pytest #59
Workflow file for this run
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| name: pytest | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }} | |
| cancel-in-progress: true | |
| on: | |
| # pull_request: | |
| # paths: | |
| # - '**.py' | |
| # push: | |
| # branches: [main] | |
| # paths: | |
| # - '**.py' | |
| workflow_dispatch: | |
| branches: [remove-freesurfer] | |
| env: | |
| SUBJECTS_DIR: /home/runner/work/brainprint-tests/brainprint-tests/data | |
| SUBJECT_ID: test | |
| DESTINATION_DIR: /home/runner/work/brainprint-tests/brainprint-tests/dat | |
| jobs: | |
| pytest: | |
| timeout-minutes: 30 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| # os: [ubuntu, macos, windows] | |
| # python-version: [3.8, 3.9, "3.10", "3.11"] | |
| os: [ubuntu] | |
| python-version: ["3.10"] | |
| name: ${{ matrix.os }} - py${{ matrix.python-version }} | |
| runs-on: ${{ matrix.os }}-latest | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| architecture: 'x64' | |
| - name: Install package | |
| run: | | |
| python -m pip install --progress-bar off --upgrade pip setuptools wheel | |
| python -m pip install --progress-bar off .[test] | |
| - name: Create data folders | |
| run: | | |
| mkdir -p data/test/mri | |
| mkdir -p data/test/surf | |
| mkdir -p data/test/temp | |
| - name: Display system information | |
| run: brainprint-sys_info --developer | |
| - name: Download files | |
| run: | | |
| wget https://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data/buckner_data/tutorial_subjs/good_output/mri/aseg.mgz -O data/test/mri/aseg.mgz | |
| wget https://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data/buckner_data/tutorial_subjs/good_output/surf/lh.white -O data/test/surf/lh.white | |
| wget https://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data/buckner_data/tutorial_subjs/good_output/surf/rh.white -O data/test/surf/rh.white | |
| wget https://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data/buckner_data/tutorial_subjs/good_output/surf/lh.pial -O data/test/surf/lh.pial | |
| wget https://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data/buckner_data/tutorial_subjs/good_output/surf/rh.pial -O data/test/surf/rh.pial | |
| - name: Run pytest | |
| run: pytest brainprint --cov=brainprint --cov-report=xml --cov-config=pyproject.toml | |
| - name: Upload to codecov | |
| if: ${{ matrix.os == 'ubuntu' && matrix.python-version == '3.10' }} | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| files: ./coverage.xml | |
| flags: unittests # optional | |
| name: codecov-umbrella # optional | |
| fail_ci_if_error: true # optional (default = false) | |
| verbose: true # optional (default = false) | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| slug: deep-mi/BrainPrint |