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 ]
    tags: [ '*' ]
  pull_request:
    branches: [ main, develop ]
  repository_dispatch:
    types: [create-release]

jobs:

  nipype-conv:
    runs-on: ubuntu-latest
    steps:
    - name: Checkout
      uses: actions/checkout@v3
    - name: Revert version to most recent tag on upstream update
      if: github.event_name == 'repository_dispatch'
      run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}')    
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v4
    - 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/afni/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@v3
    - name: Revert version to most recent tag on upstream update
      if: github.event_name == 'repository_dispatch'
      run: git checkout $(git tag -l | 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/afni/auto
    - name: Strip auto package from gitignore so it is included in package
      run: |
        sed -i '/\/pydra\/tasks\/afni\/auto/d' .gitignore
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v4
      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 "./related-packages/fileformats[dev]" "related-packages/fileformats-extras[dev]"
        pip install ${{ matrix.pip-flags }} ".[dev]"
        python -c "import pydra.tasks.afni 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_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
        python -c "import fileformats.extras.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
  
  fileformats-test:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.8', '3.11']
    steps:
    - uses: actions/checkout@v3
    - name: Revert version to most recent tag on upstream update
      if: github.event_name == 'repository_dispatch'
      run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}')
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v4
      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[test]" "./related-packages/fileformats-extras[test]"
        python -c "import fileformats.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
    - name: Test fileformats with pytest
      run: |
        cd ./fileformats
        pytest -sv --cov fileformats.medimage_afni --cov fileformats.extras.medimage_afni --cov-report xml .

  test:
    needs: [nipype-conv, fileformats-test]
    runs-on: ubuntu-22.04
    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: Get Download cache Key
      id: cache-key
      run: echo "::set-output name=key::afni-linux-ubuntu22_amd64-7.4.1"
    - name: Cache FreeSurfer
      uses: actions/cache@v2
      with:
        path: $HOME/downloads/afni
        key: ${{ steps.cache-key.outputs.key }}
        restore-keys: |
          afni-linux-ubuntu22_amd64-7.4.1
    - name: Download FreeSurfer
      if: steps.cache-key.outputs.key != steps.cache-hit.outputs.key
      run: |
        mkdir -p $HOME/downloads/afni
        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
      shell: bash
    - name: Install Freesurfer
      env:
        FREESURFER_LICENCE: ${{ secrets.FREESURFER_LICENCE }}
      run: |
        pushd $HOME/downloads/afni
        tar -zxpf afni-linux-ubuntu22_amd64-7.4.1.tar.gz
        mv afni $HOME/
        popd
        export FREESURFER_HOME=$HOME/afni
        source $FREESURFER_HOME/SetUpFreeSurfer.sh
        echo $FREESURFER_LICENCE > $FREESURFER_HOME/license.txt
        export PATH=$FREESURFER_HOME/bin:$PATH
    - uses: actions/checkout@v3
    - name: Revert version to most recent tag on upstream update
      if: github.event_name == 'repository_dispatch'
      run: git checkout $(git tag -l | 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/afni/auto
    - name: Strip auto package from gitignore so it is included in package
      run: |
        sed -i '/\/src\/pydra\/tasks\/afni\/auto/d' .gitignore
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v4
      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.afni 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 --doctest-modules ./pydra/tasks/afni \
            --cov pydra.tasks.afni --cov-report xml
    - uses: codecov/codecov-action@v3
      if: ${{ always() }}
      with:
        files: coverage.xml,./fileformats/coverage.xml
        name: pydra-afni

  deploy-fileformats:
    needs: [devcheck, test]
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v3
      with:
        submodules: recursive
        fetch-depth: 0 
    - name: Set up Python
      uses: actions/setup-python@v4
      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 == 'push' && startsWith(github.ref, 'refs/tags')) || 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@v3
      with:
        submodules: recursive
        fetch-depth: 0 
    - name: Set up Python
      uses: actions/setup-python@v4
      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 == 'push' && startsWith(github.ref, 'refs/tags')) || 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: [deploy-fileformats-extras]
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v3
      with:
        submodules: recursive
        fetch-depth: 0
    - name: Download tasks converted from Nipype 
      uses: actions/download-artifact@v3
      with:
        name: converted-nipype
        path: pydra/tasks/afni/auto
    - name: Tag release with a post-release based on Nipype and Nipype2Pydra versions
      if: github.event_name == 'repository_dispatch'
      run: |
        TAG=$(git tag -l | tail -n 1 | awk -F post '{print $1}')
        POST=$(python -c "from pydra.tasks.afni.auto._version import *; print(post_release)")
        git checkout $TAG
        git add -f pydra/tasks/afni/auto/_version.py
        git commit -am"added auto-generated version to make new tag for package version"
        git tag ${TAG}post${POST}    
    - name: Set up Python
      uses: actions/setup-python@v4
      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\/afni\/auto/d' .gitignore
    - 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 == 'push' && startsWith(github.ref, 'refs/tags')) || 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 }}   

# 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