testing.yml

name: testing

on:
  push:
    branches: [main]
    tags: ["v*"]
  pull_request:
  workflow_dispatch:
  repository_dispatch:
    types: [pymatgen-ci-trigger]

jobs:
  lint:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - uses: actions/setup-python@v5
        with:
          python-version: "3.10"
          cache: pip
          cache-dependency-path: pyproject.toml

      - uses: pre-commit/action@v3.0.0

  test-non-ase:
    # prevent this action from running on forks
    if: github.repository == 'materialsproject/atomate2'

    services:
      local_mongodb:
        image: mongo:4.0
        ports:
          - 27017:27017

    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
    strategy:
      matrix:
        python-version: ["3.10", "3.11", "3.12"]
        split: [1, 2, 3]

    steps:
      - name: Check out repo
        uses: actions/checkout@v4

      - name: Set up micromamba
        uses: mamba-org/setup-micromamba@main

      - name: Create mamba environment
        run: |
          micromamba create -n a2 python=${{ matrix.python-version }} --yes

      - name: Install uv
        run: micromamba run -n a2 pip install uv

      - name: Install conda dependencies
        run: |
          micromamba install -n a2 -c conda-forge enumlib packmol bader --yes

      - name: Install dependencies
        run: |
          micromamba activate a2
          python -m pip install --upgrade pip
          mkdir -p ~/.abinit/pseudos
          cp -r tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4 ~/.abinit/pseudos
          uv pip install .[strict,strict-forcefields,tests,abinit]
          uv pip install torch-runstats
          uv pip install --no-deps nequip==0.5.6

      - name: Install pymatgen from master if triggered by pymatgen repo dispatch
        if: github.event_name == 'repository_dispatch' && github.event.action == 'pymatgen-ci-trigger'
        run: |
          micromamba activate a2
          uv pip install --upgrade 'git+https://github.com/materialsproject/pymatgen@${{ github.event.client_payload.pymatgen_ref }}'

      - name: Test split ${{ matrix.split }}
        env:
          MP_API_KEY: ${{ secrets.MP_API_KEY }}

        # regenerate durations file with `pytest --store-durations --durations-path tests/.pytest-split-durations`
        # Note the use of `--splitting-algorithm least_duration`.
        # This helps prevent a test split having no tests to run, and then the GH action failing, see:
        # https://github.com/jerry-git/pytest-split/issues/95
        # However this `splitting-algorithm` means that tests cannot depend sensitively on the order they're executed in.
        run: |
          micromamba activate a2
          pytest --splits 3 --group ${{ matrix.split }} --durations-path tests/.pytest-split-durations --splitting-algorithm least_duration --ignore=tests/ase --ignore=tests/openff_md --ignore=tests/openmm_md --cov=atomate2 --cov-report=xml


      - uses: codecov/codecov-action@v1
        if: matrix.python-version == '3.10' && github.repository == 'materialsproject/atomate2'
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          name: coverage${{ matrix.split }}
          file: ./coverage.xml

  test-openff:
    # prevent this action from running on forks
    if: github.repository == 'materialsproject/atomate2'

    services:
      local_mongodb:
        image: mongo:4.0
        ports:
          - 27017:27017

    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
    strategy:
      matrix:
        python-version: ["3.10","3.11","3.12"]

    steps:
      - name: Check out repo
        uses: actions/checkout@v4

      - name: Set up micromamba
        uses: mamba-org/setup-micromamba@main

      - name: Create mamba environment
        run: |
          micromamba create -n a2 python=${{ matrix.python-version }} --yes

      - name: Install uv
        run: micromamba run -n a2 pip install uv

      - name: Install conda dependencies
        run: |
          micromamba install -n a2 -c conda-forge enumlib packmol bader openbabel openff-toolkit==0.16.2 openff-interchange==0.3.22 --yes

      - name: Install dependencies
        run: |
          micromamba activate a2
          python -m pip install --upgrade pip
          uv pip install .[strict-openff,tests]

      - name: Install pymatgen from master if triggered by pymatgen repo dispatch
        if: github.event_name == 'repository_dispatch' && github.event.action == 'pymatgen-ci-trigger'
        run: |
          micromamba activate a2
          uv pip install --upgrade 'git+https://github.com/materialsproject/pymatgen@${{ github.event.client_payload.pymatgen_ref }}'

      - name: Test split ${{ matrix.split }}
        env:
          MP_API_KEY: ${{ secrets.MP_API_KEY }}

        run: |
          micromamba activate a2
          pytest tests/{openff_md,openmm_md}

  test-notebooks-and-ase:
    # prevent this action from running on forks
    if: github.repository == 'materialsproject/atomate2'
    
