Update BrukerTiffImagingExtractor
#61
Workflow file for this run
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| name: Full Tests | |
| on: | |
| schedule: | |
| - cron: "0 0 * * *" # daily | |
| pull_request: | |
| workflow_dispatch: | |
| jobs: | |
| run: | |
| name: Full tests on ${{ matrix.os }} with Python ${{ matrix.python-version }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: [3.8, 3.9, "3.10", 3.11] | |
| os: [ubuntu-latest, windows-latest, macos-latest] | |
| steps: | |
| - uses: s-weigand/setup-conda@v1 | |
| - uses: actions/checkout@v2 | |
| - run: git fetch --prune --unshallow --tags | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Global Setup | |
| run: | | |
| pip install -U pip | |
| pip install pytest-xdist | |
| git config --global user.email "[email protected]" | |
| git config --global user.name "CI Almighty" | |
| pip install wheel # needed for scanimage | |
| - name: Install roiextractors with minimal requirements | |
| run: pip install .[test] | |
| - name: Run minimal tests | |
| run: pytest tests/test_internals -n auto --dist loadscope | |
| - name: Test full installation (-e needed for codecov report) | |
| run: pip install -e .[full] | |
| - name: Get ophys_testing_data current head hash | |
| id: ophys | |
| run: echo "::set-output name=HASH_OPHYS_DATASET::$(git ls-remote https://gin.g-node.org/CatalystNeuro/ophys_testing_data.git HEAD | cut -f1)" | |
| - name: Cache ophys dataset - ${{ steps.ophys.outputs.HASH_OPHYS_DATASET }} | |
| uses: actions/cache@v2 | |
| id: cache-ophys-datasets | |
| with: | |
| path: ./ophys_testing_data | |
| key: ophys-datasets-042023-${{ matrix.os }}-${{ steps.ophys.outputs.HASH_OPHYS_DATASET }} | |
| - if: steps.cache-ophys-datasets.outputs.cache-hit == false | |
| name: Install and configure AWS CLI | |
| run: | | |
| pip install awscli==1.25.27 | |
| aws configure set aws_access_key_id ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| aws configure set aws_secret_access_key ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| - if: steps.cache-ophys-datasets.outputs.cache-hit == false | |
| name: Download data from S3 | |
| run: aws s3 cp --recursive s3://${{ secrets.S3_GIN_BUCKET }}//ophys_testing_data ./ophys_testing_data | |
| - name: Run full pytest with coverage | |
| run: pytest -n auto --dist loadscope --cov=./ --cov-report xml:./codecov.xml | |
| - if: ${{ matrix.python-version == '3.9' && matrix.os == 'ubuntu-latest'}} | |
| name: Upload full coverage to Codecov | |
| uses: codecov/codecov-action@v1 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./codecov.xml | |
| flags: unittests | |
| name: codecov-umbrella | |
| yml: ./codecov.yml |