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Merge branch 'main' into 3342-faster---touch-runs
2 parents a39ec20 + cc04085 commit 8f9db10

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‎.github/workflows/docs.yml‎

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@@ -17,42 +17,44 @@ jobs:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v4
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with:
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python-version: '3.x'
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- name: Setup doc dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -r docs/requirements.txt
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python -m pip install -r docs/requirements.txt
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python -m pip install .
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- name: Build docs
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run: |
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cd docs
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make html SPHINXOPTS="-W --keep-going -n"
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- name: Upload documentation
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uses: actions/upload-artifact@v4
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with:
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name: docs-html
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path: docs/_build/html/
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apidocs:
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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@v4
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- uses: actions/setup-python@v4
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with:
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python-version: '3.x'
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- name: Setup doc dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -r apidocs/requirements.txt
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pip install -e .
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python -m pip install -r apidocs/requirements.txt
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python -m pip install .
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- name: Build docs
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run: |
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cd apidocs
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uses: actions/upload-artifact@v4
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with:
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name: apidocs-html
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path: apidocs/_build/html/
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path: apidocs/_build/html/

‎.gitignore‎

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@@ -30,9 +30,10 @@ tests/test*/*
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playground/*
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tutorial/*
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snakemake/assets/data
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src/snakemake/assets/data
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src/snakemake/_version.py
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# pixi environments
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.pixi
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*.egg-info
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pixi.lock
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pixi.lock

‎MANIFEST.in‎

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@@ -1,6 +1,13 @@
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include versioneer.py
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include snakemake/_version.py
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global-exclude *
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include setup.py
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include pyproject.toml
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include README.md
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include LICENSE.md
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include .gitignore
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graft src
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# Include tests in sdist, otherwise only tests/test*.py are included by default
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graft tests
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global-exclude *~ *.py[cod] *.so

‎pyproject.toml‎

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@@ -1,6 +1,10 @@
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[build-system]
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requires = ["setuptools>=64", "setuptools-scm>=8"]
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build-backend = "setuptools.build_meta"
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[project]
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name = "snakemake"
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version = "8.30.0"
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dynamic = ["version"]
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description = "Workflow management system to create reproducible and scalable data analyses"
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readme = { content-type = "text/markdown", text = """
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Snakemake is a workflow management system that aims to reduce the
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[project.scripts]
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snakemake = "snakemake.cli:main"
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[build-system]
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requires = ["setuptools>=42,<76", 'tomli']
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build-backend = "setuptools.build_meta"
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[tool.setuptools.packages.find]
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include = ["snakemake", "snakemake.*"]
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[tool.setuptools.package-data]
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"*" = [
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"*.css",
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"*.sh",
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"*.html",
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"*.jinja2",
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"*.js",
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"*.svg",
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"Snakefile.*",
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"*.rst",
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]
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[tool.versioneer]
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VCS = "git"
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style = "pep440"
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tag_prefix = "v"
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versionfile_build = "snakemake/_version.py"
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versionfile_source = "snakemake/_version.py"
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[tool.setuptools_scm]
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version_file = "src/snakemake/_version.py"
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# Ignore Git hash
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local_scheme = "no-local-version"
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[tool.codespell]
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# Ref: https://github.com/codespell-project/codespell#using-a-config-file
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quality = { features = ["style"] }
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publish = { features = ["publish"] }
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#----------------------- Python Envs -------------------------
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# Python Envs
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[tool.pixi.feature.py311.dependencies]
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python = ">=3.11.0,<3.12"
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[tool.pixi.feature.py312.dependencies]
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python = ">=3.12.0,<3.13"
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#------------------------ Test -------------------------------
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# Test
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[tool.pytest.ini_options]
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addopts = "--verbose --show-capture=stderr" # --exitfirst
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markers = [
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dash = "*"
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openmpi = "*"
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#------------------------ Docs -------------------------------
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# Docs
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[tool.pixi.feature.docs.dependencies]
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sphinx = ">=7.2.6,<8"
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sphinx-argparse = ">=0.4.0,<0.6"
@@ -252,16 +236,15 @@ description = "Serve the documentation on http://localhost:8000"
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cmd = "python -m http.server 8000 --directory docs/_build/html"
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depends-on = ["build-docs"]
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#------------------------ Style -------------------------------
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# Style
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[tool.pixi.feature.style.dependencies]
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black = "*"
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[tool.pixi.feature.style.tasks]
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format = { cmd = "black snakemake tests/*.py", description = "Format the code" }
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format = { cmd = "black src/ tests/*.py", description = "Format the code" }
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#------------------------ publish -------------------------------
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# Publish
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[tool.pixi.feature.publish.dependencies]
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setuptools = ">=75.8.2,<76"
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twine = ">=6.1.0,<7"
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python-build = ">=1.2.2,<2"
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‎setup.py‎

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import os
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from pathlib import Path
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import sys
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source_dir = Path(__file__).parent
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sys.path.append(str(source_dir))
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import versioneer # noqa: E402
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# import Assets, while avoiding that the rest of snakemake is imported here before
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# setup has been called.
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sys.path.append(str(source_dir / "snakemake"))
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sys.path.append(str(source_dir / "src" / "snakemake"))
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from assets import Assets
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# download online assets
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Assets.deploy()
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setup(
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name="snakemake",
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version=versioneer.get_version(),
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cmdclass=versioneer.get_cmdclass(),
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use_scm_version=True,
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package_data={
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"snakemake": [
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"assets/data/**/*",

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