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‎.github/workflows/announce-release.yml‎

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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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uses: actions/checkout@v6
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- name: Post to Mastodon
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uses: snakemake/mastodon-release-post-action@v1

‎.github/workflows/codespell.yml‎

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steps:
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- name: Checkout
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uses: actions/checkout@v5
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uses: actions/checkout@v6
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- name: Codespell
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uses: codespell-project/actions-codespell@v2
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with:

‎.github/workflows/docker-publish.yml‎

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if: github.repository == 'snakemake/snakemake'
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v5
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- uses: actions/checkout@v6
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v2

‎.github/workflows/docs.yml‎

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if: github.event.pull_request.merged != true || github.ref != 'refs/heads/main'
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v5
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- uses: actions/checkout@v6
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- name: Install Pixi
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uses: prefix-dev/[email protected].1
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uses: prefix-dev/[email protected].3
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with:
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environments: "docs"
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pixi-version: v0.42.1
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if: github.event.pull_request.merged != true || github.ref != 'refs/heads/main'
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v5
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- uses: actions/checkout@v6
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- name: Install Pixi
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uses: prefix-dev/[email protected].1
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uses: prefix-dev/[email protected].3
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with:
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environments: "docs"
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pixi-version: v0.42.1

‎.github/workflows/main.yml‎

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pull-requests: write # for marocchino/sticky-pull-request-comment to create or update PR comment
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v5
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- uses: actions/checkout@v6
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- name: Install Pixi
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uses: prefix-dev/[email protected].1
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uses: prefix-dev/[email protected].3
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with:
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environments: "quality"
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pixi-version: v0.42.1
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ZENODO_SANDBOX_PAT: "${{ secrets.ZENODO_SANDBOX_PAT }}"
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CI: true
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steps:
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- uses: actions/checkout@v5
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- uses: actions/checkout@v6
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with:
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fetch-depth: 0
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- name: Install Pixi
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uses: prefix-dev/[email protected].1
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uses: prefix-dev/[email protected].3
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with:
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environments: ${{ matrix.env }}
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pixi-version: v0.42.1
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runs-on: ubuntu-latest
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needs: tests
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steps:
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- uses: actions/checkout@v5
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- uses: actions/checkout@v6
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- name: Build container image
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run: docker build .

‎.github/workflows/release-please.yml‎

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release-type: python
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token: ${{ secrets.RELEASE_PLEASE_PR_CI_TOKEN }}
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- uses: actions/checkout@v5
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- uses: actions/checkout@v6
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if: ${{ steps.release.outputs.release_created }}
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with:
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fetch-depth: 0
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- name: Set up Pixi
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if: ${{ steps.release.outputs.release_created }}
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uses: prefix-dev/[email protected].1
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uses: prefix-dev/[email protected].3
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with:
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environments: quality
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pixi-version: v0.47.0

‎CHANGELOG.md‎

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# Changelog
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## [9.14.0](https://github.com/snakemake/snakemake/compare/v9.13.7...v9.14.0) (2025-11-27)
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### Features
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* Support Hy in script directive ([#3824](https://github.com/snakemake/snakemake/issues/3824)) ([2329c9e](https://github.com/snakemake/snakemake/commit/2329c9ed7ac37b422e1b42f9f25865682b15a73d))
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### Bug Fixes
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* Add support for pathlib in `notebook` field ([#3811](https://github.com/snakemake/snakemake/issues/3811)) ([7b2180a](https://github.com/snakemake/snakemake/commit/7b2180a33c6bd8efbdb213ef0caafe7c3febbe7c))
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* Addressed race condition in workdir_handler.py ([#3844](https://github.com/snakemake/snakemake/issues/3844)) ([8dbfcfb](https://github.com/snakemake/snakemake/commit/8dbfcfb23d9fe35f28a8153180c644c384ae21ee))
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* cleanup update-marked output files of failed jobs if there was no backup to restore them ([#3843](https://github.com/snakemake/snakemake/issues/3843)) ([41f1ce8](https://github.com/snakemake/snakemake/commit/41f1ce838fdca84c764eb4126419dfc5d910308f))
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* correct Windows callable path handling ([#3832](https://github.com/snakemake/snakemake/issues/3832)) ([5caad70](https://github.com/snakemake/snakemake/commit/5caad70003bdda91a6b9965e7742c7e796a1cc12))
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* expand env vars on resources ([#3823](https://github.com/snakemake/snakemake/issues/3823)) ([fcfa1bc](https://github.com/snakemake/snakemake/commit/fcfa1bc0449a1a1fbaa9effdc4a30f264e129070))
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* fix backup for output marked by `update` ([#3839](https://github.com/snakemake/snakemake/issues/3839)) ([09c64b7](https://github.com/snakemake/snakemake/commit/09c64b7789e36d700c9806b86a0659e9a2d2b7ad))
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* Minor fixes/additions to logging module. ([#3802](https://github.com/snakemake/snakemake/issues/3802)) ([3b3986d](https://github.com/snakemake/snakemake/commit/3b3986ddc9ce6b796a465bb37c0053b3a5cce207))
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* mount local storage prefix into containers ([#3840](https://github.com/snakemake/snakemake/issues/3840)) ([f1e8b62](https://github.com/snakemake/snakemake/commit/f1e8b6293803339ba49ef1fdd7cfe451a4e9c853))
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* properly format input/output files in case of missing rule to produce them ([#3849](https://github.com/snakemake/snakemake/issues/3849)) ([69d5d24](https://github.com/snakemake/snakemake/commit/69d5d246e90b8976e9228c6e6151d0d447e782df))
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* Unpack AnnotatedString in _apply_wildcards ([#3798](https://github.com/snakemake/snakemake/issues/3798)) ([7886508](https://github.com/snakemake/snakemake/commit/7886508641ce9a1912dd94f3f2b522f8b222c050))
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### Performance Improvements
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* retrieve storage inputs immediately before scheduling jobs instead of before running the entire workflow ([#3850](https://github.com/snakemake/snakemake/issues/3850)) ([4ac6cda](https://github.com/snakemake/snakemake/commit/4ac6cdaf9a0826563535387de344b25db26c2ef1))
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## [9.13.7](https://github.com/snakemake/snakemake/compare/v9.13.6...v9.13.7) (2025-11-07)
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‎pyproject.toml‎

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"tests/test_executor_test_suite.py",
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"tests/test_api.py",
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"tests/test_internals.py",
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"tests/test_jupyter_notebook_pathlike.py",
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# the tests below were never tested in the old CI and currently fail
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# "tests/test_args.py",
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# "tests/test_output_index.py",

‎src/snakemake/common/__init__.py‎

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)
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def func_true(job):
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return True
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def get_snakemake_searchpaths():
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paths = [str(Path(__file__).parent.parent.parent)] + [
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path for path in sys.path if os.path.isdir(path)

‎src/snakemake/common/workdir_handler.py‎

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self.olddir = Path.cwd()
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self.workdir.mkdir(parents=True)
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self.workdir.mkdir(parents=True, exist_ok=True)
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os.chdir(self.workdir)
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def change_back(self):

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