test.yml

name: Build and test

on: [push, pull_request]

permissions:
  contents: read

jobs:
  build:
    name: Build package
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python 3.11
        uses: actions/setup-python@v5
        with:
          python-version: "3.11"
      - name: Install pypa/build
        run: >-
          python3 -m
          pip install
          build
          --user
      - name: Build python package
        run: python3 -m build

  test:
    name: Build distribution and run tests
    runs-on: ubuntu-latest
    needs:
      - build

    strategy:
      matrix:
        python-version: ["3.10", "3.11", "3.12"]

    steps:
      - uses: actions/checkout@v4
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}

      - name: Install dependencies
        run: |
          pip install pytest pytest-cov pytest-mock pytest-datafiles
          pip install .

      - name: Install fork of CCP-EM pipeliner
        run: |
          git clone -b diamond_tomo --single-branch https://gitlab.com/stephen-riggs/ccpem-pipeliner.git
          pip install ./ccpem-pipeliner

      - name: Test with pytest
        run: |
          PYTHONDEVMODE=1 pytest -v -ra --cov=cryoemservices --cov-report=xml --cov-branch tests

      - name: Upload to Codecov
        uses: codecov/codecov-action@v4
        with:
          name: ${{ matrix.python-version }}
          files: coverage.xml
        env:
          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
        continue-on-error: true
        timeout-minutes: 2