Update zbrains.py #7
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python | |
| name: Python package | |
| on: | |
| push: | |
| branches: [ "main" ] | |
| pull_request: | |
| branches: [ "main" ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.8", "3.9", "3.10"] | |
| steps: | |
| - name: Install System Dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y sshpass sshfs | |
| sudo apt-get install libglu1 | |
| - name: Install Connectome Workbench | |
| run: | | |
| wget https://www.humanconnectome.org/storage/app/media/workbench/workbench-linux64-v1.5.0.zip | |
| unzip workbench-linux64-v1.5.0.zip -d /home/runner/work | |
| echo 'export PATH=$PATH:/home/runner/work/workbench/bin_linux64' >> ~/.bashrc | |
| source ~/.bashrc | |
| /home/runner/work/workbench/bin_linux64/wb_command -version | |
| - name: Connect to Proxy | |
| run: | | |
| sshpass -p ${{ secrets.PASSWORD }} ssh -v -o StrictHostKeyChecking=no ${{ secrets.USER }}@login.bic.mni.mcgill.ca 'nc -q0 login.bic.mni.mcgill.ca 22' & | |
| - name: Create Mount Point | |
| run: | | |
| sudo mkdir -p /mnt/z | |
| sudo chown -R $(whoami) /mnt/z | |
| - name: Mount Filesystem | |
| run: | | |
| sshfs ${{ secrets.USER }}@login.bic.mni.mcgill.ca:/data/mica1/03_projects/ian/pytest_data /mnt/z -v -o password_stdin <<<"${{ secrets.PASSWORD }}" | |
| ls /mnt/z/BIDS_MICs_Test | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install flake8 pytest | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Test with pytest | |
| run: | | |
| pytest |