Update the load_data method of the database readers #269
Workflow file for this run
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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://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Run Test with PyTest and Codecov | |
| on: | |
| push: | |
| branches: [ dev ] | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| build: | |
| # Don't run on forked repos. | |
| if: github.repository_owner == 'DeepPSP' | |
| runs-on: ubuntu-20.04 | |
| strategy: | |
| matrix: | |
| python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Clear unnecessary system components | |
| run: | | |
| echo "Free space:" | |
| df -h | |
| sudo rm -rf /usr/local/lib/android # will release about 10 GB if you don't need Android | |
| sudo rm -rf /usr/share/dotnet # will release about 20GB if you don't need .NET | |
| sudo rm -rf /opt/ghc | |
| sudo rm -rf /usr/local/share/boost | |
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| - name: Install system libraries | |
| run: | | |
| sudo apt update | |
| sudo apt install build-essential ffmpeg libsm6 libxext6 libsndfile1 -y | |
| - name: Set up Ruby | |
| uses: ruby/setup-ruby@v1 | |
| with: | |
| ruby-version: '3.0' # Not needed with a .ruby-version file | |
| bundler-cache: true # runs 'bundle install' and caches installed gems automatically | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' # caching pip dependencies | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip setuptools wheel | |
| python -m pip install -r requirements.txt | |
| python -m pip install pytest pytest-xdist pytest-cov # Testing packages | |
| python -m pip uninstall torch-ecg --yes # Remove if already installed | |
| python setup.py install_egg_info # Workaround https://github.com/pypa/pip/issues/4537 | |
| python -m pip install -e .[dev] | |
| python -m pip freeze | |
| - name: Install nsrr and download a samll part of SHHS to do test | |
| # ref. https://github.com/DeepPSP/nsrr-automate | |
| run: | | |
| gem install nsrr --no-document | |
| nsrr download shhs/polysomnography/edfs/shhs1/ --file="^shhs1\-20010.*\.edf" --token=${{ secrets.NSRR_TOKEN }} | |
| nsrr download shhs/polysomnography/annotations-events-nsrr/shhs1/ --file="^shhs1\-20010.*\-nsrr\.xml" --token=${{ secrets.NSRR_TOKEN }} | |
| nsrr download shhs/polysomnography/annotations-events-profusion/shhs1/ --file="^shhs1\-20010.*\-profusion\.xml" --token=${{ secrets.NSRR_TOKEN }} | |
| nsrr download shhs/polysomnography/annotations-rpoints/shhs1/ --file="^shhs1\-20010.*\-rpoint\.csv" --token=${{ secrets.NSRR_TOKEN }} | |
| nsrr download shhs/datasets/ --shallow --token=${{ secrets.NSRR_TOKEN }} | |
| nsrr download shhs/datasets/hrv-analysis/ --token=${{ secrets.NSRR_TOKEN }} | |
| mkdir -p ~/tmp/nsrr-data/ | |
| mv shhs/ ~/tmp/nsrr-data/ | |
| du -sh ~/tmp/nsrr-data/* | |
| - name: Run test with pytest and collect coverage | |
| run: | | |
| pytest -v -s \ | |
| --cov=torch_ecg \ | |
| --ignore=test/test_pipelines \ | |
| test | |
| - name: Upload coverage to Codecov | |
| if: matrix.python-version == '3.8' | |
| uses: codecov/codecov-action@v3 | |
| - name: Remove downloaded NSRR data | |
| run: | | |
| rm -rf ~/tmp/nsrr-data/ |