ci.yaml

name: CI
run-name: "${{ github.event_name }}: ${{ github.ref }}"

on:
  push:
  pull_request:
    branches:
      - "master"
  schedule:
    - cron: "0 3 * * 1"  # weekly on Monday
  workflow_dispatch:

jobs:
  test:
    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [macOS-latest, ubuntu-latest]
        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
    env:
      CI_OS: ${{ matrix.os }}
      PYVER: ${{ matrix.python-version }}
      PACKAGE: "opencadd"

    steps:
      - uses: actions/checkout@v4

      - name: Additional info about the build
        shell: bash
        run: |
          uname -a
          df -h
          ulimit -a

      - name: 'Setup conda environment'
        uses: mamba-org/setup-micromamba@v1
        with:
          create-args: python=${{ matrix.python-version }}
          environment-file: devtools/conda-envs/test_env.yaml
          micromamba-version: latest
          generate-run-shell: true
          init-shell: bash
          condarc: |
            channels:
              - conda-forge
              - defaults
              - bioconda

      # TODO: Remove this step when patched theseus makes it to CF
      - name: Build patched mmligner
        shell: micromamba-shell {0}
        run: |
          micromamba install conda-build
          conda build devtools/conda-recipes/mmligner/

      - name: Install package
        shell: micromamba-shell {0}
        run: |
          micromamba install -c local mmligner pip
          python -m pip install . --no-deps
          micromamba list

      - name: Run tests
        shell: micromamba-shell {0}
        run: |
          pytest -v --cov=${PACKAGE} --cov-report=xml --color=yes ${PACKAGE}/tests/

      - name: CodeCov
        if: github.event_name == 'push' && github.ref_name == 'master'
        uses: codecov/codecov-action@v1
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          file: ./coverage.xml
          flags: unittests
          yml: ./.codecov.yml

  #############
  lint-format:
    runs-on: ubuntu-latest
    env:
      PACKAGE: "opencadd"

    steps:
      - name: Checkout the code
        uses: actions/checkout@v4

      - name: 'Setup Python'
        uses: actions/setup-python@v5
        with:
          python-version: '3.x'

      - name: Install linter and formatter
        run: |
          python -m pip install pylint black

      - name: Run pylint
        run: pylint $PACKAGE/

      - name: Run black check
        if: always()
        run: black --check -l 99 $PACKAGE/