Minimal and Full Tests #1349
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| name: Minimal and Full Tests | |
| on: | |
| schedule: | |
| - cron: "0 16 * * *" # Daily at noon EST | |
| workflow_call: | |
| secrets: | |
| AWS_ACCESS_KEY_ID: | |
| required: true | |
| AWS_SECRET_ACCESS_KEY: | |
| required: true | |
| S3_GIN_BUCKET: | |
| required: true | |
| workflow_dispatch: | |
| jobs: | |
| run: | |
| name: ${{ matrix.os }} 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, macos-latest, windows-latest] | |
| steps: | |
| - uses: s-weigand/setup-conda@v1 | |
| - uses: actions/checkout@v3 | |
| - run: git fetch --prune --unshallow --tags | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Global Setup | |
| run: | | |
| python -m pip install -U pip # Official recommended way | |
| pip install pytest-xdist | |
| git config --global user.email "CI@example.com" | |
| git config --global user.name "CI Almighty" | |
| pip install wheel # Needed for scan image | |
| - name: Install neuroconv with minimal requirements | |
| run: pip install .[test] | |
| - name: Run import tests | |
| run: | | |
| pytest tests/imports.py::TestImportStructure::test_top_level | |
| pytest tests/imports.py::TestImportStructure::test_tools | |
| pytest tests/imports.py::TestImportStructure::test_datainterfaces | |
| - name: Run minimal tests | |
| run: pytest tests/test_minimal -rsx -n auto --dist loadscope | |
| - name: Install with ecephys requirements | |
| run: pip install .[ecephys] | |
| - name: Run ecephys tests | |
| run: pytest tests/test_ecephys -rsx -n auto --dist loadscope | |
| - name: Install with ophys requirements | |
| run: pip install .[ophys] | |
| - name: Run ophys tests | |
| run: pytest tests/test_ophys -rsx -n auto --dist loadscope | |
| - name: Install with behavior requirements | |
| run: pip install .[behavior] | |
| - name: Run behavior tests | |
| run: pytest tests/test_behavior -rsx -n auto --dist loadscope | |
| - name: Install with icephys requirements | |
| run: pip install .[icephys] | |
| #- name: Run icephys tests # There are no icephys specific tests without data | |
| # run: pytest tests/test_icephys -rsx -n auto --dist loadscope | |
| - name: Install full requirements (-e needed for codecov report) | |
| run: pip install -e .[full] | |
| - name: Get ephy_testing_data current head hash | |
| id: ephys | |
| run: echo "::set-output name=HASH_EPHY_DATASET::$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)" | |
| - name: Cache ephys dataset - ${{ steps.ephys.outputs.HASH_EPHY_DATASET }} | |
| uses: actions/cache@v3 | |
| id: cache-ephys-datasets | |
| with: | |
| path: ./ephy_testing_data | |
| key: ephys-datasets-2023-06-26-${{ matrix.os }}-${{ steps.ephys.outputs.HASH_EPHY_DATASET }} | |
| - name: Get ophys_testing_data current head hash | |
| id: ophys | |
| run: echo "::set-output name=HASH_OPHYS_DATASET::$(git ls-remote https://gin.g-node.org/CatalystNeuro/ophys_testing_data.git HEAD | cut -f1)" | |
| - name: Cache ophys dataset - ${{ steps.ophys.outputs.HASH_OPHYS_DATASET }} | |
| uses: actions/cache@v3 | |
| id: cache-ophys-datasets | |
| with: | |
| path: ./ophys_testing_data | |
| key: ophys-datasets-2022-08-18-${{ matrix.os }}-${{ steps.ophys.outputs.HASH_OPHYS_DATASET }} | |
| - name: Get behavior_testing_data current head hash | |
| id: behavior | |
| run: echo "::set-output name=HASH_BEHAVIOR_DATASET::$(git ls-remote https://gin.g-node.org/CatalystNeuro/behavior_testing_data.git HEAD | cut -f1)" | |
| - name: Cache behavior dataset - ${{ steps.behavior.outputs.HASH_BEHAVIOR_DATASET }} | |
| uses: actions/cache@v3 | |
| id: cache-behavior-datasets | |
| with: | |
| path: ./behavior_testing_data | |
| key: behavior-datasets-2023-07-26-${{ matrix.os }}-${{ steps.behavior.outputs.HASH_behavior_DATASET }} | |
| - if: steps.cache-ephys-datasets.outputs.cache-hit != 'true' || steps.cache-ophys-datasets.outputs.cache-hit != 'true' || steps.cache-behavior-datasets.outputs.cache-hit != 'true' | |
| name: Install and configure AWS CLI | |
| run: | | |
| pip install awscli | |
| 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-ephys-datasets.outputs.cache-hit != 'true' | |
| name: Download ephys dataset from S3 | |
| run: aws s3 cp --recursive ${{ secrets.S3_GIN_BUCKET }}/ephy_testing_data ./ephy_testing_data | |
| - if: steps.cache-ophys-datasets.outputs.cache-hit != 'true' | |
| name: Download ophys dataset from S3 | |
| run: aws s3 cp --recursive ${{ secrets.S3_GIN_BUCKET }}/ophys_testing_data ./ophys_testing_data | |
| - if: steps.cache-behavior-datasets.outputs.cache-hit != 'true' | |
| name: Download behavior dataset from S3 | |
| run: aws s3 cp --recursive ${{ secrets.S3_GIN_BUCKET }}/behavior_testing_data ./behavior_testing_data | |
| - name: Run full pytest with coverage | |
| run: pytest -rsx -n auto --dist loadscope --cov=./ --cov-report xml:./codecov.xml | |
| - name: Upload full coverage to Codecov | |
| if: ${{ matrix.python-version == '3.9' && matrix.os == 'ubuntu-latest' }} | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./codecov.xml | |
| flags: unittests | |
| name: codecov-umbrella | |
| yml: ./codecov.yml |