Adding function for overlaying multiple segmentations onto image. #182
Workflow file for this run
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| name: Main Testing | |
| on: | |
| push: | |
| branches: | |
| - master | |
| paths-ignore: | |
| - '**.md' | |
| pull_request: | |
| branches: | |
| - master | |
| paths-ignore: | |
| - '**.md' | |
| concurrency: | |
| group: ci-${{ github.head_ref || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.10' | |
| - name: Install and run black for notebooks | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install black[jupyter] | |
| black --check --diff --verbose Python | |
| test: | |
| needs: lint | |
| strategy: | |
| matrix: #using macos-13 because pyenchant doesn't work on macos-latest (macos 14, arm64 architecture) | |
| os: [macos-13, windows-latest, ubuntu-latest] | |
| python-version: ['3.8', '3.11'] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # fetch all history for all branches, required for the changed-files action | |
| - uses: actions/cache@v4 | |
| id: cache | |
| with: | |
| path: | | |
| Data | |
| key: notebook-data-${{ hashFiles('Data/manifest.json') }} | |
| restore-keys: | | |
| notebook-data-${{ hashFiles('Data/manifest.json') }} | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| # on windows, the pyenchant package includes enchant | |
| - name: Install enchant on non windows systems | |
| shell: bash | |
| run: | | |
| if [ "$RUNNER_OS" == "Linux" ]; then | |
| sudo apt-get update | |
| sudo apt-get install enchant-2 | |
| elif [ "$RUNNER_OS" == "macOS" ]; then | |
| brew update-reset | |
| brew install enchant | |
| fi | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install -r requirements_dev.txt | |
| - name: Download data | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: python Utilities/downloaddata.py Data/ Data/manifest.json | |
| - name: Get list of Python notebooks to test | |
| id: nbl | |
| uses: tj-actions/changed-files@v45 | |
| with: | |
| files: Python/*.ipynb | |
| - name: Run the notebooks test | |
| shell: bash | |
| if: steps.nbl.outputs.any_changed == 'true' | |
| env: | |
| SIMPLE_ITK_MEMORY_CONSTRAINED_ENVIRONMENT: 1 | |
| run: | | |
| test_files="${{ steps.nbl.outputs.all_changed_files }}" | |
| # on windows the paths use backslashes, so replace with forward slashes | |
| if [ "$RUNNER_OS" == "Windows" ]; then | |
| test_files="${test_files//\\//}" | |
| fi | |
| for nb_file in ${test_files}; do | |
| # the substring contains the file paths, extract the basename for usage with pytest | |
| pytest -v --tb=short tests/test_notebooks.py::Test_notebooks::test_python_notebook["${nb_file##*/}"] | |
| done | |
| - name: Run the scripts test | |
| env: | |
| SIMPLE_ITK_MEMORY_CONSTRAINED_ENVIRONMENT: 1 | |
| run: | | |
| pytest -v --tb=short tests/test_scripts.py |