pythonpackage.yml

# 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

name: Python package

on:
  push:
    branches: [ '**' ]
    tags: [ '*' ]
  pull_request:
    branches: [ master, 'maint/*' ]
  schedule:
    - cron: '0 0 * * *'

concurrency:
  group: python-${{ github.ref }}
  cancel-in-progress: true

jobs:
  job_metadata:
    if: github.repository == 'nipreps/niworkflows'
    runs-on: ubuntu-latest
    outputs:
      commit_message: ${{ steps.get_commit_message.outputs.commit_message }}
      version: ${{ steps.show_version.outputs.version }}
    steps:
      - name: Checkout
        uses: actions/checkout@v4
        with:
          fetch-depth: 0
      - name: Print head git commit message
        id: get_commit_message
        run: |
          if [[ -z "$COMMIT_MSG" ]]; then
            COMMIT_MSG=$(git show -s --format=%s $REF)
          fi
          echo commit_message=$COMMIT_MSG | tee -a $GITHUB_OUTPUT
        env:
          COMMIT_MSG: ${{ github.event.head_commit.message }}
          REF: ${{ github.event.pull_request.head.sha }}
      - name: Detect version
        id: show_version
        run: |
          if [[ "$GITHUB_REF" == refs/tags/* ]]; then
            VERSION=${GITHUB_REF##*/}
          else
            pipx run hatch version  # Once to avoid output of initial setup
            VERSION=$( pipx run hatch version )
          fi
          echo version=$VERSION | tee -a $GITHUB_OUTPUT

  build:
    if: github.repository == 'nipreps/niworkflows'
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
      with:
        fetch-depth: 0
    - name: Set up Python 3
      uses: actions/setup-python@v5
      with:
        python-version: 3
    - name: Display Python version
      run: python -c "import sys; print(sys.version)"
    - name: Build niworkflows
      run: pipx run build
    - name: Check distributions
      run: pipx run twine check dist/*
    - uses: actions/upload-artifact@v3
      with:
        name: dist
        path: dist/

  get_data:
    if: github.repository == 'nipreps/niworkflows'
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0}
    steps:
    - name: Create test data directory
      run: mkdir -p $HOME/.cache/stanford-crn
    - name: Load test data cache
      uses: actions/cache@v4
      id: stanford-crn
      with:
        path: ~/.cache/stanford-crn/
        key: data-v0-${{ github.ref_name }}-${{ github.sha }}
        restore-keys: |
          data-v0-${{ github.ref_name }}-
          data-v0-
    - name: Setup conda
      uses: conda-incubator/setup-miniconda@v3
      with:
        auto-activate-base: true
        activate-environment: ""
    - name: Verify environment
      run: |
        conda info
        which python
    - name: Install datalad
      run: |
        python -m pip install datalad-installer
        datalad-installer --sudo ok git-annex
        python -m pip install datalad datalad-osf
        datalad wtf
    - name: Pacify git
      run: |
        git config --global user.email "github@niworkflows.ci"
        git config --global user.name "Niworkflows Action"
    - name: Fetch test data
      run: |
        DS=$HOME/.cache/stanford-crn
        datalad install -r -s https://github.com/nipreps-data/niworkflows-data.git $DS
        cd $DS
        git -C BIDS-examples-1-enh-ds054 checkout enh/ds054
        datalad update -r --merge -d .
        datalad get -J 2 -r ds000003 ds000030/sub-10228/func

  test:
    needs: [build, get_data, job_metadata]
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.9", "3.10", "3.11", "3.12"]
        install: [repo]
        include:
          - python-version: "3.12"
            install: sdist
          - python-version: "3.12"
            install: wheel
          - python-version: "3.12"
            install: editable

