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Merge branch 'main' into params_serialize
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‎.github/workflows/main.yml‎

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@@ -58,12 +58,13 @@ jobs:
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cp test-environment.yml test-environment-${{ matrix.py_ver }}.yml
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sed -E -i 's/- python.+/- python =${{ matrix.py_ver }}/' test-environment-${{ matrix.py_ver }}.yml
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- name: Setup snakemke environment
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uses: mamba-org/setup-micromamba@v1
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- name: Setup snakemake environment
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uses: conda-incubator/setup-miniconda@v3
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with:
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miniforge-version: latest
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environment-file: test-environment-${{ matrix.py_ver }}.yml
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environment-name: snakemake
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cache-environment: true
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auto-update-conda: true
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- name: Install snakemake from source
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shell: bash -el {0}
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sudo apt-get update
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sudo apt install -y stress git wget openmpi-bin libopenmpi-dev apptainer
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# See https://github.com/apptainer/apptainer/pull/2262
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- name: Disable apparmor namespace restrictions for apptainer
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run: |
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sudo sh -c 'echo kernel.apparmor_restrict_unprivileged_userns=0 \
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>/etc/sysctl.d/90-disable-userns-restrictions.conf'
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sudo sysctl -p /etc/sysctl.d/90-disable-userns-restrictions.conf
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- name: Test local
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env:
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CI: true
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print(line, end="")
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- name: Setup snakemake environment
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uses: mamba-org/setup-micromamba@v1
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uses: conda-incubator/setup-miniconda@v3
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with:
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miniforge-version: latest
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environment-file: test-environment.yml
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environment-name: snakemake
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init-shell: powershell
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cache-environment: true
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auto-update-conda: true
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- name: Install snakemake from source
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run: |

‎.gitignore‎

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tests/test*/*
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playground/*
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tutorial/*
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snakemake/assets/data

‎CHANGELOG.md‎

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‎Dockerfile‎

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@@ -19,7 +19,7 @@ RUN micromamba create -q -y -c bioconda -c conda-forge -n snakemake \
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snakemake-minimal --only-deps && \
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eval "$(micromamba shell hook --shell bash)" && \
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micromamba activate /opt/conda/envs/snakemake && \
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micromamba install -c conda-forge mamba && \
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micromamba install -c conda-forge conda && \
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micromamba clean --all -y
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ENV PATH /opt/conda/envs/snakemake/bin:/opt/conda/envs/apptainer/bin:${PATH}

‎MANIFEST.in‎

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include versioneer.py
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include snakemake/_version.py
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include LICENSE.md
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# Include tests in sdist, otherwise only tests/test*.py are included by default
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graft tests

‎apidocs/api_reference/snakemake_api.rst‎

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with api.SnakemakeApi(
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settings.OutputSettings(
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verbose=True,
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verbose=False,
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show_failed_logs=True,
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),
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) as snakemake_api:
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dag_api = workflow_api.dag()
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# Go on by calling methods of the dag api.
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.. autosummary::
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:toctree: _autosummary
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:template: module_template.rst

‎doc-environment.yml‎

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channels:
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- conda-forge
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dependencies:
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- python >=3.7
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- python >=3.11
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- datrie
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- wrapt
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- pyyaml
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- requests
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- appdirs
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- docutils
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- ratelimiter
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- throttler
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- configargparse
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- jsonschema
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- gitpython
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- sphinx
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- pip
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- pip:
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- sphinxcontrib-napoleon
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- snakemake-interface-common >=1.17.0
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- snakemake-interface-executor-plugins >=9.1.0
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- snakemake-interface-storage-plugins >=3.2.3
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- sphinx-argparse
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- sphinx_rtd_theme
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- sphinxawesome-theme
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- docutils
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- recommonmark
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- commonmark

‎docs/_static/custom.css‎

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#content {
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overflow-x: auto;
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}
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code {
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font-family: monospace !important;
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}

‎docs/conf.py‎

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"sphinxarg.ext",
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"sphinx.ext.autosectionlabel",
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"myst_parser",
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"sphinxawesome_theme.highlighting",
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]
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html_css_files = ["custom.css"]

‎docs/executing/caching.rst‎

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would instruct Snakemake to cache and reuse the results of the rules ``download_data`` and ``create_index``.
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The environment variable definition that happens in the first line (defining the location of the cache) should of course be done only once and system wide in reality.
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When Snakemake is executed without a shared filesystem (e.g., in the cloud, see :ref:`cloud`), the environment variable has to point to a location compatible with the given remote provider (e.g. an S3 or Google Storage bucket).
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When Snakemake is executed without a shared filesystem (e.g., in the cloud, see :ref:`tutorial-cloud`), the environment variable has to point to a location compatible with the given remote provider (e.g. an S3 or Google Storage bucket).
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In any case, the provided location should be shared between all workflows of your group, institute or computing environment, in order to benefit from the reuse of previously obtained intermediate results.
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Alternatively, rules can be marked as eligible for caching via the ``cache`` directive:

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