ENH: Add an additional environment to tox to run notebooks
#200
Workflow file for this run
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| name: Unit and integration tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - maint/* | |
| pull_request: | |
| branches: | |
| - main | |
| - maint/* | |
| # Allow job to be triggered manually from GitHub interface | |
| workflow_dispatch: | |
| defaults: | |
| run: | |
| shell: bash | |
| # Force tox and pytest to use color | |
| env: | |
| FORCE_COLOR: true | |
| TEST_DATA_HOME: /home/runner/eddymotion-tests/ | |
| ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS: 4 | |
| ANTSPATH: /usr/share/miniconda/bin/ | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| permissions: | |
| contents: read | |
| jobs: | |
| stable: | |
| # Unit tests only on Linux/Python 3.12 | |
| runs-on: 'ubuntu-latest' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| - name: Install ANTs | |
| run: | | |
| conda install -c conda-forge ants=2.5 | |
| - name: Install datalad | |
| run: | | |
| python -m pip install datalad-installer | |
| datalad-installer --sudo ok git-annex | |
| python -m pip install datalad datalad-osf | |
| datalad wtf | |
| - uses: actions/cache/restore@v4 | |
| with: | |
| path: /home/runner/eddymotion-tests/ | |
| key: data-v0 | |
| - name: Get test data with DataLad | |
| run: | | |
| if [[ ! -d "${TEST_DATA_HOME}" ]]; then | |
| datalad install -rg --source=https://gin.g-node.org/nipreps-data/tests-eddymotion.git ${TEST_DATA_HOME} | |
| else | |
| cd ${TEST_DATA_HOME} | |
| datalad update --merge -r . | |
| datalad get -r -J4 * | |
| fi | |
| - uses: actions/cache/save@v4 | |
| with: | |
| path: /home/runner/eddymotion-tests/ | |
| key: data-v0 | |
| - name: Install tox | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install tox tox-gh-actions | |
| - name: Show tox config | |
| run: tox c | |
| - name: Run tox | |
| run: | | |
| export PATH=$ANTSPATH:$PATH | |
| tox -v --exit-and-dump-after 1200 | |
| - uses: codecov/codecov-action@v4 | |
| if: ${{ always() }} | |
| with: | |
| files: cov.xml | |
| token: ${{ secrets.CODECOV_TOKEN }} |