push-tests.yml

name: Push Tests

on:
  pull_request:
    branches:
      - "*"
  push:
    branches:
      - "main"

env:
  CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

permissions:
  id-token: write
  contents: read

jobs:
  lint:
    runs-on: ubuntu-22.04
    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 2
      - uses: actions/setup-python@v5
      - name: lint checks
        uses: pre-commit/action@v3.0.1

  unit-test-ontology-builder:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout
        uses: actions/checkout@v4
        with:
          ref: ${{ github.event.pull_request.head.ref }}
      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: 3.11
      - name: Python cache
        uses: actions/cache@v4
        with:
          path: ~/.cache/pip
          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
          restore-keys: |
            ${{ runner.os }}-pip-
      - name: Install dependencies
        run: |
          cd ./tools/ontology-builder
          pip install -r requirements.txt
          pip install -r requirements-dev.txt
      - name: Ontology builder unit tests
        run: |
          cd tools/ontology-builder 
          make coverage/run
      - name: Upload coverage results as an artifact
        uses: actions/upload-artifact@v4
        with:
          name: coverage-builder
          path: /home/runner/work/cellxgene-ontology-guide/cellxgene-ontology-guide/.coverage*
          retention-days: 3
          include-hidden-files: true

  unit-test-python-api:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout
        uses: actions/checkout@v4
        with:
          ref: ${{ github.event.pull_request.head.ref }}
      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: 3.11
      - name: Python cache
        uses: actions/cache@v4
        with:
          path: ~/.cache/pip
          key: ${{ runner.os }}-pip-${{ hashFiles('**/api/python/pyproject.toml') }}
          restore-keys: |
            ${{ runner.os }}-pip-
      - name: Install dependencies
        run: |
          cd api/python
          make install-dev
      - name: Python API unit tests
        run: |
          cd api/python
          make coverage/run
      - name: Upload coverage results as an artifact
        uses: actions/upload-artifact@v4
        with:
          name: coverage-api
          path: /home/runner/work/cellxgene-ontology-guide/cellxgene-ontology-guide/.coverage*
          retention-days: 3
          include-hidden-files: true

  submit-codecoverage:
    needs:
      - unit-test-ontology-builder
      - unit-test-python-api
    runs-on: ubuntu-22.04
    steps:
      - uses: actions/checkout@v4
        with:
          ref: ${{ github.event.pull_request.head.ref }}
      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: 3.11
      - name: install coverage
        run: pip install coverage
      - uses: actions/download-artifact@v4
        with:
          pattern: coverage-*
          merge-multiple: true
          path: .
      - name: coverage report
        run: |
          make coverage/report-xml
      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v4
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          env_vars: OS,PYTHON
          files: ./coverage.xml
          flags: unittests
          name: codecov-umbrella

  test-doc-generation:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout
        uses: actions/checkout@v4
        with:
          ref: ${{ github.event.pull_request.head.ref }}
      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: 3.11
      - name: Python cache
        uses: actions/cache@v4
        with:
          path: ~/.cache/pip
          key: ${{ runner.os }}-pip-${{ hashFiles('**/api/python/pyproject.toml') }}
          restore-keys: |
            ${{ runner.os }}-pip-
      - name: Install dependencies
        run: |
          cd api/python
          make docs/install
      - name: Test pdoc
        run: |
          cd api/python
          make docs/build