ci-cd.yaml

#This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

# For deployment, it will be necessary to create a PyPI API token and store it as a secret
# https://docs.github.com/en/actions/reference/encrypted-secrets

name: CI/CD

on:
  push:
    branches: [ main, develop ]
  pull_request:
    branches: [ main, develop ]
  release:
    types: [published]
  repository_dispatch:
    types: [create-post-release]

env:
  FSL_VERSION: 6.0.7.9
  FSL_HOME:  ${{ github.workspace }}/fsl-install

permissions:
  contents: read
  pages: write
  id-token: write

jobs:

  nipype-conv:
    runs-on: ubuntu-latest
    steps:

    - name: Checkout
      uses: actions/checkout@v4

    - name: Revert version to most recent version tag on upstream update
      if: github.event_name == 'repository_dispatch'
      run: git checkout $(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}')

    - name: Set up Python
      uses: actions/setup-python@v5

    - name: Install build dependencies
      run: python -m pip install --upgrade pip

    - name: Install requirements
      run: python -m pip install ./related-packages/fileformats -r ./nipype-auto-conv/requirements.txt

    - name: Run automatic Nipype > Pydra conversion
      run: ./nipype-auto-conv/generate

    - uses: actions/upload-artifact@v4
      with:
        name: converted-nipype
        path: pydra/tasks/fsl/auto

  devcheck:
    needs: [nipype-conv]
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.8', '3.11']  # Check oldest and newest versions
        pip-flags: ['', '--editable']
        pydra:
        - 'pydra'
        - '--editable git+https://github.com/nipype/pydra.git#egg=pydra'

    steps:

    - name: Checkout
      uses: actions/checkout@v4

    - name: Revert version to most recent version tag on upstream update
      if: github.event_name == 'repository_dispatch'
      run: git checkout $(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}')

    - name: Download tasks converted from Nipype
      uses: actions/download-artifact@v4
      with:
        name: converted-nipype
        path: pydra/tasks/fsl/auto

    - name: Strip auto package from gitignore so it is included in package
      run: |
        sed -i '/\/pydra\/tasks\/fsl\/auto/d' .gitignore
        sed -i '/^_version.py/d' .gitignore

    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}

    - name: Install build dependencies
      run: |
        python -m pip install --upgrade pip

    - name: Install Pydra
      run: |
        pushd $HOME
        pip install ${{ matrix.pydra }}
        popd
        python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"

    - name: Install task package
      run: |
        pip install ${{ matrix.pip-flags }} "./related-packages/fileformats[dev]"
        pip install ${{ matrix.pip-flags }} "related-packages/fileformats-extras[dev]"
        pip install ${{ matrix.pip-flags }} ".[dev]"
        python -c "import pydra.tasks.fsl as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
        python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
        python -c "import fileformats.medimage_fsl as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
        python -c "import fileformats.extras.medimage_fsl as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"

  test:
    needs: [nipype-conv]
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.8', '3.11']
    steps:

    - name: Removed unnecessary tools to free space
      run: |
        sudo rm -rf /usr/share/dotnet
        sudo rm -rf "$AGENT_TOOLSDIRECTORY"

    - name: Checkout repo
      uses: actions/checkout@v4

    - name: Install Minconda
      uses: conda-incubator/setup-miniconda@v3
      with:
        auto-activate-base: true
        activate-environment: ""

