaf59cdbf6bd6297a54e20b9932fe315012a4284b841938400389649c67e9fe3 From d62d4b95be76bbfd4123d1f042380d2323064b12 Mon Sep 17 00:00:00 2001 From: Packit Date: Wed, 20 Mar 2024 05:49:37 +0000 Subject: [PATCH 024/109] [packit] 8.9.0 upstream release - Resolves rhbz#2270394 Upstream tag: v8.9.0 Upstream commit: 1a9515a1 --- .gitignore | 1 + README.packit | 2 +- snakemake.spec | 2 +- sources | 2 +- 4 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 663b970..7eddcc1 100644 --- a/.gitignore +++ b/.gitignore @@ -46,3 +46,4 @@ /snakemake-8.6.0.tar.gz /snakemake-8.7.0.tar.gz /snakemake-8.8.0.tar.gz +/snakemake-8.9.0.tar.gz diff --git a/README.packit b/README.packit index 38c0a99..4afa99b 100644 --- a/README.packit +++ b/README.packit @@ -1,3 +1,3 @@ This repository is maintained by packit. https://packit.dev/ -The file was generated using packit 0.93.0.post1.dev5+g0048024e. +The file was generated using packit 0.94.0.post1.dev2+g7ce7e679. diff --git a/snakemake.spec b/snakemake.spec index 33baa38..5d1c720 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -33,7 +33,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.8.0 +Version: 8.9.0 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index bf9dca9..c41d626 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.8.0.tar.gz) = 1c4e6cf1a6f0579688d90bb17e30db7051392f97178703129305797bd8ace789aaf59cdbf6bd6297a54e20b9932fe315012a4284b841938400389649c67e9fe3 +SHA512 (snakemake-8.9.0.tar.gz) = 9ccbfcd2ccd0ddb9cf5fd78fd73abb3cf426b6890a5e789e3635226d4e78650908140ce55600421f6e1f231606c42c850480600f0320f4f2c2be7b697a291f4b From da51343d520f07316088f603e2fe957b36dd609a Mon Sep 17 00:00:00 2001 From: Packit Date: Thu, 28 Mar 2024 20:48:18 +0000 Subject: [PATCH 025/109] [packit] 8.10.4 upstream release - Resolves: rhbz#2271076 Upstream tag: v8.10.4 Upstream commit: 41994827 --- .gitignore | 1 + README.packit | 2 +- snakemake.spec | 2 +- sources | 2 +- 4 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 7eddcc1..ba7f984 100644 --- a/.gitignore +++ b/.gitignore @@ -47,3 +47,4 @@ /snakemake-8.7.0.tar.gz /snakemake-8.8.0.tar.gz /snakemake-8.9.0.tar.gz +/snakemake-8.10.4.tar.gz diff --git a/README.packit b/README.packit index 4afa99b..d401b46 100644 --- a/README.packit +++ b/README.packit @@ -1,3 +1,3 @@ This repository is maintained by packit. https://packit.dev/ -The file was generated using packit 0.94.0.post1.dev2+g7ce7e679. +The file was generated using packit 0.94.0.post1.dev8+g4b1f9717. diff --git a/snakemake.spec b/snakemake.spec index 5d1c720..82d96a6 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -33,7 +33,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.9.0 +Version: 8.10.4 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index c41d626..e79c58a 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.9.0.tar.gz) = 9ccbfcd2ccd0ddb9cf5fd78fd73abb3cf426b6890a5e789e3635226d4e78650908140ce55600421f6e1f231606c42c850480600f0320f4f2c2be7b697a291f4b +SHA512 (snakemake-8.10.4.tar.gz) = 7040831a377c1f1e598770eff2090b2c01ba0b5ee6688d71e6c40d9ac5ebe03b9b49175f9ad192ff41c4e6a76b213b56a18b11032b7055d23b43d5a750ed1691 From 025292d9bc2b35cd36e111aa7560b80be7375f9f Mon Sep 17 00:00:00 2001 From: Packit Date: Thu, 4 Apr 2024 21:58:13 +0000 Subject: [PATCH 026/109] Update to 8.10.6 upstream release - Resolves: rhbz#2273536 Upstream tag: v8.10.6 Upstream commit: b3c1dd4b Commit authored by Packit automation (https://packit.dev/) --- .gitignore | 1 + README.packit | 2 +- snakemake.spec | 2 +- sources | 2 +- 4 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index ba7f984..64b843f 100644 --- a/.gitignore +++ b/.gitignore @@ -48,3 +48,4 @@ /snakemake-8.8.0.tar.gz /snakemake-8.9.0.tar.gz /snakemake-8.10.4.tar.gz +/snakemake-8.10.6.tar.gz diff --git a/README.packit b/README.packit index d401b46..67f09b6 100644 --- a/README.packit +++ b/README.packit @@ -1,3 +1,3 @@ This repository is maintained by packit. https://packit.dev/ -The file was generated using packit 0.94.0.post1.dev8+g4b1f9717. +The file was generated using packit 0.94.1.post1.dev6+g1c8e91f7. diff --git a/snakemake.spec b/snakemake.spec index 82d96a6..7b0df96 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -33,7 +33,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.10.4 +Version: 8.10.6 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index e79c58a..c9c3484 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.10.4.tar.gz) = 7040831a377c1f1e598770eff2090b2c01ba0b5ee6688d71e6c40d9ac5ebe03b9b49175f9ad192ff41c4e6a76b213b56a18b11032b7055d23b43d5a750ed1691 +SHA512 (snakemake-8.10.6.tar.gz) = 46a65dab9974b068c6efbe5d35e8b5f44f468f35bc332b25ba02d38cbb9af89f672b0c0997f4e7f3bc229b03221c89901144ee509c516bd4043eea3ec8884649 From 081b1da0656a3e68b36f559cc1d8b27d26432e92 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Thu, 28 Mar 2024 23:46:53 -0400 Subject: [PATCH 027/109] Add an rpmlintrc file [skip changelog] --- snakemake.rpmlintrc | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 snakemake.rpmlintrc diff --git a/snakemake.rpmlintrc b/snakemake.rpmlintrc new file mode 100644 index 0000000..c607fe2 --- /dev/null +++ b/snakemake.rpmlintrc @@ -0,0 +1,15 @@ +# It is normal that extras metapackages should not have documentation, or any +# files at all. +addFilter(r"\+\w+.noarch: W: no-documentation") +# These extras were removed with Snakemake 8.0 and have no equivalent +# replacements. +addFilter(r" obsolete-not-provided snakemake\+(azure|google-cloud)$") +# The -doc subpackage was removed and has no equivalent replacement. +addFilter(r" obsolete-not-provided snakemake-doc$") +# Not a spelling error +addFilter(r"spelling-error \('([Mm]etapackage)s?',") +# Some small files may incidentally have duplicate contents. Because they are +# small in size and few in number, it is not worth the spec-file complexity to +# hardlink them (which would itself trigger an rpmlint warning about +# cross-directory hardlinking). +addFilter(r"files-duplicate .*/snakemake/.*/remote/[^/]+\.py") From d2dca029b56fa4cdd8530914f1e20807aab4ff6c Mon Sep 17 00:00:00 2001 From: Packit Date: Sat, 13 Apr 2024 06:31:01 +0000 Subject: [PATCH 028/109] Update to 8.10.7 upstream release - Resolves: rhbz#2274843 Upstream tag: v8.10.7 Upstream commit: 6abd8269 Commit authored by Packit automation (https://packit.dev/) --- .gitignore | 1 + README.packit | 2 +- snakemake.spec | 2 +- sources | 2 +- 4 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 64b843f..eb5d8bc 100644 --- a/.gitignore +++ b/.gitignore @@ -49,3 +49,4 @@ /snakemake-8.9.0.tar.gz /snakemake-8.10.4.tar.gz /snakemake-8.10.6.tar.gz +/snakemake-8.10.7.tar.gz diff --git a/README.packit b/README.packit index 67f09b6..60cc823 100644 --- a/README.packit +++ b/README.packit @@ -1,3 +1,3 @@ This repository is maintained by packit. https://packit.dev/ -The file was generated using packit 0.94.1.post1.dev6+g1c8e91f7. +The file was generated using packit 0.94.2. diff --git a/snakemake.spec b/snakemake.spec index 7b0df96..b3f2cd0 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -33,7 +33,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.10.6 +Version: 8.10.7 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index c9c3484..9697843 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.10.6.tar.gz) = 46a65dab9974b068c6efbe5d35e8b5f44f468f35bc332b25ba02d38cbb9af89f672b0c0997f4e7f3bc229b03221c89901144ee509c516bd4043eea3ec8884649 +SHA512 (snakemake-8.10.7.tar.gz) = ed26217107be4f7e416f3fbb14c27f85316fc4b9b298975181e2794bd33d3220659d128f8e31da1f23024dee9efd480c170d7ba2a9155f2bbaace97727ad2a7f From 5e9b8d14d454046ce061ba1a3e0db9416f269591 Mon Sep 17 00:00:00 2001 From: Packit Date: Sat, 20 Apr 2024 12:02:30 +0000 Subject: [PATCH 029/109] Update to 8.10.8 upstream release - Resolves: rhbz#2276195 Upstream tag: v8.10.8 Upstream commit: 84658188 Commit authored by Packit automation (https://packit.dev/) --- .gitignore | 1 + snakemake.spec | 2 +- sources | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.gitignore b/.gitignore index eb5d8bc..08fe0eb 100644 --- a/.gitignore +++ b/.gitignore @@ -50,3 +50,4 @@ /snakemake-8.10.4.tar.gz /snakemake-8.10.6.tar.gz /snakemake-8.10.7.tar.gz +/snakemake-8.10.8.tar.gz diff --git a/snakemake.spec b/snakemake.spec index b3f2cd0..f33776d 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -33,7 +33,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.10.7 +Version: 8.10.8 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 9697843..b374304 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.10.7.tar.gz) = ed26217107be4f7e416f3fbb14c27f85316fc4b9b298975181e2794bd33d3220659d128f8e31da1f23024dee9efd480c170d7ba2a9155f2bbaace97727ad2a7f +SHA512 (snakemake-8.10.8.tar.gz) = a2571503f5179bb648f89ef3bb9a30bafcc2c04caa8fe9b5843f7065b9a8065872bbc78fd7bf9963f7e349a8fb8f1882d0ee792ba9e2711d463459960f46c72b From eac859e659b3264077724c122ea0f3c17a589b5a Mon Sep 17 00:00:00 2001 From: Packit Date: Thu, 25 Apr 2024 11:03:24 +0000 Subject: [PATCH 030/109] Update to 8.11.0 upstream release - Resolves: rhbz#2276195 Upstream tag: v8.11.0 Upstream commit: a988cef3 Commit authored by Packit automation (https://packit.dev/) --- .gitignore | 1 + README.packit | 2 +- snakemake.spec | 2 +- sources | 2 +- 4 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 08fe0eb..473eaa0 100644 --- a/.gitignore +++ b/.gitignore @@ -51,3 +51,4 @@ /snakemake-8.10.6.tar.gz /snakemake-8.10.7.tar.gz /snakemake-8.10.8.tar.gz +/snakemake-8.11.0.tar.gz diff --git a/README.packit b/README.packit index 60cc823..bee8d88 100644 --- a/README.packit +++ b/README.packit @@ -1,3 +1,3 @@ This repository is maintained by packit. https://packit.dev/ -The file was generated using packit 0.94.2. +The file was generated using packit 0.95.0. diff --git a/snakemake.spec b/snakemake.spec index f33776d..e75c6f1 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -33,7 +33,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.10.8 +Version: 8.11.0 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index b374304..425e166 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.10.8.tar.gz) = a2571503f5179bb648f89ef3bb9a30bafcc2c04caa8fe9b5843f7065b9a8065872bbc78fd7bf9963f7e349a8fb8f1882d0ee792ba9e2711d463459960f46c72b +SHA512 (snakemake-8.11.0.tar.gz) = 4246c5f3e60f55e3070456f0e472b582b4ff130a5a49f05a6a1d8feefccac6fa49572ea759873c12c19dfc85ce0cf2d81ec80e6e33670a5b357413396b2e9898 From d86078cae402e7e58ccae32cf1f01e13807833e6 Mon Sep 17 00:00:00 2001 From: Packit Date: Wed, 1 May 2024 13:09:57 +0000 Subject: [PATCH 031/109] Update to 8.11.1 upstream release - Resolves: rhbz#2278140 Upstream tag: v8.11.1 Upstream commit: fc70c901 Commit authored by Packit automation (https://packit.dev/) --- .gitignore | 1 + README.packit | 2 +- snakemake.spec | 2 +- sources | 2 +- 4 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 473eaa0..84d13fc 100644 --- a/.gitignore +++ b/.gitignore @@ -52,3 +52,4 @@ /snakemake-8.10.7.tar.gz /snakemake-8.10.8.tar.gz /snakemake-8.11.0.tar.gz +/snakemake-8.11.1.tar.gz diff --git a/README.packit b/README.packit index bee8d88..066b312 100644 --- a/README.packit +++ b/README.packit @@ -1,3 +1,3 @@ This repository is maintained by packit. https://packit.dev/ -The file was generated using packit 0.95.0. +The file was generated using packit 0.95.0.post1.dev8+gce6bd577. diff --git a/snakemake.spec b/snakemake.spec index e75c6f1..7d2fe46 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -33,7 +33,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.11.0 +Version: 8.11.1 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 425e166..c49b3e8 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.11.0.tar.gz) = 4246c5f3e60f55e3070456f0e472b582b4ff130a5a49f05a6a1d8feefccac6fa49572ea759873c12c19dfc85ce0cf2d81ec80e6e33670a5b357413396b2e9898 +SHA512 (snakemake-8.11.1.tar.gz) = 1180c3f82e096e6f060d507281c1569b6da7fdb26860f211aa41f00b2059eaa732e60de4d8471d0570c8ecb3bbef871a3c7a0d4564bfb2bbe598a4ad79aa6f67 From 6d711792e4d73ca02880d795b8c4b16d9da71a5c Mon Sep 17 00:00:00 2001 From: Packit Date: Sat, 4 May 2024 04:24:15 +0000 Subject: [PATCH 032/109] Update to 8.11.3 upstream release - Resolves: rhbz#2278739 Upstream tag: v8.11.3 Upstream commit: 4a4eb408 Commit authored by Packit automation (https://packit.dev/) --- .gitignore | 1 + snakemake.spec | 2 +- sources | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.gitignore b/.gitignore index 84d13fc..5da0d1b 100644 --- a/.gitignore +++ b/.gitignore @@ -53,3 +53,4 @@ /snakemake-8.10.8.tar.gz /snakemake-8.11.0.tar.gz /snakemake-8.11.1.tar.gz +/snakemake-8.11.3.tar.gz diff --git a/snakemake.spec b/snakemake.spec index 7d2fe46..46478a9 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -33,7 +33,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.11.1 +Version: 8.11.3 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index c49b3e8..249f163 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.11.1.tar.gz) = 1180c3f82e096e6f060d507281c1569b6da7fdb26860f211aa41f00b2059eaa732e60de4d8471d0570c8ecb3bbef871a3c7a0d4564bfb2bbe598a4ad79aa6f67 +SHA512 (snakemake-8.11.3.tar.gz) = c65030a64afc3b78b82aaa14c092fd06a3ec545ab718e99a950fdd09f11311e38655a0d5a8a795cbeddb2937bbc9c39692a3d8f4ddf2ead99db9c3721289cdbc From 602611c48efd6818b903288198b4d1e9955c893a Mon Sep 17 00:00:00 2001 From: Packit Date: Fri, 17 May 2024 16:03:44 +0000 Subject: [PATCH 033/109] Update to 8.11.6 upstream release - Resolves: rhbz#2280990 Upstream tag: v8.11.6 Upstream commit: 3eeecc67 Commit authored by Packit automation (https://packit.dev/) --- .gitignore | 1 + README.packit | 2 +- snakemake.spec | 2 +- sources | 2 +- 4 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 5da0d1b..b5edb99 100644 --- a/.gitignore +++ b/.gitignore @@ -54,3 +54,4 @@ /snakemake-8.11.0.tar.gz /snakemake-8.11.1.tar.gz /snakemake-8.11.3.tar.gz +/snakemake-8.11.6.tar.gz diff --git a/README.packit b/README.packit index 066b312..97de583 100644 --- a/README.packit +++ b/README.packit @@ -1,3 +1,3 @@ This repository is maintained by packit. https://packit.dev/ -The file was generated using packit 0.95.0.post1.dev8+gce6bd577. +The file was generated using packit 0.96.0.post1.dev4+gc5b1ea8e. diff --git a/snakemake.spec b/snakemake.spec index 46478a9..6215d86 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -33,7 +33,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.11.3 +Version: 8.11.6 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 249f163..00e585a 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.11.3.tar.gz) = c65030a64afc3b78b82aaa14c092fd06a3ec545ab718e99a950fdd09f11311e38655a0d5a8a795cbeddb2937bbc9c39692a3d8f4ddf2ead99db9c3721289cdbc +SHA512 (snakemake-8.11.6.tar.gz) = b250bdeccc275962337507a1e945133bd08969c6d9871ceb53d5914d8e3f406c53e57dd2c6a31bc5b92e6c6ad78f33e98e3050794cd0477bf1053c1138ced93c From 181278104723a6902a58d83cc117b595a5d92ab4 Mon Sep 17 00:00:00 2001 From: Packit Date: Mon, 27 May 2024 21:15:46 +0000 Subject: [PATCH 034/109] Update to 8.12.0 upstream release - Resolves: rhbz#2283549 Upstream tag: v8.12.0 Upstream commit: 0fe04591 Commit authored by Packit automation (https://packit.dev/) --- .gitignore | 1 + README.packit | 2 +- snakemake.spec | 2 +- sources | 2 +- 4 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index b5edb99..a148989 100644 --- a/.gitignore +++ b/.gitignore @@ -55,3 +55,4 @@ /snakemake-8.11.1.tar.gz /snakemake-8.11.3.tar.gz /snakemake-8.11.6.tar.gz +/snakemake-8.12.0.tar.gz diff --git a/README.packit b/README.packit index 97de583..2fa216c 100644 --- a/README.packit +++ b/README.packit @@ -1,3 +1,3 @@ This repository is maintained by packit. https://packit.dev/ -The file was generated using packit 0.96.0.post1.dev4+gc5b1ea8e. +The file was generated using packit 0.97.1.post1.dev4+g1268842e. diff --git a/snakemake.spec b/snakemake.spec index 6215d86..d06a4d9 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -33,7 +33,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.11.6 +Version: 8.12.0 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 00e585a..c501890 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.11.6.tar.gz) = b250bdeccc275962337507a1e945133bd08969c6d9871ceb53d5914d8e3f406c53e57dd2c6a31bc5b92e6c6ad78f33e98e3050794cd0477bf1053c1138ced93c +SHA512 (snakemake-8.12.0.tar.gz) = 11535ecbdb6a119573d8dffed2057d77ecd926b867af90d0b167a73d814adfd26b3cee24c6104f2bf4d099f6acf8ca0118250d8cf9a14d2f7d6db43448296ba6 From cd1330a4a1a96fbcd30620b71cbc6119bbd11ab6 Mon Sep 17 00:00:00 2001 From: Packit Date: Thu, 6 Jun 2024 10:39:52 +0000 Subject: [PATCH 035/109] Update to 8.13.0 upstream release - Resolves: rhbz#2290700 Upstream tag: v8.13.0 Upstream commit: 6f3669d4 Commit authored by Packit automation (https://packit.dev/) --- .gitignore | 1 + README.packit | 2 +- snakemake.spec | 2 +- sources | 2 +- 4 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index a148989..f166e79 100644 --- a/.gitignore +++ b/.gitignore @@ -56,3 +56,4 @@ /snakemake-8.11.3.tar.gz /snakemake-8.11.6.tar.gz /snakemake-8.12.0.tar.gz +/snakemake-8.13.0.tar.gz diff --git a/README.packit b/README.packit index 2fa216c..d2b528d 100644 --- a/README.packit +++ b/README.packit @@ -1,3 +1,3 @@ This repository is maintained by packit. https://packit.dev/ -The file was generated using packit 0.97.1.post1.dev4+g1268842e. +The file was generated using packit 0.97.1.post1.dev6+gc8c0314a. diff --git a/snakemake.spec b/snakemake.spec index d06a4d9..0100802 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -33,7 +33,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.12.0 +Version: 8.13.0 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index c501890..8eb490c 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.12.0.tar.gz) = 11535ecbdb6a119573d8dffed2057d77ecd926b867af90d0b167a73d814adfd26b3cee24c6104f2bf4d099f6acf8ca0118250d8cf9a14d2f7d6db43448296ba6 +SHA512 (snakemake-8.13.0.tar.gz) = 80f0f73e56e12b97e0e089b1a5b04e49e5a5ea5a2f1ad6a24cffafd1ddf8aa549432215f6a7887e3001df1f7ae14f99a0cada2bc11e06ba58f5b423fedd845dc From 8d2f3045b39adcf1935d6d79b0ba8c57ab36495c Mon Sep 17 00:00:00 2001 From: Python Maint Date: Sun, 9 Jun 2024 17:13:15 +0200 Subject: [PATCH 036/109] Bootstrap for Python 3.13 --- snakemake.spec | 1 + 1 file changed, 1 insertion(+) diff --git a/snakemake.spec b/snakemake.spec index 0100802..eb1e8af 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -1,3 +1,4 @@ +%global _with_bootstrap 1 # Work around a series of circular test dependencies: # # python-snakemake-interface-report-plugins From b146c067953992e6ffff66b4fd13bf0b719980b9 Mon Sep 17 00:00:00 2001 From: Python Maint Date: Sun, 9 Jun 2024 22:43:12 +0200 Subject: [PATCH 037/109] Rebuilt for Python 3.13 --- snakemake.spec | 1 - 1 file changed, 1 deletion(-) diff --git a/snakemake.spec b/snakemake.spec index eb1e8af..0100802 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -1,4 +1,3 @@ -%global _with_bootstrap 1 # Work around a series of circular test dependencies: # # python-snakemake-interface-report-plugins From 037c3fd10dbb7b22bae8c8a959e5e7a97b705907 Mon Sep 17 00:00:00 2001 From: Packit Date: Wed, 12 Jun 2024 19:25:59 +0000 Subject: [PATCH 038/109] Update to 8.14.0 upstream release - Resolves: rhbz#2292066 Upstream tag: v8.14.0 Upstream commit: f49d2993 Commit authored by Packit automation (https://packit.dev/) --- .gitignore | 1 + snakemake.spec | 2 +- sources | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.gitignore b/.gitignore index f166e79..3d86d9a 100644 --- a/.gitignore +++ b/.gitignore @@ -57,3 +57,4 @@ /snakemake-8.11.6.tar.gz /snakemake-8.12.0.tar.gz /snakemake-8.13.0.tar.gz +/snakemake-8.14.0.tar.gz diff --git a/snakemake.spec b/snakemake.spec index 0100802..c6c0453 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -33,7 +33,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.13.0 +Version: 8.14.0 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 8eb490c..7937648 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.13.0.tar.gz) = 80f0f73e56e12b97e0e089b1a5b04e49e5a5ea5a2f1ad6a24cffafd1ddf8aa549432215f6a7887e3001df1f7ae14f99a0cada2bc11e06ba58f5b423fedd845dc +SHA512 (snakemake-8.14.0.tar.gz) = 372b75b20b7e26a2a64e8461c6c757328884fd73db9f9ba6582e8e01ea0764ebf20cc13ab5a1815d68241a2626d7dbef8fa4a87340fdb63024bc8f1e9d93b40c From 93f4a579116f832e2485afa166e87e949fb1842f Mon Sep 17 00:00:00 2001 From: Packit Date: Fri, 5 Jul 2024 16:15:39 +0000 Subject: [PATCH 039/109] Update to 8.15.2 upstream release - Resolves: rhbz#2295978 Upstream tag: v8.15.2 Upstream commit: c707ea8d Commit authored by Packit automation (https://packit.dev/) --- .gitignore | 1 + README.packit | 2 +- snakemake.spec | 2 +- sources | 2 +- 4 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 3d86d9a..43771f5 100644 --- a/.gitignore +++ b/.gitignore @@ -58,3 +58,4 @@ /snakemake-8.12.0.tar.gz /snakemake-8.13.0.tar.gz /snakemake-8.14.0.tar.gz +/snakemake-8.15.2.tar.gz diff --git a/README.packit b/README.packit index d2b528d..f2be23e 100644 --- a/README.packit +++ b/README.packit @@ -1,3 +1,3 @@ This repository is maintained by packit. https://packit.dev/ -The file was generated using packit 0.97.1.post1.dev6+gc8c0314a. +The file was generated using packit 0.97.3.post1.dev7+g1954e49a. diff --git a/snakemake.spec b/snakemake.spec index c6c0453..399e8f4 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -33,7 +33,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.14.0 +Version: 8.15.2 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 7937648..8be8c00 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.14.0.tar.gz) = 372b75b20b7e26a2a64e8461c6c757328884fd73db9f9ba6582e8e01ea0764ebf20cc13ab5a1815d68241a2626d7dbef8fa4a87340fdb63024bc8f1e9d93b40c +SHA512 (snakemake-8.15.2.tar.gz) = 8f6165664fe238cfa5b74013795a1640e473f1b07ff6de9187ef4a6857a90aa515f4b9bee3980ed247a1894a76ebb467a960024893091314f61e4051e13aad4c From 7c2af27c4e8d496583abfdc855bac738a4fa485e Mon Sep 17 00:00:00 2001 From: Packit Date: Wed, 10 Jul 2024 12:51:31 +0000 Subject: [PATCH 040/109] Update to 8.16.0 upstream release - Resolves: rhbz#2297081 Upstream tag: v8.16.0 Upstream commit: 838b2fce Commit authored by Packit automation (https://packit.dev/) --- .gitignore | 1 + README.packit | 2 +- snakemake.spec | 6 +++++- sources | 2 +- 4 files changed, 8 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 43771f5..08917b6 100644 --- a/.gitignore +++ b/.gitignore @@ -59,3 +59,4 @@ /snakemake-8.13.0.tar.gz /snakemake-8.14.0.tar.gz /snakemake-8.15.2.tar.gz +/snakemake-8.16.0.tar.gz diff --git a/README.packit b/README.packit index f2be23e..2499381 100644 --- a/README.packit +++ b/README.packit @@ -1,3 +1,3 @@ This repository is maintained by packit. https://packit.dev/ -The file was generated using packit 0.97.3.post1.dev7+g1954e49a. +The file was generated using packit 0.98.0. diff --git a/snakemake.spec b/snakemake.spec index 399e8f4..57b8a18 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -33,7 +33,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.15.2 +Version: 8.16.0 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses @@ -168,6 +168,10 @@ k="${k-}${k+ and }not test_deploy_sources" # Plus, this would add an unwanted BuildRequires on %%{py3_dist Pillow}. ignore="${ignore-} --ignore-glob=tests/test_conda_python_3_7_script/*" +# Error collecting tests in tests/test_script_py/scripts/test_explicit_import.py +# https://github.com/snakemake/snakemake/issues/2961 +ignore="${ignore-} --ignore=tests/test_script_py/scripts/test_explicit_import.py" + %pytest -v -k "${k-}" ${ignore-} %endif diff --git a/sources b/sources index 8be8c00..fcc662e 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.15.2.tar.gz) = 8f6165664fe238cfa5b74013795a1640e473f1b07ff6de9187ef4a6857a90aa515f4b9bee3980ed247a1894a76ebb467a960024893091314f61e4051e13aad4c +SHA512 (snakemake-8.16.0.tar.gz) = 29b6ba6da5dbbd347dee45114b949c976973555c9234f8a150dcd83e4af1638c1773590320bc44284cf20ea445efb377dcf9199921ed2b4d62bad3a60a41af3c From 8fd651c4ad8d26dc3fa85501230ade874ffc84ab Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Tue, 16 Jul 2024 10:15:21 -0400 Subject: [PATCH 041/109] Patch for pulp 2.8.0 --- snakemake-7.32.4-pulp-2.8.patch | 12 ++++++++++++ snakemake.spec | 6 ++++++ 2 files changed, 18 insertions(+) create mode 100644 snakemake-7.32.4-pulp-2.8.patch diff --git a/snakemake-7.32.4-pulp-2.8.patch b/snakemake-7.32.4-pulp-2.8.patch new file mode 100644 index 0000000..f26dd34 --- /dev/null +++ b/snakemake-7.32.4-pulp-2.8.patch @@ -0,0 +1,12 @@ +diff -Naur snakemake-7.32.4-original/snakemake/__init__.py snakemake-7.32.4/snakemake/__init__.py +--- snakemake-7.32.4-original/snakemake/__init__.py 2023-09-18 10:42:36.000000000 -0400 ++++ snakemake-7.32.4/snakemake/__init__.py 2024-07-16 10:12:09.542270257 -0400 +@@ -1604,7 +1604,7 @@ + try: + import pulp + +- lp_solvers = pulp.list_solvers(onlyAvailable=True) ++ lp_solvers = pulp.listSolvers(onlyAvailable=True) + except ImportError: + # Dummy list for the case that pulp is not available + # This only happened when building docs. diff --git a/snakemake.spec b/snakemake.spec index 46fd73f..baadeeb 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -32,6 +32,9 @@ BuildArch: noarch # Since we build the docs as a PDF, we can’t include an animated GIF demo. # Patch out the image reference and the text referring to it. Patch: snakemake-7.11.0-docs-no-animated-demo.patch +# Fix compatibility with python-pulp 2.8.0 +# Downstream-only since snakemake 7.x is no longer developed, and 8.x is OK +Patch: snakemake-7.32.4-pulp-2.8.patch BuildRequires: python3-devel @@ -42,6 +45,9 @@ Requires: vim-filesystem Provides: vim-snakemake = %{version}-%{release} +# The patch for pulp 2.8 is not backwards-compatible with 2.7. +Requires: (%{py3_dist pulp} >= 2.8 if %{py3_dist pulp}) + %if %{with tests} # See test-environment.yml for a listing of test dependencies, along with a lot # of other cruft. From 9eee5a00ac4654880d736c8a2e1bea0ec778303d Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 20 Jul 2024 05:56:20 +0000 Subject: [PATCH 042/109] Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild From c4f747fd42ef7e59fd9f717c2c3f36809dc5dc55 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Thu, 1 Aug 2024 15:04:10 -0400 Subject: [PATCH 043/109] Rely on python-unversioned-command - This seems to be the best compromise around portable remote execution --- snakemake.spec | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/snakemake.spec b/snakemake.spec index 57b8a18..6aa7ecc 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -54,6 +54,15 @@ BuildRequires: python3-devel 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 @@ -96,9 +105,7 @@ BuildRequires: %{py3_dist google-cloud-storage} sed -r -i '1{/^#!