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:
  nireports_version: <set-nireports-version-here>
  nireports_install_dir:  ${{ github.workspace }}/install

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 -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/nireports

  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/nireports

    - name: Strip auto package from gitignore so it is included in package
      run: |
        sed -i '/\/pydra\/tasks\/nireports/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 }} ".[dev]"
        python -c "import pydra.tasks.nireports as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
        python -c "import pydra 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: Revert version to most recent version tag on Nipype or Nipype2Pydra update
      if: github.event_name == 'repository_dispatch'
      run: git checkout $(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}')

    - name: Cache nireports Install
      id: cache-install
      uses: actions/cache@v4
      with:
        path: ${{ env.nireports_install_dir }}
        key: nireports-${{ env.nireports_version }}-${{ runner.os }}

    - name: Install nireports Package
      if: steps.cache-install.outputs.cache-hit != 'true'
      run: |
        echo "NOT IMPLEMENTED YET (install at nireports_install_dir: $nireports_install_dir)"
        exit 1  # This is a placeholder, replace this line and the one above with the installation procedure
        echo "PATH=${{ env.nireports_install_dir }}/bin:$PATH" >> $GITHUB_ENV
    
    - name: Download tasks converted from Nipype 
      uses: actions/download-artifact@v4
      with:
        name: converted-nipype
        path: pydra/tasks/nireports

    - 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\/nireports/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 ".[test]"
        python -c "import pydra.tasks.nireports 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/nireports
        --cov pydra.tasks.nireports
        --cov-report xml

    - name: Upload to CodeCov
      uses: codecov/codecov-action@v3
      if: ${{ always() }}
      with:
        files: coverage.xml
        name: pydra-nireports

  deploy:
    needs: [nipype-conv, test]
    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/nireports

    - 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\/nireports/d' .gitignore
        cat .gitignore

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

    - name: Generate post-release tag based on Nipype and Nipype2Pydra versions
      id: post_release_tag
      run: |
        POST=$(python -c "from pydra.tasks.nireports._post_release import post_release; print(post_release)")
        echo "TAG=${{ 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/nireports
        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        


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

      - 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.POST_RELEASE_PAT }}" -H "Accept: application/vnd.github.everest-preview+json"
          "https://api.github.com/repos/nipype/pydra-nireports/dispatches"
          -d '{
            "event_type": "progress-report",
            "client_payload": ${{ steps.generate-report.output.progress_report }}
          }'
        env:
          PAT: ${{ env.PROGRESS_REPORT_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