add github actions test for nnunet inference #1
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| name: Run nnunet tests on all OS | |
| on: | |
| push: | |
| paths-ignore: | |
| - '**.md' | |
| jobs: | |
| run-tests: | |
| strategy: | |
| matrix: | |
| # os: [ubuntu-latest, windows-latest, macos-latest] # fails on windows until https://github.com/MIC-DKFZ/nnUNet/issues/2396 is resolved | |
| os: [ubuntu-latest, macos-latest] | |
| python-version: ["3.10"] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Download and extract weights and download example file | |
| # use python instead of curl to avoid the need to install curl (more difficult for macos) | |
| run: | | |
| mkdir -p $HOME/github_actions_nnunet/results | |
| python -c "import urllib.request; urllib.request.urlretrieve('https://github.com/wasserth/TotalSegmentator/releases/download/v2.0.0-weights/Dataset300_body_6mm_1559subj.zip', '$HOME/github_actions_nnunet/results/tmp_download_file.zip')" | |
| unzip -o $HOME/github_actions_nnunet/results/tmp_download_file.zip -d $HOME/github_actions_nnunet/results | |
| rm $HOME/github_actions_nnunet/results/tmp_download_file.zip | |
| python -c "import urllib.request; urllib.request.urlretrieve('https://github.com/wasserth/TotalSegmentator/raw/refs/tags/v2.4.0/tests/reference_files/example_ct_sm.nii.gz', '$HOME/github_actions_nnunet/example_ct_sm.nii.gz')" | |
| - name: Install dependencies on Ubuntu | |
| if: runner.os == 'Linux' | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install pytest Cython | |
| pip install torch==2.4.0 -f https://download.pytorch.org/whl/cpu | |
| pip install . | |
| - name: Install dependencies on Windows / MacOS | |
| if: runner.os == 'Windows' || runner.os == 'macOS' | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install pytest Cython | |
| pip install torch==2.4.0 | |
| pip install . | |
| - name: Run test script | |
| run: python tests/integration_tests/run_nnunet_inference.py |