openfe/.github/workflows/ci.yaml

name: "CI"
on:
  pull_request:
    branches:
      - main
   # Skip CI if changed files only affect the following folders
   # - docs: documentation changes don't need code validation
   # See here for more details: https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#example-excluding-paths
    paths-ignore:
      - "docs/*"
      - ".readthedocs.yaml"
  push:
    branches:
      - main
  schedule:
    - cron: "0 4 * * *"
  workflow_dispatch:
  release:
    types:
      - published

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

defaults:
  run:
    shell: bash -leo pipefail {0}

jobs:
  tests:
    runs-on: ${{ matrix.os }}
    name: "💻-${{matrix.os }} 🐍-${{ matrix.python-version }} oechem: ${{ matrix.openeye }}"
    strategy:
      fail-fast: false
      matrix:
        os: ["ubuntu-latest", "macos-latest"]
        python-version:
          - "3.11"
          - "3.12"
          - "3.13"
        openeye: ["no"]
        include: # NOTE: openeye does not yet support 3.13.
          - os: "ubuntu-latest"
            python-version: "3.11"
            openeye: "yes"
          - os: "macos-latest"
            python-version: "3.12"
            openeye: "yes"

    env:
      OE_LICENSE: ${{ github.workspace }}/oe_license.txt

    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0

      - name: Get current date
        id: date
        run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}"

      - name: "Setup Micromamba"
        uses: mamba-org/setup-micromamba@v2
        with:
          environment-file: environment.yml
          environment-name: openfe_env
          cache-environment: true
          cache-downloads: true
          cache-environment-key: environment-${{ steps.date.outputs.date }}
          cache-downloads-key: downloads-${{ steps.date.outputs.date }}
          create-args: >-
            python=${{ matrix.python-version }}
            pydantic=${{ matrix.pydantic-version }}
          init-shell: bash

      - name: "Install OpenEye"
        if: ${{ !github.event.pull_request.head.repo.fork
                && matrix.openeye == 'yes' }}
        env:
          OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }}
        run: |
          echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE}
          micromamba install -c openeye openeye-toolkits
          python -c "import openeye; assert openeye.oechem.OEChemIsLicensed(), 'oechem license check failed!'"

      - name: "Install"
        run: python -m pip install --no-deps -e .

      - name: "Environment Information"
        run: |
          micromamba info
          micromamba list
          pip list

      - name: "Test imports"
        run: |
          # if we add more to this, consider changing to for + env vars
          python -Ic "import openfe; print(openfe.__version__)"

      - name: "Run tests"
        env:
          # Set the OFE_SLOW_TESTS to True if running a Cron job
          OFE_SLOW_TESTS: ${{ fromJSON('{"false":"false","true":"true"}')[github.event_name != 'pull_request'] }}
          DUECREDIT_ENABLE: 'yes'
        run: |
          pytest -n auto -v --cov=openfe --cov=openfecli --cov-report=xml --durations=10

      - name: codecov-pr
        if: ${{ github.repository == 'OpenFreeEnergy/openfe'
                && github.event_name == 'pull_request' }}
        uses: codecov/codecov-action@v4
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          file: coverage.xml
          fail_ci_if_error: False
          verbose: True
          flags: fast-tests

      - name: codecov-merge
        # we only want to upload a slow report if
        # 1) it isn't a schedule run
        # 2) it wasn't from a PR (we don't run slow tests on PRs)
        if: ${{ github.repository == 'OpenFreeEnergy/openfe'  
                && github.event_name != 'schedule'            
                && github.event_name != 'pull_request' }}     
        uses: codecov/codecov-action@v4
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          file: coverage.xml
          fail_ci_if_error: False
          verbose: True
          flags: slow-tests