pipeline.yml

name: Pipeline

on:
  push:
    branches: [ main ]
  pull_request:

jobs:
  black:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
    - uses: psf/black@stable
      with:
        options: "--check --diff"
        src: ./src/${{ github.event.repository.name }}

  black_fix:  # in most cases pre-commit is faster
    needs: [black]
    if: failure()
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
      with:
        token: ${{ secrets.DEPENDABOT_WORKFLOW_TOKEN }}
        ref: ${{ github.event.pull_request.head.ref }} # Check out the head of the actual branch, not the PR
        fetch-depth: 0 # otherwise, you will fail to push refs to dest repo
    - name: format black
      uses: psf/black@stable
      with:
        options: ""
        src: "./src/${{ github.event.repository.name }}"
    - name: commit
      run: |
        git config --local user.email "pyiron@mpie.de"
        git config --local user.name "pyiron-runner"
        git commit -m "Format black" -a
    - name: push
      uses: ad-m/github-push-action@master
      with:
        github_token: ${{ secrets.DEPENDABOT_WORKFLOW_TOKEN }}
        branch: ${{ github.event.pull_request.head.ref }}

  mypy:
    needs: [black]
    runs-on: ubuntu-latest
    steps:
      - name: Setup Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.14"
          architecture: x64
      - name: Checkout
        uses: actions/checkout@v4
      - name: Test
        run: |
          pip install mypy types-PyYAML types-paramiko
          mypy --ignore-missing-imports src/${{ github.event.repository.name }}

  coverage:
    needs: [black]
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - name: Setup environment
        run: |
          cp .ci_support/environment.yml environment.yml
          echo "- flux-core =0.81.0" >> environment.yml
          echo -e "channels:\n  - conda-forge\n" > .condarc
          mkdir -p /home/runner/.ssh
          echo "test.rebex.net,195.144.107.198 ecdsa-sha2-nistp256 AAAAE2VjZHNhLXNoYTItbmlzdHAyNTYAAAAIbmlzdHAyNTYAAABBBLZcZopPvkxYERubWeSrWOSHpxJdR14WFVES/Q3hFguTn6L+0EANqYcbRXhGBUV6SjR7SaxZACXSxOzgCtG4kwc=" > /home/runner/.ssh/known_hosts
      - name: Setup Mambaforge
        uses: conda-incubator/setup-miniconda@v3
        with:
          python-version: '3.13'
          miniforge-version: latest
          condarc-file: .condarc
          environment-file: environment.yml
      - name: Install
        shell: bash -l {0}
        run: pip install . --no-deps --no-build-isolation
      - name: Test
        shell: bash -l {0}
        run: >
          flux start
          coverage run
      - name: Collect Coverage
        shell: bash -l {0}
        run: coverage xml
      - name: Upload coverage reports to Codecov
        uses: codecov/codecov-action@v5
        with:
          token: ${{ secrets.CODECOV_TOKEN }}

  minimal:
    needs: [black]
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - name: Setup environment
        run: echo -e "channels:\n  - conda-forge\n" > .condarc
      - name: Setup Mambaforge
        uses: conda-incubator/setup-miniconda@v3
        with:
          python-version: '3.14'
          miniforge-version: latest
          condarc-file: .condarc
          environment-file: .ci_support/environment-mini.yml
      - name: Test
        shell: bash -l {0}
        run: |
          pip install . --no-deps --no-build-isolation
          python -m unittest discover tests

  notebooks:
    needs: [black]
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - name: Merge Notebook environment
        run: |
          cp binder/environment.yml environment.yml
          tail --lines=+4 .ci_support/environment-notebooks.yml >> environment.yml
          echo -e "channels:\n  - conda-forge\n" > .condarc
      - name: Setup Mambaforge
        uses: conda-incubator/setup-miniconda@v3
        with:
          python-version: "3.13"
          miniforge-version: latest
          condarc-file: .condarc
          environment-file: environment.yml
      - name: Install
        shell: bash -l {0}
        run: |
          pip install . --no-deps --no-build-isolation
          mkdir config
          cp -r tests/static/flux config
      - name: Notebooks with config
        shell: bash -l {0}
        run: >
          flux start
          papermill notebooks/example_config.ipynb example-config-out.ipynb -k "python3"
      - name: Notebooks dynamic
        shell: bash -l {0}
        run: >
          flux start
          papermill notebooks/example_queue_type.ipynb example-queue-type-out.ipynb -k "python3"

  pip_check:
    needs: [black]
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - name: Conda config
        run: echo -e "channels:\n  - conda-forge\n" > .condarc
      - name: Setup Mambaforge
        uses: conda-incubator/setup-miniconda@v3
        with:
          python-version: '3.14'
          miniforge-version: latest
          condarc-file: .condarc
          environment-file: .ci_support/environment.yml
      - name: Pip check
        shell: bash -l {0}
        run: |
          pip install tomlkit
          python .ci_support/check.py
          cat pyproject.toml
          pip install . --no-deps --no-build-isolation
          pip check

  uv_check:
    needs: [black]
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
    - uses: astral-sh/setup-uv@v7
    - name: Install the project and pip check
      shell: bash -l {0}
      run: |
        uv sync --all-extras --dev
        pip check

  unittest_matrix:
    needs: [black]
    runs-on: ${{ matrix.operating-system }}
    strategy:
      matrix:
        include:
          - operating-system: macos-latest
            python-version: '3.14'

