Address change in pandas 2.x value_counts(). #108
Workflow file for this run
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| name: GitHub Actions | |
| on: | |
| push: | |
| branches: | |
| - master | |
| paths-ignore: | |
| - '**.md' | |
| pull_request: | |
| branches: | |
| - master | |
| paths-ignore: | |
| - '**.md' | |
| workflow_dispatch: | |
| # manually trigger workflow with a boolean value indicating whether to use the | |
| # SimpleITK package from test PyPi (pre-release testing) | |
| inputs: | |
| testPyPi: | |
| description: 'Use test PyPi?' | |
| required: true | |
| type: boolean | |
| schedule: | |
| # run testing on the first of each month 5am ET / 9am UTC | |
| - cron: '0 9 1 * *' | |
| concurrency: | |
| group: ci-${{ github.head_ref || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.9 | |
| - 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: | |
| os: [macos-latest, windows-latest] | |
| python-version: ['3.8', '3.10'] | |
| inputs: ["00_ or 01_ or 02_ or 03_ or 04_ or 05_ or 10_ or 20_ or 21_ or 22_ or 300_ or 30_ or 31_ or 32_ or 33_ or 34_ or 35_ or 36_", "51_ or 55_ or 56_ or 60_ or 61_ or 62_ or 63_ or 64_ or 65_ or 66_ or 67_ or 68_ or 69_ or 70_ or 71_" | |
| ] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/cache@v3 | |
| id: cache | |
| with: | |
| path: | | |
| Data | |
| key: notebook-data-${{ hashFiles('Data/manifest.json') }} | |
| restore-keys: | | |
| notebook-data-${{ hashFiles('Data/manifest.json') }} | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| 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: Install SimpleITK from test PyPi from manually launched workflow | |
| if: ${{ inputs.testPyPi }} | |
| run: pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple SimpleITK | |
| - name: Download data | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: python Utilities/downloaddata.py Data/ Data/manifest.json | |
| - name: run the test | |
| env: | |
| SIMPLE_ITK_MEMORY_CONSTRAINED_ENVIRONMENT: 1 | |
| run: | | |
| pytest -v --tb=short -k "${{matrix.inputs}}" tests/test_notebooks.py::Test_notebooks::test_python_notebook | |
| pytest -v --tb=short tests/test_scripts.py |