    - name: Install fsl Packages
      run: >-
        conda install -c conda-forge -c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
        ciftilib cli11 elc fsl-add_module fsl-armawrap fsl-asl_mfree fsl-avwutils fsl-base
        fsl-basil fsl-basisfield fsl-baycest fsl-bet2 fsl-bianca fsl-biancadata fsl-bint
        fsl-cluster fsl-copain fsl-cprob fsl-cudimot fsl-data_atlases
        fsl-data_atlases_xtract fsl-data_first_models_317_bin fsl-data_first_models_336_bin fsl-data_linearmni
        fsl-data_omm fsl-data_possum fsl-data_standard fsl-deface fsl-discreteopt fsl-dpm fsl-dwssfp
        fsl-easyfeat fsl-eddy fsl-eddy_qc fsl-fabber_core fsl-fabber_models_asl fsl-fabber_models_cest
        fsl-fabber_models_dce fsl-fabber_models_dsc fsl-fabber_models_dualecho fsl-fabber_models_dwi
        fsl-fabber_models_pet fsl-fabber_models_qbold fsl-fabber_models_t1 fsl-fast4 fsl-fastpdlib
        fsl-fdt fsl-feat5 fsl-film fsl-filmbabe fsl-first fsl-first_lib fsl-flameo
        fsl-flirt fsl-fnirt fsl-fugue fsl-get_standard fsl-giftiio fsl-gps
        fsl-gui-desktop fsl-installer fsl-lesions fsl-libgdc fsl-libmeshutils fsl-libvis fsl-load_dicom fsl-mcflirt
        fsl-melodic fsl-meshclass fsl-misc_c fsl-misc_scripts fsl-misc_tcl fsl-miscmaths fsl-miscvis
        fsl-mist fsl-mm fsl-msm fsl-msmreglib fsl-mvdisc fsl-nets fsl-newimage
        fsl-newmesh fsl-newnifti fsl-newran fsl-oxford_asl fsl-possum fsl-ptx2 fsl-pyfeeds
        fsl-pyfeeds-tests fsl-qboot fsl-randomise fsl-relax fsl-shapemodel fsl-siena fsl-slicetimer
        fsl-sub fsl-sub-plugin-sge fsl-sub-plugin-slurm fsl-surface fsl-susan fsl-swe fsl-tbss
        fsl-topup fsl-utils fsl-vbm fsl-verbena fsl-vtkio fsl-warpfns fsl-wire fsl-xtract fsl-xtract_data
        fsl-znzlib fsl_mrs fsl_sub fsl_sub_plugin_sge fsl_sub_plugin_slurm

    - name: Download tasks converted from Nipype
      uses: actions/download-artifact@v4
      with:
        name: converted-nipype
        path: pydra/tasks/fsl/auto

    - name: Show the contents of the auto-generated tasks
      run: tree pydra

    - name: Strip auto package from gitignore so it is included in package
      run: |
        sed -i '/\/pydra\/tasks\/fsl\/auto/d' .gitignore

    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}

    - name: Install build dependencies
      run: |
        python -m pip install --upgrade pip

    - name: Install task package
      run: |
        pip install "./related-packages/fileformats" "./related-packages/fileformats-extras" ".[test]"
        python -c "import pydra.tasks.fsl as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
        python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"

    - name: Test with pytest
      run: >-
        pytest -sv
        ./pydra/tasks/fsl
        ./related-packages/fileformats
        ./related-packages/fileformats-extras
        --cov pydra.tasks.fsl
        --cov fileformats.medimage_fsl
        --cov fileformats.extras.medimage_fsl
        --cov-report xml

    - name: Upload to CodeCov
      uses: codecov/codecov-action@v4
      if: ${{ always() }}
      with:
        files: coverage.xml
        name: pydra-fsl


  deploy-fileformats:
    needs: [devcheck, test]
    runs-on: ubuntu-latest
    steps:

    - uses: actions/checkout@v4
      with:
        submodules: recursive
        fetch-depth: 0

    - name: Set up Python
      uses: actions/setup-python@v5
      with:
        python-version: '3.11'

    - name: Install build tools
      run: python -m pip install build twine

    - name: Build source and wheel distributions
      run: python -m build ./related-packages/fileformats

    - name: Check distributions
      run: twine check ./related-packages/fileformats/dist/*

    - name: Check for PyPI token on tag
      id: deployable
      if: github.event_name == 'release' || github.event_name == 'repository_dispatch'
      env:
        PYPI_API_TOKEN: "${{ secrets.PYPI_FILEFORMATS_API_TOKEN }}"
      run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi

