Modifying the shard_num read for templates to indicate that data_path flag needs to be passed as an integer
#461
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: GaNDLF TaskRunner | |
| on: | |
| pull_request: | |
| branches: [ develop ] | |
| permissions: | |
| contents: read | |
| env: | |
| # A workaround for long FQDN names provided by GitHub actions. | |
| FQDN: "localhost" | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: "3.10" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install typer==0.11.1 | |
| pip install torch==2.3.1+cpu torchvision torchaudio --extra-index-url https://download.pytorch.org/whl/cpu | |
| pip install . | |
| - name: Install GaNDLF | |
| run: | | |
| git clone https://github.com/MLCommons/GaNDLF.git ./gandlf | |
| cd gandlf | |
| git fetch --tags | |
| echo "Checkout the latest GaNDLF tag" | |
| latestTag=$(git describe --tags "$(git rev-list --tags --max-count=1)") | |
| git checkout $latestTag | |
| - name: GaNDLF Task Runner Test | |
| run: | | |
| cd gandlf | |
| pwd | |
| pip install -e . | |
| pip uninstall onnx -y | |
| cat ./GANDLF/version.py | |
| echo "Download data and Split CSVs into training and validation" | |
| # python -c "from testing.test_full import test_generic_download_data, test_generic_constructTrainingCSV; test_generic_download_data(); test_generic_constructTrainingCSV()" | |
| pytest --cov=. --cov-report=xml -k "prepare_data_for_ci" | |
| head -n 1 testing/data/train_2d_rad_segmentation.csv > /home/runner/work/openfl/openfl/valid.csv | |
| tail -n +9 testing/data/train_2d_rad_segmentation.csv >> /home/runner/work/openfl/openfl/valid.csv | |
| head -n 8 testing/data/train_2d_rad_segmentation.csv > /home/runner/work/openfl/openfl/train.csv | |
| cp testing/config_segmentation.yaml /home/runner/work/openfl/openfl/config_segmentation.yaml | |
| echo "DEBUG display the config file" | |
| cat /home/runner/work/openfl/openfl/config_segmentation.yaml | |
| echo "Initialize OpenFL plan" | |
| ## from docs | |
| export WORKSPACE_TEMPLATE=gandlf_seg_test | |
| export WORKSPACE_PATH=./my_federation | |
| fx workspace create --prefix ${WORKSPACE_PATH} --template ${WORKSPACE_TEMPLATE} | |
| cd ${WORKSPACE_PATH} | |
| mkdir ./data/one | |
| mkdir ./data/two | |
| cp /home/runner/work/openfl/openfl/*.csv ./data/one/ | |
| cp /home/runner/work/openfl/openfl/*.csv ./data/two/ | |
| ## from docs | |
| # fx plan initialize --gandlf_config ../testing/config_segmentation.yaml | |
| cd /home/runner/work/openfl/openfl | |
| ls | |
| file "/home/runner/work/openfl/openfl/config_segmentation.yaml" | |
| ## for 2d data, only a single change is needed in the gandlf config | |
| sed -i 's/# n_channels: 3/num_channels: 3/g' "/home/runner/work/openfl/openfl/config_segmentation.yaml" | |
| ## for 3d data, the following changes are needed in the gandlf config -- commented out for now | |
| # sed -i 's/dimension: 2/dimension: 3/g' "/home/runner/work/openfl/openfl/config_segmentation.yaml" | |
| # sed -i 's/0,255/0,1/g' "/home/runner/work/openfl/openfl/config_segmentation.yaml" | |
| # sed -i 's/128,128/32,32,32/g' "/home/runner/work/openfl/openfl/config_segmentation.yaml" | |
| python -m tests.github.test_gandlf --template gandlf_seg_test --fed_workspace aggregator --col1 one --col2 two --rounds-to-train 1 --gandlf_config "/home/runner/work/openfl/openfl/config_segmentation.yaml" | |