fix(devop): code coverage failing #2698
Workflow file for this run
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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/[email protected] | |
- 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 | |
include-hidden-files: true | |
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 | |
include-hidden-files: true | |
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 | |
include-hidden-files: true | |
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 | |
include-hidden-files: true | |
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: | |
token: ${{ secrets.CODECOV_TOKEN }} | |
env_vars: OS,PYTHON | |
files: ./coverage.xml | |
flags: unittests | |
name: codecov-umbrella |