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‎.github/workflows/ci.yml

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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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jobs:
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formatting:
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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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- name: Install poetry
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run: pipx 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: "3.9"
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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 black --check .
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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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- name: Install poetry
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run: pipx 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: "3.9"
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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 code
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run: poetry run flake8
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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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- name: Install poetry
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run: pipx 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: "3.9"
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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 tests/tests.py
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- name: Run Coverage
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run: poetry run coverage report -m

‎.github/workflows/conventional-prs.yml

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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/[email protected]
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

‎.github/workflows/release-please.yml

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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-storage-plugin-s3
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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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- uses: actions/checkout@v3
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- uses: actions/setup-python@v2
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with:
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python-version: "3.9"
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- name: Install poetry
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run: pipx 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: "3.9"
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cache: poetry
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- name: Install Dependencies using Poetry
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run: |
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pip install connection-pool # because it is incompatible with poetry
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poetry install
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- name: Publish to PyPi
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env:
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PYPI_USERNAME: __token__
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PYPI_PASSWORD: ${{ secrets.PYPI_TOKEN }}
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run: poetry publish --build --username $PYPI_USERNAME --password $PYPI_PASSWORD

‎.gitignore

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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py,cover
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.hypothesis/
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.pytest_cache/
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cover/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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.pybuilder/
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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# For a library or package, you might want to ignore these files since the code is
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# intended to run in multiple environments; otherwise, check them in:
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# .python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# poetry
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# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
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# This is especially recommended for binary packages to ensure reproducibility, and is more
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# commonly ignored for libraries.
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# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
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#poetry.lock
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# pdm
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# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
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#pdm.lock
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# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
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# in version control.
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# https://pdm.fming.dev/#use-with-ide
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.pdm.toml
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# pytype static type analyzer
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.pytype/
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# Cython debug symbols
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cython_debug/
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# PyCharm
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# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
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# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
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# and can be added to the global gitignore or merged into this file. For a more nuclear
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# option (not recommended) you can uncomment the following to ignore the entire idea folder.
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#.idea/
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poetry.lock

‎LICENSE

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MIT License
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Copyright (c) 2023 Snakemake Community
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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.

‎README.md

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# snakemake-storage-plugin-s3
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A Snakemake storage plugin for S3 API storage (AWS S3, MinIO, etc.)

‎pyproject.toml

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[tool.poetry]
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name = "snakemake-storage-plugin-s3"
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version = "0.1.0"
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description = "A Snakemake storage plugin for S3 API storage (AWS S3, MinIO, etc.)"
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authors = ["Johannes Koester <[email protected]>"]
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readme = "README.md"
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[tool.poetry.dependencies]
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python = "^3.9"
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snakemake-interface-common = "^1.10.0"
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snakemake-interface-storage-plugins = "^1.0.0"
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boto3 = "^1.28.55"
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botocore = "^1.31.55"
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[tool.poetry.group.dev.dependencies]
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black = "^23.9.1"
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flake8 = "^6.1.0"
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coverage = "^7.3.1"
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pytest = "^7.4.2"
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snakemake = "^7.32.4"
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[build-system]
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requires = ["poetry-core"]
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build-backend = "poetry.core.masonry.api"

‎setup.cfg

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[flake8]
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# Recommend matching the black line length (default 88),
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# rather than using the flake8 default of 79:
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max-line-length = 88
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extend-ignore =
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# See https://github.com/PyCQA/pycodestyle/issues/373
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E203,

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