/d}' \ snakemake/executors/jobscript.sh \ snakemake/executors/google_lifesciences_helper.py -# Fix calls to unversioned Python interpreter -sed -r -i 's@"python"@"%{python3}"@g' tests/test_linting.py -sed -r -i 's@python -m@"%{python3} -m@g' tests/tests.py + # Copy and rename nano and vim extensions readmes for use in the main # documentation directory. for editor in nano vim From 2100ec62b6af175996f5057b739915ac8d8855d9 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Thu, 1 Aug 2024 12:44:53 -0400 Subject: [PATCH 044/109] Run tests the way upstream expects - The result is that we run many more tests --- snakemake.rpmlintrc | 2 + snakemake.spec | 162 +++++++++++++++++++++++++++++++++++++------- 2 files changed, 138 insertions(+), 26 deletions(-) diff --git a/snakemake.rpmlintrc b/snakemake.rpmlintrc index c607fe2..4a4b850 100644 --- a/snakemake.rpmlintrc +++ b/snakemake.rpmlintrc @@ -13,3 +13,5 @@ addFilter(r"spelling-error \('([Mm]etapackage)s?',") # hardlink them (which would itself trigger an rpmlint warning about # cross-directory hardlinking). addFilter(r"files-duplicate .*/snakemake/.*/remote/[^/]+\.py") +# This is, unfortunately, intentional. See the comments in the spec file. +addFilter(r" python-leftover-require python-unversioned-command$") diff --git a/snakemake.spec b/snakemake.spec index 6aa7ecc..b19328e 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -3,11 +3,12 @@ # 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-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: # @@ -17,12 +18,19 @@ # 2. BOOTSTRAP: snakemake # 3. python-snakemake-executor-plugin-cluster-generic, # python-snakemake-storage-plugin-http, -# python-snakemake-storage-plugin-s3 +# python-snakemake-storage-plugin-s3, +# python-snakemake-storage-plugin-fs # 4. snakemake, python-snakemake-interface-executor-plugins, # python-snakemake-interface-storage-plugins, # python-snakemake-interface-report-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 +# Run tests that require conda? +# https://bugzilla.redhat.com/show_bug.cgi?id=2300602 +%bcond conda_tests %{expr:!0%{?fc41}} %global _description %{expand: The Snakemake workflow management system is a tool to create reproducible and @@ -77,12 +85,30 @@ Obsoletes: snakemake+google-cloud < 8.1.0-1 Obsoletes: snakemake-doc < 8.2.1-2 %if %{with tests} +# For several tests (either apptainer or singularity-ce should work): +BuildRequires: (apptainer or singularity-ce) +%if %{with conda_tests} +# For several tests +BuildRequires: conda +%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 + # 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 @@ -156,30 +182,114 @@ find '%{buildroot}%{_datadir}/vim/vimfiles' \ %pyproject_check_import -e '*.tests*' -e 'snakemake.executors.flux' %if %{with tests} -# Needs a network connection: -ignore="${ignore-} --ignore-glob=tests/test_google_lifesciences/*" +%if %{without network_tests} +# The following require network access (and pass if it is available). +k="${k-}${k+ and }not test_ancient" +k="${k-}${k+ and }not test_containerized" +k="${k-}${k+ and }not test_default_storage" +k="${k-}${k+ and }not test_default_storage_local_job" +k="${k-}${k+ and }not test_github_issue78" +k="${k-}${k+ and }not test_issue1083" +k="${k-}${k+ and }not test_load_metawrapper" +k="${k-}${k+ and }not test_module_complex" +k="${k-}${k+ and }not test_module_complex2" +k="${k-}${k+ and }not test_module_report" +k="${k-}${k+ and }not test_module_with_script" +k="${k-}${k+ and }not test_modules_meta_wrapper" +k="${k-}${k+ and }not test_modules_prefix" +k="${k-}${k+ and }not test_output_file_cache_storage" +k="${k-}${k+ and }not test_report" +k="${k-}${k+ and }not test_report_dir" +k="${k-}${k+ and }not test_report_display_code" +k="${k-}${k+ and }not test_report_zip" +k="${k-}${k+ and }not test_rule_inheritance_globals" +k="${k-}${k+ and }not test_storage" +%endif -# Needs a network connection (plus, there are some unresolved -# unversioned-python-command issues which we hope are confined to the test -# code): -k="${k-}${k+ and }not test_deploy_sources" +# This requires network access, and also fails mysteriously, without a clear +# error message. Since the test involves a container, we assume there are a lot +# of things that could be going on that don’t reflect real problems. +k="${k-}${k+ and }not test_shell_exec" -# ______ ERROR collecting tests/test_conda_python_script/test_script.py ______ -# import file mismatch: -# imported module 'test_script' has this __file__ attribute: -# /builddir/build/BUILD/snakemake-7.31.1/tests/test_conda_python_3_7_script/test_script.py -# which is not the same as the test file we want to collect: -# /builddir/build/BUILD/snakemake-7.31.1/tests/test_conda_python_script/test_script.py -# HINT: remove __pycache__ / .pyc files and/or use a unique basename for your test file modules -# -# Plus, this would add an unwanted BuildRequires on %%{py3_dist Pillow}. -ignore="${ignore-} --ignore-glob=tests/test_conda_python_3_7_script/*" +%if %{without conda_tests} +# The following require conda (but not mamba) +k="${k-}${k+ and }not test_singularity_conda" +k="${k-}${k+ and }not test_containerized" +%endif -# Error collecting tests in tests/test_script_py/scripts/test_explicit_import.py -# https://github.com/snakemake/snakemake/issues/2961 -ignore="${ignore-} --ignore=tests/test_script_py/scripts/test_explicit_import.py" +# The following require cwltool, +# https://github.com/common-workflow-language/cwltool, which is not packaged. +# They might also require network access. +k="${k-}${k+ and }not test_cwl_singularity" -%pytest -v -k "${k-}" ${ignore-} +# The following require mamba, which is not packaged. (We do have micromamba, +# but that does not suffice.) They might also require network access. +k="${k-}${k+ and }not test_archive" +k="${k-}${k+ and }not test_conda" +k="${k-}${k+ and }not test_conda_create_envs_only" +k="${k-}${k+ and }not test_conda_custom_prefix" +k="${k-}${k+ and }not test_conda_function" +k="${k-}${k+ and }not test_conda_global" +k="${k-}${k+ and }not test_conda_named" +k="${k-}${k+ and }not test_conda_pin_file" +k="${k-}${k+ and }not test_conda_python_3_7_script" +k="${k-}${k+ and }not test_conda_python_script" +k="${k-}${k+ and }not test_converting_path_for_r_script" +k="${k-}${k+ and }not test_deploy_hashing" +k="${k-}${k+ and }not test_deploy_script" +k="${k-}${k+ and }not test_issue1093" +k="${k-}${k+ and }not test_issue635" +k="${k-}${k+ and }not test_jupyter_notebook" +k="${k-}${k+ and }not test_jupyter_notebook_draft" +k="${k-}${k+ and }not test_prebuilt_conda_script" +k="${k-}${k+ and }not test_script" +k="${k-}${k+ and }not test_script_pre_py39" +k="${k-}${k+ and }not test_wrapper" +k="${k-}${k+ and }not test_wrapper_local_git_prefix" + +# The following require the “pep” extra. They might also require network +# access. +k="${k-}${k+ and }not test_modules_peppy" +k="${k-}${k+ and }not test_pep_pathlib" +k="${k-}${k+ and }not test_peppy" + +# TODO: What is the root cause here? +# E AssertionError: expected error on execution +k="${k-}${k+ and }not test_strict_mode" + +# TODO: What is the root cause here? +# /usr/bin/bash: line 1: /usr/bin/activate: No such file or directory +# /usr/bin/bash: line 1: /builddir/.bashrc: No such file or directory +# Activating conda environment: .snakemake/conda/e4dc474209c43f7737d680b3f7ada436_ +# /usr/bin/bash: line 1: Tm: command not found +k="${k-}${k+ and }not test_upstream_conda" + +%if 0%{?fedora} > 40 +# TODO: What is the root cause here? +# Is it Python 3.13? A dependency version? Something else? +# E AssertionError: wrong result produced for file 'test.1.out': +# E ------found------ +# E 1 +# E -----expected----- +# E 1 +# E 1 +# E 1 +# E ----------------- +k="${k-}${k+ and }not test_group_job_resources_with_pipe" +%endif + +# See discussion in https://github.com/snakemake/snakemake/issues/2961 +# regarding running individual tests explicitly rather than letting pytest +# discover them freely, and see the “Test local” step in +# .github/workflows/main.yml for the list of tests that should be run. +# - tests/test_api.py requires network access and S3 credentials +%pytest -v -k "${k-}" ${ignore-} \ + tests/tests.py \ + tests/test_expand.py \ + tests/test_io.py \ + tests/test_schema.py \ + tests/test_linting.py \ + tests/test_executor_test_suite.py %endif %files -f %{pyproject_files} From 471052edf0d9f91abd20a56d73c81c761a63100f Mon Sep 17 00:00:00 2001 From: Packit Date: Tue, 13 Aug 2024 12:03:20 +0000 Subject: [PATCH 045/109] Update to 8.17.0 upstream release - Resolves: rhbz#2304309 Upstream tag: v8.17.0 Upstream commit: 7e2d075f Commit authored by Packit automation (https://packit.dev/) --- .gitignore | 1 + README.packit | 2 +- snakemake.spec | 2 +- sources | 2 +- 4 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 08917b6..9b9643c 100644 --- a/.gitignore +++ b/.gitignore @@ -60,3 +60,4 @@ /snakemake-8.14.0.tar.gz /snakemake-8.15.2.tar.gz /snakemake-8.16.0.tar.gz +/snakemake-8.17.0.tar.gz diff --git a/README.packit b/README.packit index 2499381..4df53f3 100644 --- a/README.packit +++ b/README.packit @@ -1,3 +1,3 @@ This repository is maintained by packit. https://packit.dev/ -The file was generated using packit 0.98.0. +The file was generated using packit 0.100.1. diff --git a/snakemake.spec b/snakemake.spec index b19328e..3e070ea 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -41,7 +41,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.16.0 +Version: 8.17.0 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index fcc662e..07a641a 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.16.0.tar.gz) = 29b6ba6da5dbbd347dee45114b949c976973555c9234f8a150dcd83e4af1638c1773590320bc44284cf20ea445efb377dcf9199921ed2b4d62bad3a60a41af3c +SHA512 (snakemake-8.17.0.tar.gz) = 54b8dccc4d6e3a79ff28ef3768cdfc99d7e038a5105f75c506ac1e04301baa6c42b663c62c1d8fe750899d37a810e9164765f497b025880a732070d90ccee942 From 6dad0db8625bc6dd8fdd4e7c943153a1a8afe10d Mon Sep 17 00:00:00 2001 From: Packit Date: Thu, 15 Aug 2024 10:21:14 +0000 Subject: [PATCH 046/109] Update to 8.18.0 upstream release - Resolves: rhbz#2305095 Upstream tag: v8.18.0 Upstream commit: 1b08a797 Commit authored by Packit automation (https://packit.dev/) --- .gitignore | 1 + snakemake.spec | 2 +- sources | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.gitignore b/.gitignore index 9b9643c..171125e 100644 --- a/.gitignore +++ b/.gitignore @@ -61,3 +61,4 @@ /snakemake-8.15.2.tar.gz /snakemake-8.16.0.tar.gz /snakemake-8.17.0.tar.gz +/snakemake-8.18.0.tar.gz diff --git a/snakemake.spec b/snakemake.spec index 3e070ea..960612a 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -41,7 +41,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.17.0 +Version: 8.18.0 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 07a641a..4eaff45 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.17.0.tar.gz) = 54b8dccc4d6e3a79ff28ef3768cdfc99d7e038a5105f75c506ac1e04301baa6c42b663c62c1d8fe750899d37a810e9164765f497b025880a732070d90ccee942 +SHA512 (snakemake-8.18.0.tar.gz) = 0db4b1a8fe9182ed7dc6dce61f4d7ff6f67d77c970dc309db906219398d11c34c5c81d6094ce7a16d08481d0039c871bc5b29c0824b1623037cab7e07952c4cd From 92fc68568d678368ea5cf37ad6e3fa76a07245ad Mon Sep 17 00:00:00 2001 From: Packit Date: Fri, 23 Aug 2024 01:52:59 +0000 Subject: [PATCH 047/109] Update to 8.18.2 upstream release - Resolves: rhbz#2307480 Upstream tag: v8.18.2 Upstream commit: 9a600464 Commit authored by Packit automation (https://packit.dev/) --- .gitignore | 1 + README.packit | 2 +- snakemake.spec | 2 +- sources | 2 +- 4 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 171125e..a45cbe7 100644 --- a/.gitignore +++ b/.gitignore @@ -62,3 +62,4 @@ /snakemake-8.16.0.tar.gz /snakemake-8.17.0.tar.gz /snakemake-8.18.0.tar.gz +/snakemake-8.18.2.tar.gz diff --git a/README.packit b/README.packit index 4df53f3..94a5d96 100644 --- a/README.packit +++ b/README.packit @@ -1,3 +1,3 @@ This repository is maintained by packit. https://packit.dev/ -The file was generated using packit 0.100.1. +The file was generated using packit 0.100.2.post1.dev4+g31a74ebd. diff --git a/snakemake.spec b/snakemake.spec index 960612a..dd47fbe 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -41,7 +41,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.18.0 +Version: 8.18.2 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 4eaff45..c6b761f 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (snakemake-8.18.0.tar.gz) = 0db4b1a8fe9182ed7dc6dce61f4d7ff6f67d77c970dc309db906219398d11c34c5c81d6094ce7a16d08481d0039c871bc5b29c0824b1623037cab7e07952c4cd +SHA512 (snakemake-8.18.2.tar.gz) = a8ed98541fcf60236c6a1507d4d0088a14e2d5af9ba4d6059e9314fb49b4534a3a64b52b1725a20ab3f415f187748c0c82b93880ef232d90593a0b81a7809af7 From 29add5f4310b54b63b04e87bff45541a8a40b179 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Thu, 22 Aug 2024 23:29:02 -0400 Subject: [PATCH 048/109] No longer conditionalize conda tests We can now install conda in F41. --- snakemake.spec | 5 ----- 1 file changed, 5 deletions(-) diff --git a/snakemake.spec b/snakemake.spec index dd47fbe..60d5008 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -28,9 +28,6 @@ # Run tests that require network access? This only makes sense for local mock # builds in combination with --enable-network. %bcond network_tests 0 -# Run tests that require conda? -# https://bugzilla.redhat.com/show_bug.cgi?id=2300602 -%bcond conda_tests %{expr:!0%{?fc41}} %global _description %{expand: The Snakemake workflow management system is a tool to create reproducible and @@ -211,11 +208,9 @@ k="${k-}${k+ and }not test_storage" # of things that could be going on that don’t reflect real problems. k="${k-}${k+ and }not test_shell_exec" -%if %{without conda_tests} # The following require conda (but not mamba) k="${k-}${k+ and }not test_singularity_conda" k="${k-}${k+ and }not test_containerized" -%endif # The following require cwltool, # https://github.com/common-workflow-language/cwltool, which is not packaged. From 8e7fe404d8aa7161458f71c7e300822aa1304078 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Fri, 20 Sep 2024 08:25:21 -0400 Subject: [PATCH 049/109] =?UTF-8?q?Stop=20trying=20to=20generate=20BR?= =?UTF-8?q?=E2=80=99s=20from=20removed=20extras?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit [skip changelog --- snakemake.spec | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/snakemake.spec b/snakemake.spec index 60d5008..d19b0ea 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -138,7 +138,7 @@ done %generate_buildrequires # Generate BR’s for all supported extras to ensure they do not FTI -%pyproject_buildrequires -x reports,messaging,google-cloud,azure +%pyproject_buildrequires -x reports,messaging %build %pyproject_wheel From 4ec1c48d904c81f8d59f1c766e2700a3560745c7 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Sun, 13 Oct 2024 16:25:27 -0400 Subject: [PATCH 050/109] Allow pulp 2.9 --- 3138.patch | 22 ++++++++++++++++++++++ snakemake.spec | 4 ++++ 2 files changed, 26 insertions(+) create mode 100644 3138.patch diff --git a/3138.patch b/3138.patch new file mode 100644 index 0000000..2871efc --- /dev/null +++ b/3138.patch @@ -0,0 +1,22 @@ +From d6d4e80f6787d5c7db47c46641200b66c9e85b1d Mon Sep 17 00:00:00 2001 +From: "Benjamin A. Beasley" +Date: Sun, 13 Oct 2024 07:21:35 -0400 +Subject: [PATCH] chore(deps): allow pulp 2.9 + +--- + setup.cfg | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/setup.cfg b/setup.cfg +index c96ee37bf..055c24d23 100644 +--- a/setup.cfg ++++ b/setup.cfg +@@ -46,7 +46,7 @@ install_requires = + nbformat + packaging + psutil +- pulp >=2.3.1,<2.9 # pulp introduced a breaking change from 2.7 to 2.8. Hence we should always pin to the minor version. ++ pulp >=2.3.1,<2.10 # pulp introduced a breaking change from 2.7 to 2.8. Hence we should always pin to the minor version. + pyyaml + requests >=2.8.1,<3.0 + reretry diff --git a/snakemake.spec b/snakemake.spec index d19b0ea..0eb54f4 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -53,6 +53,10 @@ License: MIT AND Unlicense URL: https://snakemake.readthedocs.io/en/stable/index.html Source: https://github.com/snakemake/snakemake/archive/v%{version}/snakemake-%{version}.tar.gz +# chore(deps): allow pulp 2.9 +# https://github.com/snakemake/snakemake/pull/3138 +Patch: https://github.com/snakemake/snakemake/pull/3138.patch + BuildArch: noarch BuildRequires: python3-devel From f603c042a70f899c7043a4f0de72411e2a9d9320 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sun, 19 Jan 2025 11:04:54 +0000 Subject: [PATCH 051/109] Rebuilt for https://fedoraproject.org/wiki/Fedora_42_Mass_Rebuild From fa2f73be8821027edfdd4ddb47b1c1ab14f2f9b2 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Tue, 18 Mar 2025 22:12:31 -0400 Subject: [PATCH 052/109] Update to 8.30.0 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Add a weak dependency on R-core - An asset bundle for offline HTML report generation is now included; this has required significant additional “machinery” to package properly, and adds many terms to the License field. --- .gitignore | 2 + ...k-around-setuptools-76-hash-mismatch.patch | 54 ++ ...e-texts-for-things-bundled-in-the-as.patch | 677 ++++++++++++++++++ 3138.patch | 22 - get_assets | 88 +++ snakemake-8.30.0-modified-assets.patch | 44 ++ snakemake.spec | 458 +++++++++--- sources | 3 +- 8 files changed, 1218 insertions(+), 130 deletions(-) create mode 100644 0001-Revert-chore-work-around-setuptools-76-hash-mismatch.patch create mode 100644 0001-chore-Add-license-texts-for-things-bundled-in-the-as.patch delete mode 100644 3138.patch create mode 100755 get_assets create mode 100644 snakemake-8.30.0-modified-assets.patch diff --git a/.gitignore b/.gitignore index a45cbe7..6554fb6 100644 --- a/.gitignore +++ b/.gitignore @@ -63,3 +63,5 @@ /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 diff --git a/0001-Revert-chore-work-around-setuptools-76-hash-mismatch.patch b/0001-Revert-chore-work-around-setuptools-76-hash-mismatch.patch new file mode 100644 index 0000000..509268a --- /dev/null +++ b/0001-Revert-chore-work-around-setuptools-76-hash-mismatch.patch @@ -0,0 +1,54 @@ +From 9d99c1c7fc2bb7ebfcba570fe64f07b0646f294a Mon Sep 17 00:00:00 2001 +From: "Benjamin A. Beasley" +Date: Tue, 18 Mar 2025 22:18:47 -0400 +Subject: [PATCH] Revert "chore: work around setuptools 76 hash mismatch from + March 9, 2025 (#3370)" + +This reverts commit 477e5f80d781334afcd549c612823caba1ef6299. +--- + pyproject.toml | 3 +-- + test-environment.yml | 5 ++--- + 2 files changed, 3 insertions(+), 5 deletions(-) + +diff --git a/pyproject.toml b/pyproject.toml +index 52229b4d..275a4655 100644 +--- a/pyproject.toml ++++ b/pyproject.toml +@@ -1,8 +1,7 @@ + [build-system] + build-backend = "setuptools.build_meta" + requires = [ +- # TODO relax upper bound, as of March 9 2025 there is a hash mismatch in setuptools on pypi +- "setuptools>=42,<76", ++ "setuptools>=42", + 'tomli; python_version < "3.11"', + ] + +diff --git a/test-environment.yml b/test-environment.yml +index 6b778458..df8a30de 100644 +--- a/test-environment.yml ++++ b/test-environment.yml +@@ -4,7 +4,6 @@ channels: + - nodefaults + dependencies: + - python >=3.11 +- - setuptools + - yte + - packaging + - boto3 +@@ -58,10 +57,10 @@ dependencies: + - nodejs # for cwltool + - immutables + - conda +- - cwltool +- - cwl-utils + - pip + - pip: ++ - cwltool ++ - cwl-utils + - snakemake-interface-executor-plugins >=9.3.1 + - snakemake-executor-plugin-cluster-generic >=1.0.9 + - snakemake-storage-plugin-http +-- +2.48.1 + diff --git a/0001-chore-Add-license-texts-for-things-bundled-in-the-as.patch b/0001-chore-Add-license-texts-for-things-bundled-in-the-as.patch new file mode 100644 index 0000000..759db2d --- /dev/null +++ b/0001-chore-Add-license-texts-for-things-bundled-in-the-as.patch @@ -0,0 +1,677 @@ +From 5d4175e75a0981d9d925ecde4297d3b568c403c2 Mon Sep 17 00:00:00 2001 +From: Ben Beasley +Date: Tue, 11 Mar 2025 11:46:53 -0400 +Subject: [PATCH] chore: Add license texts for things bundled in the assets + (#3099) +MIME-Version: 1.0 +Content-Type: text/plain; charset=UTF-8 +Content-Transfer-Encoding: 8bit + + +This PR is intended to apply on top of +https://github.com/snakemake/snakemake/pull/3098; see that PR for the +first two commits. + +From there, I attempted to account for all of the NPM packages that are +bundled in `vega/vega.js` via dependencies. I made an effort to verify +that every license file added in this commit actually corresponds to +some code present in `vega.js`. + +Next, I inspected `vega.js` for comments indicating that particular +routines were copied, derived, or adapted from other projects, and added +the license files for those projects. I didn’t attempt to judge whether +or not any of snippets might be distant enough from their inspirations +that they could perhaps claim not to be derived works under a particular +set of copyright laws – I just took the attributions at their word. + +Almost all of these licenses are ones (like `MIT`, `Apache-2.0`, `ISC` +or `BSD-3-Clause`) that require including the copyright and permission +statements (the license text) in copies and derived works, so while this +work is fussy, tedious, and unrewarding, it would seem to be necessary. + +So far, I only dug through `vega.js`. I still need to check if there is +anything in `vega-lite.js` or `vega-embed.js` that isn’t already +accounted for in `vega.js`, and I need to look at the other libraries +too. Still, I thought I should post my work in progress in case it +collected any feedback. + + +### QC + + +* [ ] The PR contains a test case for the changes or the changes are +already covered by an existing test case. **N/A – this change is not +really testable – except that building the package confirms the +checksums match.** +* [x] The documentation (`docs/`) is updated to reflect the changes or +this is not necessary (e.g. if the change does neither modify the +language nor the behavior or functionalities of Snakemake). **N/A – no +documentation update is believed to be necessary.** + + + +## Summary by CodeRabbit + +- **New Features** +- Added numerous new assets and dependencies related to the Vega +library, enhancing functionality. +- Expanded package declarations for various D3 modules and other +libraries in the reporting system. +- Introduced a new class for executing Xonsh scripts, allowing for more +scripting options. +- Added a new rule for running Python scripts in a Conda environment, +improving workflow flexibility. +- Enhanced documentation with a new "Maintainers" section and expanded +resources. + - Introduced a new test suite for validating Conda functionalities. +- Enhanced data validation capabilities using both Pandas and Polars for +handling sample data. + +- **Bug Fixes** +- Ensured that licenses and versions are accurately maintained for +various libraries. +- Improved error handling for Windows-specific issues in the testing +framework. + + +--------- + +Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com> +Co-authored-by: Johannes Köster +--- + snakemake/assets/__init__.py | 400 ++++++++++++++++++ + .../report/html_reporter/data/packages.py | 137 ++++++ + 2 files changed, 537 insertions(+) + +diff --git a/snakemake/assets/__init__.py b/snakemake/assets/__init__.py +index 123bf130..ac343e25 100644 +--- a/snakemake/assets/__init__.py ++++ b/snakemake/assets/__init__.py +@@ -93,6 +93,262 @@ class Assets: + sha256="b75f7ed0af20dedadf92c52bc236161bcf0d294ff2e6e34ca76403203349f71d", + version="5.21.0", + ), ++ # Begin dependencies for vega, included in vega/vega.js ++ # Versions from https://github.com/vega/vega/blob/v5.21.0/yarn.lock. ++ # Via vega-crossfilter, vega-encode, vega-format, ++ # vega-functions, vega-geo, vega-regression, vega-scale, vega-statistics, ++ # vega-time, vega-transforms, vega-view; and via d3-geo (via vega-functions, ++ # vega-geo, vega-projection); and via d3-geo-projection (via vega-projection) ++ # ++ # This has its own dependency, internmap (1.0.1); however, while we can ++ # find code from vega-crossfilter and d3-array in vega.js, there does ++ # not appear to be any code from internmap after tree-shaking. ++ "d3-array/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/d3/d3-array/refs/tags/v{version}/LICENSE", ++ sha256="0747bebeb06b10954913149be9b9a8bdf6fad3e6fdcbd9f9524e7a94c13d2cea", ++ version="2.12.1", ++ ), ++ # Via vega-format ++ "d3-format/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/d3/d3-format/refs/tags/v{version}/LICENSE", ++ sha256="7eea8533ea92bd8c32a901e89ecb0305890905bb12711449565ddff96891146d", ++ version="2.0.0", ++ ), ++ # Via vega-format ++ "d3-time-format/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/d3/d3-time-format/refs/tags/v{version}/LICENSE", ++ sha256="7a3cb0e5055874e67db9aa2d5fe26de23204fa994ffbad198901ffe9c812a717", ++ version="3.0.0", ++ ), ++ # Via vega-time, vega-view; and via d3-time-format (via vega-format) ++ "d3-time/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/d3/d3-time/refs/tags/v{version}/LICENSE", ++ sha256="e1211892da0b0e0585b7aebe8f98c1274fba15bafe47fa1f4ee8a7a502c06304", ++ version="2.1.1", ++ ), ++ # Via vega-encode, vega-scale ++ "d3-interpolate/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/d3/d3-interpolate/refs/tags/v{version}/LICENSE", ++ sha256="e1211892da0b0e0585b7aebe8f98c1274fba15bafe47fa1f4ee8a7a502c06304", ++ version="2.0.1", ++ ), ++ # Via vega-functions, vega-geo; and via d3-interpolate (via vega-encode) ++ "d3-color/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/d3/d3-color/refs/tags/v{version}/LICENSE", ++ sha256="e1211892da0b0e0585b7aebe8f98c1274fba15bafe47fa1f4ee8a7a502c06304", ++ version="2.0.0", ++ ), ++ # Via vega-scale ++ "d3-scale/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/d3/d3-scale/refs/tags/v{version}/LICENSE", ++ sha256="7eea8533ea92bd8c32a901e89ecb0305890905bb12711449565ddff96891146d", ++ version="3.3.0", ++ ), ++ # Via vega-expression (vega-lite also depends on vega-expression) ++ # The license file included in the NPM package does not exist directly ++ # in https://github.com/DefinitelyTyped/DefinitelyTyped, so we use an ++ # unpkg URL to reference the contents of the NPM package instead. ++ "@types-estree/LICENSE": Asset( ++ url="https://unpkg.com/@types/estree@{version}/LICENSE", ++ sha256="c2cfccb812fe482101a8f04597dfc5a9991a6b2748266c47ac91b6a5aae15383", ++ version="0.0.50", ++ ), ++ # Via