    - name: Upload to PyPI
      if: steps.deployable.outputs.DEPLOY
      uses: pypa/gh-action-pypi-publish@release/v1
      with:
        user: __token__
        password: ${{ secrets.PYPI_FILEFORMATS_API_TOKEN }}
        packages-dir: ./related-packages/fileformats/dist

  deploy-fileformats-extras:
    needs: [deploy-fileformats]
    runs-on: ubuntu-latest
    steps:

    - uses: actions/checkout@v4
      with:
        submodules: recursive
        fetch-depth: 0

    - name: Set up Python
      uses: actions/setup-python@v5
      with:
        python-version: '3.11'

    - name: Install build tools
      run: python -m pip install build twine

    - name: Build source and wheel distributions
      run: python -m build ./related-packages/fileformats-extras

    - name: Check distributions
      run: twine check ./related-packages/fileformats-extras/dist/*

    - name: Check for PyPI token on tag
      id: deployable
      if: github.event_name == 'release' || github.event_name == 'repository_dispatch'
      env:
        PYPI_API_TOKEN: "${{ secrets.PYPI_FILEFORMATS_EXTRAS_API_TOKEN }}"
      run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi

    - name: Upload to PyPI
      if: steps.deployable.outputs.DEPLOY
      uses: pypa/gh-action-pypi-publish@release/v1
      with:
        user: __token__
        password: ${{ secrets.PYPI_FILEFORMATS_EXTRAS_API_TOKEN }}
        packages-dir: ./related-packages/fileformats-extras/dist

  deploy:
    needs: [nipype-conv, test, deploy-fileformats, deploy-fileformats-extras]
    runs-on: ubuntu-latest
    steps:

    - name: Checkout repository
      uses: actions/checkout@v4
      with:
        submodules: recursive
        fetch-depth: 0

    - name: Set up Git user
      run: |
        git config --local user.email "action@github.com"
        git config --local user.name "GitHub Action"

    - name: Get latest version tag
      id: latest_tag
      run: |
        git fetch --tags
        echo "TAG=$(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}')" >> $GITHUB_OUTPUT

    - name: Revert to latest tag
      if: github.event_name == 'repository_dispatch'
      run: git checkout ${{ steps.latest_tag.outputs.TAG }}

    - name: Download tasks converted from Nipype
      uses: actions/download-artifact@v4
      with:
        name: converted-nipype
        path: pydra/tasks/fsl/auto

    - name: Show the contents of the auto-generated tasks
      run: tree pydra

    - name: Set up Python
      uses: actions/setup-python@v5
      with:
        python-version: '3.11'

    - name: Install build tools
      run: python -m pip install build twine

    - name: Strip auto package from gitignore so it is included in package
      run: |
        sed -i '/\/pydra\/tasks\/fsl\/auto/d' .gitignore
        cat .gitignore

    - name: Install task package to calculate post-release tag
      run: |
        pip install "./related-packages/fileformats" "./related-packages/fileformats-extras" ".[test]"

    - name: Generate post-release tag based on Nipype and Nipype2Pydra versions
      id: post_release_tag
      run: |
        POST=$(python -c "from pydra.tasks.fsl.auto._post_release import *; print(post_release)")
        echo "TAG=${{ steps.latest_tag.outputs.TAG }}post${POST}" >> $GITHUB_OUTPUT

    - name: Add auto directory to git repo
      if: github.event_name == 'release' || github.event_name == 'repository_dispatch'
      run: |
        git add pydra/tasks/fsl/auto
        git commit -am"added auto-generated version to make new tag for package version"
        git status

    - name: Overwrite the tag of release event with latest commit (i.e. including the auto directory)
      if: github.event_name == 'release'
      run: |
        git tag -d ${{ steps.latest_tag.outputs.TAG }};
        git tag ${{ steps.latest_tag.outputs.TAG }};

    - name: Tag repo with the post-release
      if: github.event_name == 'repository_dispatch'
      run: git tag ${{ steps.post_release_tag.outputs.TAG }}

    - name: Build source and wheel distributions
      run: python -m build .

