Add compatibility for urls in generate_inputs
#1165
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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://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Test workflow | |
| on: | |
| push: | |
| branches: | |
| - '*' | |
| - '!push-action/*' | |
| pull_request: | |
| branches: | |
| - '*' | |
| - '!push-action/*' | |
| paths: | |
| - snakebids/** | |
| - scripts/** | |
| jobs: | |
| quality: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Install | |
| uses: khanlab/actions/.github/actions/[email protected] | |
| with: | |
| python-version: '3.11' | |
| install-library: true | |
| # run python style checks | |
| - name: Poetry Lock Check | |
| run: poetry check --lock | |
| # Check that running update-bids doesn't change any files | |
| - name: update-bids check | |
| run: | | |
| poetry run poe update-bids | |
| git diff --quiet || ( | |
| git diff | |
| echo 'bids specs out of date, run `poetry run poe update-bids`' | |
| exit 1 | |
| ) | |
| - name: Formatting | |
| run: poetry run ruff format snakebids --check | |
| - name: Linting | |
| run: poetry run ruff check snakebids | |
| - name: pyright | |
| run: poetry run pyright snakebids | |
| build-cache-env: | |
| runs-on: ubuntu-latest | |
| needs: [ 'quality' ] | |
| strategy: | |
| matrix: | |
| python-version: ['3.8', '3.9', '3.10', '3.11', '3.12'] | |
| steps: | |
| - uses: khanlab/actions/.github/actions/[email protected] | |
| id: setup | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: setup docker | |
| uses: ./.github/actions/build-test-container | |
| with: | |
| python-version: ${{ steps.setup.outputs.python-version }} | |
| test: | |
| runs-on: ubuntu-latest | |
| needs: [ 'build-cache-env' ] | |
| strategy: | |
| matrix: | |
| python-version: ['3.8', '3.9', '3.10', '3.11', '3.12'] | |
| split: ['1', '2', '3', '4', '5'] | |
| fail-fast: false | |
| steps: | |
| - name: install | |
| uses: khanlab/actions/.github/actions/[email protected] | |
| id: setup | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| install-library: true | |
| - name: build docker test container | |
| uses: ./.github/actions/build-test-container | |
| with: | |
| python-version: ${{ steps.setup.outputs.python-version }} | |
| load: true | |
| - name: Test with pytest | |
| env: | |
| HYPOTHESIS_PROFILE: pr | |
| run: >- | |
| poetry run pytest -n auto --splits 5 --group ${{ matrix.split }} | |
| --cov=snakebids --cov-report=xml | |
| --doctest-modules --ignore=docs | |
| --ignore=snakebids/project_template --benchmark-disable | |
| - name: save coverage report | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-${{ matrix.python-version }}-${{ matrix.split }} | |
| path: ./coverage.xml | |
| upload_coverage: | |
| runs-on: ubuntu-latest | |
| needs: [ test ] | |
| steps: | |
| - name: checkout repository | |
| uses: actions/checkout@v4 | |
| - name: download coverage reports | |
| uses: actions/download-artifact@v4 | |
| with: | |
| pattern: coverage-* | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| verbose: true | |
| fail_ci_if_error: true | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} |