vega-force ++ "d3-force/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/d3/d3-force/refs/tags/v{version}/LICENSE", ++ sha256="e1211892da0b0e0585b7aebe8f98c1274fba15bafe47fa1f4ee8a7a502c06304", ++ version="2.1.1", ++ ), ++ # Via d3-force (via vega-force) ++ "d3-dispatch/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/d3/d3-dispatch/refs/tags/v{version}/LICENSE", ++ sha256="e1211892da0b0e0585b7aebe8f98c1274fba15bafe47fa1f4ee8a7a502c06304", ++ version="2.0.0", ++ ), ++ # Via d3-force (via vega-force) ++ "d3-quadtree/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/d3/d3-quadtree/refs/tags/v{version}/LICENSE", ++ sha256="e1211892da0b0e0585b7aebe8f98c1274fba15bafe47fa1f4ee8a7a502c06304", ++ version="2.0.0", ++ ), ++ # Via vega-view; and via d3-force (via vega-force) ++ "d3-timer/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/d3/d3-timer/refs/tags/v{version}/LICENSE", ++ sha256="e1211892da0b0e0585b7aebe8f98c1274fba15bafe47fa1f4ee8a7a502c06304", ++ version="2.0.0", ++ ), ++ # Via vega-functions, vega-geo, vega-projection (directly and via ++ # d3-geo-projection) ++ "d3-geo/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/d3/d3-geo/refs/tags/v{version}/LICENSE", ++ sha256="c3c9d41a75b64963748657932167ec4c56404b8fd557d4f89c9eeda6e2fdf39a", ++ version="2.0.2", ++ ), ++ # Via vega-hierarchy ++ "d3-hierarchy/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/d3/d3-hierarchy/refs/tags/v{version}/LICENSE", ++ sha256="e1211892da0b0e0585b7aebe8f98c1274fba15bafe47fa1f4ee8a7a502c06304", ++ version="2.0.0", ++ ), ++ # Via vega-loader ++ # This has its own dependencies (commander 2.20.3, iconv-lite 0.4.24, ++ # rw 1.3.3), but they are all used only in the command-line tools ++ # rather than in the library that is bundled in vega.js. ++ "d3-dsv/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/d3/d3-dsv/refs/tags/v{version}/LICENSE", ++ sha256="8b5304265ccedbd17567aa14a0dc6b9bf4013fee44964c46aa54fdf8527d6a68", ++ version="2.0.0", ++ ), ++ # Via vega-loader; also from vega-geo/src/util/contours.js, "Based on ++ # https://github.com/topojson/topojson-client/blob/v3.0.0/src/stitch.js" ++ # This has its own dependency (commander 2.20.3), but it is used only ++ # in the command-line tools rather than in the library that is bundled ++ # in vega.js. Dependency node-fetch 2.6.4, via vega-loader, is not ++ # used for browser builds. ++ "topojson-client/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/topojson/topojson-client/refs/tags/v{version}/LICENSE", ++ sha256="4c4d15b635e04e691825a76db7d33f7f2033b55669a7430011694f31e6c65999", ++ version="3.1.0", ++ ), ++ # Via vega-projection ++ # This has its own dependencies (commander 2.20.3, resolve 1.20.0), but ++ # they are all used only in the command-line tools rather than in the ++ # library that is bundled in vega.js. ++ "d3-geo-projection/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/d3/d3-geo-projection/refs/tags/v{version}/LICENSE", ++ sha256="4108a126a74cc35d4d5ae39ca5d0cc926fa7c8ec40e459a0c6d3481c69decbd8", ++ version="3.0.0", ++ ), ++ # Via vega-scenegraph (directly and via d3-shape) ++ "d3-path/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/d3/d3-path/refs/tags/v{version}/LICENSE", ++ sha256="b8265327ab678f554800e71188b1cc6b1ff57522e292d2b1c0be66f27cf328b6", ++ version="2.0.0", ++ ), ++ # Via vega-scenegraph ++ "d3-shape/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/d3/d3-shape/refs/tags/v{version}/LICENSE", ++ sha256="7eea8533ea92bd8c32a901e89ecb0305890905bb12711449565ddff96891146d", ++ version="2.1.0", ++ ), ++ # Via vega-voronoi ++ "d3-delaunay/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/d3/d3-delaunay/refs/tags/v{version}/LICENSE", ++ sha256="d19bf35c4080eea32e098a9c8d62540ffd425611ac8dfc856a233f0357d8b02e", ++ version="5.2.0", ++ ), ++ # Via d3-delaunay (via vega-voronoi) ++ "delaunator/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/mapbox/delaunator/refs/tags/v{version}/LICENSE", ++ sha256="27043d1a6a0e1985fde12660decbbd3b23c67de900b00609c90d4f0aa492f425", ++ version="4.0.1", ++ ), ++ # End dependencies for vega, included in vega/vega.js ++ # Begin copied/derived/adapted code in vega, included in vega/vega.js ++ # From vega-util/src/lruCache.js, "adapted from ++ # https://github.com/dominictarr/hashlru/ (MIT License)". Version 1.0.4 ++ # was the current version when the function was added to vega, in ++ # commit f153863f3575bff1b42294c9cb065d80afb757ff on 2020-02-28. ++ "hashlru/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/dominictarr/hashlru/refs/tags/v{version}/LICENSE", ++ sha256="08e4bd7a280eaaf1fbcaad9dad1fb94412477fcdd1cf81660988303297e5e1d1", ++ version="1.0.4", ++ ), ++ # From ++ # vega-statistics/src/regression/{poly,r-squared,pow,log,linear}.js, ++ # "Adapted from d3-regression by Harry Stevens". Version 1.2.1 was the ++ # current version when the functions were added to vega, in commit ++ # 71610e4456a3a4145435d83f8458748ba137a2a3 2019-05-10. That release was ++ # not tagged in git, so we use the corresponding commit hash. ++ "d3-regression/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/HarryStevens/d3-regression/e23d40a663dffba14b92cb42d9989de3a32894b5/LICENSE", ++ sha256="d210203f922101502894baf700b9a392e323a26e4b603ab166c57e09a6e773b5", ++ version="1.2.1", ++ ), ++ # From vega-statistics/src/regression/poly.js, "Adapted from ++ # d3-regression by Harry Stevens [...] which was adapted from ++ # regression-js by Tom Alexander" Version 2.0.1 was the current version ++ # when the functions were added to vega, in commit ++ # 71610e4456a3a4145435d83f8458748ba137a2a3 2019-05-10. ++ "regression/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/Tom-Alexander/regression-js/refs/tags/{version}/LICENSE", ++ sha256="2f932f5cfb9b042cc6c0089ee8004b33e3746ffeab879341dbd453c150524307", ++ version="2.0.1", ++ ), ++ # From vega-statistics/src/regression/loess.js, "Adapted from ++ # science.js by Jason Davies". Version 1.9.3 was the current version ++ # when the functions were added to vega, in commit ++ # 71610e4456a3a4145435d83f8458748ba137a2a3 on 2019-05-10. ++ "science/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/jasondavies/science.js/refs/tags/v{version}/LICENSE", ++ sha256="3bd1fdf686ffcad175daddcb36ee28599ac8f090b6cec2c7654118c8a6f3d4c9", ++ version="1.9.3", ++ ), ++ # From src/quickselect.js in d3-array, "Based on ++ # https://github.com/mourner/quickselect". Version 2.0.0 was the ++ # current version when the file was added to d3-array, in commit ++ # d447c2a31cd6aacf54a40b22c29620f7e17bbd7e on 2018-11-10. ++ "quickselect/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/mourner/quickselect/refs/tags/v{version}/LICENSE", ++ sha256="597034cb7c11c916ad407344ea99a0b08e3c443a6b4421460f1d23c411c69707", ++ version="2.0.0", ++ ), ++ # From vega-statistics/src/normal.js, "Ported from Apache Commons ++ # Math". Version 3.6.1 was the current version when this implementation ++ # of erfinv was added to vega, in commit ++ # c26050f21b0c95620f8f1a3094056716ec6c5aaa on 2019-09-26. ++ "commons-math/LICENSE.txt": Asset( ++ url="https://raw.githubusercontent.com/apache/commons-math/refs/tags/MATH_3_6_1/LICENSE.txt", ++ sha256="64f23963615950bad9ddd31569a7f09afbbe11b81d94873ffd9b1cac6081a11d", ++ version="3.6.1", ++ ), ++ "commons-math/NOTICE.txt": Asset( ++ url="https://raw.githubusercontent.com/apache/commons-math/refs/tags/MATH_3_6_1/NOTICE.txt", ++ sha256="5495442a32bfc2b93b4a8f2c34c5c218d16cca434aa5684fb953d9419120e3fa", ++ version="3.6.1", ++ ), ++ # From vega-expression/src/parser.js, "The following expression parser ++ # is based on Esprima (http://esprima.org/)." Unusually, the original ++ # license text is reproduced in the source file, so we could get by ++ # without a separate license file (and in fact the license file lacks ++ # the necessary copyright statement present in the code) but we add it ++ # for consistency. Version 2.2.0 was the last version of Esprima that ++ # had a copyright statement in esprima.js attributing specific ++ # individual contributors, as reproduced in the vega source. ++ "esprima/LICENSE.BSD": Asset( ++ url="https://raw.githubusercontent.com/jquery/esprima/refs/tags/{version}/LICENSE.BSD", ++ sha256="0e74697a68cebdcd61502c30fe80ab7f9e341d995dcd452023654d57133534b1", ++ version="2.2.0", ++ ), ++ # From vega-scenegraph/src/path/arc.js, "Copied from Inkscape svgtopdf, ++ # thanks!" We cannot find the original implementation in Inkscape or ++ # anywhere else, so we do not add a license file for this snippet. ++ # From vega-scenegraph/src/path/parse.js, "Path parsing and rendering ++ # code adapted from fabric.js -- Thanks!" This was added in commit ++ # 82932143de7cef4187a34026689df12abaa25959 on 2018-12-20, and the ++ # current release of fabric.js at that time was 2.4.5. ++ "fabric/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/fabricjs/fabric.js/refs/tags/v{version}/LICENSE", ++ sha256="9f6c2cc99aa9c618df93fed7d1cf7279d4e329d92dd2ce5e96173c73ce305055", ++ version="2.4.5", ++ ), ++ # From vega-geo/src/util/{contours,density2D}.js, "Implementation ++ # adapted from d3/d3-contour. Thanks!" When these routines were added ++ # in 0ab6b730a7e576d33d00e12063855bb132194191 on 2019-11-11, the latest ++ # version was 1.3.2. ++ "d3-contour/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/d3/d3-contour/refs/tags/v{version}/LICENSE", ++ sha256="5f5dcce265668080a60fbdc513f6f8ef21466780bcaa331e64ee39df19e63b30", ++ version="1.3.2", ++ ), ++ # From vega-geo/src/util/contours.js, "Based on ++ # https://github.com/mbostock/shapefile/blob/v0.6.2/shp/polygon.js" ++ "shapefile/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/mbostock/shapefile/refs/tags/v{version}/LICENSE.txt", ++ sha256="c16529a9d5b8802982abd714a6823344e24b0cb5131596bc343927ead605d708", ++ version="0.6.2", ++ ), ++ # End copied/derived/adapted code in vega, included in vega/vega.js + "vega-lite/vega-lite.js": Asset( + url="https://cdnjs.cloudflare.com/ajax/libs/vega-lite/{version}/vega-lite.js", + sha256="6eb7f93121cd9f44cf8640244f87c5e143f87c7a0b6cd113da4a9e41e3adf0aa", +@@ -103,6 +359,57 @@ class Assets: + sha256="f618900fd0d64046963b29f40590cdd1e341a2f41449f99110d82fd81fea808c", + version="5.2.0", + ), ++ # Begin dependencies for vega-lite, included in vega-lite/vega-lite.js ++ # Versions from https://github.com/vega/vega-lite/blob/v5.2.0/yarn.lock. ++ "@types-clone/LICENSE": Asset( ++ url="https://unpkg.com/@types/clone@{version}/LICENSE", ++ 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", ++ version="2.1.2", ++ ), ++ "fast-deep-equal/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/epoberezkin/fast-deep-equal/refs/tags/v{version}/LICENSE", ++ sha256="7bf9b2de73a6b356761c948d0e9eeb4be6c1270bd04c79cd489c1e400ffdfc1a", ++ version="3.1.3", ++ ), ++ "fast-json-stable-stringify/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/epoberezkin/fast-json-stable-stringify/refs/tags/v{version}/LICENSE", ++ sha256="a833d366242c298cf1b10263516572fb8dcbe68eb5072cdcac2b4546e2b4eb36", ++ version="2.1.0", ++ ), ++ "json-stringify-pretty-compact/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/lydell/json-stringify-pretty-compact/refs/tags/v{version}/LICENSE", ++ sha256="d0800a7c9b5f723f7fe029f75d3a9ae44173178b9729d1521e18371ab24ae97a", ++ version="3.0.0", ++ ), ++ # The tslib package is among vega-lite's direct dependencies, and the ++ # yarn.lock file shows three versions could be included: 2.2.0, 2.1.0 ++ # (both MIT-licensed), and 1.1.0 (Apache-2.0-licensed). However, we ++ # found no trace of any of these in the actual vega-lite.js bundle. ++ # ---- ++ # The following packages are part of vega, and are already covered by ++ # vega/LICENSE. ++ # - vega-event-selector: no dependencies ++ # - vega-expression: depends on vega-util, @types/estree (already ++ # covered as one of vega's dependencies) ++ # - vega-util (no dependencies; includes code from hashlru, already ++ # covered as one of vega's dependencies) ++ # ---- ++ # End dependencies for vega-lite, included in vega-lite/vega-lite.js ++ # Begin copied/derived/adapted code in vega-lite, included in vega-lite/vega-lite.js ++ # - hashlru is included in vega-util; already covered as one of vega's dependencies ++ # End copied/derived/adapted code in vega-lite, included in vega-lite/vega-lite.js + "vega-embed/vega-embed.js": Asset( + url="https://cdnjs.cloudflare.com/ajax/libs/vega-embed/{version}/vega-embed.js", + sha256="4e546c1f86eb200333606440e92f76e2940b905757018d9672cd1708e4e6ff0a", +@@ -113,6 +420,78 @@ class Assets: + sha256="32df67148f0fc3db0eb9e263a7b75d07f1eb14c61955005a4a39c6918d10d137", + version="6.20.8", + ), ++ # Begin dependencies for vega-embed, included in vega-embed/vega-embed.js ++ # Versions from https://github.com/vega/vega-embed/blob/v6.20.8/yarn.lock. ++ "fast-json-patch/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/Starcounter-Jack/JSON-Patch/refs/tags/v{version}/LICENSE.txt", ++ sha256="26593d78926902a82eb9bc7e40d1811fc381055f23516b92fe48ca8399bf02df", ++ version="3.1.0", ++ ), ++ # json-stringify-pretty-compact 3.0.0 is already covered as one of ++ # vega's dependencies ++ # ---- ++ # There are four versions of the semver package in yarn.lock (5.7.1, ++ # 6.3.0, 7.0.0, 7.3.5), but it appears that only one copy remains in ++ # the vega-embed.js bundle. The bundle has a compareBuild function, ++ # added in 6.1.0. It does not export a "tokens" list, added in 6.3.0 ++ # and present in 7.0.0, but that is not conclusive because the package ++ # was split into separate source files to improve tree-shaking. By ++ # 7.3.5, the first line of the SemVer class constructor changes to ++ # "options = parseOptions(options)", and this does match what we see in ++ # the bundle, so we conclude that we have semver 7.3.5. In any case, ++ # the ISC license was unchanged across all four versions. ++ "semver/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/npm/node-semver/refs/tags/v{version}/LICENSE", ++ sha256="4ec3d4c66cd87f5c8d8ad911b10f99bf27cb00cdfcff82621956e379186b016b", ++ version="7.3.5", ++ ), ++ # The tslib package is among vega-embed's direct dependencies, and the ++ # yarn.lock file shows four versions could be included: 2.3.1, 2.1.0, ++ # 1.14.1 (all MIT-licensed), and 1.1.0 (Apache-2.0-licensed). However, ++ # we found no trace of any of these in the actual vega-embed.js bundle. ++ # ---- ++ # The following packages are part of vega, and are already covered by ++ # vega/LICENSE. ++ # - vega-interpreter: no dependencies ++ # ---- ++ # This is not part of https://github.com/vega/vega, as far as we can ++ # tell, so we handle it separately. The repository ++ # https://github.com/vega/schema linked from NPM appears to contain ++ # only JSON schemas, not JavaScript source code, so we use an unpkg URL ++ # to reference the contents of the NPM package instead. ++ "vega-schema-url-parser/LICENSE": Asset( ++ url="https://unpkg.com/vega-schema-url-parser@{version}/LICENSE", ++ sha256="eeb1606fda238f623c36d1eb5e27c33b986a446445340b220c141097424af045", ++ version="2.2.0", ++ ), ++ "vega-themes/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/vega/vega-themes/refs/tags/v{version}/LICENSE", ++ sha256="ceb75fa4fbebbc381c0465442a502ffc13b73f36ccb385a66bcd5f55869e3979", ++ version="2.10.0", ++ ), ++ # Depends on vega-util, which is already covered in vega ++ "vega-tooltip/LICENSE": Asset( ++ url="https://raw.githubusercontent.com/vega/vega-tooltip/refs/tags/v{version}/LICENSE", ++ sha256="93cd20d9cee8c77c080d1a585e3b07644ad2c8e9ccdfc86e350136884d62d935", ++ version="0.28.0", ++ ), ++ # End dependencies for vega-embed, included in vega-embed/vega-embed.js ++ # Begin copied/derived/adapted code in vega-embed, included in vega-embed/vega-embed.js ++ # - hashlru is included in vega-util (via vega-tooltip); already ++ # covered as one of vega's dependencies ++ # - _areEquals() is based on fast-deep-equal; already covered as one of ++ # vega-lite's dependencies ++ # - googlecharts theme in vega-themes carries its own copyright statement, ++ # Copyright 2020 Google LLC. ++ # ++ # Use of this source code is governed by a BSD-style ++ # license that can be found in the LICENSE file or at ++ # https://developers.google.com/open-source/licenses/bsd ++ # No plain-text version of that URL is available, and the license has ++ # the same BSD-3-Clause permission statement as vega-themes itself, ++ # so we consider the combination of vega-themes/LICENSE and the ++ # copyright statement in the source code sufficient. ++ # End copied/derived/adapted code in vega-embed, included in vega-embed/vega-embed.js + "heroicons/LICENSE": Asset( + url="https://raw.githubusercontent.com/tailwindlabs/heroicons/refs/tags/v{version}/LICENSE", + sha256="75523ddd65d9620bea09f84e89d0c373b4205a3708b8a1e9f9598a5438a3e641", +@@ -128,6 +507,27 @@ class Assets: + sha256="f657f99d3fb9647db92628e96007aabb46e5f04f33e49999075aab8e250ca7ce", + version="15.7.2", + ), ++ # Begin dependencies for prop-types, included in prop-types/prop-types.min.js ++ # Versions from https://github.com/facebook/prop-types/blob/v15.7.2/yarn.lock ++ # ---- ++ # The loose-envify package is among prop-types's direct dependencies, ++ # and the yarn.lock file shows two versions could be included: 1.4.0 ++ # and 1.3.1 (both MIT-licensed). However, we found no trace of ++ # loose-envify code in the actual prop-types.min.js bundle, so it ++ # appears this dependency was removed in tree-shaking, along with its ++ # dependency js-tokens (3.0.0 and/or 4.0.0). ++ # ---- ++ # The object-assign package (version 4.1.1) is among prop-types's ++ # direct dependencies, but we found no trace of it in the actual ++ # prop-types.min.js bundle, so it appears this dependency (a polyfill) ++ # was removed in tree-shaking. ++ # ---- ++ # The react-is package (version 16.8.1) is among prop-types's ++ # direct dependencies, but we found no trace of it in the actual ++ # prop-types.min.js bundle, so it appears this dependency was removed ++ # in tree-shaking. ++ # ---- ++ # End dependencies for prop-types, included in prop-types/prop-types.min.js + } + + @classmethod +diff --git a/snakemake/report/html_reporter/data/packages.py b/snakemake/report/html_reporter/data/packages.py +index 963a4c10..2b8e364f 100644 +--- a/snakemake/report/html_reporter/data/packages.py ++++ b/snakemake/report/html_reporter/data/packages.py +@@ -38,14 +38,151 @@ def get_packages(): + source_path="vega/vega.js", + license_path="vega/LICENSE", + ), ++ # Begin dependencies for vega, included in vega/vega.js ++ "d3-array": Package( ++ license_path="d3-array/LICENSE", ++ ), ++ "d3-format": Package( ++ license_path="d3-format/LICENSE", ++ ), ++ "d3-time-format": Package( ++ license_path="d3-time-format/LICENSE", ++ ), ++ "d3-time": Package( ++ license_path="d3-time/LICENSE", ++ ), ++ "d3-interpolate": Package( ++ license_path="d3-interpolate/LICENSE", ++ ), ++ "d3-color": Package( ++ license_path="d3-color/LICENSE", ++ ), ++ "d3-scale": Package( ++ license_path="d3-scale/LICENSE", ++ ), ++ "@types-estree": Package( ++ license_path="@types-estree/LICENSE", ++ ), ++ "d3-force": Package( ++ license_path="d3-force/LICENSE", ++ ), ++ "d3-dispatch": Package( ++ license_path="d3-dispatch/LICENSE", ++ ), ++ "d3-quadtree": Package( ++ license_path="d3-quadtree/LICENSE", ++ ), ++ "d3-timer": Package( ++ license_path="d3-timer/LICENSE", ++ ), ++ "d3-geo": Package( ++ license_path="d3-geo/LICENSE", ++ ), ++ "d3-hierarchy": Package( ++ license_path="d3-hierarchy/LICENSE", ++ ), ++ "d3-dsv": Package( ++ license_path="d3-dsv/LICENSE", ++ ), ++ "topojson-client": Package( ++ license_path="topojson-client/LICENSE", ++ ), ++ "d3-geo-projection": Package( ++ license_path="d3-geo-projection/LICENSE", ++ ), ++ "d3-path": Package( ++ license_path="d3-path/LICENSE", ++ ), ++ "d3-shape": Package( ++ license_path="d3-shape/LICENSE", ++ ), ++ "d3-delaunay": Package( ++ license_path="d3-delaunay/LICENSE", ++ ), ++ "delaunator": Package( ++ license_path="delaunator/LICENSE", ++ ), ++ # End dependencies for vega, included in vega/vega.js ++ # Begin copied/derived/adapted code in vega, included in vega/vega.js ++ "hashlru": Package( ++ license_path="hashlru/LICENSE", ++ ), ++ "d3-regression": Package( ++ license_path="d3-regression/LICENSE", ++ ), ++ "regression": Package( ++ license_path="regression/LICENSE", ++ ), ++ "science": Package( ++ license_path="science/LICENSE", ++ ), ++ "quickselect": Package( ++ license_path="quickselect/LICENSE", ++ ), ++ "commons-math": Package( ++ license_path="commons-math/LICENSE.txt", ++ # This must be included with LICENSE.txt. ++ notice="commons-math/NOTICE.txt", ++ ), ++ "esprima": Package( ++ license_path="esprima/LICENSE.BSD", ++ ), ++ "fabric": Package( ++ license_path="fabric/LICENSE", ++ ), ++ "d3-contour": Package( ++ license_path="d3-contour/LICENSE", ++ ), ++ # End copied/derived/adapted code in vega, included in vega/vega.js + "vega-lite": Package( + source_path="vega-lite/vega-lite.js", + license_path="vega-lite/LICENSE", + ), ++ # Begin dependencies for vega-lite, included in vega-lite/vega-lite.js ++ # (excluding those shared with vega and therefore already documented) ++ "@types-clone": Package( ++ license_path="@types-estree/LICENSE", ++ ), ++ "array-flat-polyfill": Package( ++ license_path="array-flat-polyfill/LICENSE", ++ ), ++ "clone": Package( ++ license_path="clone/LICENSE", ++ ), ++ "fast-deep-equal": Package( ++ license_path="fast-deep-equal/LICENSE", ++ ), ++ "fast-json-stable-stringify": Package( ++ license_path="fast-json-stable-stringify/LICENSE", ++ ), ++ "json-stringify-pretty-compact": Package( ++ license_path="json-stringify-pretty-compact/LICENSE", ++ ), ++ # End dependencies for vega-lite, included in vega-lite/vega-lite.js ++ # Any copied/derived/adapted code in vega-lite is shared with vega. + "vega-embed": Package( + source_path="vega-embed/vega-embed.js", + license_path="vega-embed/LICENSE", + ), ++ # Begin dependencies for vega-embed, included in vega-embed/vega-embed.js ++ # (excluding those shared with vega/vega-lite and therefore already documented) ++ "fast-json-patch": Package( ++ license_path="fast-json-patch/LICENSE", ++ ), ++ "semver": Package( ++ license_path="semver/LICENSE", ++ ), ++ "vega-schema-url-parser": Package( ++ license_path="vega-schema-url-parser/LICENSE", ++ ), ++ "vega-themes": Package( ++ license_path="vega-themes/LICENSE", ++ ), ++ "vega-tooltip": Package( ++ license_path="vega-tooltip/LICENSE", ++ ), ++ # End dependencies for vega-embed, included in vega-embed/vega-embed.js ++ # Any copied/derived/adapted code in vega-embed is shared with vega and/or vega-lite. + "heroicons": Package( + license_path="heroicons/LICENSE", + ), +-- +2.48.1 + diff --git a/3138.patch b/3138.patch deleted file mode 100644 index 2871efc..0000000 --- a/3138.patch +++ /dev/null @@ -1,22 +0,0 @@ -From d6d4e80f6787d5c7db47c46641200b66c9e85b1d Mon Sep 17 00:00:00 2001 -From: "Benjamin A. Beasley" -Date: Sun, 13 Oct 2024 07:21:35 -0400 -Subject: [PATCH] chore(deps): allow pulp 2.9 - ---- - setup.cfg | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/setup.cfg b/setup.cfg -index c96ee37bf..055c24d23 100644 ---- a/setup.cfg -+++ b/setup.cfg -@@ -46,7 +46,7 @@ install_requires = - nbformat - packaging - psutil -- pulp >=2.3.1,<2.9 # pulp introduced a breaking change from 2.7 to 2.8. Hence we should always pin to the minor version. -+ pulp >=2.3.1,<2.10 # pulp introduced a breaking change from 2.7 to 2.8. Hence we should always pin to the minor version. - pyyaml - requests >=2.8.1,<3.0 - reretry diff --git a/get_assets b/get_assets new file mode 100755 index 0000000..85a81ca --- /dev/null +++ b/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' "${XDIR}/snakemake/assets/")" + +echo "==== Apply patches ====" 1>&2 +spectool --list-files "${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}/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='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' \ + "${XDIR}/snakemake/assets" +then + echo 'MANUAL AUDIT REQUIRED' 1>&2 + exit 1 +fi +# Remove license file and the directory containing it +rm -rv "${XDIR}/snakemake/assets/data/array-flat-polyfill" +echo "--> Search for missed CC0-1.0 licenses" 1>&2 +if grep -ErinI '\bCC0\b' "${XDIR}/snakemake/assets" +then + echo 'MANUAL AUDIT REQUIRED' 1>&2 + exit 1 +fi + +echo "==== Archive assets ====" 1>&2 +RESULT="${XDIR}-assets.tar.zst" +ls -ld "${XDIR}/snakemake/assets/" +# https://www.gnu.org/software/tar/manual/html_section/Reproducibility.html +TZ=UTC LC_ALL=C tar \ + --create \ + --sort=name \ + --format=posix \ + --numeric-owner --owner=0 --group=0 \ + --mode=go+u,go-w \ + --pax-option='delete=atime,delete=ctime' \ + --clamp-mtime --mtime="@${MTIME}" \ + --directory="${XDIR}" \ + snakemake/assets/data | + zstdmt --ultra -22 > "${RESULT}" + +mv -v "${RESULT}" "${DIST_GIT}" diff --git a/snakemake-8.30.0-modified-assets.patch b/snakemake-8.30.0-modified-assets.patch new file mode 100644 index 0000000..8946d82 --- /dev/null +++ b/snakemake-8.30.0-modified-assets.patch @@ -0,0 +1,44 @@ +diff -Naur snakemake-8.30.0-original/snakemake/assets/__init__.py snakemake-8.30.0/snakemake/assets/__init__.py +--- snakemake-8.30.0-original/snakemake/assets/__init__.py 2025-03-19 10:16:19.899201489 -0400 ++++ snakemake-8.30.0/snakemake/assets/__init__.py 2025-03-19 10:20:34.376310829 -0400 +@@ -349,9 +349,12 @@ + 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( +@@ -366,13 +369,6 @@ + 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-8.30.0-original/snakemake/report/html_reporter/data/packages.py snakemake-8.30.0/snakemake/report/html_reporter/data/packages.py +--- snakemake-8.30.0-original/snakemake/report/html_reporter/data/packages.py 2025-03-19 10:16:19.900335558 -0400 ++++ snakemake-8.30.0/snakemake/report/html_reporter/data/packages.py 2025-03-19 10:16:47.850551627 -0400 +@@ -143,9 +143,6 @@ + "@types-clone": Package( + license_path="@types-estree/LICENSE", + ), +- "array-flat-polyfill": Package( +- license_path="array-flat-polyfill/LICENSE", +- ), + "clone": Package( + license_path="clone/LICENSE", + ), diff --git a/snakemake.spec b/snakemake.spec index 0eb54f4..a2dd730 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -28,6 +28,9 @@ # 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 %global _description %{expand: The Snakemake workflow management system is a tool to create reproducible and @@ -38,24 +41,136 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.18.2 -Release: %autorelease +Version: 8.30.0 +Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses -# The entire project is (SPDX) MIT, except: -# - versioneer.py is Unlicense -# - snakemake/_version.py says: -# This file is released into the public domain. -# which would be LicenseRef-Fedora-Public-Domain, except that the comments in -# versioneer.py make it clear that Unlicense is intended for the generated -# files as well. -License: MIT AND Unlicense +# The primary license for Snakemake is MIT; versioneer contributes Unlicense, +# and 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: +# - snakemake/assets/data/vega/vega.js +# +# BSD-3-Clause AND MIT: +# - snakemake/assets/data/vega-lite/vega-lite.js +# +# BSD-3-Clause AND ISC AND MIT: +# - 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. +# - snakemake/assets/data/prop-types/prop-types.min.js +# - snakemake/assets/data/tailwindcss/tailwind.css +# +# Unlicense: +# - versioneer.py +# - snakemake/_version.py (which says “This file is released into the public +# domain,” but the comments in versioneer.py make it clear that Unlicense is +# intended for the generated files as well) +# +# == License breakdown for 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 for 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 for 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 AND + Unlicense + } URL: https://snakemake.readthedocs.io/en/stable/index.html -Source: https://github.com/snakemake/snakemake/archive/v%{version}/snakemake-%{version}.tar.gz +%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 -# chore(deps): allow pulp 2.9 -# https://github.com/snakemake/snakemake/pull/3138 -Patch: https://github.com/snakemake/snakemake/pull/3138.patch +# Upstream upper-bounded the version of setuptools to work around a hash +# mismatch in setuptools 76 on PyPI observed on March 9, 2025. The system +# setuptools is fine. The upper-bound was removed in a later release. Here we +# revert it as a downstream-only patch. +Patch: 0001-Revert-chore-work-around-setuptools-76-hash-mismatch.patch + +# chore: Add license texts for things bundled in the assets +# https://github.com/snakemake/snakemake/pull/3099 +# Rebased on v8.30.0 +Patch: 0001-chore-Add-license-texts-for-things-bundled-in-the-as.patch + +# 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-8.30.0-modified-assets.patch BuildArch: noarch @@ -75,7 +190,165 @@ 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 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. + +# snakemake/assets/data/react/react.production.min.js +Provides: bundled(npm(react)) = 18.2.0 +# snakemake/assets/data/react/react-dom.production.min.js +Provides: bundled(npm(react-dom)) = 18.2.0 + +# snakemake/assets/data/vega/vega.js +Provides: bundled(npm(vega)) = 5.21.0 +# Bundled in 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 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 snakemake/assets/data/vega/vega.js in the form of copied, derived, +# or adapted snippets. See notes in 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 + +# 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 snakemake/assets/data/vega-lite/vega-lite.js as dependencies: +# See notes in 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 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 snakemake/assets/data/vega-lite/vega-lite.js in the form of +# copied, derived, or adapted snippets. See notes in +# snakemake/assets/__init__.py. +#Provides: bundled(npm(hashlru)) = 1.0.4 + +# 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 snakemake/assets/data/vega-embed/vega-embed.js as dependencies: +# See notes in 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 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 snakemake/assets/data/vega-embed/vega-embed.js in the form of +# copied, derived, or adapted snippets. See notes in +# 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 + +# snakemake/assets/data/prop-types/prop-types.min.js +Provides: bundled(npm(prop-types)) = 15.7.2 + # These extras were removed upstream in Snakemake 8.0.0. Retain the Obsoletes # until F40 reaches EOL so we have a clean upgrade path. Obsoletes: snakemake+azure < 8.1.0-1 @@ -89,8 +362,12 @@ Obsoletes: snakemake-doc < 8.2.1-2 # For several tests (either apptainer or singularity-ce should work): BuildRequires: (apptainer or singularity-ce) %if %{with conda_tests} -# For several tests +# 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 @@ -99,7 +376,7 @@ BuildRequires: graphviz # For test_github_issue1158: BuildRequires: strace # For test_benchmark and test_benchmark_jsonl: -BuildRequires: stress +BuildRequires: stress-ng # See test-environment.yml for a listing of test dependencies, along with a lot # of other cruft. @@ -119,13 +396,17 @@ BuildRequires: %{py3_dist google-cloud-storage} %description %_description + # No metapackage for “pep” extra because the following are not packaged: # - python3-eido # - python3-peppy %pyproject_extras_subpkg -n snakemake reports messaging + %prep %autosetup -n snakemake-%{version} -p1 +%setup -q -T -D -a 1 -c -n snakemake-%{version} + %py3_shebang_fix . # Remove shebangs from non-executable scripts. The Python script is executable # in the source tree but will be installed without executable permissions. @@ -140,17 +421,41 @@ do cp -vp "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 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 >> snakemake/assets/__init__.py < 40 -# TODO: What is the root cause here? -# Is it Python 3.13? A dependency version? Something else? -# E AssertionError: wrong result produced for file 'test.1.out': -# E ------found------ -# E 1 -# E -----expected----- -# E 1 -# E 1 -# E 1 -# E ----------------- -k="${k-}${k+ and }not test_group_job_resources_with_pipe" -%endif - # 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 “Test local” step in -# .github/workflows/main.yml for the list of tests that should be run. +# 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-}" ${ignore-} \ - tests/tests.py \ - tests/test_expand.py \ - tests/test_io.py \ - tests/test_schema.py \ - tests/test_linting.py \ - tests/test_executor_test_suite.py + tests/tests.py \ +%if %{with conda_tests} + tests/tests_using_conda.py \ %endif + tests/test_expand.py \ + tests/test_io.py \ + tests/test_schema.py \ + tests/test_linting.py \ + tests/test_executor_test_suite.py \ + tests/test_internals.py +%endif + %files -f %{pyproject_files} %doc CHANGELOG.md @@ -309,5 +552,6 @@ k="${k-}${k+ and }not test_group_job_resources_with_pipe" %{_datadir}/vim/vimfiles/ftplugin/snakemake/ %{_datadir}/vim/vimfiles/syntax/snakemake.vim + %changelog %autochangelog diff --git a/sources b/sources index c6b761f..a5dc5cd 100644 --- a/sources +++ b/sources @@ -1 +1,2 @@ -SHA512 (snakemake-8.18.2.tar.gz) = a8ed98541fcf60236c6a1507d4d0088a14e2d5af9ba4d6059e9314fb49b4534a3a64b52b1725a20ab3f415f187748c0c82b93880ef232d90593a0b81a7809af7 +SHA512 (snakemake-8.30.0.tar.gz) = f8e5f09377b55cd2394dbc6ce82e221a52a7f7a4a6fb70d57f72297ee5d3cb045f4fbbb24c589b6785d9edeaa0ce6ba13cb54f26470918166ed49af4497f0ebe +SHA512 (snakemake-8.30.0-assets.tar.zst) = beadfe2c8a2b41e927b20420cdec88670acc6111283f413260213d70e6e5f9e6007249b83f889a043810ab72b89e3963d5732be79873ace6637c3b7675c21e19 From af2d0a81b49b658fb764550121d2ef385bf99f4c Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Thu, 8 May 2025 06:52:33 -0400 Subject: [PATCH 053/109] F41+: Use the provisional pyproject declarative buildsystem --- snakemake.spec | 40 ++++++++++++++-------------------------- 1 file changed, 14 insertions(+), 26 deletions(-) diff --git a/snakemake.spec b/snakemake.spec index a2dd730..f7c19f3 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -172,9 +172,13 @@ Patch: 0001-chore-Add-license-texts-for-things-bundled-in-the-as.patch # the substring "modified-assets" in the patch name. Patch: snakemake-8.30.0-modified-assets.patch -BuildArch: noarch +BuildSystem: pyproject +# Generate BR’s for all supported extras to ensure they do not FTI +BuildOption(generate_buildrequires): -x reports,messaging +BuildOption(install): -l snakemake +BuildOption(check): -e '*.tests*' -BuildRequires: python3-devel +BuildArch: noarch BuildRequires: help2man @@ -407,13 +411,6 @@ BuildRequires: %{py3_dist google-cloud-storage} %autosetup -n snakemake-%{version} -p1 %setup -q -T -D -a 1 -c -n snakemake-%{version} -%py3_shebang_fix . -# Remove shebangs from non-executable scripts. The Python script is executable -# in the source tree but will be installed without executable permissions. -sed -r -i '1{/^#!/d}' \ - snakemake/executors/jobscript.sh \ - snakemake/executors/google_lifesciences_helper.py - # Copy and rename nano and vim extensions readmes for use in the main # documentation directory. for editor in nano vim @@ -440,18 +437,14 @@ Assets.spec["tailwindcss/tailwind.css"].sha256 = "$( EOF -%generate_buildrequires -# Generate BR’s for all supported extras to ensure they do not FTI -%pyproject_buildrequires -x reports,messaging +%install -a +# Fix shebangs (no /usr/env shebangs) +%py3_shebang_fix %{buildroot}%{python3_sitelib} %{buildroot}%{_bindir} - -%build -%pyproject_wheel - - -%install -%pyproject_install -%pyproject_save_files -l snakemake +# 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/google_lifesciences_helper.py # Mark license files in the asset bundle. sed -r -i 's@^.*/(LICEN[CS]E|NOTICE)[^/]*$@%%license &@' %{pyproject_files} @@ -476,12 +469,7 @@ find '%{buildroot}%{_datadir}/vim/vimfiles' \ -type f -name 'README.*' -print -delete -%check -# Even if we are running the tests, this is useful; it could turn up import -# errors that would only be revealed by tests we had to disable (e.g. due to -# network access). -%pyproject_check_import -e '*.tests*' - +%check -a %if %{with tests} %if %{without network_tests} # The following require network access (at least DNS) and pass if it is From 8d09f652b86ece3829ef5e1d6c6399985476b570 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Thu, 8 May 2025 07:12:42 -0400 Subject: [PATCH 054/109] Update .rpmlintrc file for latest rpmlint and snakemake versions --- snakemake.rpmlintrc | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/snakemake.rpmlintrc b/snakemake.rpmlintrc index 4a4b850..1640ec5 100644 --- a/snakemake.rpmlintrc +++ b/snakemake.rpmlintrc @@ -11,7 +11,15 @@ addFilter(r"spelling-error \('([Mm]etapackage)s?',") # Some small files may incidentally have duplicate contents. Because they are # small in size and few in number, it is not worth the spec-file complexity to # hardlink them (which would itself trigger an rpmlint warning about -# cross-directory hardlinking). +# cross-directory hardlinking). This includes some of the web/report assed +# license files. addFilter(r"files-duplicate .*/snakemake/.*/remote/[^/]+\.py") +addFilter(r"files-duplicate .*/snakemake/.*/tests/.*/caption\.rst") +addFilter(r"files-duplicate .*/snakemake/assets/data/.*/LICEN[CS]E.*") # This is, unfortunately, intentional. See the comments in the spec file. addFilter(r" python-leftover-require python-unversioned-command$") +# This Source cannot be a URL because we must use a script to generate it, as +# documented in the spec file. +addFilter(r" invalid-url Source[0-9]+: snakemake-.*-assets\.tar\.zst$") +# Bogus; it is a perfectly fine zstandard file. +addFilter(r" inconsistent-file-extension snakemake-.*-assets\.tar\.zst$") From 7632af6245536a990e89207c1d94f0326708467c Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Fri, 21 Mar 2025 13:53:26 -0400 Subject: [PATCH 055/109] Update to 9.3.3 (close RHBZ#2309617) --- .gitignore | 2 + ...k-around-setuptools-76-hash-mismatch.patch | 54 -- ...e-texts-for-things-bundled-in-the-as.patch | 677 ------------------ get_assets | 16 +- ...h => snakemake-9.1.1-modified-assets.patch | 18 +- snakemake.rpmlintrc | 13 +- snakemake.spec | 155 ++-- sources | 4 +- 8 files changed, 113 insertions(+), 826 deletions(-) delete mode 100644 0001-Revert-chore-work-around-setuptools-76-hash-mismatch.patch delete mode 100644 0001-chore-Add-license-texts-for-things-bundled-in-the-as.patch rename snakemake-8.30.0-modified-assets.patch => snakemake-9.1.1-modified-assets.patch (69%) diff --git a/.gitignore b/.gitignore index 6554fb6..aa2543e 100644 --- a/.gitignore +++ b/.gitignore @@ -65,3 +65,5 @@ /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 diff --git a/0001-Revert-chore-work-around-setuptools-76-hash-mismatch.patch b/0001-Revert-chore-work-around-setuptools-76-hash-mismatch.patch deleted file mode 100644 index 509268a..0000000 --- a/0001-Revert-chore-work-around-setuptools-76-hash-mismatch.patch +++ /dev/null @@ -1,54 +0,0 @@ -From 9d99c1c7fc2bb7ebfcba570fe64f07b0646f294a Mon Sep 17 00:00:00 2001 -From: "Benjamin A. Beasley" -Date: Tue, 18 Mar 2025 22:18:47 -0400 -Subject: [PATCH] Revert "chore: work around setuptools 76 hash mismatch from - March 9, 2025 (#3370)" - -This reverts commit 477e5f80d781334afcd549c612823caba1ef6299. ---- - pyproject.toml | 3 +-- - test-environment.yml | 5 ++--- - 2 files changed, 3 insertions(+), 5 deletions(-) - -diff --git a/pyproject.toml b/pyproject.toml -index 52229b4d..275a4655 100644 ---- a/pyproject.toml -+++ b/pyproject.toml -@@ -1,8 +1,7 @@ - [build-system] - build-backend = "setuptools.build_meta" - requires = [ -- # TODO relax upper bound, as of March 9 2025 there is a hash mismatch in setuptools on pypi -- "setuptools>=42,<76", -+ "setuptools>=42", - 'tomli; python_version < "3.11"', - ] - -diff --git a/test-environment.yml b/test-environment.yml -index 6b778458..df8a30de 100644 ---- a/test-environment.yml -+++ b/test-environment.yml -@@ -4,7 +4,6 @@ channels: - - nodefaults - dependencies: - - python >=3.11 -- - setuptools - - yte - - packaging - - boto3 -@@ -58,10 +57,10 @@ dependencies: - - nodejs # for cwltool - - immutables - - conda -- - cwltool -- - cwl-utils - - pip - - pip: -+ - cwltool -+ - cwl-utils - - snakemake-interface-executor-plugins >=9.3.1 - - snakemake-executor-plugin-cluster-generic >=1.0.9 - - snakemake-storage-plugin-http --- -2.48.1 - diff --git a/0001-chore-Add-license-texts-for-things-bundled-in-the-as.patch b/0001-chore-Add-license-texts-for-things-bundled-in-the-as.patch deleted file mode 100644 index 759db2d..0000000 --- a/0001-chore-Add-license-texts-for-things-bundled-in-the-as.patch +++ /dev/null @@ -1,677 +0,0 @@ -From 5d4175e75a0981d9d925ecde4297d3b568c403c2 Mon Sep 17 00:00:00 2001 -From: Ben Beasley -Date: Tue, 11 Mar 2025 11:46:53 -0400 -Subject: [PATCH] chore: Add license texts for things bundled in the assets - (#3099) -MIME-Version: 1.0 -Content-Type: text/plain; charset=UTF-8 -Content-Transfer-Encoding: 8bit - - -This PR is intended to apply on top of -https://github.com/snakemake/snakemake/pull/3098; see that PR for the -first two commits. - -From there, I attempted to account for all of the NPM packages that are -bundled in `vega/vega.js` via dependencies. I made an effort to verify -that every license file added in this commit actually corresponds to -some code present in `vega.js`. - -Next, I inspected `vega.js` for comments indicating that particular -routines were copied, derived, or adapted from other projects, and added -the license files for those projects. I didn’t attempt to judge whether -or not any of snippets might be distant enough from their inspirations -that they could perhaps claim not to be derived works under a particular -set of copyright laws – I just took the attributions at their word. - -Almost all of these licenses are ones (like `MIT`, `Apache-2.0`, `ISC` -or `BSD-3-Clause`) that require including the copyright and permission -statements (the license text) in copies and derived works, so while this -work is fussy, tedious, and unrewarding, it would seem to be necessary. - -So far, I only dug through `vega.js`. I still need to check if there is -anything in `vega-lite.js` or `vega-embed.js` that isn’t already -accounted for in `vega.js`, and I need to look at the other libraries -too. Still, I thought I should post my work in progress in case it -collected any feedback. - - -### QC - - -* [ ] The PR contains a test case for the changes or the changes are -already covered by an existing test case. **N/A – this change is not -really testable – except that building the package confirms the -checksums match.** -* [x] The documentation (`docs/`) is updated to reflect the changes or -this is not necessary (e.g. if the change does neither modify the -language nor the behavior or functionalities of Snakemake). **N/A – no -documentation update is believed to be necessary.** - - - -## Summary by CodeRabbit - -- **New Features** -- Added numerous new assets and dependencies related to the Vega -library, enhancing functionality. -- Expanded package declarations for various D3 modules and other -libraries in the reporting system. -- Introduced a new class for executing Xonsh scripts, allowing for more -scripting options. -- Added a new rule for running Python scripts in a Conda environment, -improving workflow flexibility. -- Enhanced documentation with a new "Maintainers" section and expanded -resources. - - Introduced a new test suite for validating Conda functionalities. -- Enhanced data validation capabilities using both Pandas and Polars for -handling sample data. - -- **Bug Fixes** -- Ensured that licenses and versions are accurately maintained for -various libraries. -- Improved error handling for Windows-specific issues in the testing -framework. - - ---------- - -Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com> -Co-authored-by: Johannes Köster ---- - snakemake/assets/__init__.py | 400 ++++++++++++++++++ - .../report/html_reporter/data/packages.py | 137 ++++++ - 2 files changed, 537 insertions(+) - -diff --git a/snakemake/assets/__init__.py b/snakemake/assets/__init__.py -index 123bf130..ac343e25 100644 ---- a/snakemake/assets/__init__.py -+++ b/snakemake/assets/__init__.py -@@ -93,6 +93,262 @@ class Assets: - sha256="b75f7ed0af20dedadf92c52bc236161bcf0d294ff2e6e34ca76403203349f71d", - version="5.21.0", - ), -+ # Begin dependencies for vega, included in vega/vega.js -+ # Versions from https://github.com/vega/vega/blob/v5.21.0/yarn.lock. -+ # Via vega-crossfilter, vega-encode, vega-format, -+ # vega-functions, vega-geo, vega-regression, vega-scale, vega-statistics, -+ # vega-time, vega-transforms, vega-view; and via d3-geo (via vega-functions, -+ # vega-geo, vega-projection); and via d3-geo-projection (via vega-projection) -+ # -+ # This has its own dependency, internmap (1.0.1); however, while we can -+ # find code from vega-crossfilter and d3-array in vega.js, there does -+ # not appear to be any code from internmap after tree-shaking. -+ "d3-array/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/d3/d3-array/refs/tags/v{version}/LICENSE", -+ sha256="0747bebeb06b10954913149be9b9a8bdf6fad3e6fdcbd9f9524e7a94c13d2cea", -+ version="2.12.1", -+ ), -+ # Via vega-format -+ "d3-format/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/d3/d3-format/refs/tags/v{version}/LICENSE", -+ sha256="7eea8533ea92bd8c32a901e89ecb0305890905bb12711449565ddff96891146d", -+ version="2.0.0", -+ ), -+ # Via vega-format -+ "d3-time-format/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/d3/d3-time-format/refs/tags/v{version}/LICENSE", -+ sha256="7a3cb0e5055874e67db9aa2d5fe26de23204fa994ffbad198901ffe9c812a717", -+ version="3.0.0", -+ ), -+ # Via vega-time, vega-view; and via d3-time-format (via vega-format) -+ "d3-time/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/d3/d3-time/refs/tags/v{version}/LICENSE", -+ sha256="e1211892da0b0e0585b7aebe8f98c1274fba15bafe47fa1f4ee8a7a502c06304", -+ version="2.1.1", -+ ), -+ # Via vega-encode, vega-scale -+ "d3-interpolate/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/d3/d3-interpolate/refs/tags/v{version}/LICENSE", -+ sha256="e1211892da0b0e0585b7aebe8f98c1274fba15bafe47fa1f4ee8a7a502c06304", -+ version="2.0.1", -+ ), -+ # Via vega-functions, vega-geo; and via d3-interpolate (via vega-encode) -+ "d3-color/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/d3/d3-color/refs/tags/v{version}/LICENSE", -+ sha256="e1211892da0b0e0585b7aebe8f98c1274fba15bafe47fa1f4ee8a7a502c06304", -+ version="2.0.0", -+ ), -+ # Via vega-scale -+ "d3-scale/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/d3/d3-scale/refs/tags/v{version}/LICENSE", -+ sha256="7eea8533ea92bd8c32a901e89ecb0305890905bb12711449565ddff96891146d", -+ version="3.3.0", -+ ), -+ # Via vega-expression (vega-lite also depends on vega-expression) -+ # The license file included in the NPM package does not exist directly -+ # in https://github.com/DefinitelyTyped/DefinitelyTyped, so we use an -+ # unpkg URL to reference the contents of the NPM package instead. -+ "@types-estree/LICENSE": Asset( -+ url="https://unpkg.com/@types/estree@{version}/LICENSE", -+ sha256="c2cfccb812fe482101a8f04597dfc5a9991a6b2748266c47ac91b6a5aae15383", -+ version="0.0.50", -+ ), -+ # Via vega-force -+ "d3-force/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/d3/d3-force/refs/tags/v{version}/LICENSE", -+ sha256="e1211892da0b0e0585b7aebe8f98c1274fba15bafe47fa1f4ee8a7a502c06304", -+ version="2.1.1", -+ ), -+ # Via d3-force (via vega-force) -+ "d3-dispatch/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/d3/d3-dispatch/refs/tags/v{version}/LICENSE", -+ sha256="e1211892da0b0e0585b7aebe8f98c1274fba15bafe47fa1f4ee8a7a502c06304", -+ version="2.0.0", -+ ), -+ # Via d3-force (via vega-force) -+ "d3-quadtree/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/d3/d3-quadtree/refs/tags/v{version}/LICENSE", -+ sha256="e1211892da0b0e0585b7aebe8f98c1274fba15bafe47fa1f4ee8a7a502c06304", -+ version="2.0.0", -+ ), -+ # Via vega-view; and via d3-force (via vega-force) -+ "d3-timer/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/d3/d3-timer/refs/tags/v{version}/LICENSE", -+ sha256="e1211892da0b0e0585b7aebe8f98c1274fba15bafe47fa1f4ee8a7a502c06304", -+ version="2.0.0", -+ ), -+ # Via vega-functions, vega-geo, vega-projection (directly and via -+ # d3-geo-projection) -+ "d3-geo/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/d3/d3-geo/refs/tags/v{version}/LICENSE", -+ sha256="c3c9d41a75b64963748657932167ec4c56404b8fd557d4f89c9eeda6e2fdf39a", -+ version="2.0.2", -+ ), -+ # Via vega-hierarchy -+ "d3-hierarchy/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/d3/d3-hierarchy/refs/tags/v{version}/LICENSE", -+ sha256="e1211892da0b0e0585b7aebe8f98c1274fba15bafe47fa1f4ee8a7a502c06304", -+ version="2.0.0", -+ ), -+ # Via vega-loader -+ # This has its own dependencies (commander 2.20.3, iconv-lite 0.4.24, -+ # rw 1.3.3), but they are all used only in the command-line tools -+ # rather than in the library that is bundled in vega.js. -+ "d3-dsv/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/d3/d3-dsv/refs/tags/v{version}/LICENSE", -+ sha256="8b5304265ccedbd17567aa14a0dc6b9bf4013fee44964c46aa54fdf8527d6a68", -+ version="2.0.0", -+ ), -+ # Via vega-loader; also from vega-geo/src/util/contours.js, "Based on -+ # https://github.com/topojson/topojson-client/blob/v3.0.0/src/stitch.js" -+ # This has its own dependency (commander 2.20.3), but it is used only -+ # in the command-line tools rather than in the library that is bundled -+ # in vega.js. Dependency node-fetch 2.6.4, via vega-loader, is not -+ # used for browser builds. -+ "topojson-client/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/topojson/topojson-client/refs/tags/v{version}/LICENSE", -+ sha256="4c4d15b635e04e691825a76db7d33f7f2033b55669a7430011694f31e6c65999", -+ version="3.1.0", -+ ), -+ # Via vega-projection -+ # This has its own dependencies (commander 2.20.3, resolve 1.20.0), but -+ # they are all used only in the command-line tools rather than in the -+ # library that is bundled in vega.js. -+ "d3-geo-projection/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/d3/d3-geo-projection/refs/tags/v{version}/LICENSE", -+ sha256="4108a126a74cc35d4d5ae39ca5d0cc926fa7c8ec40e459a0c6d3481c69decbd8", -+ version="3.0.0", -+ ), -+ # Via vega-scenegraph (directly and via d3-shape) -+ "d3-path/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/d3/d3-path/refs/tags/v{version}/LICENSE", -+ sha256="b8265327ab678f554800e71188b1cc6b1ff57522e292d2b1c0be66f27cf328b6", -+ version="2.0.0", -+ ), -+ # Via vega-scenegraph -+ "d3-shape/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/d3/d3-shape/refs/tags/v{version}/LICENSE", -+ sha256="7eea8533ea92bd8c32a901e89ecb0305890905bb12711449565ddff96891146d", -+ version="2.1.0", -+ ), -+ # Via vega-voronoi -+ "d3-delaunay/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/d3/d3-delaunay/refs/tags/v{version}/LICENSE", -+ sha256="d19bf35c4080eea32e098a9c8d62540ffd425611ac8dfc856a233f0357d8b02e", -+ version="5.2.0", -+ ), -+ # Via d3-delaunay (via vega-voronoi) -+ "delaunator/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/mapbox/delaunator/refs/tags/v{version}/LICENSE", -+ sha256="27043d1a6a0e1985fde12660decbbd3b23c67de900b00609c90d4f0aa492f425", -+ version="4.0.1", -+ ), -+ # End dependencies for vega, included in vega/vega.js -+ # Begin copied/derived/adapted code in vega, included in vega/vega.js -+ # From vega-util/src/lruCache.js, "adapted from -+ # https://github.com/dominictarr/hashlru/ (MIT License)". Version 1.0.4 -+ # was the current version when the function was added to vega, in -+ # commit f153863f3575bff1b42294c9cb065d80afb757ff on 2020-02-28. -+ "hashlru/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/dominictarr/hashlru/refs/tags/v{version}/LICENSE", -+ sha256="08e4bd7a280eaaf1fbcaad9dad1fb94412477fcdd1cf81660988303297e5e1d1", -+ version="1.0.4", -+ ), -+ # From -+ # vega-statistics/src/regression/{poly,r-squared,pow,log,linear}.js, -+ # "Adapted from d3-regression by Harry Stevens". Version 1.2.1 was the -+ # current version when the functions were added to vega, in commit -+ # 71610e4456a3a4145435d83f8458748ba137a2a3 2019-05-10. That release was -+ # not tagged in git, so we use the corresponding commit hash. -+ "d3-regression/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/HarryStevens/d3-regression/e23d40a663dffba14b92cb42d9989de3a32894b5/LICENSE", -+ sha256="d210203f922101502894baf700b9a392e323a26e4b603ab166c57e09a6e773b5", -+ version="1.2.1", -+ ), -+ # From vega-statistics/src/regression/poly.js, "Adapted from -+ # d3-regression by Harry Stevens [...] which was adapted from -+ # regression-js by Tom Alexander" Version 2.0.1 was the current version -+ # when the functions were added to vega, in commit -+ # 71610e4456a3a4145435d83f8458748ba137a2a3 2019-05-10. -+ "regression/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/Tom-Alexander/regression-js/refs/tags/{version}/LICENSE", -+ sha256="2f932f5cfb9b042cc6c0089ee8004b33e3746ffeab879341dbd453c150524307", -+ version="2.0.1", -+ ), -+ # From vega-statistics/src/regression/loess.js, "Adapted from -+ # science.js by Jason Davies". Version 1.9.3 was the current version -+ # when the functions were added to vega, in commit -+ # 71610e4456a3a4145435d83f8458748ba137a2a3 on 2019-05-10. -+ "science/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/jasondavies/science.js/refs/tags/v{version}/LICENSE", -+ sha256="3bd1fdf686ffcad175daddcb36ee28599ac8f090b6cec2c7654118c8a6f3d4c9", -+ version="1.9.3", -+ ), -+ # From src/quickselect.js in d3-array, "Based on -+ # https://github.com/mourner/quickselect". Version 2.0.0 was the -+ # current version when the file was added to d3-array, in commit -+ # d447c2a31cd6aacf54a40b22c29620f7e17bbd7e on 2018-11-10. -+ "quickselect/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/mourner/quickselect/refs/tags/v{version}/LICENSE", -+ sha256="597034cb7c11c916ad407344ea99a0b08e3c443a6b4421460f1d23c411c69707", -+ version="2.0.0", -+ ), -+ # From vega-statistics/src/normal.js, "Ported from Apache Commons -+ # Math". Version 3.6.1 was the current version when this implementation -+ # of erfinv was added to vega, in commit -+ # c26050f21b0c95620f8f1a3094056716ec6c5aaa on 2019-09-26. -+ "commons-math/LICENSE.txt": Asset( -+ url="https://raw.githubusercontent.com/apache/commons-math/refs/tags/MATH_3_6_1/LICENSE.txt", -+ sha256="64f23963615950bad9ddd31569a7f09afbbe11b81d94873ffd9b1cac6081a11d", -+ version="3.6.1", -+ ), -+ "commons-math/NOTICE.txt": Asset( -+ url="https://raw.githubusercontent.com/apache/commons-math/refs/tags/MATH_3_6_1/NOTICE.txt", -+ sha256="5495442a32bfc2b93b4a8f2c34c5c218d16cca434aa5684fb953d9419120e3fa", -+ version="3.6.1", -+ ), -+ # From vega-expression/src/parser.js, "The following expression parser -+ # is based on Esprima (http://esprima.org/)." Unusually, the original -+ # license text is reproduced in the source file, so we could get by -+ # without a separate license file (and in fact the license file lacks -+ # the necessary copyright statement present in the code) but we add it -+ # for consistency. Version 2.2.0 was the last version of Esprima that -+ # had a copyright statement in esprima.js attributing specific -+ # individual contributors, as reproduced in the vega source. -+ "esprima/LICENSE.BSD": Asset( -+ url="https://raw.githubusercontent.com/jquery/esprima/refs/tags/{version}/LICENSE.BSD", -+ sha256="0e74697a68cebdcd61502c30fe80ab7f9e341d995dcd452023654d57133534b1", -+ version="2.2.0", -+ ), -+ # From vega-scenegraph/src/path/arc.js, "Copied from Inkscape svgtopdf, -+ # thanks!" We cannot find the original implementation in Inkscape or -+ # anywhere else, so we do not add a license file for this snippet. -+ # From vega-scenegraph/src/path/parse.js, "Path parsing and rendering -+ # code adapted from fabric.js -- Thanks!" This was added in commit -+ # 82932143de7cef4187a34026689df12abaa25959 on 2018-12-20, and the -+ # current release of fabric.js at that time was 2.4.5. -+ "fabric/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/fabricjs/fabric.js/refs/tags/v{version}/LICENSE", -+ sha256="9f6c2cc99aa9c618df93fed7d1cf7279d4e329d92dd2ce5e96173c73ce305055", -+ version="2.4.5", -+ ), -+ # From vega-geo/src/util/{contours,density2D}.js, "Implementation -+ # adapted from d3/d3-contour. Thanks!" When these routines were added -+ # in 0ab6b730a7e576d33d00e12063855bb132194191 on 2019-11-11, the latest -+ # version was 1.3.2. -+ "d3-contour/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/d3/d3-contour/refs/tags/v{version}/LICENSE", -+ sha256="5f5dcce265668080a60fbdc513f6f8ef21466780bcaa331e64ee39df19e63b30", -+ version="1.3.2", -+ ), -+ # From vega-geo/src/util/contours.js, "Based on -+ # https://github.com/mbostock/shapefile/blob/v0.6.2/shp/polygon.js" -+ "shapefile/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/mbostock/shapefile/refs/tags/v{version}/LICENSE.txt", -+ sha256="c16529a9d5b8802982abd714a6823344e24b0cb5131596bc343927ead605d708", -+ version="0.6.2", -+ ), -+ # End copied/derived/adapted code in vega, included in vega/vega.js - "vega-lite/vega-lite.js": Asset( - url="https://cdnjs.cloudflare.com/ajax/libs/vega-lite/{version}/vega-lite.js", - sha256="6eb7f93121cd9f44cf8640244f87c5e143f87c7a0b6cd113da4a9e41e3adf0aa", -@@ -103,6 +359,57 @@ class Assets: - sha256="f618900fd0d64046963b29f40590cdd1e341a2f41449f99110d82fd81fea808c", - version="5.2.0", - ), -+ # Begin dependencies for vega-lite, included in vega-lite/vega-lite.js -+ # Versions from https://github.com/vega/vega-lite/blob/v5.2.0/yarn.lock. -+ "@types-clone/LICENSE": Asset( -+ url="https://unpkg.com/@types/clone@{version}/LICENSE", -+ 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", -+ version="2.1.2", -+ ), -+ "fast-deep-equal/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/epoberezkin/fast-deep-equal/refs/tags/v{version}/LICENSE", -+ sha256="7bf9b2de73a6b356761c948d0e9eeb4be6c1270bd04c79cd489c1e400ffdfc1a", -+ version="3.1.3", -+ ), -+ "fast-json-stable-stringify/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/epoberezkin/fast-json-stable-stringify/refs/tags/v{version}/LICENSE", -+ sha256="a833d366242c298cf1b10263516572fb8dcbe68eb5072cdcac2b4546e2b4eb36", -+ version="2.1.0", -+ ), -+ "json-stringify-pretty-compact/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/lydell/json-stringify-pretty-compact/refs/tags/v{version}/LICENSE", -+ sha256="d0800a7c9b5f723f7fe029f75d3a9ae44173178b9729d1521e18371ab24ae97a", -+ version="3.0.0", -+ ), -+ # The tslib package is among vega-lite's direct dependencies, and the -+ # yarn.lock file shows three versions could be included: 2.2.0, 2.1.0 -+ # (both MIT-licensed), and 1.1.0 (Apache-2.0-licensed). However, we -+ # found no trace of any of these in the actual vega-lite.js bundle. -+ # ---- -+ # The following packages are part of vega, and are already covered by -+ # vega/LICENSE. -+ # - vega-event-selector: no dependencies -+ # - vega-expression: depends on vega-util, @types/estree (already -+ # covered as one of vega's dependencies) -+ # - vega-util (no dependencies; includes code from hashlru, already -+ # covered as one of vega's dependencies) -+ # ---- -+ # End dependencies for vega-lite, included in vega-lite/vega-lite.js -+ # Begin copied/derived/adapted code in vega-lite, included in vega-lite/vega-lite.js -+ # - hashlru is included in vega-util; already covered as one of vega's dependencies -+ # End copied/derived/adapted code in vega-lite, included in vega-lite/vega-lite.js - "vega-embed/vega-embed.js": Asset( - url="https://cdnjs.cloudflare.com/ajax/libs/vega-embed/{version}/vega-embed.js", - sha256="4e546c1f86eb200333606440e92f76e2940b905757018d9672cd1708e4e6ff0a", -@@ -113,6 +420,78 @@ class Assets: - sha256="32df67148f0fc3db0eb9e263a7b75d07f1eb14c61955005a4a39c6918d10d137", - version="6.20.8", - ), -+ # Begin dependencies for vega-embed, included in vega-embed/vega-embed.js -+ # Versions from https://github.com/vega/vega-embed/blob/v6.20.8/yarn.lock. -+ "fast-json-patch/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/Starcounter-Jack/JSON-Patch/refs/tags/v{version}/LICENSE.txt", -+ sha256="26593d78926902a82eb9bc7e40d1811fc381055f23516b92fe48ca8399bf02df", -+ version="3.1.0", -+ ), -+ # json-stringify-pretty-compact 3.0.0 is already covered as one of -+ # vega's dependencies -+ # ---- -+ # There are four versions of the semver package in yarn.lock (5.7.1, -+ # 6.3.0, 7.0.0, 7.3.5), but it appears that only one copy remains in -+ # the vega-embed.js bundle. The bundle has a compareBuild function, -+ # added in 6.1.0. It does not export a "tokens" list, added in 6.3.0 -+ # and present in 7.0.0, but that is not conclusive because the package -+ # was split into separate source files to improve tree-shaking. By -+ # 7.3.5, the first line of the SemVer class constructor changes to -+ # "options = parseOptions(options)", and this does match what we see in -+ # the bundle, so we conclude that we have semver 7.3.5. In any case, -+ # the ISC license was unchanged across all four versions. -+ "semver/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/npm/node-semver/refs/tags/v{version}/LICENSE", -+ sha256="4ec3d4c66cd87f5c8d8ad911b10f99bf27cb00cdfcff82621956e379186b016b", -+ version="7.3.5", -+ ), -+ # The tslib package is among vega-embed's direct dependencies, and the -+ # yarn.lock file shows four versions could be included: 2.3.1, 2.1.0, -+ # 1.14.1 (all MIT-licensed), and 1.1.0 (Apache-2.0-licensed). However, -+ # we found no trace of any of these in the actual vega-embed.js bundle. -+ # ---- -+ # The following packages are part of vega, and are already covered by -+ # vega/LICENSE. -+ # - vega-interpreter: no dependencies -+ # ---- -+ # This is not part of https://github.com/vega/vega, as far as we can -+ # tell, so we handle it separately. The repository -+ # https://github.com/vega/schema linked from NPM appears to contain -+ # only JSON schemas, not JavaScript source code, so we use an unpkg URL -+ # to reference the contents of the NPM package instead. -+ "vega-schema-url-parser/LICENSE": Asset( -+ url="https://unpkg.com/vega-schema-url-parser@{version}/LICENSE", -+ sha256="eeb1606fda238f623c36d1eb5e27c33b986a446445340b220c141097424af045", -+ version="2.2.0", -+ ), -+ "vega-themes/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/vega/vega-themes/refs/tags/v{version}/LICENSE", -+ sha256="ceb75fa4fbebbc381c0465442a502ffc13b73f36ccb385a66bcd5f55869e3979", -+ version="2.10.0", -+ ), -+ # Depends on vega-util, which is already covered in vega -+ "vega-tooltip/LICENSE": Asset( -+ url="https://raw.githubusercontent.com/vega/vega-tooltip/refs/tags/v{version}/LICENSE", -+ sha256="93cd20d9cee8c77c080d1a585e3b07644ad2c8e9ccdfc86e350136884d62d935", -+ version="0.28.0", -+ ), -+ # End dependencies for vega-embed, included in vega-embed/vega-embed.js -+ # Begin copied/derived/adapted code in vega-embed, included in vega-embed/vega-embed.js -+ # - hashlru is included in vega-util (via vega-tooltip); already -+ # covered as one of vega's dependencies -+ # - _areEquals() is based on fast-deep-equal; already covered as one of -+ # vega-lite's dependencies -+ # - googlecharts theme in vega-themes carries its own copyright statement, -+ # Copyright 2020 Google LLC. -+ # -+ # Use of this source code is governed by a BSD-style -+ # license that can be found in the LICENSE file or at -+ # https://developers.google.com/open-source/licenses/bsd -+ # No plain-text version of that URL is available, and the license has -+ # the same BSD-3-Clause permission statement as vega-themes itself, -+ # so we consider the combination of vega-themes/LICENSE and the -+ # copyright statement in the source code sufficient. -+ # End copied/derived/adapted code in vega-embed, included in vega-embed/vega-embed.js - "heroicons/LICENSE": Asset( - url="https://raw.githubusercontent.com/tailwindlabs/heroicons/refs/tags/v{version}/LICENSE", - sha256="75523ddd65d9620bea09f84e89d0c373b4205a3708b8a1e9f9598a5438a3e641", -@@ -128,6 +507,27 @@ class Assets: - sha256="f657f99d3fb9647db92628e96007aabb46e5f04f33e49999075aab8e250ca7ce", - version="15.7.2", - ), -+ # Begin dependencies for prop-types, included in prop-types/prop-types.min.js -+ # Versions from https://github.com/facebook/prop-types/blob/v15.7.2/yarn.lock -+ # ---- -+ # The loose-envify package is among prop-types's direct dependencies, -+ # and the yarn.lock file shows two versions could be included: 1.4.0 -+ # and 1.3.1 (both MIT-licensed). However, we found no trace of -+ # loose-envify code in the actual prop-types.min.js bundle, so it -+ # appears this dependency was removed in tree-shaking, along with its -+ # dependency js-tokens (3.0.0 and/or 4.0.0). -+ # ---- -+ # The object-assign package (version 4.1.1) is among prop-types's -+ # direct dependencies, but we found no trace of it in the actual -+ # prop-types.min.js bundle, so it appears this dependency (a polyfill) -+ # was removed in tree-shaking. -+ # ---- -+ # The react-is package (version 16.8.1) is among prop-types's -+ # direct dependencies, but we found no trace of it in the actual -+ # prop-types.min.js bundle, so it appears this dependency was removed -+ # in tree-shaking. -+ # ---- -+ # End dependencies for prop-types, included in prop-types/prop-types.min.js - } - - @classmethod -diff --git a/snakemake/report/html_reporter/data/packages.py b/snakemake/report/html_reporter/data/packages.py -index 963a4c10..2b8e364f 100644 ---- a/snakemake/report/html_reporter/data/packages.py -+++ b/snakemake/report/html_reporter/data/packages.py -@@ -38,14 +38,151 @@ def get_packages(): - source_path="vega/vega.js", - license_path="vega/LICENSE", - ), -+ # Begin dependencies for vega, included in vega/vega.js -+ "d3-array": Package( -+ license_path="d3-array/LICENSE", -+ ), -+ "d3-format": Package( -+ license_path="d3-format/LICENSE", -+ ), -+ "d3-time-format": Package( -+ license_path="d3-time-format/LICENSE", -+ ), -+ "d3-time": Package( -+ license_path="d3-time/LICENSE", -+ ), -+ "d3-interpolate": Package( -+ license_path="d3-interpolate/LICENSE", -+ ), -+ "d3-color": Package( -+ license_path="d3-color/LICENSE", -+ ), -+ "d3-scale": Package( -+ license_path="d3-scale/LICENSE", -+ ), -+ "@types-estree": Package( -+ license_path="@types-estree/LICENSE", -+ ), -+ "d3-force": Package( -+ license_path="d3-force/LICENSE", -+ ), -+ "d3-dispatch": Package( -+ license_path="d3-dispatch/LICENSE", -+ ), -+ "d3-quadtree": Package( -+ license_path="d3-quadtree/LICENSE", -+ ), -+ "d3-timer": Package( -+ license_path="d3-timer/LICENSE", -+ ), -+ "d3-geo": Package( -+ license_path="d3-geo/LICENSE", -+ ), -+ "d3-hierarchy": Package( -+ license_path="d3-hierarchy/LICENSE", -+ ), -+ "d3-dsv": Package( -+ license_path="d3-dsv/LICENSE", -+ ), -+ "topojson-client": Package( -+ license_path="topojson-client/LICENSE", -+ ), -+ "d3-geo-projection": Package( -+ license_path="d3-geo-projection/LICENSE", -+ ), -+ "d3-path": Package( -+ license_path="d3-path/LICENSE", -+ ), -+ "d3-shape": Package( -+ license_path="d3-shape/LICENSE", -+ ), -+ "d3-delaunay": Package( -+ license_path="d3-delaunay/LICENSE", -+ ), -+ "delaunator": Package( -+ license_path="delaunator/LICENSE", -+ ), -+ # End dependencies for vega, included in vega/vega.js -+ # Begin copied/derived/adapted code in vega, included in vega/vega.js -+ "hashlru": Package( -+ license_path="hashlru/LICENSE", -+ ), -+ "d3-regression": Package( -+ license_path="d3-regression/LICENSE", -+ ), -+ "regression": Package( -+ license_path="regression/LICENSE", -+ ), -+ "science": Package( -+ license_path="science/LICENSE", -+ ), -+ "quickselect": Package( -+ license_path="quickselect/LICENSE", -+ ), -+ "commons-math": Package( -+ license_path="commons-math/LICENSE.txt", -+ # This must be included with LICENSE.txt. -+ notice="commons-math/NOTICE.txt", -+ ), -+ "esprima": Package( -+ license_path="esprima/LICENSE.BSD", -+ ), -+ "fabric": Package( -+ license_path="fabric/LICENSE", -+ ), -+ "d3-contour": Package( -+ license_path="d3-contour/LICENSE", -+ ), -+ # End copied/derived/adapted code in vega, included in vega/vega.js - "vega-lite": Package( - source_path="vega-lite/vega-lite.js", - license_path="vega-lite/LICENSE", - ), -+ # Begin dependencies for vega-lite, included in vega-lite/vega-lite.js -+ # (excluding those shared with vega and therefore already documented) -+ "@types-clone": Package( -+ license_path="@types-estree/LICENSE", -+ ), -+ "array-flat-polyfill": Package( -+ license_path="array-flat-polyfill/LICENSE", -+ ), -+ "clone": Package( -+ license_path="clone/LICENSE", -+ ), -+ "fast-deep-equal": Package( -+ license_path="fast-deep-equal/LICENSE", -+ ), -+ "fast-json-stable-stringify": Package( -+ license_path="fast-json-stable-stringify/LICENSE", -+ ), -+ "json-stringify-pretty-compact": Package( -+ license_path="json-stringify-pretty-compact/LICENSE", -+ ), -+ # End dependencies for vega-lite, included in vega-lite/vega-lite.js -+ # Any copied/derived/adapted code in vega-lite is shared with vega. - "vega-embed": Package( - source_path="vega-embed/vega-embed.js", - license_path="vega-embed/LICENSE", - ), -+ # Begin dependencies for vega-embed, included in vega-embed/vega-embed.js -+ # (excluding those shared with vega/vega-lite and therefore already documented) -+ "fast-json-patch": Package( -+ license_path="fast-json-patch/LICENSE", -+ ), -+ "semver": Package( -+ license_path="semver/LICENSE", -+ ), -+ "vega-schema-url-parser": Package( -+ license_path="vega-schema-url-parser/LICENSE", -+ ), -+ "vega-themes": Package( -+ license_path="vega-themes/LICENSE", -+ ), -+ "vega-tooltip": Package( -+ license_path="vega-tooltip/LICENSE", -+ ), -+ # End dependencies for vega-embed, included in vega-embed/vega-embed.js -+ # Any copied/derived/adapted code in vega-embed is shared with vega and/or vega-lite. - "heroicons": Package( - license_path="heroicons/LICENSE", - ), --- -2.48.1 - diff --git a/get_assets b/get_assets index 85a81ca..c69a1cd 100755 --- a/get_assets +++ b/get_assets @@ -25,7 +25,7 @@ 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}/snakemake/assets/")" +MTIME="$(stat --format='%Y' "${XDIR}/src/snakemake/assets/")" echo "==== Apply patches ====" 1>&2 spectool --list-files "${SPEC}" | @@ -40,14 +40,14 @@ spectool --list-files "${SPEC}" | done echo "==== Download assets ====" 1>&2 -PYTHONPATH="${PWD}/${XDIR}/snakemake" python3 <<'EOF' +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='snakemake/assets/data/vega-lite/vega-lite.js' +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}/${target}" 1>&2 @@ -55,15 +55,15 @@ sed -r -i '/^[[:blank:]]*Array\.prototype\.flat[[:blank:]]*\|\|/d' \ "${XDIR}/${target}" echo '--> Search for vestiges of array-flat-polyfill' 1>&2 if grep -ErinI 'defineProperty\(Array\.prototype,[[:blank:]]*.flat' \ - "${XDIR}/snakemake/assets" + "${XDIR}/src/snakemake/assets" then echo 'MANUAL AUDIT REQUIRED' 1>&2 exit 1 fi # Remove license file and the directory containing it -rm -rv "${XDIR}/snakemake/assets/data/array-flat-polyfill" +rm -rv "${XDIR}/src/snakemake/assets/data/array-flat-polyfill" echo "--> Search for missed CC0-1.0 licenses" 1>&2 -if grep -ErinI '\bCC0\b' "${XDIR}/snakemake/assets" +if grep -ErinI '\bCC0\b' "${XDIR}/src/snakemake/assets" then echo 'MANUAL AUDIT REQUIRED' 1>&2 exit 1 @@ -71,7 +71,7 @@ fi echo "==== Archive assets ====" 1>&2 RESULT="${XDIR}-assets.tar.zst" -ls -ld "${XDIR}/snakemake/assets/" +ls -ld "${XDIR}/src/snakemake/assets/" # https://www.gnu.org/software/tar/manual/html_section/Reproducibility.html TZ=UTC LC_ALL=C tar \ --create \ @@ -82,7 +82,7 @@ TZ=UTC LC_ALL=C tar \ --pax-option='delete=atime,delete=ctime' \ --clamp-mtime --mtime="@${MTIME}" \ --directory="${XDIR}" \ - snakemake/assets/data | + src/snakemake/assets/data | zstdmt --ultra -22 > "${RESULT}" mv -v "${RESULT}" "${DIST_GIT}" diff --git a/snakemake-8.30.0-modified-assets.patch b/snakemake-9.1.1-modified-assets.patch similarity index 69% rename from snakemake-8.30.0-modified-assets.patch rename to snakemake-9.1.1-modified-assets.patch index 8946d82..6aa4419 100644 --- a/snakemake-8.30.0-modified-assets.patch +++ b/snakemake-9.1.1-modified-assets.patch @@ -1,7 +1,7 @@ -diff -Naur snakemake-8.30.0-original/snakemake/assets/__init__.py snakemake-8.30.0/snakemake/assets/__init__.py ---- snakemake-8.30.0-original/snakemake/assets/__init__.py 2025-03-19 10:16:19.899201489 -0400 -+++ snakemake-8.30.0/snakemake/assets/__init__.py 2025-03-19 10:20:34.376310829 -0400 -@@ -349,9 +349,12 @@ +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 @@ -15,7 +15,7 @@ diff -Naur snakemake-8.30.0-original/snakemake/assets/__init__.py snakemake-8.30 version="5.2.0", ), "vega-lite/LICENSE": Asset( -@@ -366,13 +369,6 @@ +@@ -428,13 +431,6 @@ sha256="c2cfccb812fe482101a8f04597dfc5a9991a6b2748266c47ac91b6a5aae15383", version="2.1.1", ), @@ -29,12 +29,12 @@ diff -Naur snakemake-8.30.0-original/snakemake/assets/__init__.py snakemake-8.30 "clone/LICENSE": Asset( url="https://raw.githubusercontent.com/pvorb/clone/refs/tags/v{version}/LICENSE", sha256="3fb0857ef0133928cf72c88dfc464e931486e88778961eedec25585e2321507f", -diff -Naur snakemake-8.30.0-original/snakemake/report/html_reporter/data/packages.py snakemake-8.30.0/snakemake/report/html_reporter/data/packages.py ---- snakemake-8.30.0-original/snakemake/report/html_reporter/data/packages.py 2025-03-19 10:16:19.900335558 -0400 -+++ snakemake-8.30.0/snakemake/report/html_reporter/data/packages.py 2025-03-19 10:16:47.850551627 -0400 +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-estree/LICENSE", + license_path="@types-clone/LICENSE", ), - "array-flat-polyfill": Package( - license_path="array-flat-polyfill/LICENSE", diff --git a/snakemake.rpmlintrc b/snakemake.rpmlintrc index 1640ec5..83eecf6 100644 --- a/snakemake.rpmlintrc +++ b/snakemake.rpmlintrc @@ -11,15 +11,14 @@ addFilter(r"spelling-error \('([Mm]etapackage)s?',") # Some small files may incidentally have duplicate contents. Because they are # small in size and few in number, it is not worth the spec-file complexity to # hardlink them (which would itself trigger an rpmlint warning about -# cross-directory hardlinking). This includes some of the web/report assed -# license files. +# cross-directory hardlinking). addFilter(r"files-duplicate .*/snakemake/.*/remote/[^/]+\.py") addFilter(r"files-duplicate .*/snakemake/.*/tests/.*/caption\.rst") +# Similarly, we expect that there will be some duplicate license files for web +# assets, and it is not worthwhile to attempt to symlink or hardlink these. addFilter(r"files-duplicate .*/snakemake/assets/data/.*/LICEN[CS]E.*") # This is, unfortunately, intentional. See the comments in the spec file. addFilter(r" python-leftover-require python-unversioned-command$") -# This Source cannot be a URL because we must use a script to generate it, as -# documented in the spec file. -addFilter(r" invalid-url Source[0-9]+: snakemake-.*-assets\.tar\.zst$") -# Bogus; it is a perfectly fine zstandard file. -addFilter(r" inconsistent-file-extension snakemake-.*-assets\.tar\.zst$") +# The assets bundle needs to be generated with a script, so it has no URL (and +# .tar.zst is perfectly legitimate). +addFilter(r" (invalid-url|inconsistent-file-extension).* snakemake-.*-assets\.tar\.zst") diff --git a/snakemake.spec b/snakemake.spec index f7c19f3..113bda7 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -41,37 +41,31 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 8.30.0 +Version: 9.3.3 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses -# The primary license for Snakemake is MIT; versioneer contributes Unlicense, -# and web assets contribute a variety of other licenses. +# 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: -# - snakemake/assets/data/vega/vega.js +# - src/snakemake/assets/data/vega/vega.js # # BSD-3-Clause AND MIT: -# - snakemake/assets/data/vega-lite/vega-lite.js +# - src/snakemake/assets/data/vega-lite/vega-lite.js # # BSD-3-Clause AND ISC AND MIT: -# - snakemake/assets/data/vega-embed/vega-embed.js +# - 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. -# - snakemake/assets/data/prop-types/prop-types.min.js -# - snakemake/assets/data/tailwindcss/tailwind.css +# - src/snakemake/assets/data/prop-types/prop-types.min.js +# - src/snakemake/assets/data/tailwindcss/tailwind.css # -# Unlicense: -# - versioneer.py -# - snakemake/_version.py (which says “This file is released into the public -# domain,” but the comments in versioneer.py make it clear that Unlicense is -# intended for the generated files as well) -# -# == License breakdown for snakemake/assets/data/vega/vega.js == +# == License breakdown: src/snakemake/assets/data/vega/vega.js == # # The primary license for npm(vega) is BSD-3-Clause. The bundle contains: # @@ -101,7 +95,7 @@ Summary: Workflow management system to create reproducible and scalable d # MIT-0: # - npm(fabric), bundled as a copied, derived, or adapted snippet # -# == License breakdown for snakemake/assets/data/vega-lite/vega-lite.js == +# == 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: # @@ -116,7 +110,7 @@ Summary: Workflow management system to create reproducible and scalable d # - npm(hashlru), bundled as a copied, derived, or adapted snippet # - npm(json-stringify-pretty-compact) # -# == License breakdown for snakemake/assets/data/vega-embed/vega-embed.js == +# == 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: # @@ -133,8 +127,7 @@ License: %{shrink: BSD-3-Clause AND ISC AND MIT AND - MIT-0 AND - Unlicense + MIT-0 } URL: https://snakemake.readthedocs.io/en/stable/index.html %global forgeurl https://github.com/snakemake/snakemake @@ -152,17 +145,6 @@ Source0: %{forgeurl}/archive/v%{version}/snakemake-%{version}.tar.gz Source1: snakemake-%{version}-assets.tar.zst Source2: get_assets -# Upstream upper-bounded the version of setuptools to work around a hash -# mismatch in setuptools 76 on PyPI observed on March 9, 2025. The system -# setuptools is fine. The upper-bound was removed in a later release. Here we -# revert it as a downstream-only patch. -Patch: 0001-Revert-chore-work-around-setuptools-76-hash-mismatch.patch - -# chore: Add license texts for things bundled in the assets -# https://github.com/snakemake/snakemake/pull/3099 -# Rebased on v8.30.0 -Patch: 0001-chore-Add-license-texts-for-things-bundled-in-the-as.patch - # Downstream-only: adjust the asset metadata in the sources, including # checksums, for any adjustments that happened in the get_assets script. # @@ -170,7 +152,7 @@ Patch: 0001-chore-Add-license-texts-for-things-bundled-in-the-as.patch # 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-8.30.0-modified-assets.patch +Patch: snakemake-9.1.1-modified-assets.patch BuildSystem: pyproject # Generate BR’s for all supported extras to ensure they do not FTI @@ -212,18 +194,18 @@ Provides: vim-snakemake = %{version}-%{release} # 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 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. +# 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. -# snakemake/assets/data/react/react.production.min.js +# src/snakemake/assets/data/react/react.production.min.js Provides: bundled(npm(react)) = 18.2.0 -# snakemake/assets/data/react/react-dom.production.min.js +# src/snakemake/assets/data/react/react-dom.production.min.js Provides: bundled(npm(react-dom)) = 18.2.0 -# snakemake/assets/data/vega/vega.js +# src/snakemake/assets/data/vega/vega.js Provides: bundled(npm(vega)) = 5.21.0 -# Bundled in snakemake/assets/data/vega/vega.js as dependencies: +# 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 @@ -253,7 +235,7 @@ 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 snakemake/assets/__init__.py. +# 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 @@ -275,8 +257,8 @@ 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 snakemake/assets/data/vega/vega.js in the form of copied, derived, -# or adapted snippets. See notes in snakemake/assets/__init__.py. +# 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: @@ -290,21 +272,21 @@ Provides: bundled(npm(regression)) = 2.0.1 Provides: bundled(npm(science)) = 1.9.3 Provides: bundled(npm(shapefile)) = 0.6.2 -# snakemake/assets/data/vega-lite/vega-lite.js +# 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 snakemake/assets/data/vega-lite/vega-lite.js as dependencies: -# See notes in snakemake/assets/__init__.py. +# 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 snakemake/assets/__init__.py, as well as dependencies in +# 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. @@ -312,24 +294,25 @@ Provides: bundled(npm(json-stringify-pretty-compact)) = 3.0.0 #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 snakemake/assets/data/vega-lite/vega-lite.js in the form of +# Present in src/snakemake/assets/data/vega-lite/vega-lite.js in the form of # copied, derived, or adapted snippets. See notes in -# snakemake/assets/__init__.py. +# src/snakemake/assets/__init__.py. #Provides: bundled(npm(hashlru)) = 1.0.4 -# snakemake/assets/data/vega-embed/vega-embed.js +# 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 snakemake/assets/data/vega-embed/vega-embed.js as dependencies: -# See notes in snakemake/assets/__init__.py. +# 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 snakemake/assets/__init__.py, as well as dependencies in +# 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. @@ -338,9 +321,9 @@ 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 snakemake/assets/data/vega-embed/vega-embed.js in the form of +# Present in src/snakemake/assets/data/vega-embed/vega-embed.js in the form of # copied, derived, or adapted snippets. See notes in -# snakemake/assets/__init__.py. +# 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 @@ -350,7 +333,7 @@ Provides: bundled(npm(vega-tooltip)) = 0.28.0 # the virtual Provides, just in case we have missed something. Provides: bundled(npm(heroicons)) = 1.0.3 -# snakemake/assets/data/prop-types/prop-types.min.js +# src/snakemake/assets/data/prop-types/prop-types.min.js Provides: bundled(npm(prop-types)) = 15.7.2 # These extras were removed upstream in Snakemake 8.0.0. Retain the Obsoletes @@ -419,24 +402,32 @@ do done # The CDN URL for tailwind.css does not deliver a file with a stable checksum, -# so upstream has not recorded a checksum in 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 >> snakemake/assets/__init__.py <> src/snakemake/assets/__init__.py < Date: Fri, 9 May 2025 14:24:33 +0000 Subject: [PATCH 056/109] Update to 9.3.4 upstream release - Resolves: rhbz#2309617 Upstream tag: v9.3.4 Upstream commit: 67ad5eb3 Commit authored by Packit automation (https://packit.dev/) --- .gitignore | 2 ++ README.packit | 2 +- snakemake.spec | 2 +- sources | 4 ++-- 4 files changed, 6 insertions(+), 4 deletions(-) diff --git a/.gitignore b/.gitignore index aa2543e..bb88d1c 100644 --- a/.gitignore +++ b/.gitignore @@ -67,3 +67,5 @@ /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 diff --git a/README.packit b/README.packit index 94a5d96..807ffc6 100644 --- a/README.packit +++ b/README.packit @@ -1,3 +1,3 @@ This repository is maintained by packit. https://packit.dev/ -The file was generated using packit 0.100.2.post1.dev4+g31a74ebd. +The file was generated using packit 1.6.0.post1.dev2+gd5a7662a. diff --git a/snakemake.spec b/snakemake.spec index 113bda7..129c924 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -41,7 +41,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 9.3.3 +Version: 9.3.4 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 3977284..51cff90 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.3.3.tar.gz) = 9407ba7a5d1b595396749123d92eded5140bd21acdc13994aa7184d24ae30c7d0e17c09f5f2fc9a6c3d05a0dcfc041a35db68777aa94d051dac0488a14f533ee -SHA512 (snakemake-9.3.3-assets.tar.zst) = db419e77df51340865f5feda15cda8fd70670beb5262514e02ef9b3c33fa538ef35ce175a2866814266e9d351b0bb4a49d0d18eb708295579821983d971e50d0 +SHA512 (snakemake-9.3.4.tar.gz) = 470572996c4c0da7d7dfe50f92929e8657c2c89e76df904de5f332f773dd9aab88fd39ac1e2cce49f13111caff537c2cbcb98fd85bea31fbfc6e9891f5a42509 +SHA512 (snakemake-9.3.4-assets.tar.zst) = a4d757c6ef61449caa676c32f8f847fc6786aa7e419a9ef53dd9c6110dec07139fbc9cd5f54bcb8d09356502faedc0b01190bd9b8b5243a796776ddfc744e862 From d9aa4c518ab29bc6aeec9e7a705bcbea30f1d4c0 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Fri, 9 May 2025 11:43:44 -0400 Subject: [PATCH 057/109] Stop using Packit, since we must run a script to generate the asset-bundle source --- .packit.yaml | 13 ------------- 1 file changed, 13 deletions(-) delete mode 100644 .packit.yaml diff --git a/.packit.yaml b/.packit.yaml deleted file mode 100644 index 2959457..0000000 --- a/.packit.yaml +++ /dev/null @@ -1,13 +0,0 @@ -upstream_project_url: https://github.com/snakemake/snakemake -copy_upstream_release_description: false -upstream_tag_template: v{version} - -jobs: - - job: pull_from_upstream - trigger: release - dist_git_branches: - - fedora-rawhide - - job: koji_build - trigger: commit - dist_git_branches: - - fedora-all From 191c1b2800118215f5a6e03552af11d5efc451f1 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Sat, 10 May 2025 22:13:46 -0400 Subject: [PATCH 058/109] Update .rpmlintrc file for current rpmlint --- snakemake.rpmlintrc | 2 -- 1 file changed, 2 deletions(-) diff --git a/snakemake.rpmlintrc b/snakemake.rpmlintrc index 83eecf6..ede389e 100644 --- a/snakemake.rpmlintrc +++ b/snakemake.rpmlintrc @@ -6,8 +6,6 @@ addFilter(r"\+\w+.noarch: W: no-documentation") addFilter(r" obsolete-not-provided snakemake\+(azure|google-cloud)$") # The -doc subpackage was removed and has no equivalent replacement. addFilter(r" obsolete-not-provided snakemake-doc$") -# Not a spelling error -addFilter(r"spelling-error \('([Mm]etapackage)s?',") # Some small files may incidentally have duplicate contents. Because they are # small in size and few in number, it is not worth the spec-file complexity to # hardlink them (which would itself trigger an rpmlint warning about From d4e4d6466a239b48042a51c9c32f3b8cf16cb16e Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Thu, 15 May 2025 20:20:07 -0400 Subject: [PATCH 059/109] Update to 9.4.0 (close RHBZ#2366656) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index bb88d1c..15c4c80 100644 --- a/.gitignore +++ b/.gitignore @@ -69,3 +69,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index 129c924..2781245 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -41,7 +41,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 9.3.4 +Version: 9.4.0 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 51cff90..39d38fc 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.3.4.tar.gz) = 470572996c4c0da7d7dfe50f92929e8657c2c89e76df904de5f332f773dd9aab88fd39ac1e2cce49f13111caff537c2cbcb98fd85bea31fbfc6e9891f5a42509 -SHA512 (snakemake-9.3.4-assets.tar.zst) = a4d757c6ef61449caa676c32f8f847fc6786aa7e419a9ef53dd9c6110dec07139fbc9cd5f54bcb8d09356502faedc0b01190bd9b8b5243a796776ddfc744e862 +SHA512 (snakemake-9.4.0.tar.gz) = d25646f6ebae10b08a31e3ab85b2f662ae6c118deca19814a9d0bdd6dafe58e365ce3dc83bd04ecadb937fd9d6d7dd4b69dc1ef71b6f9c17e3d3bf83e7a16448 +SHA512 (snakemake-9.4.0-assets.tar.zst) = 49d1b3340738f761dc9d45a8b43e54a7c5e6da5af1fa50f486cf865e60d850e3fffa98ae88f05fdd1f70f9e6e130a5a411b945ebdc7596b9bcd550fce0bd1c90 From b20ab7df8e40429feeacfb3b762b5a23a7248799 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Sat, 24 May 2025 08:57:21 -0400 Subject: [PATCH 060/109] Update to 9.5.1 (close RHBZ#2367769) --- .gitignore | 2 ++ snakemake.spec | 3 ++- sources | 4 ++-- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 15c4c80..145c753 100644 --- a/.gitignore +++ b/.gitignore @@ -71,3 +71,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index 2781245..9b756d9 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -41,7 +41,7 @@ Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.} Name: snakemake -Version: 9.4.0 +Version: 9.5.1 Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses @@ -467,6 +467,7 @@ find '%{buildroot}%{_datadir}/vim/vimfiles' \ # 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" diff --git a/sources b/sources index 39d38fc..30d768f 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.4.0.tar.gz) = d25646f6ebae10b08a31e3ab85b2f662ae6c118deca19814a9d0bdd6dafe58e365ce3dc83bd04ecadb937fd9d6d7dd4b69dc1ef71b6f9c17e3d3bf83e7a16448 -SHA512 (snakemake-9.4.0-assets.tar.zst) = 49d1b3340738f761dc9d45a8b43e54a7c5e6da5af1fa50f486cf865e60d850e3fffa98ae88f05fdd1f70f9e6e130a5a411b945ebdc7596b9bcd550fce0bd1c90 +SHA512 (snakemake-9.5.1.tar.gz) = e61d275e0a7fbbb17f150407268389095facd782643dac27d268d97191054a4529ac73be45f5146c74861c7a07ac8d97acf1dc5360c4f27008b1857272428050 +SHA512 (snakemake-9.5.1-assets.tar.zst) = 20d3752baaada27b996a28f6299c51f23af61f0dcb8703906c300e237e4657b8a134388759069decb00c08d4c29e511c53e43d53af83fae5e3af7b6ba4d8a3ef From 1118337fcfb52932b31ea141d61a1f911db7571b Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Thu, 29 May 2025 07:36:09 -0400 Subject: [PATCH 061/109] Allow PuLP 3.2 --- 3609.patch | 22 ++++++++++++++++++++++ snakemake.spec | 4 ++++ 2 files changed, 26 insertions(+) create mode 100644 3609.patch diff --git a/3609.patch b/3609.patch new file mode 100644 index 0000000..1c5d34f --- /dev/null +++ b/3609.patch @@ -0,0 +1,22 @@ +From 1360aae69dc344923143bf524a5d3b7d0a46ec05 Mon Sep 17 00:00:00 2001 +From: "Benjamin A. Beasley" +Date: Thu, 29 May 2025 07:33:21 -0400 +Subject: [PATCH] chore: Allow PuLP 3.2 + +--- + pyproject.toml | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/pyproject.toml b/pyproject.toml +index 646b4c4c2..124eb4c62 100644 +--- a/pyproject.toml ++++ b/pyproject.toml +@@ -41,7 +41,7 @@ dependencies = [ + "nbformat", + "packaging", + "psutil", +- "pulp>=2.3.1,<3.2", ++ "pulp>=2.3.1,<3.3", + "pyyaml", + "requests>=2.8.1,<3.0", + "reretry", diff --git a/snakemake.spec b/snakemake.spec index 9b756d9..eae52d9 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -154,6 +154,10 @@ Source2: get_assets # the substring "modified-assets" in the patch name. Patch: snakemake-9.1.1-modified-assets.patch +# chore: Allow PuLP 3.2 +# https://github.com/snakemake/snakemake/pull/3609 +Patch: %{forgeurl}/pull/3609.patch + BuildSystem: pyproject # Generate BR’s for all supported extras to ensure they do not FTI BuildOption(generate_buildrequires): -x reports,messaging From 0c5027804542e8d25e9855a4001596b4407056e8 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Thu, 12 Jun 2025 06:31:02 -0400 Subject: [PATCH 062/109] Work around broken python-google-cloud-storage --- snakemake.spec | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/snakemake.spec b/snakemake.spec index eae52d9..0bb6bb3 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -31,6 +31,9 @@ # 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 +# F43FailsToInstall: python3-google-cloud-storage +# https://bugzilla.redhat.com/show_bug.cgi?id=2371928 +%bcond gcs_tests 0 %global _description %{expand: The Snakemake workflow management system is a tool to create reproducible and @@ -162,7 +165,10 @@ BuildSystem: pyproject # Generate BR’s for all supported extras to ensure they do not FTI BuildOption(generate_buildrequires): -x reports,messaging BuildOption(install): -l snakemake -BuildOption(check): -e '*.tests*' +BuildOption(check): %{shrink: + -e '*.tests*' + %{?!with_gcs_tests:-e 'snakemake.executors.google_lifesciences_helper'} + } BuildArch: noarch @@ -382,8 +388,10 @@ BuildRequires: %{py3_dist snakemake-storage-plugin-s3} %endif # For import-testing snakemake.gui BuildRequires: %{py3_dist flask} +%if %{with google_cloud_storage_tests} # For import-testing snakemake.executors.google_lifesciences_helper: BuildRequires: %{py3_dist google-cloud-storage} +%endif %description %_description From 5a415c350b23827dddec16b451e3b2b79788e6c1 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Thu, 12 Jun 2025 06:25:25 -0400 Subject: [PATCH 063/109] Bootstrap for Python 3.14 (close RHBZ#2372222) --- snakemake.spec | 1 + 1 file changed, 1 insertion(+) diff --git a/snakemake.spec b/snakemake.spec index 0bb6bb3..87793a7 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -1,3 +1,4 @@ +%global _with_bootstrap 1 # Work around a series of circular test dependencies: # # python-snakemake-interface-report-plugins From bd2da15e7244abfc298b7b750fa0799ea6e87921 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Thu, 12 Jun 2025 11:30:23 -0400 Subject: [PATCH 064/109] Move the description lower in the spec file [skip changelog] --- snakemake.spec | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/snakemake.spec b/snakemake.spec index 87793a7..f587851 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -36,14 +36,6 @@ # https://bugzilla.redhat.com/show_bug.cgi?id=2371928 %bcond gcs_tests 0 -%global _description %{expand: -The Snakemake workflow management system is a tool to create reproducible and -scalable data analyses. Workflows are described via a human readable, Python -based language. They can be seamlessly scaled to server, cluster, grid and -cloud environments, without the need to modify the workflow definition. -Finally, Snakemake workflows can entail a description of required software, -which will be automatically deployed to any execution environment.} - Name: snakemake Version: 9.5.1 Release: %autorelease @@ -394,6 +386,14 @@ BuildRequires: %{py3_dist flask} 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 From 2d0bcdaa8b19ef25c89e62caa3551b405bfa9db6 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Thu, 12 Jun 2025 08:18:05 -0400 Subject: [PATCH 065/109] Update to a snapshot to address a Python 3.14 regression - Do a non-bootstrap build --- .gitignore | 2 ++ 3609.patch | 22 ---------------------- snakemake.spec | 50 +++++++++++++++++++++++++++++++++++++------------- sources | 4 ++-- 4 files changed, 41 insertions(+), 37 deletions(-) delete mode 100644 3609.patch diff --git a/.gitignore b/.gitignore index 145c753..addac61 100644 --- a/.gitignore +++ b/.gitignore @@ -73,3 +73,5 @@ /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 diff --git a/3609.patch b/3609.patch deleted file mode 100644 index 1c5d34f..0000000 --- a/3609.patch +++ /dev/null @@ -1,22 +0,0 @@ -From 1360aae69dc344923143bf524a5d3b7d0a46ec05 Mon Sep 17 00:00:00 2001 -From: "Benjamin A. Beasley" -Date: Thu, 29 May 2025 07:33:21 -0400 -Subject: [PATCH] chore: Allow PuLP 3.2 - ---- - pyproject.toml | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/pyproject.toml b/pyproject.toml -index 646b4c4c2..124eb4c62 100644 ---- a/pyproject.toml -+++ b/pyproject.toml -@@ -41,7 +41,7 @@ dependencies = [ - "nbformat", - "packaging", - "psutil", -- "pulp>=2.3.1,<3.2", -+ "pulp>=2.3.1,<3.3", - "pyyaml", - "requests>=2.8.1,<3.0", - "reretry", diff --git a/snakemake.spec b/snakemake.spec index f587851..574f532 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -1,4 +1,3 @@ -%global _with_bootstrap 1 # Work around a series of circular test dependencies: # # python-snakemake-interface-report-plugins @@ -36,8 +35,23 @@ # https://bugzilla.redhat.com/show_bug.cgi?id=2371928 %bcond gcs_tests 0 +# Snapshot fixes test_config_ref failing with: +# +# jsonschema.exceptions._RefResolutionError: [Errno 2] No such file or +# directory: +# 'file:/tmp/pytest-of-mockbuild/pytest-0/test_config_ref0/schema/bar.schema.yaml' +# +# Specifically, we need: +# +# fix: DeprecationWarning when using snakemake.utils.validate +# https://github.com/snakemake/snakemake/pull/3420 +# https://github.com/snakemake/snakemake/commit/cf724272eefcd9b30fb625d2e16380727bef9c3e +%global commit 6dee2b55fbfff3bdad33cecdbeb8bd55ff4586bc +%global snapdate 20250612 + Name: snakemake -Version: 9.5.1 +Version: 9.5.1^%{snapdate}git%{sub %{commit} 1 7} +%global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses @@ -133,12 +147,12 @@ URL: https://snakemake.readthedocs.io/en/stable/index.html # 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 +Source0: %{forgeurl}/archive/%{commit}/snakemake-%{commit}.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 +Source1: snakemake-%{commit}-assets.tar.zst Source2: get_assets # Downstream-only: adjust the asset metadata in the sources, including @@ -150,10 +164,6 @@ Source2: get_assets # the substring "modified-assets" in the patch name. Patch: snakemake-9.1.1-modified-assets.patch -# chore: Allow PuLP 3.2 -# https://github.com/snakemake/snakemake/pull/3609 -Patch: %{forgeurl}/pull/3609.patch - BuildSystem: pyproject # Generate BR’s for all supported extras to ensure they do not FTI BuildOption(generate_buildrequires): -x reports,messaging @@ -352,7 +362,9 @@ Obsoletes: snakemake-doc < 8.2.1-2 # For several tests (either apptainer or singularity-ce should work): BuildRequires: (apptainer or singularity-ce) %if %{with conda_tests} -# For tests/tests_using_conda.py +# 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 @@ -404,8 +416,8 @@ which will be automatically deployed to any execution environment.} %prep -%autosetup -n snakemake-%{version} -p1 -%setup -q -T -D -a 1 -c -n snakemake-%{version} +%autosetup -n snakemake-%{commit} -p1 +%setup -q -T -D -a 1 -c -n snakemake-%{commit} # Copy and rename nano and vim extensions readmes for use in the main # documentation directory. @@ -434,11 +446,11 @@ EOF %generate_buildrequires -p -export SETUPTOOLS_SCM_PRETEND_VERSION='%{version}' +export SETUPTOOLS_SCM_PRETEND_VERSION='%{srcversion}' %build -p -export SETUPTOOLS_SCM_PRETEND_VERSION='%{version}' +export SETUPTOOLS_SCM_PRETEND_VERSION='%{srcversion}' %install -a @@ -514,6 +526,18 @@ 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 this. # # FAILED ../tests/tests.py::test_update_flag - AssertionError: wrong result diff --git a/sources b/sources index 30d768f..7c73367 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.5.1.tar.gz) = e61d275e0a7fbbb17f150407268389095facd782643dac27d268d97191054a4529ac73be45f5146c74861c7a07ac8d97acf1dc5360c4f27008b1857272428050 -SHA512 (snakemake-9.5.1-assets.tar.zst) = 20d3752baaada27b996a28f6299c51f23af61f0dcb8703906c300e237e4657b8a134388759069decb00c08d4c29e511c53e43d53af83fae5e3af7b6ba4d8a3ef +SHA512 (snakemake-6dee2b55fbfff3bdad33cecdbeb8bd55ff4586bc.tar.gz) = 72b9ff9d16a59b789f8c0bdf8f5689c66b02d43df484cf5cff6a880d46d8d9d3535836e4cc0a25da4c1ceee04c6372a41f3348d172289ba101b3582a36f9ef54 +SHA512 (snakemake-6dee2b55fbfff3bdad33cecdbeb8bd55ff4586bc-assets.tar.zst) = beb90fcd88b02e7f1cf3efbe6ff88c604a4664e4c71aa3abf0a1cb16aa8a0b551bc54f64c5e02a476c246e7ef7226c04f33e0a64d1d0706272898d6498c09066 From 42c2682fdfbf6b9de756c8abff1e4d75dbad12e9 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Wed, 18 Jun 2025 08:48:50 -0400 Subject: [PATCH 066/109] Re-enable tests requiring google-cloud-storage --- snakemake.spec | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/snakemake.spec b/snakemake.spec index 574f532..b5b11ba 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -31,9 +31,7 @@ # 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 -# F43FailsToInstall: python3-google-cloud-storage -# https://bugzilla.redhat.com/show_bug.cgi?id=2371928 -%bcond gcs_tests 0 +%bcond gcs_tests 1 # Snapshot fixes test_config_ref failing with: # @@ -393,7 +391,7 @@ BuildRequires: %{py3_dist snakemake-storage-plugin-s3} %endif # For import-testing snakemake.gui BuildRequires: %{py3_dist flask} -%if %{with google_cloud_storage_tests} +%if %{with gcs_tests} # For import-testing snakemake.executors.google_lifesciences_helper: BuildRequires: %{py3_dist google-cloud-storage} %endif From 63d07bdff2b6880b95be58580711cbd4edf84076 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Mon, 23 Jun 2025 11:20:48 -0400 Subject: [PATCH 067/109] Update to 9.6.1 - Skip one flaky test --- .gitignore | 2 ++ snakemake.rpmlintrc | 5 ++--- snakemake.spec | 41 +++++++++++++++-------------------------- sources | 4 ++-- 4 files changed, 21 insertions(+), 31 deletions(-) diff --git a/.gitignore b/.gitignore index addac61..d794acb 100644 --- a/.gitignore +++ b/.gitignore @@ -75,3 +75,5 @@ /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 diff --git a/snakemake.rpmlintrc b/snakemake.rpmlintrc index ede389e..5e46a87 100644 --- a/snakemake.rpmlintrc +++ b/snakemake.rpmlintrc @@ -1,9 +1,8 @@ # It is normal that extras metapackages should not have documentation, or any # files at all. addFilter(r"\+\w+.noarch: W: no-documentation") -# These extras were removed with Snakemake 8.0 and have no equivalent -# replacements. -addFilter(r" obsolete-not-provided snakemake\+(azure|google-cloud)$") +# Removed in Snakemake 9.6 with no equivalent replacement. +addFilter(r" obsolete-not-provided snakemake\+(messaging)$") # The -doc subpackage was removed and has no equivalent replacement. addFilter(r" obsolete-not-provided snakemake-doc$") # Some small files may incidentally have duplicate contents. Because they are diff --git a/snakemake.spec b/snakemake.spec index b5b11ba..cdd0198 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -33,22 +33,8 @@ %bcond conda_tests 0 %bcond gcs_tests 1 -# Snapshot fixes test_config_ref failing with: -# -# jsonschema.exceptions._RefResolutionError: [Errno 2] No such file or -# directory: -# 'file:/tmp/pytest-of-mockbuild/pytest-0/test_config_ref0/schema/bar.schema.yaml' -# -# Specifically, we need: -# -# fix: DeprecationWarning when using snakemake.utils.validate -# https://github.com/snakemake/snakemake/pull/3420 -# https://github.com/snakemake/snakemake/commit/cf724272eefcd9b30fb625d2e16380727bef9c3e -%global commit 6dee2b55fbfff3bdad33cecdbeb8bd55ff4586bc -%global snapdate 20250612 - Name: snakemake -Version: 9.5.1^%{snapdate}git%{sub %{commit} 1 7} +Version: 9.6.1 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses @@ -145,12 +131,12 @@ URL: https://snakemake.readthedocs.io/en/stable/index.html # 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/%{commit}/snakemake-%{commit}.tar.gz +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-%{commit}-assets.tar.zst +Source1: snakemake-%{version}-assets.tar.zst Source2: get_assets # Downstream-only: adjust the asset metadata in the sources, including @@ -164,7 +150,7 @@ 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,messaging +BuildOption(generate_buildrequires): -x reports BuildOption(install): -l snakemake BuildOption(check): %{shrink: -e '*.tests*' @@ -347,14 +333,12 @@ 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 -# These extras were removed upstream in Snakemake 8.0.0. Retain the Obsoletes -# until F40 reaches EOL so we have a clean upgrade path. -Obsoletes: snakemake+azure < 8.1.0-1 -Obsoletes: snakemake+google-cloud < 8.1.0-1 # We no longer build Sphinx-generated PDF documentation. Beginning with 8.2.3, # this would require patching out sphinxawesome-theme from docs/conf.py. It’s # possible but tedious. Obsoletes: snakemake-doc < 8.2.1-2 +# 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): @@ -410,12 +394,13 @@ which will be automatically deployed to any execution environment.} # No metapackage for “pep” extra because the following are not packaged: # - python3-eido # - python3-peppy -%pyproject_extras_subpkg -n snakemake reports messaging +# Therefore, also no metapakge for “all” extra +%pyproject_extras_subpkg -n snakemake reports %prep -%autosetup -n snakemake-%{commit} -p1 -%setup -q -T -D -a 1 -c -n snakemake-%{commit} +%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. @@ -536,7 +521,7 @@ k="${k-}${k+ and }not test_jupyter_notebook_nbconvert" k="${k-}${k+ and }not test_jupyter_notebook_draft" %endif -# Flaky; so far, we have not attempted to understand or report this. +# Flaky; so far, we have not attempted to understand or report these. # # FAILED ../tests/tests.py::test_update_flag - AssertionError: wrong result # produced for file 'test.txt': @@ -547,6 +532,10 @@ k="${k-}${k+ and }not test_jupyter_notebook_draft" # bar # ----------------- k="${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 diff --git a/sources b/sources index 7c73367..5233f2e 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-6dee2b55fbfff3bdad33cecdbeb8bd55ff4586bc.tar.gz) = 72b9ff9d16a59b789f8c0bdf8f5689c66b02d43df484cf5cff6a880d46d8d9d3535836e4cc0a25da4c1ceee04c6372a41f3348d172289ba101b3582a36f9ef54 -SHA512 (snakemake-6dee2b55fbfff3bdad33cecdbeb8bd55ff4586bc-assets.tar.zst) = beb90fcd88b02e7f1cf3efbe6ff88c604a4664e4c71aa3abf0a1cb16aa8a0b551bc54f64c5e02a476c246e7ef7226c04f33e0a64d1d0706272898d6498c09066 +SHA512 (snakemake-9.6.1.tar.gz) = b90c327f2d2e6f9dd2e3bcef8d5effdffd9ee9dd43b8da55ccb6e3fae2cb6f653f54e43b34c579dc93f3e0437110394d0ae1c5d71a540e599312b14146531b2a +SHA512 (snakemake-9.6.1-assets.tar.zst) = 0337ca72f109882a93ddec8532cfa5af0b65764c2e20d9e49271f6316645031c6bf586784b8507b130503eebb17e79bd2e7e74484b1193a227423f29138fb67b From 2995ff993ef5c8485e8cc08320dd40492880471b Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Mon, 23 Jun 2025 14:06:38 -0400 Subject: [PATCH 068/109] Update bootstrapping notes There is now a test dependency on snakemake from python-snakemake-interface-common, creating a new dependency cycle. [skip changelog] --- snakemake.spec | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/snakemake.spec b/snakemake.spec index cdd0198..b89822c 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -12,7 +12,8 @@ # # A good build order is: # -# 1. BOOTSTRAP: python-snakemake-interface-executor-plugins, +# 1. BOOTSTRAP: python-snakemake-interface-common +# python-snakemake-interface-executor-plugins, # python-snakemake-interface-storage-plugins, # python-snakemake-interface-report-plugins # 2. BOOTSTRAP: snakemake From e542da4d9fc398a9be85e03d1a525ad6c8e88947 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Tue, 24 Jun 2025 07:40:54 -0400 Subject: [PATCH 069/109] Update to 9.6.2 (close RHBZ#2374535) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index d794acb..b23ece6 100644 --- a/.gitignore +++ b/.gitignore @@ -77,3 +77,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index b89822c..4c717f7 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -35,7 +35,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.6.1 +Version: 9.6.2 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 5233f2e..dcd7d56 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.6.1.tar.gz) = b90c327f2d2e6f9dd2e3bcef8d5effdffd9ee9dd43b8da55ccb6e3fae2cb6f653f54e43b34c579dc93f3e0437110394d0ae1c5d71a540e599312b14146531b2a -SHA512 (snakemake-9.6.1-assets.tar.zst) = 0337ca72f109882a93ddec8532cfa5af0b65764c2e20d9e49271f6316645031c6bf586784b8507b130503eebb17e79bd2e7e74484b1193a227423f29138fb67b +SHA512 (snakemake-9.6.2.tar.gz) = dec50a1283dd6b021b366e8e476ba27497762bd1b8e35b691a1c4d452a5c5edaa9fbb7786d5f75cb383cc7cd6b7f97707293454f2be8e39f0658d4a472cedcfe +SHA512 (snakemake-9.6.2-assets.tar.zst) = af4874401dc74ae933637bdb846f22c5a379ebee9fdde1f9f59ad0e916bd54e809609408137ce9015b1bf959562bad6d25d05c3f1714ff96afe7a9ef5edd14d8 From e492debc4778c72f64cf11e0b4e6cc3dd9c21f46 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Fri, 4 Jul 2025 14:38:27 -0400 Subject: [PATCH 070/109] Update to 9.7.1 (close RHBZ#2376436) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index b23ece6..864b71b 100644 --- a/.gitignore +++ b/.gitignore @@ -79,3 +79,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index 4c717f7..9caf37d 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -35,7 +35,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.6.2 +Version: 9.7.1 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index dcd7d56..c036835 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.6.2.tar.gz) = dec50a1283dd6b021b366e8e476ba27497762bd1b8e35b691a1c4d452a5c5edaa9fbb7786d5f75cb383cc7cd6b7f97707293454f2be8e39f0658d4a472cedcfe -SHA512 (snakemake-9.6.2-assets.tar.zst) = af4874401dc74ae933637bdb846f22c5a379ebee9fdde1f9f59ad0e916bd54e809609408137ce9015b1bf959562bad6d25d05c3f1714ff96afe7a9ef5edd14d8 +SHA512 (snakemake-9.7.1.tar.gz) = 90ce7afbdff7295acb6282f6f2ad0ee8810e24ba8dda90da67a18d38e21893edcf26cdca85f872ee926838e9f116f88339b7db483c4764b6169826dea303ca7f +SHA512 (snakemake-9.7.1-assets.tar.zst) = bb8a8cfcd97e021a9f7439472b7d019576886cfbbd4dd77b7f06113a6ebb84473dda199d48e050e03016e45524d6a56d1fb83c13debbb35b9b59a70bd5c66edc From 11f507e8a6380e46e3e51cd49501b4e2ae09ba40 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Thu, 10 Jul 2025 22:41:33 -0400 Subject: [PATCH 071/109] =?UTF-8?q?Remove=20README.packit=20since=20we=20d?