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‎.coveragerc‎

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[run]
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branch = True
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omit =
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*/_version.py

‎.flake8‎

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[flake8]
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doctests = True
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exclude =
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**/__init__.py
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*build/
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docs/sphinxext/
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docs/tools/
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docs/conf.py
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docs/source/conf.py
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max-line-length = 88
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select = C,E,F,W,B,B950
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extend-ignore = E203,E501,E129,W503
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per-file-ignores =
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__init__.py:F401,F403

‎.github/workflows/ci-cd.yaml‎

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#This workflow will install Python dependencies, run tests and lint with a variety of Python versions
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# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
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# For deployment, it will be necessary to create a PyPI API token and store it as a secret
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# https://docs.github.com/en/actions/reference/encrypted-secrets
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name: CI/CD
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on:
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push:
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branches: [ main, develop ]
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tags: [ '*' ]
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pull_request:
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branches: [ main, develop ]
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jobs:
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devcheck:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ['3.8', '3.12'] # Check oldest and newest versions
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pip-flags: ['', '--editable']
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pydra:
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- 'pydra'
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- '--editable git+https://github.com/nipype/pydra.git#egg=pydra'
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install build dependencies
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run: |
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python -m pip install --upgrade pip
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- name: Install Pydra
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run: |
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pip install ${{ matrix.pydra }}
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python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
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- name: Install task package
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run: |
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pip install ${{ matrix.pip-flags }} ".[dev]"
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python -c "import pydra.workers.CHANGEME as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
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python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
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test:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [3.7, 3.8, 3.9, '3.10']
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install build dependencies
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run: |
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python -m pip install --upgrade pip
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- name: Install task package
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run: |
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pip install ".[test]"
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python -c "import pydra.workers.CHANGEME as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
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python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
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- name: Test with pytest
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run: |
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pytest -sv --doctest-modules pydra/workers/CHANGEME \
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--cov pydra.workers.CHANGEME --cov-report xml
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- uses: codecov/codecov-action@v3
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if: ${{ always() }}
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deploy:
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needs: [devcheck, test]
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [3.9]
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steps:
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- uses: actions/checkout@v4
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with:
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submodules: recursive
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fetch-depth: 0
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install build tools
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run: python -m pip install build twine
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- name: Build source and wheel distributions
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run: python -m build
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- name: Check distributions
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run: twine check dist/*
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- uses: actions/upload-artifact@v4
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with:
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name: distributions
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path: dist/
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# Deploy on tags if PYPI_API_TOKEN is defined in the repository secrets.
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# Secrets are not accessible in the if: condition [0], so set an output variable [1]
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# [0] https://github.community/t/16928
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# [1] https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-output-parameter
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- name: Check for PyPI token on tag
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id: deployable
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if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
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env:
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PYPI_API_TOKEN: "${{ secrets.PYPI_API_TOKEN }}"
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run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi
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- name: Upload to PyPI
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if: steps.deployable.outputs.DEPLOY
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uses: pypa/gh-action-pypi-publish@37f50c210e3d2f9450da2cd423303d6a14a6e29f # v1.5.1
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with:
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user: __token__
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password: ${{ secrets.PYPI_API_TOKEN }}

‎.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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pip-wheel-metadata/
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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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# 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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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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.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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# PEP 582; used by e.g. github.com/David-OConnor/pyflow
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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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# Pycharm
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.idea
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# Vim
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.*.sw[op]
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# VS Code
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.vscode
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# Mac garbarge
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.DS_store
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# Generated files
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/pydra/workers/CHANGEME/_version.py

‎.pre-commit-config.yaml‎

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# See https://pre-commit.com for more information
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# See https://pre-commit.com/hooks.html for more hooks
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.4.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-yaml
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- id: check-added-large-files
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- repo: https://github.com/psf/black
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rev: 22.12.0
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hooks:
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- id: black

‎LICENSE‎

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Copyright 2021 Nipype developers
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Licensed under the Apache License, Version 2.0 (the "License");
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you may not use this file except in compliance with the License.
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You may obtain a copy of the License at
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http://www.apache.org/licenses/LICENSE-2.0
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Unless required by applicable law or agreed to in writing, software
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distributed under the License is distributed on an "AS IS" BASIS,
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WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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See the License for the specific language governing permissions and
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limitations under the License.

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