[ENH] Add Network Enrichment Significance Testing #300
Workflow file for this run
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| name: neuromaps-tests | |
| on: | |
| workflow_dispatch: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| jobs: | |
| check_style: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.8 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install ruff | |
| - name: Run style checks | |
| run: ruff check . | |
| codespell: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Run codespell | |
| uses: codespell-project/actions-codespell@v2 | |
| run_tests: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: ['ubuntu-latest'] | |
| python-version: ['3.8', '3.9', '3.10', '3.11', '3.12'] | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Display Python version | |
| run: python -c "import sys; print(sys.version)" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install -r requirements.txt | |
| python -m pip install pytest pytest-cov codecov | |
| python -m pip install git+https://github.com/netneurolab/netneurotools | |
| - name: Install connectome workbench | |
| run: | | |
| while true; do | |
| wget --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 0 --no-dns-cache -c \ | |
| https://www.humanconnectome.org/storage/app/media/workbench/workbench-linux64-v1.5.0.zip && break | |
| done | |
| unzip workbench-linux64-v1.5.0.zip -d ${HOME} | |
| echo "$HOME/workbench/bin_linux64" >> $GITHUB_PATH | |
| - name: Install neuromaps | |
| run: python -m pip install . | |
| - name: Print neuromaps version | |
| run: python -c "import neuromaps; print(neuromaps.__version__)" | |
| - name: Test submodule import | |
| run: | | |
| cd .. | |
| python -c "from neuromaps import parcellate; from neuromaps.datasets import available_annotations" | |
| - name: Run tests | |
| run: pytest --doctest-modules --cov=neuromaps --cov-report=xml --junitxml=junit/test-results.xml --verbose --pyargs neuromaps | |
| - uses: codecov/codecov-action@v3 | |
| with: | |
| files: ./coverage.xml | |
| verbose: true | |
| - name: Upload pytest test results | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }} | |
| path: junit/test-results.xml |