= =?UTF-8?q?on=E2=80=99t=20use=20packit?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit [skip changelog] --- README.packit | 3 --- 1 file changed, 3 deletions(-) delete mode 100644 README.packit diff --git a/README.packit b/README.packit deleted file mode 100644 index 807ffc6..0000000 --- a/README.packit +++ /dev/null @@ -1,3 +0,0 @@ -This repository is maintained by packit. -https://packit.dev/ -The file was generated using packit 1.6.0.post1.dev2+gd5a7662a. From 6632c4727967700de25c63a0b2fdb3ee7e945c4f Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Thu, 10 Jul 2025 22:42:18 -0400 Subject: [PATCH 072/109] Update to 9.8.0 (close RHBZ#2379466) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 864b71b..60fc643 100644 --- a/.gitignore +++ b/.gitignore @@ -81,3 +81,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index 9caf37d..4210b6a 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -35,7 +35,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.7.1 +Version: 9.8.0 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index c036835..7c3e51c 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.7.1.tar.gz) = 90ce7afbdff7295acb6282f6f2ad0ee8810e24ba8dda90da67a18d38e21893edcf26cdca85f872ee926838e9f116f88339b7db483c4764b6169826dea303ca7f -SHA512 (snakemake-9.7.1-assets.tar.zst) = bb8a8cfcd97e021a9f7439472b7d019576886cfbbd4dd77b7f06113a6ebb84473dda199d48e050e03016e45524d6a56d1fb83c13debbb35b9b59a70bd5c66edc +SHA512 (snakemake-9.8.0.tar.gz) = 7f9b5ea92651fcfc4ef0f97c75c1a008241c56b9f309bd600b818210f1b1d8c9aaf64a8a0db8e0eabfebce8fc88400e31d79220ee031dec519a5263426d4c9bc +SHA512 (snakemake-9.8.0-assets.tar.zst) = abc8d2062608a5d0b52681036aede4f0a07cb60dd43bd508ceb5666f7942a3c619a9c1ead2e666ade76ef6be0affbd167bf1b7f8958471a8c722ae4bd33e26c0 From 6763e6b95c2e0f4f23797c3f903bf0203c039155 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Mon, 21 Jul 2025 06:54:52 -0400 Subject: [PATCH 073/109] Update to 9.8.1 (close RHBZ#2382290) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 60fc643..5a349ce 100644 --- a/.gitignore +++ b/.gitignore @@ -83,3 +83,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index 4210b6a..48057df 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -35,7 +35,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.8.0 +Version: 9.8.1 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 7c3e51c..1f891ad 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.8.0.tar.gz) = 7f9b5ea92651fcfc4ef0f97c75c1a008241c56b9f309bd600b818210f1b1d8c9aaf64a8a0db8e0eabfebce8fc88400e31d79220ee031dec519a5263426d4c9bc -SHA512 (snakemake-9.8.0-assets.tar.zst) = abc8d2062608a5d0b52681036aede4f0a07cb60dd43bd508ceb5666f7942a3c619a9c1ead2e666ade76ef6be0affbd167bf1b7f8958471a8c722ae4bd33e26c0 +SHA512 (snakemake-9.8.1.tar.gz) = 46ddf552ef7c9e89422bd07553327df323e6f4f2462edc812957d8290182fa330e470075bd8591d854b6951cdb940cd47ce89b93450bf27ba97a70d834aad2ba +SHA512 (snakemake-9.8.1-assets.tar.zst) = 56a02a843105525be8ab73b8f1a6eb03b8aa39b660fe9c59c5f24920aa5c2567bc70c052108f35f84f11bf407225c938ef9e4c8e1067ca39072958a8ce222128 From 3049cd151a1e87a4cb1eebaa5086417a0039ea31 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Fri, 25 Jul 2025 18:28:08 +0000 Subject: [PATCH 074/109] Rebuilt for https://fedoraproject.org/wiki/Fedora_43_Mass_Rebuild From 53acdf2f4ed296525f2a82b57148cf3d2784165d Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Sat, 26 Jul 2025 07:27:59 -0400 Subject: [PATCH 075/109] Update to 9.8.2 (close RHBZ#2383550) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 5a349ce..17d41c3 100644 --- a/.gitignore +++ b/.gitignore @@ -85,3 +85,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index 48057df..2ac7b7b 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -35,7 +35,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.8.1 +Version: 9.8.2 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 1f891ad..b155f8a 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.8.1.tar.gz) = 46ddf552ef7c9e89422bd07553327df323e6f4f2462edc812957d8290182fa330e470075bd8591d854b6951cdb940cd47ce89b93450bf27ba97a70d834aad2ba -SHA512 (snakemake-9.8.1-assets.tar.zst) = 56a02a843105525be8ab73b8f1a6eb03b8aa39b660fe9c59c5f24920aa5c2567bc70c052108f35f84f11bf407225c938ef9e4c8e1067ca39072958a8ce222128 +SHA512 (snakemake-9.8.2.tar.gz) = da1d0c601493e767869916d09dbc2599174c719771ef86cfbdf4ed517bb1992c36ccff618092e373368e54b105f0961d7f4e5a775aba2750951843e18d7680e2 +SHA512 (snakemake-9.8.2-assets.tar.zst) = 71cad40b7cc73d1c74a30f9a67ebe9b0bf9de36a57b45d8e2ce5dc31b662b0cd8f740c201c8356eb74749ee6f88c2faf8aca918d6c1a9238a88991a01f528d0f From 78a56d88dd76edad9fde01d1c2eebc0733265d48 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Tue, 29 Jul 2025 14:57:22 -0400 Subject: [PATCH 076/109] Update to 9.9.0 (close RHBZ#2384291) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 17d41c3..619212c 100644 --- a/.gitignore +++ b/.gitignore @@ -87,3 +87,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index 2ac7b7b..c4f2e10 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -35,7 +35,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.8.2 +Version: 9.9.0 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index b155f8a..60f8936 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.8.2.tar.gz) = da1d0c601493e767869916d09dbc2599174c719771ef86cfbdf4ed517bb1992c36ccff618092e373368e54b105f0961d7f4e5a775aba2750951843e18d7680e2 -SHA512 (snakemake-9.8.2-assets.tar.zst) = 71cad40b7cc73d1c74a30f9a67ebe9b0bf9de36a57b45d8e2ce5dc31b662b0cd8f740c201c8356eb74749ee6f88c2faf8aca918d6c1a9238a88991a01f528d0f +SHA512 (snakemake-9.9.0.tar.gz) = 1b59332a97ef6eec1678037c49ae91d7b1e0000e8e54ff065fe1d7a8dd22e24e670a533721ba9044f8e4eb32f411d93e8f95c86459447e2515f03a243c7a8b06 +SHA512 (snakemake-9.9.0-assets.tar.zst) = 38bb59073c075d2abbd5f546a733e508ac1140941e3b97a1615ad9547536b1d3473060acd5ba78fc62b8cdfcde3ac341654c86f9aa607071fcd18ba95f70a9d5 From 49c1d6261018226cd7bfff64377bbe8daeceffe9 Mon Sep 17 00:00:00 2001 From: Python Maint Date: Fri, 15 Aug 2025 15:18:19 +0200 Subject: [PATCH 077/109] Rebuilt for Python 3.14.0rc2 bytecode From c692946a13b2b18da52abe5ff0cb3747539c8c0a Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Sat, 30 Aug 2025 01:45:02 +0100 Subject: [PATCH 078/109] Update to 9.10.0 (close RHBZ#2391749) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 619212c..07f759e 100644 --- a/.gitignore +++ b/.gitignore @@ -89,3 +89,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index c4f2e10..2e29867 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -35,7 +35,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.9.0 +Version: 9.10.0 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 60f8936..866c1a4 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.9.0.tar.gz) = 1b59332a97ef6eec1678037c49ae91d7b1e0000e8e54ff065fe1d7a8dd22e24e670a533721ba9044f8e4eb32f411d93e8f95c86459447e2515f03a243c7a8b06 -SHA512 (snakemake-9.9.0-assets.tar.zst) = 38bb59073c075d2abbd5f546a733e508ac1140941e3b97a1615ad9547536b1d3473060acd5ba78fc62b8cdfcde3ac341654c86f9aa607071fcd18ba95f70a9d5 +SHA512 (snakemake-9.10.0.tar.gz) = 96b6bcc158ec867ee6bd39cbf45c1cef75ceaa5eb7bde21a075a478af765d4261e980e5d74088b747fdddee775955d7aa672018d1e4e571d357e6cb6e708d1c4 +SHA512 (snakemake-9.10.0-assets.tar.zst) = a1653f461683db2544b82facf0de5b2b3b680da474ac24262be5454fef534ccf60373d61b267f721a7f46c93e3dcc1ea59da1b0ce42b43326404387f4b7ba127 From 85964dac50639f941b0e138c416af0ec94f40475 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Sun, 31 Aug 2025 23:48:36 +0100 Subject: [PATCH 079/109] Improve bootstrapping instructions in the spec file --- snakemake.spec | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/snakemake.spec b/snakemake.spec index 2e29867..4f12fb1 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -1,7 +1,8 @@ # Work around a series of circular test dependencies: # -# python-snakemake-interface-report-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─────────────────╮ @@ -24,6 +25,7 @@ # 4. snakemake, python-snakemake-interface-executor-plugins, # python-snakemake-interface-storage-plugins, # python-snakemake-interface-report-plugins +# python-snakemake-interface-scheduler-plugins %bcond bootstrap 0 %bcond tests %{without bootstrap} # Run tests that require network access? This only makes sense for local mock From 2fbc8e9875f1bdc32498177a0a180da5bcd532be Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Mon, 1 Sep 2025 16:58:11 +0100 Subject: [PATCH 080/109] Update to 9.10.1 (close RHBZ#2392414) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 07f759e..59d7ff3 100644 --- a/.gitignore +++ b/.gitignore @@ -91,3 +91,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index 4f12fb1..f30401d 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -37,7 +37,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.10.0 +Version: 9.10.1 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 866c1a4..4230228 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.10.0.tar.gz) = 96b6bcc158ec867ee6bd39cbf45c1cef75ceaa5eb7bde21a075a478af765d4261e980e5d74088b747fdddee775955d7aa672018d1e4e571d357e6cb6e708d1c4 -SHA512 (snakemake-9.10.0-assets.tar.zst) = a1653f461683db2544b82facf0de5b2b3b680da474ac24262be5454fef534ccf60373d61b267f721a7f46c93e3dcc1ea59da1b0ce42b43326404387f4b7ba127 +SHA512 (snakemake-9.10.1.tar.gz) = 3d248583335f21e7b5c715d1e58f3e560a9d3397e94fabfe27220ea6e8ca0aee90ee2e8f355b4c2c76b09e163d5ca878b1dff31f329088d00857335a949b7a0c +SHA512 (snakemake-9.10.1-assets.tar.zst) = 8023e083c8144a1d89c427103532865be0f1119108dd4d7bce3d5c9b1695875c55be4693f83e2d6952d7b8dce466ddc09b730efb6b46e17a838436d1ddd06932 From 55844897254f51bf0c3d286b326f31c47deae5ea Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Sat, 6 Sep 2025 06:34:39 +0100 Subject: [PATCH 081/109] Update to 9.11.0 (close RHBZ#2393559) --- .gitignore | 2 ++ 3728.patch | 23 +++++++++++++++++++++++ snakemake.spec | 6 +++++- sources | 4 ++-- 4 files changed, 32 insertions(+), 3 deletions(-) create mode 100644 3728.patch diff --git a/.gitignore b/.gitignore index 59d7ff3..ebcb9d5 100644 --- a/.gitignore +++ b/.gitignore @@ -93,3 +93,5 @@ /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 diff --git a/3728.patch b/3728.patch new file mode 100644 index 0000000..0a283e5 --- /dev/null +++ b/3728.patch @@ -0,0 +1,23 @@ +From 840ad0bc3ecfaa3a2490c08551b16b0d0346e2ad Mon Sep 17 00:00:00 2001 +From: "Benjamin A. Beasley" +Date: Sat, 6 Sep 2025 06:52:55 +0100 +Subject: [PATCH] Fix invalid escape sequences in a doc string + +Make the doc string for snakemake.resources.is_ordinary_string a raw string. +--- + src/snakemake/resources.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/snakemake/resources.py b/src/snakemake/resources.py +index 442165240..08804677d 100644 +--- a/src/snakemake/resources.py ++++ b/src/snakemake/resources.py +@@ -662,7 +662,7 @@ def infer_resources(name, value, resources: dict): + + + def is_ordinary_string(val): +- """ ++ r""" + Check if a string is an ordinary string. + Ordinary strings are not evaluated and are not + expected to be python expressions and be returned as is. diff --git a/snakemake.spec b/snakemake.spec index f30401d..c1ede56 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -37,7 +37,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.10.1 +Version: 9.11.0 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses @@ -151,6 +151,10 @@ Source2: get_assets # the substring "modified-assets" in the patch name. Patch: snakemake-9.1.1-modified-assets.patch +# fix: invalid escape sequences in a doc string +# https://github.com/snakemake/snakemake/pull/3728 +Patch: %{forgeurl}/pull/3728.patch + BuildSystem: pyproject # Generate BR’s for all supported extras to ensure they do not FTI BuildOption(generate_buildrequires): -x reports diff --git a/sources b/sources index 4230228..0599532 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.10.1.tar.gz) = 3d248583335f21e7b5c715d1e58f3e560a9d3397e94fabfe27220ea6e8ca0aee90ee2e8f355b4c2c76b09e163d5ca878b1dff31f329088d00857335a949b7a0c -SHA512 (snakemake-9.10.1-assets.tar.zst) = 8023e083c8144a1d89c427103532865be0f1119108dd4d7bce3d5c9b1695875c55be4693f83e2d6952d7b8dce466ddc09b730efb6b46e17a838436d1ddd06932 +SHA512 (snakemake-9.11.0.tar.gz) = 20148afe4df683e8fadc2138ce8de0c9fcf8d0597581b3d9d305f631419529b5c60011a2a061c33285694d6cf64927ffa436636bfe07c89d2e5970d244c284a0 +SHA512 (snakemake-9.11.0-assets.tar.zst) = 54c66f1286b00424e816af852baae97e83ad25135f5f0898aba7b761e9a5a15bd2a66073249258741be15d86ddc1cdc6b54820848244e668eafc637b1832a235 From 7d007c5ffc2e2a90d1c2406c81292f5a30c3141f Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Tue, 9 Sep 2025 22:10:29 +0100 Subject: [PATCH 082/109] Update to 9.11.2 (close RHBZ#2393854) --- .gitignore | 2 ++ 3728.patch | 23 ----------------------- snakemake.spec | 6 +----- sources | 4 ++-- 4 files changed, 5 insertions(+), 30 deletions(-) delete mode 100644 3728.patch diff --git a/.gitignore b/.gitignore index ebcb9d5..a1f2edc 100644 --- a/.gitignore +++ b/.gitignore @@ -95,3 +95,5 @@ /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 diff --git a/3728.patch b/3728.patch deleted file mode 100644 index 0a283e5..0000000 --- a/3728.patch +++ /dev/null @@ -1,23 +0,0 @@ -From 840ad0bc3ecfaa3a2490c08551b16b0d0346e2ad Mon Sep 17 00:00:00 2001 -From: "Benjamin A. Beasley" -Date: Sat, 6 Sep 2025 06:52:55 +0100 -Subject: [PATCH] Fix invalid escape sequences in a doc string - -Make the doc string for snakemake.resources.is_ordinary_string a raw string. ---- - src/snakemake/resources.py | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/src/snakemake/resources.py b/src/snakemake/resources.py -index 442165240..08804677d 100644 ---- a/src/snakemake/resources.py -+++ b/src/snakemake/resources.py -@@ -662,7 +662,7 @@ def infer_resources(name, value, resources: dict): - - - def is_ordinary_string(val): -- """ -+ r""" - Check if a string is an ordinary string. - Ordinary strings are not evaluated and are not - expected to be python expressions and be returned as is. diff --git a/snakemake.spec b/snakemake.spec index c1ede56..21046bf 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -37,7 +37,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.11.0 +Version: 9.11.2 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses @@ -151,10 +151,6 @@ Source2: get_assets # the substring "modified-assets" in the patch name. Patch: snakemake-9.1.1-modified-assets.patch -# fix: invalid escape sequences in a doc string -# https://github.com/snakemake/snakemake/pull/3728 -Patch: %{forgeurl}/pull/3728.patch - BuildSystem: pyproject # Generate BR’s for all supported extras to ensure they do not FTI BuildOption(generate_buildrequires): -x reports diff --git a/sources b/sources index 0599532..536b8aa 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.11.0.tar.gz) = 20148afe4df683e8fadc2138ce8de0c9fcf8d0597581b3d9d305f631419529b5c60011a2a061c33285694d6cf64927ffa436636bfe07c89d2e5970d244c284a0 -SHA512 (snakemake-9.11.0-assets.tar.zst) = 54c66f1286b00424e816af852baae97e83ad25135f5f0898aba7b761e9a5a15bd2a66073249258741be15d86ddc1cdc6b54820848244e668eafc637b1832a235 +SHA512 (snakemake-9.11.2.tar.gz) = ac504138e532b0824bb1c822052da401b3f05cae77217c34097dd371cae505d0835585f7986e0e8b980da8fd6b3cae7d5a7be6b893c29b97d1f1bb78e5208f20 +SHA512 (snakemake-9.11.2-assets.tar.zst) = db2b89499cad3fb36c40ed59f2521545183cc914f21c60bd58dce990ce50783436ba9cf9adc4ae3bd948baa60352d0e8640b57dcdae41154ab865baf28390f27 From 1bdd3403b6904d611b1ed2989eb6b8d150753a67 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Thu, 18 Sep 2025 10:55:42 +0100 Subject: [PATCH 083/109] Allow PuLP 3.3 --- 3745.patch | 22 ++++++++++++++++++++++ snakemake.spec | 4 ++++ 2 files changed, 26 insertions(+) create mode 100644 3745.patch diff --git a/3745.patch b/3745.patch new file mode 100644 index 0000000..4689e7a --- /dev/null +++ b/3745.patch @@ -0,0 +1,22 @@ +From f8551ac19e7782dde0bd9e0102efcae038a06515 Mon Sep 17 00:00:00 2001 +From: "Benjamin A. Beasley" +Date: Thu, 18 Sep 2025 10:51:08 +0100 +Subject: [PATCH] chore: Allow PuLP 3.3 + +--- + pyproject.toml | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/pyproject.toml b/pyproject.toml +index fcc8b33a7..97a0dfc86 100644 +--- a/pyproject.toml ++++ b/pyproject.toml +@@ -42,7 +42,7 @@ dependencies = [ + "nbformat", + "packaging >=24.0", + "psutil", +- "pulp>=2.3.1,<3.3", ++ "pulp>=2.3.1,<3.4", + "pyyaml", + "referencing", + "requests>=2.8.1,<3.0", diff --git a/snakemake.spec b/snakemake.spec index 21046bf..66af1cf 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -151,6 +151,10 @@ Source2: get_assets # the substring "modified-assets" in the patch name. Patch: snakemake-9.1.1-modified-assets.patch +# chore: Allow PuLP 3.3 +# https://github.com/snakemake/snakemake/pull/3745 +Patch: %{forgeurl}/pull/3745.patch + BuildSystem: pyproject # Generate BR’s for all supported extras to ensure they do not FTI BuildOption(generate_buildrequires): -x reports From bf49773d1e7f30e74931b8face41c220bf696f95 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Thu, 18 Sep 2025 11:58:36 +0100 Subject: [PATCH 084/109] Update to 9.11.3 (close RHBZ#2396346) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index a1f2edc..1c505d1 100644 --- a/.gitignore +++ b/.gitignore @@ -97,3 +97,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index 66af1cf..34b5576 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -37,7 +37,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.11.2 +Version: 9.11.3 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 536b8aa..0bad91d 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.11.2.tar.gz) = ac504138e532b0824bb1c822052da401b3f05cae77217c34097dd371cae505d0835585f7986e0e8b980da8fd6b3cae7d5a7be6b893c29b97d1f1bb78e5208f20 -SHA512 (snakemake-9.11.2-assets.tar.zst) = db2b89499cad3fb36c40ed59f2521545183cc914f21c60bd58dce990ce50783436ba9cf9adc4ae3bd948baa60352d0e8640b57dcdae41154ab865baf28390f27 +SHA512 (snakemake-9.11.3.tar.gz) = 05f2c03c6845ab95fc5e5a6f43bfad7ff6d8f8333e5b1d16fd5c805091f18252b7d015c07f004b2293238cef3895ecb6bd39f839a425473d490c0a45bb569766 +SHA512 (snakemake-9.11.3-assets.tar.zst) = 5c7a3e998d03e90ae78e0f0c337b8225b22757cf2bc72f38746e4a1a2d3888672fc00642cc0f0e318118b40fcd59a251f5e2dfae918155304ab5ae280b41f6d2 From 8b0c20d7272c259de330f623c1b0e43af3c6550b Mon Sep 17 00:00:00 2001 From: Python Maint Date: Fri, 19 Sep 2025 14:57:00 +0200 Subject: [PATCH 085/109] Rebuilt for Python 3.14.0rc3 bytecode From d982d3f4926e9d5dca8645e73818ebfe8c0af0f4 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Sat, 20 Sep 2025 07:33:41 +0100 Subject: [PATCH 086/109] Update to 9.11.4 (close RHBZ#2396635) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 1c505d1..8d75f92 100644 --- a/.gitignore +++ b/.gitignore @@ -99,3 +99,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index 34b5576..8287366 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -37,7 +37,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.11.3 +Version: 9.11.4 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 0bad91d..a7494b3 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.11.3.tar.gz) = 05f2c03c6845ab95fc5e5a6f43bfad7ff6d8f8333e5b1d16fd5c805091f18252b7d015c07f004b2293238cef3895ecb6bd39f839a425473d490c0a45bb569766 -SHA512 (snakemake-9.11.3-assets.tar.zst) = 5c7a3e998d03e90ae78e0f0c337b8225b22757cf2bc72f38746e4a1a2d3888672fc00642cc0f0e318118b40fcd59a251f5e2dfae918155304ab5ae280b41f6d2 +SHA512 (snakemake-9.11.4.tar.gz) = 64ac937e8fa54aab117d7ad13604626e503a3348c4377412f69e8a9b487dbdb7d9507ea6c87b1dc591c68e5c47b555f26181e0f2d0dbb1aa4a98a26841df56c9 +SHA512 (snakemake-9.11.4-assets.tar.zst) = 11fb5c1c5e9ba84ebe1bb07f26e347e575ce41ee7472705696c20fa113030594dd7247060151d939f389abe2953fef027945b1bc3d6daf1995417a1d42799b54 From 22ee3e7ef606d9e11bfc57bf03eb45eb7286c3b6 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Wed, 24 Sep 2025 14:17:51 +0100 Subject: [PATCH 087/109] Update to 9.11.5 (close RHBZ#2397632) --- .gitignore | 2 ++ 3745.patch | 22 ---------------------- snakemake.spec | 6 +----- sources | 4 ++-- 4 files changed, 5 insertions(+), 29 deletions(-) delete mode 100644 3745.patch diff --git a/.gitignore b/.gitignore index 8d75f92..7d2a490 100644 --- a/.gitignore +++ b/.gitignore @@ -101,3 +101,5 @@ /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 diff --git a/3745.patch b/3745.patch deleted file mode 100644 index 4689e7a..0000000 --- a/3745.patch +++ /dev/null @@ -1,22 +0,0 @@ -From f8551ac19e7782dde0bd9e0102efcae038a06515 Mon Sep 17 00:00:00 2001 -From: "Benjamin A. Beasley" -Date: Thu, 18 Sep 2025 10:51:08 +0100 -Subject: [PATCH] chore: Allow PuLP 3.3 - ---- - pyproject.toml | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/pyproject.toml b/pyproject.toml -index fcc8b33a7..97a0dfc86 100644 ---- a/pyproject.toml -+++ b/pyproject.toml -@@ -42,7 +42,7 @@ dependencies = [ - "nbformat", - "packaging >=24.0", - "psutil", -- "pulp>=2.3.1,<3.3", -+ "pulp>=2.3.1,<3.4", - "pyyaml", - "referencing", - "requests>=2.8.1,<3.0", diff --git a/snakemake.spec b/snakemake.spec index 8287366..0a92916 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -37,7 +37,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.11.4 +Version: 9.11.5 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses @@ -151,10 +151,6 @@ Source2: get_assets # the substring "modified-assets" in the patch name. Patch: snakemake-9.1.1-modified-assets.patch -# chore: Allow PuLP 3.3 -# https://github.com/snakemake/snakemake/pull/3745 -Patch: %{forgeurl}/pull/3745.patch - BuildSystem: pyproject # Generate BR’s for all supported extras to ensure they do not FTI BuildOption(generate_buildrequires): -x reports diff --git a/sources b/sources index a7494b3..fc50c87 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.11.4.tar.gz) = 64ac937e8fa54aab117d7ad13604626e503a3348c4377412f69e8a9b487dbdb7d9507ea6c87b1dc591c68e5c47b555f26181e0f2d0dbb1aa4a98a26841df56c9 -SHA512 (snakemake-9.11.4-assets.tar.zst) = 11fb5c1c5e9ba84ebe1bb07f26e347e575ce41ee7472705696c20fa113030594dd7247060151d939f389abe2953fef027945b1bc3d6daf1995417a1d42799b54 +SHA512 (snakemake-9.11.5.tar.gz) = e244c7015c383dc5d524e67d80e0591aaa7c992978fddcc325897804c2f51bd81875dc8eaba685b918187bfa82d32c7eac2c84b693174e63b29136c5fec26320 +SHA512 (snakemake-9.11.5-assets.tar.zst) = 6ab60f2b562f8f6fc1720b2be0b72648acffcc477848acf9ebf61d658cb8d55ea68ab0d06e495f52245c3aac265378b24df0b3d80e4d1210d5eacb77717c6bc5 From 49ba85d394df12925c377f664f80fcde67879a39 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Thu, 25 Sep 2025 20:45:14 +0100 Subject: [PATCH 088/109] Update to 9.11.6 (close RHBZ#2398149) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 7d2a490..90054ce 100644 --- a/.gitignore +++ b/.gitignore @@ -103,3 +103,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index 0a92916..382ec4b 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -37,7 +37,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.11.5 +Version: 9.11.6 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index fc50c87..b4b843c 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.11.5.tar.gz) = e244c7015c383dc5d524e67d80e0591aaa7c992978fddcc325897804c2f51bd81875dc8eaba685b918187bfa82d32c7eac2c84b693174e63b29136c5fec26320 -SHA512 (snakemake-9.11.5-assets.tar.zst) = 6ab60f2b562f8f6fc1720b2be0b72648acffcc477848acf9ebf61d658cb8d55ea68ab0d06e495f52245c3aac265378b24df0b3d80e4d1210d5eacb77717c6bc5 +SHA512 (snakemake-9.11.6.tar.gz) = 8f4abb3dbc68bcff307daefc4bdd74a6e720dba8b2ee5bda898c9ec7c20d00dae966a05909e3e0a62112d1f8638ea69af721b0348eaf0941fd5141530029079d +SHA512 (snakemake-9.11.6-assets.tar.zst) = 7cbc90f9addd4e898ccd8794ca075edf43e42478f23f86cef8469ba83a883ebccddc253d23ef69429c6c167d5a2283cfe6176829241baa5e63608654a3e23f40 From 76f30d52d7eaf216fba00cbb44675f806dc4220b Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Wed, 1 Oct 2025 11:08:13 +0100 Subject: [PATCH 089/109] Update to 9.11.7 (close RHBZ#2400624) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 90054ce..175deb4 100644 --- a/.gitignore +++ b/.gitignore @@ -105,3 +105,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index 382ec4b..11bda59 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -37,7 +37,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.11.6 +Version: 9.11.7 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index b4b843c..acf73ee 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.11.6.tar.gz) = 8f4abb3dbc68bcff307daefc4bdd74a6e720dba8b2ee5bda898c9ec7c20d00dae966a05909e3e0a62112d1f8638ea69af721b0348eaf0941fd5141530029079d -SHA512 (snakemake-9.11.6-assets.tar.zst) = 7cbc90f9addd4e898ccd8794ca075edf43e42478f23f86cef8469ba83a883ebccddc253d23ef69429c6c167d5a2283cfe6176829241baa5e63608654a3e23f40 +SHA512 (snakemake-9.11.7.tar.gz) = 15a73b771a08ff56cc38b8343e47c3a04e748ee34057835f1373d01aa2833dfb6d63ca1eda531d14439ecf5c3816be83ffc106346d835cbafda4dd1405234d90 +SHA512 (snakemake-9.11.7-assets.tar.zst) = 7511c835a016fc9733477b9f9a0d007150875cb47eb23a306f5679fe0721c15efc014611dd03d02131a1bcd87f8e659c6def05ea06ac4000d2c12bf59ec1addf From a29585e0cb3a6a70c733d52a9c1ac29ddb901340 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Thu, 2 Oct 2025 06:48:15 +0100 Subject: [PATCH 090/109] Update bootstrapping documentation in the spec file [skip changelog] --- snakemake.spec | 35 +++++++++++++++++++++-------------- 1 file changed, 21 insertions(+), 14 deletions(-) diff --git a/snakemake.spec b/snakemake.spec index 11bda59..540cba8 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -1,8 +1,9 @@ # Work around a series of circular test dependencies: # -# python-snakemake-interface-scheduler-plugins -# │￪ python-snakemake-interface-report-plugins -# ￬│ ￬￪ ⬐───╮ +# 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─────────────────╮ @@ -13,19 +14,25 @@ # # A good build order is: # -# 1. BOOTSTRAP: python-snakemake-interface-common -# python-snakemake-interface-executor-plugins, -# python-snakemake-interface-storage-plugins, -# python-snakemake-interface-report-plugins -# 2. BOOTSTRAP: snakemake -# 3. python-snakemake-executor-plugin-cluster-generic, -# python-snakemake-storage-plugin-http, -# python-snakemake-storage-plugin-s3, -# python-snakemake-storage-plugin-fs -# 4. snakemake, python-snakemake-interface-executor-plugins, -# python-snakemake-interface-storage-plugins, +# 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-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 From a10f95af582d245e812f42a1033489782e2b8f37 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Thu, 2 Oct 2025 06:59:04 +0100 Subject: [PATCH 091/109] Add snakemake-logger-plugin-rich to bootstrapping docs [skip changelog] --- snakemake.spec | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/snakemake.spec b/snakemake.spec index 540cba8..23274f2 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -1,6 +1,7 @@ # Work around a series of circular test dependencies: # -# python-snakemake-interface-logger-plugins +# ⬐─python-snakemake-logger-plugin-rich🠔────╮ +# python-snakemake-interface-logger-plugins─╯ # │￪python-snakemake-interface-scheduler-plugins # │││￪ python-snakemake-interface-report-plugins # ￬│￬│ ￬￪ ⬐───╮ @@ -24,6 +25,7 @@ # 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 From 9ca79712ed3ecfc270cb811211d473012d389101 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Thu, 2 Oct 2025 13:04:14 +0100 Subject: [PATCH 092/109] Update to 9.11.8 (close RHBZ#2401000) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 175deb4..c0e2069 100644 --- a/.gitignore +++ b/.gitignore @@ -107,3 +107,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index 23274f2..4aa9289 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -46,7 +46,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.11.7 +Version: 9.11.8 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index acf73ee..5d98ff9 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.11.7.tar.gz) = 15a73b771a08ff56cc38b8343e47c3a04e748ee34057835f1373d01aa2833dfb6d63ca1eda531d14439ecf5c3816be83ffc106346d835cbafda4dd1405234d90 -SHA512 (snakemake-9.11.7-assets.tar.zst) = 7511c835a016fc9733477b9f9a0d007150875cb47eb23a306f5679fe0721c15efc014611dd03d02131a1bcd87f8e659c6def05ea06ac4000d2c12bf59ec1addf +SHA512 (snakemake-9.11.8.tar.gz) = 0ce8cac3544f281867751c00abf18ffcdc53b743ac28f31f2cd6b065342bad1bedde2ba75ddc14e168f39247c1d94377dac2a394cfb2ee7317b300ee6d950cae +SHA512 (snakemake-9.11.8-assets.tar.zst) = bbb1ba14fd1ba56e51afe57939a449dcbaa1a942edb7c313b7b2f01c154431e4413b5cd92513a7c1a950bacd6fb261dda5e54b8be7e2bf93fa5c09a7ac7b2d09 From d6336b26064e16fb8e8de865d97bf9ed53e35b10 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Fri, 3 Oct 2025 19:45:53 +0100 Subject: [PATCH 093/109] Update to 9.11.9 (close RHBZ#2401257) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index c0e2069..23b1f19 100644 --- a/.gitignore +++ b/.gitignore @@ -109,3 +109,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index 4aa9289..e5c894a 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -46,7 +46,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.11.8 +Version: 9.11.9 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 5d98ff9..8bf1f77 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.11.8.tar.gz) = 0ce8cac3544f281867751c00abf18ffcdc53b743ac28f31f2cd6b065342bad1bedde2ba75ddc14e168f39247c1d94377dac2a394cfb2ee7317b300ee6d950cae -SHA512 (snakemake-9.11.8-assets.tar.zst) = bbb1ba14fd1ba56e51afe57939a449dcbaa1a942edb7c313b7b2f01c154431e4413b5cd92513a7c1a950bacd6fb261dda5e54b8be7e2bf93fa5c09a7ac7b2d09 +SHA512 (snakemake-9.11.9.tar.gz) = f591fe7a61dc283ca9f6c8aa9e63e1cce2efab28ae031ce087d3f74f63f34b3aa4c183aa652d44fa692ef20e81bd2b9d4403bf31a1abd51a6cea25746a1433fe +SHA512 (snakemake-9.11.9-assets.tar.zst) = 228a5c515d1e8ea70078d13eff838002f5c39b074ab63802e3f140b99780dcefaa8c146d304601d706b107d9a0757b3fadf6f99f5e4558402780aad95ab29dee From f1a429bd2b40348ad732e59bed78dad316715cd0 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Sat, 4 Oct 2025 17:19:20 +0100 Subject: [PATCH 094/109] Update to 9.12.0 (close RHBZ#2401452) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 23b1f19..31cc6d1 100644 --- a/.gitignore +++ b/.gitignore @@ -111,3 +111,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index e5c894a..100c777 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -46,7 +46,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.11.9 +Version: 9.12.0 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 8bf1f77..261b0e8 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.11.9.tar.gz) = f591fe7a61dc283ca9f6c8aa9e63e1cce2efab28ae031ce087d3f74f63f34b3aa4c183aa652d44fa692ef20e81bd2b9d4403bf31a1abd51a6cea25746a1433fe -SHA512 (snakemake-9.11.9-assets.tar.zst) = 228a5c515d1e8ea70078d13eff838002f5c39b074ab63802e3f140b99780dcefaa8c146d304601d706b107d9a0757b3fadf6f99f5e4558402780aad95ab29dee +SHA512 (snakemake-9.12.0.tar.gz) = 623c3e868def3435a2aa03ea6854e0b8081314afa2f80b15c1e8b42180bc3f0a1b69418dff6638e462443c715bf108b7310e08481fddabc2e6eff182b89562ff +SHA512 (snakemake-9.12.0-assets.tar.zst) = c6fca1bfc3cd33cb0daff39aa40bf50cb38f30c41d37177a5503d51c942932ea4e322de9fb3d55f807e90b56e1e1840cff76dffc8018f49a9b3006d1dce4ba3f From e1fc4d3135f0606ecc938e6bfd6ac04d7d351522 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Sat, 11 Oct 2025 09:08:46 +0100 Subject: [PATCH 095/109] Update to 9.13.0 (close RHBZ#2403096) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 31cc6d1..5545107 100644 --- a/.gitignore +++ b/.gitignore @@ -113,3 +113,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index 100c777..e28ee82 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -46,7 +46,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.12.0 +Version: 9.13.0 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 261b0e8..6596610 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.12.0.tar.gz) = 623c3e868def3435a2aa03ea6854e0b8081314afa2f80b15c1e8b42180bc3f0a1b69418dff6638e462443c715bf108b7310e08481fddabc2e6eff182b89562ff -SHA512 (snakemake-9.12.0-assets.tar.zst) = c6fca1bfc3cd33cb0daff39aa40bf50cb38f30c41d37177a5503d51c942932ea4e322de9fb3d55f807e90b56e1e1840cff76dffc8018f49a9b3006d1dce4ba3f +SHA512 (snakemake-9.13.0.tar.gz) = 1b7fd3bf1088a6c59075a0dcf7b2dba7a8cb99aeccb40327972ba56dd6db649369b5559426f435f5c39c3dcdd19584cf7c8a5b3b398c1425d51425bf250d25ad +SHA512 (snakemake-9.13.0-assets.tar.zst) = 6cfb22a399539e05b77bca07e40440d9ab636867683a64ac8dc0daea45868fdba7262786c2ef25facbcd7f2d1677c1bab0cff15039f8b0e2d0b38b9a2a4deed6 From 5cadab948250e7b695a7cf736af376d8e75cef6d Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Sat, 11 Oct 2025 22:44:55 +0100 Subject: [PATCH 096/109] Update to 9.13.1 (close RHBZ#2403281) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 5545107..1e704b2 100644 --- a/.gitignore +++ b/.gitignore @@ -115,3 +115,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index e28ee82..1f43fcc 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -46,7 +46,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.13.0 +Version: 9.13.1 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 6596610..d826892 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.13.0.tar.gz) = 1b7fd3bf1088a6c59075a0dcf7b2dba7a8cb99aeccb40327972ba56dd6db649369b5559426f435f5c39c3dcdd19584cf7c8a5b3b398c1425d51425bf250d25ad -SHA512 (snakemake-9.13.0-assets.tar.zst) = 6cfb22a399539e05b77bca07e40440d9ab636867683a64ac8dc0daea45868fdba7262786c2ef25facbcd7f2d1677c1bab0cff15039f8b0e2d0b38b9a2a4deed6 +SHA512 (snakemake-9.13.1.tar.gz) = 702df63c2ff4bf140c43d71a5b548f5ec0483ffc57efdf7427b3e588a95610ea4187dfb437808fca272fb3f898a104e0de82fb1e388328612754367bf823b7ca +SHA512 (snakemake-9.13.1-assets.tar.zst) = 385a8f9250bed48c9560049afac60f5ce16d8613d95bac8d98c26152e5021a898a9fef6e2246250674bcbf39dc3288f64673af528a270d7ea4859a0ff90af009 From b33ad800c44e17464a0f7dac1cdac8e0fde1b94e Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Sun, 12 Oct 2025 21:31:03 +0100 Subject: [PATCH 097/109] Update to 9.13.2 (close RHBZ#2403372) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 1e704b2..5316ad7 100644 --- a/.gitignore +++ b/.gitignore @@ -117,3 +117,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index 1f43fcc..e1ff18d 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -46,7 +46,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.13.1 +Version: 9.13.2 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index d826892..463b889 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.13.1.tar.gz) = 702df63c2ff4bf140c43d71a5b548f5ec0483ffc57efdf7427b3e588a95610ea4187dfb437808fca272fb3f898a104e0de82fb1e388328612754367bf823b7ca -SHA512 (snakemake-9.13.1-assets.tar.zst) = 385a8f9250bed48c9560049afac60f5ce16d8613d95bac8d98c26152e5021a898a9fef6e2246250674bcbf39dc3288f64673af528a270d7ea4859a0ff90af009 +SHA512 (snakemake-9.13.2.tar.gz) = b627643e7280151def2e64df2784d629d3624853c5255bbe1a9376d407dce6c2db03d8e74fbfe290fcfbc289487c59254da6655dd1654333529f298ae7488ca9 +SHA512 (snakemake-9.13.2-assets.tar.zst) = fba2847ce74081f58b2980844223d63dcc5c4a851aeac9f23b5fb3ed0d8a8e567b0134991428cdf069ad55a83c6dbc4568a201d0d68410a2f01801d72233a47b From 9622b94e7ca658445f51064696360e4245435fd4 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Sat, 18 Oct 2025 07:59:02 +0100 Subject: [PATCH 098/109] Update to 9.13.3 (close RHBZ#2404796) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 5316ad7..72ef63d 100644 --- a/.gitignore +++ b/.gitignore @@ -119,3 +119,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index e1ff18d..f8f6258 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -46,7 +46,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.13.2 +Version: 9.13.3 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 463b889..383df73 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.13.2.tar.gz) = b627643e7280151def2e64df2784d629d3624853c5255bbe1a9376d407dce6c2db03d8e74fbfe290fcfbc289487c59254da6655dd1654333529f298ae7488ca9 -SHA512 (snakemake-9.13.2-assets.tar.zst) = fba2847ce74081f58b2980844223d63dcc5c4a851aeac9f23b5fb3ed0d8a8e567b0134991428cdf069ad55a83c6dbc4568a201d0d68410a2f01801d72233a47b +SHA512 (snakemake-9.13.3.tar.gz) = fc5caa283fce7c3a29f1b194f977aba56303415b617bc296f24a4441d820d8bd71cd2583ec190de091918da79d56a1952f802006d13f16fc34970da04fb8a19c +SHA512 (snakemake-9.13.3-assets.tar.zst) = 004e39509e0f07ce9c0aec23bbb84c35fcb1df726d32701fd6e6f2771149b83e818c5544fb7536ffdb4455ced9187a2d2d8298064e99d0527cbe28a0b6284116 From b46acc103dae800bb8578a76edbbe30e76059d12 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Wed, 22 Oct 2025 23:22:16 +0100 Subject: [PATCH 099/109] Update to 9.13.4 (close RHBZ#2405879) --- snakemake.spec | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/snakemake.spec b/snakemake.spec index f8f6258..b40249d 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -46,7 +46,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.13.3 +Version: 9.13.4 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses From a38036f1787e5bc31909a43b12e098d89cb29bc4 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Wed, 22 Oct 2025 23:24:30 +0100 Subject: [PATCH 100/109] Update to 9.13.4 (close RHBZ#2405879) --- .gitignore | 2 ++ sources | 4 ++-- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.gitignore b/.gitignore index 72ef63d..2d9bbb2 100644 --- a/.gitignore +++ b/.gitignore @@ -121,3 +121,5 @@ /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 diff --git a/sources b/sources index 383df73..73d0557 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.13.3.tar.gz) = fc5caa283fce7c3a29f1b194f977aba56303415b617bc296f24a4441d820d8bd71cd2583ec190de091918da79d56a1952f802006d13f16fc34970da04fb8a19c -SHA512 (snakemake-9.13.3-assets.tar.zst) = 004e39509e0f07ce9c0aec23bbb84c35fcb1df726d32701fd6e6f2771149b83e818c5544fb7536ffdb4455ced9187a2d2d8298064e99d0527cbe28a0b6284116 +SHA512 (snakemake-9.13.4.tar.gz) = 6e67385b0e0803b0d9715397fd9f3e260ce9525e5d65bbd010aade860a2c3848db84275c932dfd4e7916b5ce770670a5627e335cc51aa08d1538819e1d86c1f4 +SHA512 (snakemake-9.13.4-assets.tar.zst) = 77824e736e10db417c1cee72eb2dfa6551636385547c686d08692d9bdef88566bf9d41cbc692897151cac8cba5c889fc2140d07347e2a326c381c4e8b863600e From 26ec5d763ceb0b7e99b2e030162a2f98a17f434c Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Tue, 4 Nov 2025 20:10:09 +0000 Subject: [PATCH 101/109] Update to 9.13.5 (close RHBZ#2412283) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 2d9bbb2..b436057 100644 --- a/.gitignore +++ b/.gitignore @@ -123,3 +123,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index b40249d..de03fe6 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -46,7 +46,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.13.4 +Version: 9.13.5 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 73d0557..6e22136 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.13.4.tar.gz) = 6e67385b0e0803b0d9715397fd9f3e260ce9525e5d65bbd010aade860a2c3848db84275c932dfd4e7916b5ce770670a5627e335cc51aa08d1538819e1d86c1f4 -SHA512 (snakemake-9.13.4-assets.tar.zst) = 77824e736e10db417c1cee72eb2dfa6551636385547c686d08692d9bdef88566bf9d41cbc692897151cac8cba5c889fc2140d07347e2a326c381c4e8b863600e +SHA512 (snakemake-9.13.5.tar.gz) = 8143220351a58fbf84ea3dbc0e1238d8829e830765d6cd4079c05f65a5619b19976775428fb719b393a8f699ece2544f3b03bed8f7d2c5afa6a969c2ceb8aa54 +SHA512 (snakemake-9.13.5-assets.tar.zst) = c8081a803eda7d33a345cc025f76fc90413b3b24caf86917250f9f943c58a4824831a6d6353f15fe267e2c485edc5b7ca10c7bb7a2142529c572f1b0466fa1b1 From d7bc3ba40d7a8fd4626503a3664ff457f1217bad Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Thu, 6 Nov 2025 22:32:13 +0000 Subject: [PATCH 102/109] Update to 9.13.6 (close RHBZ#2413244) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index b436057..9f7bb1f 100644 --- a/.gitignore +++ b/.gitignore @@ -125,3 +125,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index de03fe6..5c90643 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -46,7 +46,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.13.5 +Version: 9.13.6 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 6e22136..e175b36 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.13.5.tar.gz) = 8143220351a58fbf84ea3dbc0e1238d8829e830765d6cd4079c05f65a5619b19976775428fb719b393a8f699ece2544f3b03bed8f7d2c5afa6a969c2ceb8aa54 -SHA512 (snakemake-9.13.5-assets.tar.zst) = c8081a803eda7d33a345cc025f76fc90413b3b24caf86917250f9f943c58a4824831a6d6353f15fe267e2c485edc5b7ca10c7bb7a2142529c572f1b0466fa1b1 +SHA512 (snakemake-9.13.6.tar.gz) = b879b8dc4e3539202804852b61fb6acd0022d895cb13485ce67b784b6de7044557f8765a96e5a527f2a806332f90c563d4688a302aa4ad37b7d22f0a7e8885d2 +SHA512 (snakemake-9.13.6-assets.tar.zst) = b1c49d74e108996284664a034ce19f35df8bab6f2a9e4627cc7c7ee6410e68bd8cf07d9bd5f84fc65d4eae63af0a3fd478556509f137af8c5ccfaef0d8e1b90c From cc9bf4074438fdfe310ff2235516af651e98ebc4 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Fri, 7 Nov 2025 22:55:35 +0000 Subject: [PATCH 103/109] Update to 9.13.7 (close RHBZ#2413438) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 9f7bb1f..40b70dc 100644 --- a/.gitignore +++ b/.gitignore @@ -127,3 +127,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index 5c90643..21f3176 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -46,7 +46,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.13.6 +Version: 9.13.7 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index e175b36..a8d342a 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.13.6.tar.gz) = b879b8dc4e3539202804852b61fb6acd0022d895cb13485ce67b784b6de7044557f8765a96e5a527f2a806332f90c563d4688a302aa4ad37b7d22f0a7e8885d2 -SHA512 (snakemake-9.13.6-assets.tar.zst) = b1c49d74e108996284664a034ce19f35df8bab6f2a9e4627cc7c7ee6410e68bd8cf07d9bd5f84fc65d4eae63af0a3fd478556509f137af8c5ccfaef0d8e1b90c +SHA512 (snakemake-9.13.7.tar.gz) = 4e1b90448ccb7395d082d186380a71ce3b74aae4058fc031e145b5ac93466d6928990e80930cf9745558308eb99a09ddc1a5c038cc02e129193246e4fc0c73e5 +SHA512 (snakemake-9.13.7-assets.tar.zst) = 48d9d9ec9172f7709b4c2f09a777e008a2d3b199b1f33e574c46001f6f15972f41e68eb8009854e92ae57d19f4fb82bb76033927c81098766e5e213428916eac From 8af8519b466b8a3c64eb7e7d04ee21d29f023cee Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Sun, 7 Dec 2025 08:11:25 +0000 Subject: [PATCH 104/109] Remove rpmlintrc filters for duplicate files MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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] --- snakemake.rpmlintrc | 9 --------- 1 file changed, 9 deletions(-) diff --git a/snakemake.rpmlintrc b/snakemake.rpmlintrc index 5e46a87..b0e2093 100644 --- a/snakemake.rpmlintrc +++ b/snakemake.rpmlintrc @@ -5,15 +5,6 @@ addFilter(r"\+\w+.noarch: W: no-documentation") addFilter(r" obsolete-not-provided snakemake\+(messaging)$") # The -doc subpackage was removed and has no equivalent replacement. addFilter(r" obsolete-not-provided snakemake-doc$") -# Some small files may incidentally have duplicate contents. Because they are -# small in size and few in number, it is not worth the spec-file complexity to -# hardlink them (which would itself trigger an rpmlint warning about -# cross-directory hardlinking). -addFilter(r"files-duplicate .*/snakemake/.*/remote/[^/]+\.py") -addFilter(r"files-duplicate .*/snakemake/.*/tests/.*/caption\.rst") -# Similarly, we expect that there will be some duplicate license files for web -# assets, and it is not worthwhile to attempt to symlink or hardlink these. -addFilter(r"files-duplicate .*/snakemake/assets/data/.*/LICEN[CS]E.*") # This is, unfortunately, intentional. See the comments in the spec file. addFilter(r" python-leftover-require python-unversioned-command$") # The assets bundle needs to be generated with a script, so it has no URL (and From 10027bf8e1cda3d68364e076c9f2c2d66940b633 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Sat, 6 Dec 2025 22:58:43 +0000 Subject: [PATCH 105/109] Update to 9.14.2 (close RHBZ#2419388) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 40b70dc..ebe240f 100644 --- a/.gitignore +++ b/.gitignore @@ -129,3 +129,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index 21f3176..c4bf85c 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -46,7 +46,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.13.7 +Version: 9.14.2 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index a8d342a..630a653 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.13.7.tar.gz) = 4e1b90448ccb7395d082d186380a71ce3b74aae4058fc031e145b5ac93466d6928990e80930cf9745558308eb99a09ddc1a5c038cc02e129193246e4fc0c73e5 -SHA512 (snakemake-9.13.7-assets.tar.zst) = 48d9d9ec9172f7709b4c2f09a777e008a2d3b199b1f33e574c46001f6f15972f41e68eb8009854e92ae57d19f4fb82bb76033927c81098766e5e213428916eac +SHA512 (snakemake-9.14.2.tar.gz) = d0ce77fb9befa69c1228f5704d2fa621af9823eab3a795052926a10b4f9a6f3a3a7e2c832071f82f817342118a965a0f173e2461c02015b5852cb668cba86417 +SHA512 (snakemake-9.14.2-assets.tar.zst) = 26cde64e03c5621378c1487ccfb286d372191b8819ad1360ce8aaf9cc50a414dcb748090cef36bf8d3596b6b528b5401f9c605f0e63446e58fa008c32ed7af1f From ff6c9d4c0fc3159d36caa4a13985e10de41df588 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Mon, 8 Dec 2025 12:13:39 +0000 Subject: [PATCH 106/109] Update to 9.14.3 (close RHBZ#2420015) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index ebe240f..d2d4fe0 100644 --- a/.gitignore +++ b/.gitignore @@ -131,3 +131,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index c4bf85c..572e67c 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -46,7 +46,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.14.2 +Version: 9.14.3 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 630a653..55a1a69 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.14.2.tar.gz) = d0ce77fb9befa69c1228f5704d2fa621af9823eab3a795052926a10b4f9a6f3a3a7e2c832071f82f817342118a965a0f173e2461c02015b5852cb668cba86417 -SHA512 (snakemake-9.14.2-assets.tar.zst) = 26cde64e03c5621378c1487ccfb286d372191b8819ad1360ce8aaf9cc50a414dcb748090cef36bf8d3596b6b528b5401f9c605f0e63446e58fa008c32ed7af1f +SHA512 (snakemake-9.14.3.tar.gz) = 6118c45ee94c4fc6e9bd8715e88f57409ebc9c640e5b60fd02970031eb20baa6cd6a16f41228539f2ac294e7f3f55ee6479ad000913019876cdd16bc921d93a0 +SHA512 (snakemake-9.14.3-assets.tar.zst) = 1590964477556b44a5f49c8d22fedf3e2996617f725940aa2419b8d0c1dfece6ff09fa6eca89be9bf66d16e28962864df9b81ec11edd6670009e0c1f6bdfb021 From dcb86aad44d6c178eb6c63958a76933e715e647d Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Tue, 9 Dec 2025 10:50:33 +0000 Subject: [PATCH 107/109] Update to 9.14.4 (close RHBZ#2420467) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index d2d4fe0..a094a77 100644 --- a/.gitignore +++ b/.gitignore @@ -133,3 +133,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index 572e67c..e081f16 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -46,7 +46,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.14.3 +Version: 9.14.4 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 55a1a69..7456ca9 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.14.3.tar.gz) = 6118c45ee94c4fc6e9bd8715e88f57409ebc9c640e5b60fd02970031eb20baa6cd6a16f41228539f2ac294e7f3f55ee6479ad000913019876cdd16bc921d93a0 -SHA512 (snakemake-9.14.3-assets.tar.zst) = 1590964477556b44a5f49c8d22fedf3e2996617f725940aa2419b8d0c1dfece6ff09fa6eca89be9bf66d16e28962864df9b81ec11edd6670009e0c1f6bdfb021 +SHA512 (snakemake-9.14.4.tar.gz) = 474bbb6e8e80addf80c74f98a9d9420e04d3fdd0de901788e6dc35f01b1e1bc717ef7052db8e44557ef683568f456b7155176fe47938b1612b7d6dfeb942bff3 +SHA512 (snakemake-9.14.4-assets.tar.zst) = c41c3b22666e00705b58692039c85a61f0dce40211bdf199170a73eebc977a3023cdd8cf1b2a4295a3c8e02df0473465091e80493838789b963eead25825f6dc From 33176932354c4a13fa03090674c697a19d0b00cb Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Wed, 17 Dec 2025 06:56:48 +0000 Subject: [PATCH 108/109] Update to 9.14.5 (close RHBZ#2422268) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index a094a77..f4a2b4e 100644 --- a/.gitignore +++ b/.gitignore @@ -135,3 +135,5 @@ /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 diff --git a/snakemake.spec b/snakemake.spec index e081f16..e4d20e7 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -46,7 +46,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.14.4 +Version: 9.14.5 %global srcversion %(echo '%{version}' | cut -d '^' -f 1) Release: %autorelease Summary: Workflow management system to create reproducible and scalable data analyses diff --git a/sources b/sources index 7456ca9..1c037fc 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.14.4.tar.gz) = 474bbb6e8e80addf80c74f98a9d9420e04d3fdd0de901788e6dc35f01b1e1bc717ef7052db8e44557ef683568f456b7155176fe47938b1612b7d6dfeb942bff3 -SHA512 (snakemake-9.14.4-assets.tar.zst) = c41c3b22666e00705b58692039c85a61f0dce40211bdf199170a73eebc977a3023cdd8cf1b2a4295a3c8e02df0473465091e80493838789b963eead25825f6dc +SHA512 (snakemake-9.14.5.tar.gz) = 11d6a7e97812aa5d3ca04eaf132fc876077dbe113d4d38e8aa5b93bc63279bdf34e7f2e6135e923f03f7c05dc198a512729b2f25827f6b73f31f481aa4139272 +SHA512 (snakemake-9.14.5-assets.tar.zst) = 1e0872939c028ebde9ddf027c8748d15b42f83784c8c32b6d6fa3fb20dd5ff2a3533036486714e88a84819f9c0221daf470e300b976f9eab8d8e97cbbb94d636 From 76223058e853d6d02f7fa22239c83bcf922881b3 Mon Sep 17 00:00:00 2001 From: "Benjamin A. Beasley" Date: Thu, 8 Jan 2026 20:39:08 +0000 Subject: [PATCH 109/109] Update to 9.14.6 (close RHBZ#2428070) --- .gitignore | 2 ++ snakemake.spec | 2 +- sources | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index f4a2b4e..8624a3d 100644 --- a/.gitignore +++ b/.gitignore @@ -137,3 +137,5 @@ /snakemake-9.14.4-assets.tar.zst /snakemake-9.14.5.tar.gz /snakemake-9.14.5-assets.tar.zst +/snakemake-9.14.6.tar.gz +/snakemake-9.14.6-assets.tar.zst diff --git a/snakemake.spec b/snakemake.spec index e4d20e7..6bb8fdb 100644 --- a/snakemake.spec +++ b/snakemake.spec @@ -46,7 +46,7 @@ %bcond gcs_tests 1 Name: snakemake -Version: 9.14.5 +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 diff --git a/sources b/sources index 1c037fc..ac14f3c 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (snakemake-9.14.5.tar.gz) = 11d6a7e97812aa5d3ca04eaf132fc876077dbe113d4d38e8aa5b93bc63279bdf34e7f2e6135e923f03f7c05dc198a512729b2f25827f6b73f31f481aa4139272 -SHA512 (snakemake-9.14.5-assets.tar.zst) = 1e0872939c028ebde9ddf027c8748d15b42f83784c8c32b6d6fa3fb20dd5ff2a3533036486714e88a84819f9c0221daf470e300b976f9eab8d8e97cbbb94d636 +SHA512 (snakemake-9.14.6.tar.gz) = 3858d5610271fbf3617e3b88b10b55546ddb2eafffa929a882bf5584c91f85280fa7c5b25bae8951e4feb5aa9568ba51c0979c35b37472d03e1efc239392f1ae +SHA512 (snakemake-9.14.6-assets.tar.zst) = c58043d640c14cdb4057b515ee65d8c8eb76a4abf34d7ebae70cc929023df780ef234dd5a8fa9d76a96bb1aceda8dab1c8f5337d72ff6bb9ae7d6b82c10a16a7