New single-cell modules (and archiving old one) #3184
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python | |
| name: Test Python package | |
| on: | |
| push: | |
| branches: ["main"] | |
| pull_request: | |
| branches: ["main"] | |
| jobs: | |
| check-formatting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: psf/black@stable | |
| with: | |
| src: "proteobench" | |
| version: "~=23.0" | |
| lint-and-test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.11", "3.12", "3.13"] | |
| 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: | | |
| python -m pip install --upgrade pip | |
| python -m pip install flake8 flake8-bugbear flake8-comprehensions pytest | |
| # Install the web extra so the webinterface (streamlit) tests run instead of being skipped. | |
| python -m pip install .[web] | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Lint with flake8 plugins (bugbear, comprehensions) | |
| run: | | |
| # Non-blocking: report bugbear (B) and comprehensions (C4) issues as warnings | |
| flake8 proteobench --count --exit-zero --select=B,C4 --max-line-length=120 --statistics | |
| - name: Test with pytest | |
| run: | | |
| pytest | |
| - name: ensure paramater documentation is up-to-date | |
| run: | | |
| cd docs | |
| python parse_tables.py | |
| if git diff -- parsing_overview.tsv | grep .; then | |
| echo "Error: Parameters overview not updated, run in docs folder: python parse_tables.py" | |
| exit 1 | |
| fi | |
| - name: ensure module grid documentation is up-to-date | |
| run: | | |
| cd docs | |
| python generate_module_grid.py | |
| if git diff -- module_grid_generated.rst | grep .; then | |
| echo "Error: Module grid not updated, run in docs folder: python generate_module_grid.py" | |
| exit 1 | |
| fi | |
| - name: check if parse settings TOMLs changed | |
| id: toml_changed | |
| run: | | |
| if git diff --name-only origin/main...HEAD | grep -q 'io_parse_settings.*\.toml'; then | |
| echo "changed=true" >> $GITHUB_OUTPUT | |
| else | |
| echo "changed=false" >> $GITHUB_OUTPUT | |
| fi | |
| - name: ensure input files documentation tables are up-to-date | |
| if: steps.toml_changed.outputs.changed == 'true' | |
| run: | | |
| cd docs | |
| python generate_input_tables.py | |
| if git diff -- modules/dda/*.md modules/dia/*.md | grep .; then | |
| echo "Error: Input files tables not updated, run: cd docs && python generate_input_tables.py" | |
| exit 1 | |
| fi | |
| - name: check contributing-institutes logo symlink | |
| run: bash scripts/check_contributing_institutes_symlink.sh | |