Adding annotation of potential doublets to anndata obs #822
Workflow file for this run
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#schema: https://github.com/softprops/github-actions-schemas/blob/master/workflow.json | |
name: "Test" | |
on: | |
push: | |
branches: [main, dev] | |
pull_request: | |
branches: [main, dev] | |
workflow_dispatch: | |
permissions: | |
id-token: write | |
actions: write | |
contents: read | |
packages: write | |
env: | |
ANNOY_COMPILER_ARGS: "-DANNOYLIB_MULTITHREADED_BUILD,-mno-avx512f" | |
jobs: | |
pre_job: | |
continue-on-error: true | |
runs-on: ubuntu-latest | |
# Map a step output to a job output | |
outputs: | |
should_skip: ${{ steps.skip_check.outputs.should_skip }} | |
paths_result: ${{ steps.skip_check.outputs.paths_result }} | |
steps: | |
- id: skip_check | |
uses: fkirc/skip-duplicate-actions@v5 | |
if: ${{ !github.event.act }} | |
with: | |
concurrent_skipping: "same_content_newer" | |
skip_after_successful_duplicate: "true" | |
do_not_skip: '["workflow_dispatch"]' | |
paths_filter: | | |
python: | |
paths: | |
- 'pyproject.toml' | |
- 'poetry.lock' | |
- 'src/pixelator/**' | |
- 'tests/**' | |
paths_ignore: | |
- 'tests/**/*.md' | |
test: | |
name: Test - python ${{ matrix.py }} | |
if: needs.pre_job.outputs.should_skip == '{}' || !fromJSON(needs.pre_job.outputs.paths_result).python.should_skip | |
runs-on: ubuntu-latest | |
needs: [pre_job] | |
strategy: | |
fail-fast: false | |
matrix: | |
py: | |
- "3.11" | |
- "3.10" | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Set up Python environment | |
uses: ./.github/actions/setup-python | |
with: | |
python-version: ${{ matrix.py }} | |
- uses: supplypike/setup-bin@v3 | |
with: | |
uri: 'https://opengene.org/fastp/fastp' | |
name: 'fastp' | |
version: '0.23.4' | |
- name: Install and configure Poetry | |
uses: snok/install-poetry@v1 | |
- name: Install tox | |
run: python -m pip install tox-gh>=1.2 | |
- name: Setup test suite | |
run: tox -vv --notest | |
- name: Run test suite | |
run: tox --skip-pkg-install | |
test-coverage: | |
name: "Check the test coverage" | |
runs-on: ubuntu-latest | |
needs: | |
- pre_job | |
if: needs.pre_job.outputs.should_skip == '{}' || !fromJSON(needs.pre_job.outputs.paths_result).python.should_skip | |
steps: | |
- name: Checkout | |
uses: actions/checkout@v4 | |
- name: Set up Python environment | |
uses: ./.github/actions/setup-python | |
with: | |
python-version: "3.11" | |
- name: Install and configure Poetry | |
uses: snok/install-poetry@v1 | |
- name: Install dependencies | |
run: | | |
poetry install --with dev | |
- name: Run test suite | |
run: | | |
poetry run pytest --cov=src/ | |
- name: Upload coverage reports to Codecov | |
uses: codecov/codecov-action@v3 | |
env: | |
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
test-workflow: | |
name: Test small workflow - ${{ matrix.case }} | |
runs-on: ubuntu-latest | |
needs: [ pre_job ] | |
strategy: | |
fail-fast: false | |
matrix: | |
case: | |
- mpx_v1 | |
- mpx_v2 | |
if: needs.pre_job.outputs.should_skip == '{}' || !fromJSON(needs.pre_job.outputs.paths_result).python.should_skip | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Set up Python environment | |
uses: ./.github/actions/setup-python | |
with: | |
python-version: "3.11" | |
- uses: supplypike/setup-bin@v3 | |
with: | |
uri: 'https://opengene.org/fastp/fastp' | |
name: 'fastp' | |
version: '0.23.2' | |
- name: Install and configure Poetry | |
uses: snok/install-poetry@v1 | |
- name: Install dependencies | |
run: | | |
poetry install --with dev | |
- name: Run workflow tests | |
run: | | |
poetry run pytest -s -m "workflow_test" --basetemp=/tmp/pytest-results tests/integration/test_small_${{ matrix.case }}.yaml --log-cli-level=DEBUG |