test.yml

---
on:
  push:
    branches:
    - main
    - maint/*
    tags:
    - '*'
  pull_request:
    branches:
    - main
    - maint/*

defaults:
  run:
    shell: bash

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

permissions:
  contents: read

jobs:
  check_skip_flags:
    name: Check skip flags
    runs-on: ubuntu-latest
    outputs:
      head-commit-message: ${{ steps.get_head_commit_message.outputs.headCommitMsg }}
    steps:
    - name: Get repo
      uses: actions/checkout@v3
      with:
        ref: ${{ github.event.pull_request.head.sha }}
    - name: Print head git commit message
      id: get_head_commit_message
      run: echo "headCommitMsg=$(git show -s --format=%s)" >> $GITHUB_OUTPUT

  download-test-data:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v3
      with:
        fetch-depth: 0
    - uses: actions/cache@v3
      id: cache
      env:
        cache-name: ds000017
      with:
        path: /home/runner/work/giga_auto_qc/giga_auto_qc/giga_auto_qc/data/test_data
        key: ${{ env.cache-name }}

    - if: ${{ steps.cache.outputs.cache-hit != 'true' }}
      name: Download fmriprep derivative of ds000017
      id: download
      run: |
        mkdir -p /home/runner/work/giga_auto_qc/giga_auto_qc/giga_auto_qc/data/test_data
        cd /home/runner/work/giga_auto_qc/giga_auto_qc/giga_auto_qc/data/test_data
        wget --retry-connrefused \
          --waitretry=5 \
          --read-timeout=20 \
          --timeout=15 \
          -t 0 \
          -q \
          -O ds000017.tar.gz \
          "https://zenodo.org/record/8091903/files/ds000017-fmriprep22.0.1-downsampled-nosurface.tar.gz?download=1"
        tar -xzf ds000017.tar.gz
        rm ds000017.tar.gz

  build:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v3
      with:
        fetch-depth: 0
    - uses: actions/setup-python@v4
      with:
        python-version: 3
    - run: pip install --upgrade build twine
    - name: Build sdist and wheel
      run: python -m build
    - run: twine check dist/*
    - name: Upload sdist and wheel artifacts
      uses: actions/upload-artifact@v3
      with:
        name: dist
        path: dist/
    - name: Build git archive
      run: mkdir archive && git archive -v -o archive/archive.tgz HEAD
    - name: Upload git archive artifact
      uses: actions/upload-artifact@v3
      with:
        name: archive
        path: archive/

  test-package:
    runs-on: ubuntu-latest
    needs: [build]
    strategy:
      matrix:
        package: [wheel, sdist, archive]
    steps:
    - name: Download sdist and wheel artifacts
      if: matrix.package != 'archive'
      uses: actions/download-artifact@v3
      with:
        name: dist
        path: dist/
    - name: Download git archive artifact
      if: matrix.package == 'archive'
      uses: actions/download-artifact@v3
      with:
        name: archive
        path: archive/
    - uses: actions/setup-python@v4
      with:
        python-version: 3
    - name: Display Python version
      run: python -c "import sys; print(sys.version)"
    - name: Update pip
      run: pip install --upgrade pip
    - name: Install wheel
      if: matrix.package == 'wheel'
      run: pip install dist/*.whl
    - name: Install sdist
      if: matrix.package == 'sdist'
      run: pip install dist/*.tar.gz
    - name: Install archive
      if: matrix.package == 'archive'
      run: pip install archive/archive.tgz

  test-coverage:
    runs-on: ubuntu-latest
    needs: [build, download-test-data, check_skip_flags]
    strategy:
      matrix:
        python-version: ['3.8', '3.9', '3.10', '3.11']
    steps:
    - uses: actions/checkout@v2
      name: Set up Python ${{ matrix.python-version }}
    - uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}

    - name: Restore cached data ds000017
      id: cache
      uses: actions/cache/restore@v3
      with:
        path: /home/runner/work/giga_auto_qc/giga_auto_qc/giga_auto_qc/data/test_data
        key: ds000017

    - name: Install build dependencies
      run: python -m pip install --upgrade pip
    - name: Install task package
      run: pip install -e .[test]

    - name: Test with pytest - ignore smoke test.
      if: ${{ !contains(needs.check_skip_flags.outputs.head-commit-message, 'full_test') }}
      run: |
        pytest -m "not smoke" --cov=giga_auto_qc --cov-report=xml --doctest-modules -v --pyargs giga_auto_qc

    - name: Full test - run all the test to generate accurate coverage report.
      if: ${{ contains(needs.check_skip_flags.outputs.head-commit-message, 'full_test') }} || ${{ github.event.pull_request.merged }}
      run: pytest --cov=giga_auto_qc --cov-report=xml --doctest-modules -v --pyargs giga_auto_qc

    - uses: codecov/codecov-action@v3
      if: ${{ always() }}
      with:
        token: ${{ secrets.CODECOV_TOKEN }}

  docker:
    # build and test docker image
    if: ${{ contains(needs.check_skip_flags.outputs.head-commit-message, 'full_test') }}
    runs-on: ubuntu-latest
    needs: [download-test-data, check_skip_flags]
    steps:
    - uses: actions/checkout@v3
    - name: Build the Docker image
      run: |
        user_name="bids"
        docker build . --file Dockerfile --tag ${user_name}/giga_auto_qc
        mkdir -p "${HOME}/docker"
        docker save "${user_name}/giga_auto_qc" > "${HOME}/docker/image.tar"

    - name: Restore cached data ds000017
      id: cache
      uses: actions/cache/restore@v3
      with:
        path: /home/runner/work/giga_auto_qc/giga_auto_qc/giga_auto_qc/data/test_data
        key: ds000017

    - name: Test the Docker image
      run: |
        docker load -i ${HOME}/docker/image.tar
        docker run --rm --read-only \
          -v /home/runner/work/giga_auto_qc/giga_auto_qc/giga_auto_qc/data/test_data:/test_data \
          -v ./outputs:/outputs \
          -v ./outputs/working_dir:/work \
          bids/giga_auto_qc \
          /test_data/ds000017-fmriprep22.0.1-downsampled-nosurface \
          /outputs \
          participant \
          --participant_label 1 \
          --reindex-bids

    - name: Upload output artifact
      uses: actions/upload-artifact@v3
      with:
        name: connectome
        path: ./outputs/
    - name: Upload docker image artifact
      uses: actions/upload-artifact@v3
      with:
        name: docker-image
        path: ${HOME}/docker/image.tar

  # publish:
  #   runs-on: ubuntu-latest
  #   needs: [test-package, test-coverage]
  #   if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
  #   steps:
  #   - uses: actions/download-artifact@v3
  #     with:
  #       name: dist
  #       path: dist/
  #   - uses: pypa/gh-action-pypi-publish@release/v1
  #     with:
  #       user: __token__
  #       password: ${{ secrets.PYPI_API_TOKEN }}