Minor bugfix #63
Workflow file for this run
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| # Workflow to build nii2dcm, run unit tests and then execute command line interface (CLI) end-to-end | |
| name: Build & Test nii2dcm | |
| on: | |
| pull_request: | |
| jobs: | |
| venv-build-and-test: | |
| name: venv + E2E | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ ubuntu-latest ] | |
| python-version: [ '3.9' ] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Python packages | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install setuptools wheel | |
| pip install flake8 pytest pytest-cov | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| - name: Display installed pip packages | |
| run: | | |
| pip list | |
| - name: Setup flake8 annotations | |
| uses: rbialon/flake8-annotations@v1 | |
| - 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: Build nii2dcm | |
| run: | | |
| pip install . | |
| - name: Test nii2dcm install | |
| run: | | |
| nii2dcm -h | |
| nii2dcm -v | |
| - name: Run unit tests | |
| run: | | |
| pytest tests/ | |
| - name: Test DicomMRISVR creation | |
| run: | | |
| # run nii2dcm | |
| mkdir output | |
| nii2dcm tests/data/DicomMRISVR/t2-svr-atlas-35wk.nii.gz ./output -d SVR | |
| ls ./output | |
| # assert DICOM files exist | |
| [ -f "./output/IM_0001.dcm" ] && echo "Output DICOM file exists" || exit 1 | |
| - name: Build pytest coverage file | |
| run: | | |
| pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=nii2dcm tests/ | tee pytest-coverage.txt ; echo $? | |
| - name: Pytest coverage comment | |
| id: coverageComment | |
| uses: MishaKav/pytest-coverage-comment@main | |
| with: | |
| pytest-coverage-path: ./pytest-coverage.txt | |
| junitxml-path: ./pytest.xml | |
| - name: Update Coverage Badge | |
| uses: schneegans/dynamic-badges-action@v1.7.0 | |
| with: | |
| auth: ${{ secrets.PYTEST_COVERAGE_COMMENT }} | |
| gistID: 57ef8057d04f67dbe6e64df410b83079 | |
| filename: nii2dcm-pytest-coverage-comment.json | |
| label: Coverage Report | |
| message: ${{ steps.coverageComment.outputs.coverage }} | |
| color: ${{ steps.coverageComment.outputs.color }} | |
| namedLogo: python | |
| container-build-and-test: | |
| name: Container | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ ubuntu-latest ] | |
| python-version: [ '3.9' ] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Build container | |
| run: | | |
| docker build -t nii2dcm --progress=plain --no-cache . | |
| docker ps | |
| - name: Test nii2dcm container | |
| run: | | |
| docker run nii2dcm -h | |
| echo "nii2dcm version:" | |
| docker run nii2dcm -v |