snakemake-executor-plugin-finished 0.1.0__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- snakemake_executor_plugin_finished-0.1.0/.github/workflows/ci.yml +70 -0
- snakemake_executor_plugin_finished-0.1.0/.github/workflows/conventional-prs.yml +16 -0
- snakemake_executor_plugin_finished-0.1.0/.github/workflows/release-please.yml +43 -0
- snakemake_executor_plugin_finished-0.1.0/.gitignore +21 -0
- snakemake_executor_plugin_finished-0.1.0/CHANGELOG.md +8 -0
- snakemake_executor_plugin_finished-0.1.0/LICENSE +21 -0
- snakemake_executor_plugin_finished-0.1.0/PKG-INFO +11 -0
- snakemake_executor_plugin_finished-0.1.0/README.md +23 -0
- snakemake_executor_plugin_finished-0.1.0/pixi.lock +1355 -0
- snakemake_executor_plugin_finished-0.1.0/pyproject.toml +42 -0
- snakemake_executor_plugin_finished-0.1.0/setup.cfg +7 -0
- snakemake_executor_plugin_finished-0.1.0/src/snakemake_executor_plugin_finished/__init__.py +15 -0
- snakemake_executor_plugin_finished-0.1.0/src/snakemake_executor_plugin_finished/executor.py +107 -0
- snakemake_executor_plugin_finished-0.1.0/tests/test_executor.py +134 -0
- snakemake_executor_plugin_finished-0.1.0/tests/test_plugin.py +16 -0
- snakemake_executor_plugin_finished-0.1.0/tests/test_smoke.py +7 -0
- snakemake_executor_plugin_finished-0.1.0/tests/tests.py +1 -0
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name: CI
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on:
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push:
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branches:
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- main
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pull_request:
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env:
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PYTHON_VERSION: 3.11
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jobs:
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linting:
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runs-on: ubuntu-latest
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steps:
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- name: Check out the code
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uses: actions/checkout@v3
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- uses: actions/setup-python@v4
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with:
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python-version: ${{ env.PYTHON_VERSION }}
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- name: Install poetry
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run: pip install poetry
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- name: Determine dependencies
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run: poetry lock
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- uses: actions/setup-python@v4
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with:
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python-version: ${{ env.PYTHON_VERSION }}
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cache: poetry
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- name: Install Dependencies using Poetry
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run: poetry install
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- name: Check formatting
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run: poetry run ruff format --check .
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- name: Lint
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run: poetry run ruff check .
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testing:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/setup-python@v4
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with:
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python-version: ${{ env.PYTHON_VERSION }}
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- name: Install poetry
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run: pip install poetry
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- name: Determine dependencies
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run: poetry lock
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- uses: actions/setup-python@v4
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with:
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python-version: ${{ env.PYTHON_VERSION }}
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cache: poetry
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- name: Install dependencies
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run: poetry install
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- name: Run pytest
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run: poetry run coverage run -m pytest
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- name: Run Coverage
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run: poetry run coverage report -m
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name: PR
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on:
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pull_request_target:
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types:
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- opened
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- reopened
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- edited
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- synchronize
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jobs:
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title-format:
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runs-on: ubuntu-latest
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steps:
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- uses: amannn/action-semantic-pull-request@v3.4.0
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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on:
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push:
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branches:
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- main
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name: release-please
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jobs:
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release-please:
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runs-on: ubuntu-latest
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outputs:
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release_created: ${{ steps.release.outputs.release_created }}
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steps:
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- uses: GoogleCloudPlatform/release-please-action@v3
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id: release
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with:
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release-type: python
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package-name: snakemake-executor-plugin-finished
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token: ${{ secrets.RELEASE_PLEASE_PR_CI_TOKEN }}
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publish:
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runs-on: ubuntu-latest
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needs: release-please
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if: ${{ needs.release-please.outputs.release_created }}
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steps:
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- name: Check out the code
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uses: actions/checkout@v4
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- name: Setup pixi
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uses: prefix-dev/setup-pixi@v0
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with:
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cache: false
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locked: false
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- name: Build source and wheel distribution + check build
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run: |
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pixi run -e dev check-build
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- name: Publish to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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user: __token__
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password: ${{ secrets.PYPI_TOKEN }}
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# pixi environments
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.pixi/*
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!.pixi/config.toml
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# Python
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__pycache__/
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*.py[cod]
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*.egg-info/
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.pytest_cache/
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.ruff_cache/
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.mypy_cache/
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# Build artifacts
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build/
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dist/
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coverage-report/
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htmlcov/
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.coverage
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# Snakemake
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.snakemake/
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MIT License
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Copyright (c) 2026 Andrey Rozenberg
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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Metadata-Version: 2.4
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Name: snakemake-executor-plugin-finished
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Version: 0.1.0
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Summary: Snakemake executor plugin that marks targets as finished
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Project-URL: Repository, https://github.com/alephreish/snakemake-executor-plugin-finished
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Project-URL: Documentation, https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/finished.html
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Author-email: Andrey Rozenberg <alephreish@gmail.com>
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License-File: LICENSE
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Requires-Python: <4.0,>=3.11
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Requires-Dist: snakemake-interface-common<2,>=1.23.0
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Requires-Dist: snakemake-interface-executor-plugins<10,>=9.0.0
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# snakemake-executor-plugin-finished
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Snakemake executor plugin that marks specified targets as finished without running jobs. This provides a way to tell Snakemake that the corresponding targets should not be re-created, e.g. in cases of cosmetic changes to the code, non-essential modifications of the environment definition or other modifications that trigger a re-run but are known in advance to have no effect on the output.
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## Installation
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```bash
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pip install snakemake-executor-plugin-finished
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```
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or
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```bash
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pip install git+https://github.com/alephreish/snakemake-executor-plugin-finished
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```
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## Usage
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```bash
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snakemake --executor finished <target1> <target2>
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```
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The executor will mark the matching jobs as finished, touch the outputs, and fail if any requested target files do not exist. If nothing triggers a re-run, no modifications are made to the metadata or timestamps of the correspondign outputs.
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