push_tests.yml

name: Push tests

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

jobs:

  lint:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout
        uses: actions/checkout@v4
        with:
          ref: ${{ github.event.pull_request.head.ref }}
      - uses: actions/setup-python@v5
      - name: Pre-commit checks
        uses: pre-commit/action@v3.0.1
      - name: Install dependencies
        run: |
          pip install -r ./requirements-dev.txt
      # We can't have mypy in the pre-commit hook without having it run on all files
      # in the repo, because (probably) the --all-files argument in pre-commit overrides
      # the more narrow specifying of files in pyproject.toml
      # TODO: Remove this if/when all files are mypy-compliant
      - name: Run mypy
        run: |
          mypy --config-file pyproject.toml

  unit-tests-cli:
    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: "3.10"
      - 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: |
          pip install -r ./requirements-dev.txt
          pip install -e ./cellxgene_schema_cli
      - name: cellxgene_schema_cli Unit tests
        run: make unit-test
      - name: Upload coverage results as an artifact
        uses: actions/upload-artifact@v4
        with:
          name: coverage-cli
          path: ./.coverage*
          retention-days: 3

  unit-tests-migration-assistant:
    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: "3.10"
      - 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: |
          pip install -r scripts/migration_assistant/requirements.txt
          pip install -r ./requirements-dev.txt
      - name: migration_assistant Unit tests
        run: make migration-assistant-tests
      - name: Upload coverage results as an artifact
        uses: actions/upload-artifact@v4
        with:
          name: coverage-migration-assisstant
          path: ./.coverage*
          retention-days: 3

  unit-test-ontology-dry-run:
    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: "3.10"
      - 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: |
          pip install -r scripts/schema_bump_dry_run_ontologies/requirements.txt
          pip install -r ./requirements-dev.txt
      - name: Ontology Dry Run Unit Tests
        run: make ontology-dry-run-tests
      - name: Upload coverage results as an artifact
        uses: actions/upload-artifact@v4
        with:
          name: coverage-ontology-dry-run
          path: ./.coverage*
          retention-days: 3

  unit-test-genes-dry-run:
    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: "3.10"
      - 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: |
          pip install -r scripts/schema_bump_dry_run_genes/requirements.txt
          pip install -r ./requirements-dev.txt
      - name: Gene Dry Run Unit Tests
        run: make gene-dry-run-tests
      - name: Upload coverage results as an artifact
        uses: actions/upload-artifact@v4
        with:
          name: coverage-genes-dry-run
          path: ./.coverage*
          retention-days: 3

  submit-codecoverage:
    needs:
      - unit-test-genes-dry-run
      - unit-test-ontology-dry-run
      - unit-tests-migration-assistant
      - unit-tests-cli
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0
          ref:
            ${{ github.event.pull_request.head.ref }}
      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: '3.10'
      - name: Install dependencies
        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:
          env_vars: OS,PYTHON
          files: ./coverage.xml
          flags: unittests
          name: codecov-umbrella