FIX: Re-add run entity to electrodes.tsv (#1722) #1
Workflow file for this run
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| name: "schemacode_ci" | |
| on: | |
| push: | |
| branches: | |
| - "master" | |
| tags: | |
| - "schema-*" | |
| pull_request: | |
| branches: | |
| - "*" | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.11"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: "Install build dependencies" | |
| run: pip install --upgrade build twine | |
| - name: "Install test dependencies on tag" | |
| run: pip install --upgrade pytest pyyaml pandas tabulate markdown-it-py pyparsing | |
| if: ${{ startsWith(github.ref, 'refs/tags/schema-') }} | |
| - name: "Build archive on tag" | |
| run: pytest tools/schemacode/bidsschematools -k make_archive | |
| env: | |
| BIDSSCHEMATOOLS_RELEASE: 1 | |
| if: ${{ startsWith(github.ref, 'refs/tags/schema-') }} | |
| - name: "Build source distribution and wheel" | |
| run: python -m build tools/schemacode | |
| - name: "Check distribution metadata" | |
| run: twine check tools/schemacode/dist/* | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: dist | |
| path: tools/schemacode/dist/ | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| needs: [build] | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] | |
| include: | |
| - os: macos-latest | |
| python-version: 3 | |
| - os: windows-latest | |
| python-version: 3 | |
| name: ${{ matrix.os }} with Python ${{ matrix.python-version }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: "Set up Python" | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| allow-prereleases: true | |
| - name: "Display Python version" | |
| run: python -c "import sys; print(sys.version)" | |
| - name: "Fetch packages" | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: dist | |
| path: dist/ | |
| - name: "Install package" | |
| run: | | |
| pip install $( ls dist/*.whl )[all] | |
| - name: "Run tests" | |
| run: | | |
| python -m pytest -vs --pyargs bidsschematools -m "not validate_schema" \ | |
| --cov-append --cov-report=xml --cov=bidsschematools --doctest-modules | |
| - name: Upload artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: unit_${{ matrix.os }}_${{ matrix.python-version }} | |
| path: coverage.xml | |
| if: success() | |
| publish: | |
| runs-on: ${{ matrix.os }} | |
| name: Publish Python Package | |
| needs: [test] | |
| if: github.event_name == 'push' | |
| strategy: | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.11"] | |
| steps: | |
| - name: "Fetch packages" | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: dist | |
| path: dist/ | |
| - name: "Test PyPI upload" | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.TEST_PYPI_API_TOKEN }} | |
| repository_url: https://test.pypi.org/legacy/ | |
| skip_existing: true | |
| - name: "Upload to PyPI (on tags)" | |
| if: startsWith(github.ref, 'refs/tags/schema-') | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} | |
| validate_schema: | |
| runs-on: ubuntu-latest | |
| name: Validate schema | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set Up Python environment | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install the schemacode package | |
| run: | | |
| python -m pip install --progress-bar off --upgrade pip setuptools wheel | |
| python -m pip install -e ./tools/schemacode[all] | |
| - name: Run schema validation tests | |
| run: python -m pytest --pyargs bidsschematools -m "validate_schema" --cov-append --cov-report=xml --cov=bidsschematools | |
| - name: Upload artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: schema_validation | |
| path: coverage.xml | |
| if: success() | |
| upload_to_codecov: | |
| runs-on: "ubuntu-latest" | |
| name: Upload coverage | |
| needs: [test, validate_schema] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Download artifacts | |
| uses: actions/download-artifact@v4 | |
| - name: Upload to CodeCov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} # not required but might help API rate limits | |
| fail_ci_if_error: true |