166 using sopa as module in workflow leads to name error the name paths is unknown in this context #152
Workflow file for this run
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| name: ci | |
| on: | |
| push: | |
| branches: [master] | |
| tags: | |
| - v* | |
| pull_request: | |
| branches: [master, dev] | |
| jobs: | |
| pre-commit: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v3 | |
| - uses: pre-commit/[email protected] | |
| build: | |
| needs: [pre-commit] | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.10", "3.11.8"] | |
| steps: | |
| #---------------------------------------------- | |
| # check-out repo and set-up python | |
| #---------------------------------------------- | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Set up python ${{ matrix.python-version }} | |
| id: setup-python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| #---------------------------------------------- | |
| # install & configure poetry | |
| #---------------------------------------------- | |
| - name: Install Poetry | |
| uses: snok/install-poetry@v1 | |
| with: | |
| virtualenvs-create: true | |
| virtualenvs-in-project: true | |
| installer-parallel: true | |
| #---------------------------------------------- | |
| # load cached venv if cache exists | |
| #---------------------------------------------- | |
| - name: Load cached venv | |
| id: cached-poetry-dependencies | |
| uses: actions/cache@v3 | |
| with: | |
| path: .venv | |
| key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }} | |
| #---------------------------------------------- | |
| # install dependencies if cache does not exist | |
| #---------------------------------------------- | |
| - name: Install dependencies | |
| if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' | |
| run: poetry install --extras "dev cellpose snakemake" --no-interaction | |
| #---------------------------------------------- | |
| # perform tasks | |
| #---------------------------------------------- | |
| - name: Tests | |
| run: poetry run pytest | |
| - name: Snakemake | |
| run: cd workflow && poetry run snakemake --config sdata_path=tuto.zarr --configfile=config/toy/uniform_cellpose.yaml -c1 | |
| - name: Deploy doc | |
| if: contains(github.ref, 'tags') | |
| run: poetry run mkdocs gh-deploy --force | |
| publish: | |
| needs: [build] | |
| if: contains(github.ref, 'tags') | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Build and publish to pypi | |
| uses: JRubics/[email protected] | |
| with: | |
| python_version: "3.10" | |
| pypi_token: ${{ secrets.PYPI_TOKEN }} |