    # It seems like anything torch-dependent and tblite can't be installed in the same environment
    # without the tblite tests failing in CI, see, e.g.:
    # https://github.com/tblite/tblite/issues/116
    # Outside of CI, having torch installed but not loaded seems not to affect tblite
    # Set off ASE tests here, where tblite-dependent tests live
    services:
      local_mongodb:
        image: mongo:4.0
        ports:
          - 27017:27017

    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
    strategy:
      matrix:
        python-version: ["3.10", "3.11", "3.12"]

    steps:
      - name: Check out repo
        uses: actions/checkout@v4

      - name: Set up micromamba
        uses: mamba-org/setup-micromamba@main

      - name: Create mamba environment
        run: |
          micromamba create -n a2 python=${{ matrix.python-version }} --yes

      - name: Install uv
        run: micromamba run -n a2 pip install uv

      - name: Install conda dependencies
        run: |
          micromamba install -n a2 -c conda-forge enumlib packmol bader openbabel openff-toolkit==0.16.2 openff-interchange==0.3.22 --yes

      - name: Install dependencies
        run: |
          micromamba activate a2
          python -m pip install --upgrade pip
          uv pip install .[strict,tests]

      - name: Install pymatgen from master if triggered by pymatgen repo dispatch
        if: github.event_name == 'repository_dispatch' && github.event.action == 'pymatgen-ci-trigger'
        run: uv pip install --upgrade 'git+https://github.com/materialsproject/pymatgen@${{ github.event.client_payload.pymatgen_ref }}'

      - name: Test Notebooks
        run: |
          micromamba activate a2
          pytest --nbmake ./tutorials --ignore=./tutorials/openmm_tutorial.ipynb --ignore=./tutorials/force_fields

      - name: Test ASE
        env:
          MP_API_KEY: ${{ secrets.MP_API_KEY }}
        run: |
          micromamba activate a2
          pytest --splits 1 --group 1 --cov=atomate2 --cov-report=xml tests/ase

      - uses: codecov/codecov-action@v1
        if: matrix.python-version == '3.10' && github.repository == 'materialsproject/atomate2'
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          file: ./coverage.xml

  test-force-field-notebook:
    # prevent this action from running on forks
    if: github.repository == 'materialsproject/atomate2'

    services:
      local_mongodb:
        image: mongo:4.0
        ports:
          - 27017:27017

    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
    strategy:
      matrix:
        python-version: ["3.10", "3.11", "3.12"]

    steps:
      - name: Check out repo
        uses: actions/checkout@v4

      - name: Set up micromamba
        uses: mamba-org/setup-micromamba@main

      - name: Create mamba environment
        run: |
          micromamba create -n a2 python=${{ matrix.python-version }} --yes

      - name: Install uv
        run: micromamba run -n a2 pip install uv

      - name: Install conda dependencies
        run: |
          micromamba install -n a2 -c conda-forge enumlib packmol bader openbabel openff-toolkit==0.16.2 openff-interchange==0.3.22 --yes

      - name: Install dependencies
        run: |
          micromamba activate a2
          python -m pip install --upgrade pip
          mkdir -p ~/.abinit/pseudos
          cp -r tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4 ~/.abinit/pseudos
          uv pip install .[strict,strict-forcefields,tests,abinit]
          uv pip install torch-runstats
          uv pip install --no-deps nequip==0.5.6

      - name: Install pymatgen from master if triggered by pymatgen repo dispatch
        if: github.event_name == 'repository_dispatch' && github.event.action == 'pymatgen-ci-trigger'
        run: |
          micromamba activate a2
          uv pip install --upgrade 'git+https://github.com/materialsproject/pymatgen@${{ github.event.client_payload.pymatgen_ref }}'

      - name: Forcefield tutorial
        env:
          MP_API_KEY: ${{ secrets.MP_API_KEY }}

        # regenerate durations file with `pytest --store-durations --durations-path tests/.pytest-split-durations`
        # Note the use of `--splitting-algorithm least_duration`.
        # This helps prevent a test split having no tests to run, and then the GH action failing, see:
        # https://github.com/jerry-git/pytest-split/issues/95
        # However this `splitting-algorithm` means that tests cannot depend sensitively on the order they're executed in.
        run: |
          micromamba activate a2
          pytest --nbmake ./tutorials/force_fields


      - uses: codecov/codecov-action@v1
        if: matrix.python-version == '3.10' && github.repository == 'materialsproject/atomate2'
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          name: coverage
          file: ./coverage.xml



  docs:
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v4

      - uses: actions/setup-python@v5
        with:
          python-version: "3.10"
          cache: pip
          cache-dependency-path: pyproject.toml

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install .[strict,strict-forcefields,docs]

      - name: Build
        run: sphinx-build docs docs_build

  automerge:
    needs: [lint, test-non-ase, test-notebooks-and-ase, test-force-field-notebook, docs]
    runs-on: ubuntu-latest

    permissions:
      pull-requests: write
      contents: write

    steps:
      - uses: fastify/github-action-merge-dependabot@v3