          - operating-system: windows-latest
            python-version: '3.14'

          - operating-system: ubuntu-24.04-arm
            python-version: '3.14'

          - operating-system: ubuntu-22.04-arm
            python-version: '3.14'

          - operating-system: ubuntu-latest
            python-version: '3.14'

          - operating-system: ubuntu-latest
            python-version: '3.13'

          - operating-system: ubuntu-latest
            python-version: '3.12'

          - operating-system: ubuntu-latest
            python-version: '3.11'

    steps:
      - uses: actions/checkout@v4
      - name: Conda config
        shell: bash -l {0}
        run: echo -e "channels:\n  - conda-forge\n" > .condarc
      - name: Setup Mambaforge
        uses: conda-incubator/setup-miniconda@v3
        with:
          python-version: ${{ matrix.python-version }}
          miniforge-version: latest
          condarc-file: .condarc
          environment-file: .ci_support/environment.yml
      - name: Test
        shell: bash -l {0}
        run: |
          mkdir -p ~/.ssh
          echo "test.rebex.net,195.144.107.198 ecdsa-sha2-nistp256 AAAAE2VjZHNhLXNoYTItbmlzdHAyNTYAAAAIbmlzdHAyNTYAAABBBLZcZopPvkxYERubWeSrWOSHpxJdR14WFVES/Q3hFguTn6L+0EANqYcbRXhGBUV6SjR7SaxZACXSxOzgCtG4kwc=" > ~/.ssh/known_hosts
          pip install . --no-deps --no-build-isolation
          python -m unittest discover tests

  unittest_old:
    needs: [black]
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - name: Conda config
        run: echo -e "channels:\n  - conda-forge\n" > .condarc
      - name: Setup Mambaforge
        uses: conda-incubator/setup-miniconda@v3
        with:
          python-version: '3.9'
          miniforge-version: latest
          condarc-file: .condarc
          environment-file: .ci_support/environment-old.yml
      - name: Test
        shell: bash -l {0}
        run: |
          mkdir -p ~/.ssh
          echo "test.rebex.net,195.144.107.198 ecdsa-sha2-nistp256 AAAAE2VjZHNhLXNoYTItbmlzdHAyNTYAAAAIbmlzdHAyNTYAAABBBLZcZopPvkxYERubWeSrWOSHpxJdR14WFVES/Q3hFguTn6L+0EANqYcbRXhGBUV6SjR7SaxZACXSxOzgCtG4kwc=" > ~/.ssh/known_hosts
          pip install . --no-deps --no-build-isolation
          python -m unittest discover tests

  unittest_slurm:
    needs: [black]
    runs-on: ubuntu-latest
    services:
      mysql:
        image: mysql:8.0
        env:
          MYSQL_ROOT_PASSWORD: root
        ports:
          - "8888:3306"
        options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3
    steps:
    - uses: actions/checkout@v4
    - uses: koesterlab/setup-slurm-action@v1
      timeout-minutes: 5
    - name: Conda config
      run: echo -e "channels:\n  - conda-forge\n" > .condarc
    - uses: conda-incubator/setup-miniconda@v3
      with:
        python-version: "3.13"
        miniforge-version: latest
        condarc-file: .condarc
        environment-file: .ci_support/environment.yml
    - name: Test
      shell: bash -l {0}
      timeout-minutes: 5
      run: |
        pip install . --no-deps --no-build-isolation
        cd tests
        sinfo -o "%n %e %m %a %c %C"
        srun --mpi=list
        python -m unittest integration/test_slurm_integration.py

  unittest_flux:
    needs: [black]
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
    - name: Conda config
      run: |
        echo -e "channels:\n  - conda-forge\n" > .condarc
        echo "- flux-core=0.81.0" >> .ci_support/environment.yml
    - uses: conda-incubator/setup-miniconda@v3
      with:
        python-version: "3.13"
        miniforge-version: latest
        condarc-file: .condarc
        environment-file: .ci_support/environment.yml
    - name: Test
      shell: bash -l {0}
      timeout-minutes: 5
      run: |
        pip install . --no-deps --no-build-isolation
        cd tests
        flux start python -m unittest integration/test_flux_integration.py

  autobot:
    needs: [uv_check, unittest_old, unittest_matrix, pip_check, notebooks, minimal, coverage]
    permissions:
      contents: write
      pull-requests: write
    runs-on: ubuntu-latest
    if: (github.event.pull_request.user.login == 'dependabot[bot]' || github.event.pull_request.user.login == 'pre-commit-ci[bot]')
    steps:
      - name: Enable auto-merge for bot PRs
        run: gh pr merge --auto --squash "$PR_URL"
        env:
          PR_URL: ${{github.event.pull_request.html_url}}
          GH_TOKEN: ${{secrets.GITHUB_TOKEN}}