    - name: Check distributions
      run: twine check dist/*

    - uses: actions/upload-artifact@v4
      with:
        name: distributions
        path: dist/

    - name: Check for PyPI token on tag
      id: deployable
      if: github.event_name == 'release' || github.event_name == 'repository_dispatch'
      env:
        PYPI_API_TOKEN: "${{ secrets.PYPI_API_TOKEN }}"
      run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi

    - name: Upload to PyPI
      if: steps.deployable.outputs.DEPLOY
      uses: pypa/gh-action-pypi-publish@release/v1
      with:
        user: __token__
        password: ${{ secrets.PYPI_API_TOKEN }}

    - name: Create post-release release for releases triggered by nipype2pydra dispatches
      if: steps.deployable.outputs.DEPLOY && github.event_name == 'repository_dispatch'
      uses: actions/create-release@v1
      env:
        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions, you do not need to create your own token
      with:
        tag_name: ${{ steps.post_release_tag.outputs.TAG }}
        release_name: Release ${{ steps.post_release_tag.outputs.TAG }}
        draft: false
        prerelease: false

  # docs:
  #   needs: deploy
  #   environment:
  #     name: github-pages
  #     url: ${{ steps.deployment.outputs.page_url }}
  #   runs-on: ubuntu-latest
  #   steps:
  #     - uses: actions/checkout@v4
  #     - uses: actions/setup-python@v5
  #       with:
  #         python-version: '3.x'

  #     - name: Download tasks converted from Nipype
  #       uses: actions/download-artifact@v4
  #       with:
  #         name: converted-nipype
  #         path: pydra/tasks/freesurfer/auto

  #     - name: Install dependencies
  #       run: python -m pip install related-packages/fileformats .[doc]

  #     - name: Build docs
  #       run: |
  #         pushd docs
  #         make html
  #         popd

  #     - name: Upload artifact
  #       uses: actions/upload-pages-artifact@v3
  #       with:
  #         path: 'docs/build/html'

  #     - name: Setup GitHub Pages
  #       if: github.event_name == 'release' || github.event_name == 'repository_dispatch'
  #       uses: actions/configure-pages@v4

  #     - name: Deploy to GitHub Pages
  #       if: github.event_name == 'release' || github.event_name == 'repository_dispatch'
  #       id: deployment
  #       uses: actions/deploy-pages@v4


  # report_progress:
  #   needs: [deploy]
  #   runs-on: ubuntu-latest
  #   steps:

  #     - name: Checkout
  #       uses: actions/checkout@v4

  #     - name: Generate progress report
  #       id: generate-report
  #       run: |
  #         tools/report_progress.py outputs/progress-report.json
  #         echo "progress_report=$(cat outputs/progress-report.json)" >> $GITHUB_OUTPUT

  #     - name: Report progress to Nipype2Pydra repo
  #       if: github.event_name == 'release' || github.event_name == 'repository_dispatch'
  #       run: >-
  #         curl -XPOST -u "${{ env.REPORT_PROGRESS_PAT }}" -H "Accept: application/vnd.github.everest-preview+json"
  #         "https://api.github.com/repos/nipype/pydra-fsl/dispatches"
  #         -d '{
  #           "event_type": "progress-report",
  #           "client_payload": ${{ steps.generate-report.output.progress_report }}
  #         }'
  #       env:
  #         PAT: ${{ env.REPORT_PROGRESS_PAT }}


# Deploy on tags if PYPI_API_TOKEN is defined in the repository secrets.
# Secrets are not accessible in the if: condition [0], so set an output variable [1]
# [0] https://github.community/t/16928
# [1] https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-output-parameter