Apply suggestions from code review #617
Workflow file for this run
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| name: python | |
| on: | |
| push: | |
| pull_request: | |
| branches: | |
| - main | |
| - switch-phantoms-to-s3 | |
| workflow_call: | |
| workflow_dispatch: | |
| inputs: | |
| debug_enabled: | |
| type: boolean | |
| description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)' | |
| required: false | |
| default: false | |
| jobs: | |
| Python-Collect-Data-and-Test: | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| REAL_ECAT_TEST_PATH: ${{ github.workspace }}/OpenNeuroPET-Phantoms/sourcedata/SiemensHRRT-JHU/Hoffman.v | |
| SMALLER_ECAT_PATH: ${{ github.workspace }}/ecat_validation/ECAT7_multiframe.v.gz | |
| TEST_ECAT_PATH: ${{ github.workspace }}/ecat_validation/ECAT7_multiframe.v | |
| OUTPUT_NIFTI_PATH: ${{ github.workspace}}/pypet2bids/tests/ECAT7_multiframe.nii | |
| READ_ECAT_SAVE_AS_MATLAB: ${{ github.workspace }}/pypet2bids/tests/ECAT7_multiframe.mat | |
| NIBABEL_READ_ECAT_SAVE_AS_MATLAB: ${{ github.workspace }}/pypet2bids/tests/ECAT7_multiframe.nibabel.mat | |
| MATLAB_CODE_PATH: ${{ github.workspace }}/matlab/ | |
| strategy: | |
| matrix: | |
| os: [macOS-latest, ubuntu-latest] | |
| python: ['3.8', '3.9', '3.10'] | |
| steps: | |
| - name: Checkout Repo | |
| uses: actions/checkout@v2 | |
| - name: Cache Phantoms | |
| id: cache-phantoms | |
| uses: actions/cache@v2 | |
| with: | |
| path: US-sourced-OpenNeuroPET-Phantoms.zip | |
| key: ${{ runner.os }}-phantoms | |
| - name: Set up python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - name: Install dependencies | |
| if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' | |
| run: | | |
| cd pypet2bids | |
| python -m pip install --upgrade pip | |
| pip install poetry | |
| poetry install --with dev | |
| - name: Collect ECAT and other phantoms | |
| if: steps.cache-phantoms.outputs.cache-hit != 'true' | |
| run: "wget https://openneuropet.s3.amazonaws.com/US-sourced-OpenNeuroPET-Phantoms.zip" | |
| - name: Decompress ECAT and other phantoms | |
| run: "unzip US-sourced-OpenNeuroPET-Phantoms.zip" | |
| - name: Debug | |
| uses: mxschmitt/action-tmate@v3 | |
| if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }} | |
| timeout-minutes: 15 | |
| with: | |
| limit-access-to-actor: true | |
| - name: Test CLI --help | |
| run: | | |
| cd pypet2bids/ | |
| poetry run python3 -m pypet2bids.ecat_cli --help | |
| - name: Test CLI Ecat Dump | |
| run: | | |
| cd pypet2bids/ | |
| poetry run python3 -m pypet2bids.ecat_cli ${{ env.REAL_ECAT_TEST_PATH }} --dump | |
| # the larger real data file uses too much ram for the github runner, we use the small file for | |
| # heavy io operations instead | |
| - name: Unzip Test File(s) | |
| run: | | |
| gzip -d ${{ env.SMALLER_ECAT_PATH }} | |
| - name: Test ecatread | |
| run: "cd pypet2bids/ && poetry run python3 -m tests.test_ecatread" | |
| - name: Run All Other Python Tests w/ Pytest | |
| run: | | |
| cd pypet2bids | |
| poetry run pytest -k 'not write_pixel_data' -k 'not test_convert_pmod_to_blood' tests/ |