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Merge pull request #3 from nipype/nipype-auto-conv
Added in nipype auto convert specifications
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‎.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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repository_dispatch:
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types: [create-release]
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jobs:
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nipype-conv:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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- name: Revert version to most recent tag on upstream update
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if: github.event_name == 'repository_dispatch'
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run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}')
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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- name: Install build dependencies
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run: python -m pip install --upgrade pip
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- name: Install requirements
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run: python -m pip install ./related-packages/fileformats -r ./nipype-auto-conv/requirements.txt
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- name: Run automatic Nipype > Pydra conversion
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run: ./nipype-auto-conv/generate
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- uses: actions/upload-artifact@v3
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with:
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name: converted-nipype
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path: pydra/tasks/afni/auto
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devcheck:
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needs: [nipype-conv]
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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', '3.11'] # 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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- name: Checkout
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uses: actions/checkout@v3
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- name: Revert version to most recent tag on upstream update
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if: github.event_name == 'repository_dispatch'
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run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}')
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- name: Download tasks converted from Nipype
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uses: actions/download-artifact@v3
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with:
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name: converted-nipype
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path: pydra/tasks/afni/auto
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- name: Strip auto package from gitignore so it is included in package
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run: |
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sed -i '/\/pydra\/tasks\/afni\/auto/d' .gitignore
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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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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pushd $HOME
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pip install ${{ matrix.pydra }}
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popd
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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 "./related-packages/fileformats[dev]" "related-packages/fileformats-extras[dev]"
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pip install ${{ matrix.pip-flags }} ".[dev]"
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python -c "import pydra.tasks.afni 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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python -c "import fileformats.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
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python -c "import fileformats.extras.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
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fileformats-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: ['3.8', '3.11']
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steps:
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- uses: actions/checkout@v3
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- name: Revert version to most recent tag on upstream update
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if: github.event_name == 'repository_dispatch'
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run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}')
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install build dependencies
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run: |
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python -m pip install --upgrade pip
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- name: Install task package
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run: |
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pip install "./related-packages/fileformats[test]" "./related-packages/fileformats-extras[test]"
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python -c "import fileformats.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
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- name: Test fileformats with pytest
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run: |
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cd ./fileformats
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pytest -sv --cov fileformats.medimage_afni --cov fileformats.extras.medimage_afni --cov-report xml .
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test:
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needs: [nipype-conv, fileformats-test]
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runs-on: ubuntu-22.04
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strategy:
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matrix:
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python-version: ['3.8'] # '3.11'
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steps:
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- name: Removed unnecessary tools to free space
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run: |
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sudo rm -rf /usr/share/dotnet
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sudo rm -rf "$AGENT_TOOLSDIRECTORY"
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- name: Get Download cache Key
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id: cache-key
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run: echo "::set-output name=key::afni-linux-ubuntu22_amd64-7.4.1"
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- name: Cache FreeSurfer
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uses: actions/cache@v2
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with:
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path: $HOME/downloads/afni
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key: ${{ steps.cache-key.outputs.key }}
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restore-keys: |
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afni-linux-ubuntu22_amd64-7.4.1
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- name: Download FreeSurfer
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if: steps.cache-key.outputs.key != steps.cache-hit.outputs.key
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run: |
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mkdir -p $HOME/downloads/afni
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curl -s -o $HOME/downloads/afni/afni-linux-ubuntu22_amd64-7.4.1.tar.gz https://surfer.nmr.mgh.harvard.edu/pub/dist/afni/7.4.1/afni-linux-ubuntu22_amd64-7.4.1.tar.gz
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shell: bash
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- name: Install Freesurfer
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env:
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FREESURFER_LICENCE: ${{ secrets.FREESURFER_LICENCE }}
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run: |
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pushd $HOME/downloads/afni
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tar -zxpf afni-linux-ubuntu22_amd64-7.4.1.tar.gz
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mv afni $HOME/
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popd
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export FREESURFER_HOME=$HOME/afni
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source $FREESURFER_HOME/SetUpFreeSurfer.sh
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echo $FREESURFER_LICENCE > $FREESURFER_HOME/license.txt
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export PATH=$FREESURFER_HOME/bin:$PATH
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- uses: actions/checkout@v3
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- name: Revert version to most recent tag on upstream update
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if: github.event_name == 'repository_dispatch'
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run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}')
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- name: Download tasks converted from Nipype
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uses: actions/download-artifact@v3
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with:
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name: converted-nipype
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path: pydra/tasks/afni/auto
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- name: Strip auto package from gitignore so it is included in package
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run: |
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sed -i '/\/src\/pydra\/tasks\/afni\/auto/d' .gitignore
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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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 "./related-packages/fileformats" "./related-packages/fileformats-extras" ".[test]"
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python -c "import pydra.tasks.afni 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/tasks/afni \
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--cov pydra.tasks.afni --cov-report xml
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- uses: codecov/codecov-action@v3
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if: ${{ always() }}
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with:
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files: coverage.xml,./fileformats/coverage.xml
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name: pydra-afni
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deploy-fileformats:
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needs: [devcheck, test]
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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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with:
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submodules: recursive
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fetch-depth: 0
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: '3.11'
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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 ./related-packages/fileformats
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- name: Check distributions
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run: twine check ./related-packages/fileformats/dist/*
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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')) || github.event_name == 'repository_dispatch'
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env:
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PYPI_API_TOKEN: "${{ secrets.PYPI_FILEFORMATS_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@release/v1
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with:
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user: __token__
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password: ${{ secrets.PYPI_FILEFORMATS_API_TOKEN }}
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packages-dir: ./related-packages/fileformats/dist
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deploy-fileformats-extras:
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needs: [deploy-fileformats]
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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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with:
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submodules: recursive
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fetch-depth: 0
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: '3.11'
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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 ./related-packages/fileformats-extras
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- name: Check distributions
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run: twine check ./related-packages/fileformats-extras/dist/*
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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')) || github.event_name == 'repository_dispatch'
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env:
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PYPI_API_TOKEN: "${{ secrets.PYPI_FILEFORMATS_EXTRAS_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@release/v1
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with:
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user: __token__
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password: ${{ secrets.PYPI_FILEFORMATS_EXTRAS_API_TOKEN }}
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packages-dir: ./related-packages/fileformats-extras/dist
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deploy:
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needs: [deploy-fileformats-extras]
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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with:
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submodules: recursive
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fetch-depth: 0
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- name: Download tasks converted from Nipype
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uses: actions/download-artifact@v3
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with:
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name: converted-nipype
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path: pydra/tasks/afni/auto
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- name: Tag release with a post-release based on Nipype and Nipype2Pydra versions
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if: github.event_name == 'repository_dispatch'
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run: |
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TAG=$(git tag -l | tail -n 1 | awk -F post '{print $1}')
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POST=$(python -c "from pydra.tasks.afni.auto._version import *; print(post_release)")
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git checkout $TAG
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git add -f pydra/tasks/afni/auto/_version.py
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git commit -am"added auto-generated version to make new tag for package version"
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git tag ${TAG}post${POST}
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: '3.11'
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- name: Install build tools
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run: python -m pip install build twine
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- name: Strip auto package from gitignore so it is included in package
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run: |
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sed -i '/\/pydra\/tasks\/afni\/auto/d' .gitignore
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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@v3
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with:
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name: distributions
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path: dist/
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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')) || github.event_name == 'repository_dispatch'
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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@release/v1
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with:
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user: __token__
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password: ${{ secrets.PYPI_API_TOKEN }}
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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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