python-package.yml

# This workflow will install Python dependencies, run tests and lint with Python 3.10 and 3.11
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: Testing Linux

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

permissions:
  contents: write
  pull-requests: write

jobs:
  build:
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.10", "3.11"]
        split: [1, 2, 3, 4, 5]  # Number of splits

    steps:
    - name: Fetch Most Recent Docker Image Tag
      run: |
        TAG=$(curl -H "Accept: application/vnd.github.v3+json" \
            -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \
            https://api.github.com/orgs/autoatml/packages/container/autoplex%2Fautoplex-python-3.10/versions \
            | jq -r 'sort_by(.created_at) | reverse | .[0].metadata.container.tags[0]')
        echo "VERSION=$TAG" >> $GITHUB_ENV

    - uses: actions/checkout@v4
      with:
        fetch-depth: 0  # Fetch the entire Git history
        
    - name: Run tests using Docker image for Python ${{ matrix.python-version }}
      run: |
        docker pull ghcr.io/autoatml/autoplex/autoplex-python-${{ matrix.python-version }}:${{ env.VERSION }}

        docker run --rm \
          -v ${{ github.workspace }}:/workspace \
          -w /workspace \
          ghcr.io/autoatml/autoplex/autoplex-python-${{ matrix.python-version }}:${{ env.VERSION }} \
          bash -c "
          git config --global --add safe.directory /workspace && \
          python -m pip install --upgrade pip && \
          python -m uv cache clean && \
          python -m uv pip install --prerelease=allow '.[strict,tests,aims]' && \
          OMP_NUM_THREADS=1 pytest --cache-clear --cov=autoplex --cov-report term-missing --cov-append --splits 5 --group ${{ matrix.split }} -vv --durations-path /workspace/tests/test_data/.pytest-split-durations --store-durations -k 'not PACE'
        "

        
    - name: Upload test durations artifact
      if: matrix.python-version == '3.10'
      uses: actions/upload-artifact@v4
      with:
        name: test-durations-${{ matrix.python-version }}-${{ matrix.split }}
        include-hidden-files: true
        path: ./tests/test_data/.pytest-split-durations

    - name: Upload coverage
      if: matrix.python-version == '3.10'
      uses: actions/upload-artifact@v4
      with:
        name: coverage-${{ matrix.python-version }}-${{ matrix.split }}
        include-hidden-files: true
        path: ./.coverage

  get-pacemaker-run:
    needs: build
    runs-on: ubuntu-latest
    outputs:
      run_id: ${{ steps.get-run.outputs.run_id }}
    steps:
      - name: Get latest successful Pacemaker run ID
        id: get-run
        run: |
          RUN_ID=$(gh run list \
            --repo ${{ github.repository }} \
            --workflow="Testing Pacemaker (Python 3.10)" \
            --branch=main \
            --status=success \
            --limit=1 \
            --json databaseId \
            -q '.[0].databaseId')
          echo "run_id=$RUN_ID" >> $GITHUB_OUTPUT
        env:
          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

  commit-durations:
    if: github.repository_owner == 'autoatml' && github.ref == 'refs/heads/main'
    needs: [build, get-pacemaker-run]
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0} # enables conda/mamba env activation by reading bash profile

    steps:

    - name: Check out repo
      uses: actions/checkout@v4
    - name: Set up micromamba
      uses: mamba-org/setup-micromamba@main
    - name: Clean mamba cache
      run: |
          micromamba clean -a -y
    - name: Create mamba environment
      run: |
          micromamba create -n autoplex_tests python=3.10 --yes
    - name: Install uv
      run: micromamba run -n autoplex_tests pip install uv
    - name: Install autoplex and dependencies
      run: |
          micromamba activate autoplex_tests
          uv pip install --upgrade pip
          uv pip install --prerelease=allow .[tests,strict]
          
    - name: Download test duration artifacts
      uses: actions/download-artifact@v4
      with:
        pattern: test-durations-*

    - name: Download Pacemaker test duration artifacts
      continue-on-error: true
      uses: actions/download-artifact@v4
      with:
        pattern: test-durations-pacemaker
        run-id: ${{ needs.get-pacemaker-run.outputs.run_id }}
        github-token: ${{ secrets.GITHUB_TOKEN }}

    - name: Compute average of test durations
      run: |
        micromamba activate autoplex_tests
        python3 .github/scripts/average_test_durations.py
        rm -rf test-durations-*

    - name: Create Pull Request to push consolidated test durations
      uses: peter-evans/create-pull-request@v7
      with:
        token: ${{ secrets.ACTION_SECRET }}
        commit-message: update test durations
        title: Update test durations file
        body: Auto update test durations file
        branch: update-test-durations
        labels: |
            automated-pr
        delete-branch: true
        base: main

  coverage:
      needs: [build, get-pacemaker-run]
      runs-on: ubuntu-latest
      steps:
        - uses: actions/checkout@v4
        - name: Set up Python 3.10
          uses: actions/setup-python@v4
          with:
            python-version: '3.10'

        - name: Install Coverage
          run: |
           python -m pip install coverage[toml]

        - name: Download coverage artifacts
          continue-on-error: true
          uses: actions/download-artifact@v4
          with:
            pattern: coverage-*

        - name: Download Pacemaker coverage artifacts
          continue-on-error: true
          uses: actions/download-artifact@v4
          with:
            pattern: coverage-pacemaker
            run-id: ${{ needs.get-pacemaker-run.outputs.run_id }}
            github-token: ${{ secrets.GITHUB_TOKEN }}

        - name: Run coverage
          continue-on-error: true
          run: |
            coverage combine coverage*/.coverage*
            coverage report --show-missing

  docs:
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0} # enables conda/mamba env activation by reading bash profile

    steps:
      - name: Check out repo
        uses: actions/checkout@v4
      - name: Set up micromamba
        uses: mamba-org/setup-micromamba@main
      - name: Clean mamba cache
        run: |
            micromamba clean -a -y
      - name: Create mamba environment
        run: |
            micromamba create -n autoplex_docs python=3.10 --yes
      - name: Install uv
        run: micromamba run -n autoplex_docs pip install uv
      - name: Install autoplex and dependencies
        run: |
            micromamba activate autoplex_docs
            uv pip install --upgrade pip
            uv pip install --prerelease=allow .[docs,strict,tests,aims]

      - name: Copy tutorials
        run: |
          mkdir -p docs/user/executable
          cp -r tutorials/* docs/user/executable
          micromamba run -n autoplex_docs jupyter nbconvert --to markdown docs/user/executable/*.ipynb

      - name: Build
        run: micromamba run -n autoplex_docs sphinx-build -W docs _build