    env:
      INSTALL_TYPE: ${{ matrix.install }}

    steps:
    - uses: actions/checkout@v4
      if: matrix.install == 'repo' || matrix.install == 'editable'
      with:
        fetch-depth: 0
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    - name: Load test data cache
      uses: actions/cache@v4
      id: stanford-crn
      with:
        path: ~/.cache/stanford-crn/
        key: data-v0-${{ github.ref_name }}-${{ github.sha }}
    - name: Load TemplateFlow cache
      uses: actions/cache@v4
      id: templateflow
      with:
        path: ~/.cache/templateflow
        key: templateflow-v0-${{ github.ref_name }}-${{ strategy.job-index }}-${{ github.sha }}
        restore-keys: |
          templateflow-v0-${{ github.ref_name }}-
          templateflow-v0-
    - name: Fetch packages
      if: matrix.install == 'sdist' || matrix.install == 'wheel'
      uses: actions/download-artifact@v3
      with:
        name: dist
        path: dist/
    - name: Select archive
      run: |
        if [ "$INSTALL_TYPE" = "sdist" ]; then
          ARCHIVE=$( ls dist/*.tar.gz )
        elif [ "$INSTALL_TYPE" = "wheel" ]; then
          ARCHIVE=$( ls dist/*.whl )
        elif [ "$INSTALL_TYPE" = "repo" ]; then
          ARCHIVE="."
        elif [ "$INSTALL_TYPE" = "editable" ]; then
          ARCHIVE="-e ."
        fi
        echo "ARCHIVE=$ARCHIVE" | tee -a $GITHUB_ENV
    - name: Install package
      run: python -m pip install $ARCHIVE
    - name: Check version
      run: |
        INSTALLED_VERSION=$(python -c 'import niworkflows; print(niworkflows.__version__, end="")')
        echo "INSTALLED: \"${INSTALLED_VERSION}\""
        test "${INSTALLED_VERSION}" = "${VERSION}"
      env:
        VERSION: ${{ needs.job_metadata.outputs.version }}
    - name: Install test dependencies
      run: python -m pip install "niworkflows[tests]"
    - name: Run tests
      run: pytest -sv --doctest-modules --cov niworkflows --pyargs niworkflows
    - uses: codecov/codecov-action@v4
      name: Submit to CodeCov
      with:
        token: ${{ secrets.CODECOV_TOKEN }}

  test-pre:
    needs: [get_data, job_metadata]
    if: ${{ !contains(needs.job_metadata.outputs.commit_message, '[skip pre]') }}
    runs-on: ubuntu-latest
    strategy:
      matrix:
        # Only run --pre tests on Python versions within SPEC0 support
        python-version: ["3.11", "3.12"]
        install: [repo]
        pip-flags: ['--pre']

    env:
      INSTALL_TYPE: ${{ matrix.install }}
      PIP_FLAGS: ${{ matrix.pip-flags }}

    steps:
    - name: Debug commit message
      run: echo "${{ needs.job_metadata.outputs.commit_message }}"
    - uses: actions/checkout@v4
      with:
        fetch-depth: 0
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    - name: Load test data cache
      uses: actions/cache@v4
      id: stanford-crn
      with:
        path: ~/.cache/stanford-crn/
        key: data-v0-${{ github.ref_name }}-${{ github.sha }}
    - name: Load TemplateFlow cache
      uses: actions/cache@v4
      id: templateflow
      with:
        path: ~/.cache/templateflow
        key: templateflow-v0-${{ github.ref_name }}-${{ strategy.job-index }}-${{ github.sha }}
        restore-keys: |
          templateflow-v0-${{ github.ref_name }}-
          templateflow-v0-
    - name: Install package
      run: python -m pip install $PIP_FLAGS .
    - name: Check version
      run: |
        INSTALLED_VERSION=$(python -c 'import niworkflows; print(niworkflows.__version__, end="")')
        echo "INSTALLED: \"${INSTALLED_VERSION}\""
        test "${INSTALLED_VERSION}" = "${VERSION}"
      env:
        VERSION: ${{ needs.job_metadata.outputs.version }}
    - name: Install test dependencies
      run: python -m pip install $PIP_FLAGS "niworkflows[tests]"
    - name: Run tests
      run: pytest -sv --doctest-modules --cov niworkflows --pyargs niworkflows
    - uses: codecov/codecov-action@v4
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
      name: Submit to CodeCov

  flake8:
    if: github.event_name != 'schedule'
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
    - name: Set up Python 3
      uses: actions/setup-python@v5
      with:
        python-version: 3
    - run: pipx run flake8 niworkflows/