refactor: move UMI methods to platform/illumina.py #697
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Python package | |
| on: [push] | |
| env: | |
| POETRY_VERSION: 1.5 | |
| jobs: | |
| testing: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| PYTHON_VERSION: ["3.8", "3.9", "3.10", "3.11", "3.12"] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{matrix.PYTHON_VERSION}} | |
| uses: actions/setup-python@v1 | |
| with: | |
| python-version: ${{matrix.PYTHON_VERSION}} | |
| - name: Get full Python version | |
| id: full-python-version | |
| shell: bash | |
| run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))") | |
| - name: Install poetry | |
| shell: bash | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install poetry==${{env.POETRY_VERSION}} | |
| - name: Configure poetry | |
| shell: bash | |
| run: poetry config virtualenvs.in-project true | |
| - name: Set up cache | |
| uses: actions/cache@v2 | |
| id: cache | |
| with: | |
| path: .venv | |
| key: venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('**/poetry.lock') }} | |
| - name: Ensure cache is healthy | |
| if: steps.cache.outputs.cache-hit == 'true' | |
| shell: bash | |
| run: poetry run pip --version >/dev/null 2>&1 || rm -rf .venv | |
| - name: Check that the lock file is up to date | |
| shell: bash | |
| run: | | |
| poetry lock --check | |
| - name: Install deps | |
| shell: bash | |
| run: | | |
| poetry install --extras docs | |
| - name: Run pytest | |
| shell: bash | |
| run: | | |
| poetry run python -m pytest --cov=fgpyo --cov-report=xml --cov-branch | |
| - name: Run isort | |
| shell: bash | |
| run: | | |
| poetry run isort --force-single-line-imports --profile black fgpyo | |
| - name: Style checking | |
| shell: bash | |
| run: | | |
| poetry run black --line-length 99 --check fgpyo | |
| - name: Run lint | |
| shell: bash | |
| run: | | |
| poetry run flake8 --config=ci/flake8.cfg fgpyo | |
| - name: Run mypy | |
| shell: bash | |
| run: | | |
| poetry run mypy -p fgpyo --config=ci/mypy.ini | |
| - name: Run docs | |
| shell: bash | |
| run: | | |
| set -euo pipefail | |
| pushd docs | |
| poetry run make html | |
| popd | |
| - name: Upload code coverage | |
| uses: codecov/codecov-action@v2.1.0 |