test-ci.yml

name: CI

on:
  push:
    branches: [ "main" ]
  pull_request:
    branches: [ "main" ]

  workflow_dispatch:

jobs:
  linter-check:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout
        uses: actions/checkout@v3
      - name: Set up Python "3.10"
        uses: actions/setup-python@v4
        with:
          python-version: "3.10"
      - name: Black setup
        shell: bash
        run: pip install black ruff mypy
      - name: Black Check
        shell: bash
        run: black . --diff --color --check

  test-cpu:
    runs-on: ubuntu-latest
    needs: linter-check
    strategy:
      fail-fast: true
      matrix:
        python-version: ["3.12", "3.10"]

    steps:
      - uses: actions/checkout@v3
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install Dependencies
        shell: bash
        run: |
          python --version
          python -m pip install --upgrade pip
          python -m pip install .[test]
      - name: Run Tests
        shell: bash
        run: |
          export COVERAGE_FILE=coverage_${{ matrix.python-version }}
          pytest -n auto --ignore=tests/phantoms/test_brainweb.py --ignore=tests/phantoms/test_osf.py --cov --disable-pytest-warnings --cov-branch --cov-report=term    
      - name: Upload coverage
        if: success()
        uses: actions/upload-artifact@v4
        with:
          name: coverage_${{ matrix.python-version }}
          path: coverage_${{ matrix.python-version }}
          
  get-commit-message:
    runs-on: ubuntu-latest
    outputs:
       message: ${{ steps.get_commit_message.outputs.message }}
    steps:
       - uses: actions/checkout@v3
         with:
           ref: ${{ github.event.pull_request.head.sha }}
       - name: Get commit message
         id: get_commit_message
         run: |
            COMMIT_MESSAGE=$(git log -1 --pretty=%B)
            echo "Commit message $COMMIT_MESSAGE"
            echo "::set-output name=message::$COMMIT_MESSAGE"
    
  coverage:
    runs-on: ubuntu-latest
    needs: [test-cpu, get-commit-message]
    if: ${{ always() }}
    steps:
      - name: Checkout
        uses: actions/checkout@v3

      - name: Collect Coverages
        uses: actions/download-artifact@v4
        with:
          path: coverage_data
          pattern: coverage_*
          merge-multiple: true

      - name: Set up Python 3.10
        uses: actions/setup-python@v4
        with:
          python-version: ${{ env.PYTHON_VERSION }}
          
      - name: add the coverage tool
        shell: bash
        run: |
          python -m pip install --upgrade pip
          python -m pip install coverage[toml]
          python -m pip install -e .

      - name: Combine coverage
        run: |
          export COVERAGE_FILE=coverage_combined
          coverage combine -a coverage_data/*

      - name: Upload Combined coverage
        uses: actions/upload-artifact@v4
        with:
          name: coverage_combined
          path: coverage_combined

      - name: Reports
        run: |
          export COVERAGE_FILE=coverage_combined
          coverage xml
          coverage report
          echo COVERAGE_PERC=$(coverage report | tail -n 1 | grep -oE [0-9\.]*?% | cut -d '%' -f1) >> $GITHUB_ENV

      - name: Create a Coverage Badge
        if: ${{github.event_name == 'push'}}
        run: |
          wget https://img.shields.io/badge/coverage-${{env.COVERAGE_PERC}}%25-green -O coverage_badge.svg

      - name: Upload badge as artifact
        if: ${{github.event_name == 'push'}}
        uses: actions/upload-artifact@v4
        with:
          name: coverage_badge
          path: coverage_badge.svg

  BuildDocs:
    name: Build API Documentation
    runs-on: ubuntu-latest
    needs: get-commit-message
    if: ${{ contains(needs.get-commit-message.outputs.message, '!docs_build') || github.ref == 'refs/heads/main' }}
    steps:
      - name: Checkout
        uses: actions/checkout@v3
      
      - name: Get history and tags for SCM versioning to work
        run: |
          git fetch --prune --unshallow
          git fetch --depth=1 origin +refs/tags/*:refs/tags/*

      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: "3.10"
        
      - name: Install dependencies
        shell: bash -l {0}
        run: |
          python -m pip install --upgrade pip
          python -m pip install .[doc]
          python -m pip install -r docs/requirements.txt
      
      - name: Build API documentation
        run: |
          python -m sphinx docs docs_build
      
      - name: Display data
        run: ls -R
        working-directory: docs_build/_static
      
      - name: Upload artifact
        id: artifact-upload-step
        uses: actions/upload-artifact@v4
        with:
          # Upload the docs
          name: docs
          path: 'docs_build'
          retention-days: 5
    
  CompileDocs:
    name: Compile the coverage badge in docs
    runs-on: ubuntu-latest
    if: ${{ github.ref == 'refs/heads/main' }}
    needs: [BuildDocs, coverage]
    steps:
      - name: Get the docs_build artifact
        uses: actions/download-artifact@v4
        with:
          name: docs
          path: docs_build
          overwrite: true
    
      - name: Get the badge from CI
        uses: actions/download-artifact@v4
        with:
          name: coverage_badge
          path: docs_build/_static
          github-token: ${{ secrets.GITHUB_TOKEN }}
      
      - name: ReUpload artifacts
        uses: actions/upload-artifact@v4
        with:
          name: docs_final
          retention-days: 20
          path: docs_build