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: # Define environment variables
  ANTS_VERSION: v2.5.1
  ANTS_INSTALL_PATH: ${{ github.workspace }}/ants-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 ./related-packages/fileformats -r ./nipype-auto-conv/requirements.txt

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

    - uses: actions/upload-artifact@v3
      with:
        name: converted-nipype
        path: pydra/tasks/ants/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 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: Download tasks converted from Nipype
      uses: actions/download-artifact@v3
      with:
        name: converted-nipype
        path: pydra/tasks/ants/auto

    - name: Strip auto package from gitignore so it is included in package
      run: |
        sed -i '/\/pydra\/tasks\/ants\/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.ants 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_ants as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
        python -c "import fileformats.extras.medimage_ants as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"

  test:
    needs: [nipype-conv]
    runs-on: ubuntu-22.04
    strategy:
      matrix:
        python-version: ['3.8', '3.11']
    steps:

    - name: Install prerequisite packages
      run: sudo apt install -y cmake

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

    - name: Cache ANTs Install
      id: cache-install
      uses: actions/cache@v4
      with:
        path: ${{ env.ANTS_INSTALL_PATH }}
        key: ants-${{ env.ANTS_VERSION }}-${{ runner.os }}

    - name: Install ANTs Package
      if: steps.cache-install.outputs.cache-hit != 'true'
      run: |
        pushd ~
        git clone https://github.com/ANTsX/ANTs.git
        pushd ./ANTs
        git checkout ${{ env.ANTS_VERSION }}
        popd
        mkdir build install
        cd build
        cmake -DCMAKE_INSTALL_PREFIX=${{ env.ANTS_INSTALL_PATH }} ../ANTs
        make -j 4
        cd ANTS-build
        make install
        echo "Installation completed successfully"
        echo "PATH=${{ env.ANTS_INSTALL_PATH }}/bin:$PATH" >> $GITHUB_ENV
        echo "LD_LIBRARY_PATH=${{ env.ANTS_INSTALL_PATH }}/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
        popd

    - name: Checkout repo
      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@v3
      with:
        name: converted-nipype
        path: pydra/tasks/ants/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\/ants\/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.ants 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/ants
        ./related-packages/fileformats
        ./related-packages/fileformats-extras
        --cov pydra.tasks.ants
        --cov fileformats.medimage_ants
        --cov fileformats.extras.medimage_ants
        --cov-report xml

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


  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@v3
      with:
        name: converted-nipype
        path: pydra/tasks/ants/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\/ants\/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=$(python -c "from pydra.tasks.ants.auto._version import *; print(post_release)")
        echo "TAG=${{ 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/ants/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@v3
      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

# 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