NeuroConv Docker CLI tests #71
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| name: NeuroConv Docker CLI tests | |
| on: | |
| schedule: | |
| - cron: "0 16 * * *" # Daily at noon EST | |
| workflow_dispatch: | |
| jobs: | |
| run: | |
| name: ${{ matrix.os }} Python ${{ matrix.python-version }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.12"] | |
| os: [ubuntu-latest] #, macos-latest, windows-latest] # Seems docker might only be available for ubuntu on GitHub Actions | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - run: git fetch --prune --unshallow --tags | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Global Setup | |
| run: python -m pip install -U pip # Official recommended way | |
| - name: Install pytest and neuroconv minimal | |
| run: | | |
| pip install pytest | |
| pip install . | |
| - name: Get ephy_testing_data current head hash | |
| id: ephys | |
| run: echo "::set-output name=HASH_EPHY_DATASET::$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)" | |
| - name: Cache ephys dataset - ${{ steps.ephys.outputs.HASH_EPHY_DATASET }} | |
| uses: actions/cache@v4 | |
| id: cache-ephys-datasets | |
| with: | |
| path: ./ephy_testing_data | |
| key: ephys-datasets-2023-06-26-${{ 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 - ${{ steps.ophys.outputs.HASH_OPHYS_DATASET }} | |
| uses: actions/cache@v4 | |
| id: cache-ophys-datasets | |
| with: | |
| path: ./ophys_testing_data | |
| key: ophys-datasets-2022-08-18-${{ 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 - ${{ steps.behavior.outputs.HASH_BEHAVIOR_DATASET }} | |
| uses: actions/cache@v4 | |
| id: cache-behavior-datasets | |
| with: | |
| path: ./behavior_testing_data | |
| key: behavior-datasets-2023-07-26-${{ 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: Pull docker image | |
| run: | | |
| docker pull ghcr.io/catalystneuro/neuroconv:latest | |
| docker pull ghcr.io/catalystneuro/neuroconv:yaml_variable | |
| - name: Run docker tests | |
| run: pytest tests/docker_yaml_conversion_specification_cli.py -vv -rsx |