Add dynunet model #1058
Workflow file for this run
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| # This workflow will install Python dependencies, run tests and lint with a single version of Python | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: OpenFL-Test | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: {} | |
| jobs: | |
| openfl-test: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Free space | |
| run: | | |
| df -h | |
| sudo rm -rf /opt/ghc | |
| sudo rm -rf "/usr/local/share/boost" | |
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| sudo rm -rf "$ANDROID_SDK_ROOT" | |
| df -h | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| # Use changed-files-specific action to collect file changes. | |
| # The following commented condition applied to a step will run that step only if non-docs files have changed. | |
| # It should be applied to all functionality-related steps. | |
| # if: steps.changed-files-specific.outputs.only_modified == 'false' | |
| - name: Detect and screen file changes | |
| id: changed-files-specific | |
| uses: tj-actions/changed-files@v41 | |
| with: | |
| files: | | |
| .github/*.md | |
| .github/ISSUE_TEMPLATE/*.md | |
| .github/workflows/devcontainer.yml | |
| .github/workflows/docker-image.yml | |
| .devcontainer/** | |
| docs/** | |
| mlcube/** | |
| *.md | |
| LICENSE | |
| Dockerfile-* | |
| - name: Summarize docs and non-docs modifications | |
| run: | | |
| echo "List of docs files that have changed: ${{ steps.changed-files-specific.outputs.all_modified_files }}" | |
| echo "Changed non-docs files: ${{ steps.changed-files-specific.outputs.other_modified_files }}" | |
| # This second step is unnecessary but highly recommended because | |
| # It will cache database and saves time re-downloading it if database isn't stale. | |
| - name: Cache pip | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/setup.py') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Set up Python 3.9 | |
| if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.9 | |
| - name: Install dependencies and package | |
| if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install libvips libvips-tools -y | |
| python -m pip install --upgrade pip | |
| python -m pip install wheel | |
| pip install torch==2.2.1 torchvision==0.17.1 torchaudio==2.2.1 --index-url https://download.pytorch.org/whl/cpu | |
| pip install -e . | |
| - name: Run generic unit tests to download data and construct CSVs | |
| if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change | |
| run: | | |
| pytest --cov=. --cov-report=xml -k "prepare_data_for_ci" | |
| # openfl tests start here | |
| - name: Run OpenFL tests | |
| if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change | |
| run: | | |
| echo "Removing onnx because of protobuf version conflict" | |
| pip uninstall onnx -y | |
| echo "Installing OpenFL" | |
| git clone --depth=1 https://github.com/securefederatedai/openfl.git | |
| cd openfl | |
| git fetch --tags | |
| # echo "Checkout the latest OpenFL tag" | |
| # latestTag=$(git describe --tags "$(git rev-list --tags --max-count=1)") | |
| # git checkout $latestTag | |
| # sed -i -e 's/protobuf==3.19.6/protobuf/g' setup.py ## this should NOT be there | |
| pip install -e . | |
| cd .. | |
| echo "Copying files to appropriate directories and updated headers" | |
| head -n 1 testing/data/train_2d_rad_segmentation.csv > /home/runner/work/GaNDLF/GaNDLF/openfl/valid.csv | |
| tail -n +9 testing/data/train_2d_rad_segmentation.csv >> /home/runner/work/GaNDLF/GaNDLF/openfl/valid.csv | |
| head -n 8 testing/data/train_2d_rad_segmentation.csv > /home/runner/work/GaNDLF/GaNDLF/openfl/train.csv | |
| sed -i 's/# n_channels: 3/num_channels: 3/g' testing/config_segmentation.yaml | |
| config_to_use=$(pwd)/testing/config_segmentation.yaml | |
| cd openfl | |
| python -m tests.github.test_gandlf --template gandlf_seg_test --fed_workspace aggregator --col1 one --col2 two --rounds-to-train 1 --gandlf_config $config_to_use |