feat(ci): switch to micromamba from conda #35
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| name: Testing Inference Pipeline | |
| on: [push, pull_request] | |
| env: | |
| CI_TESTING: True | |
| jobs: | |
| build: | |
| runs-on: self-hosted | |
| steps: | |
| - name: Check out the repo | |
| uses: actions/checkout@v3 | |
| with: | |
| submodules: recursive | |
| - name: Install dependencies for deepMask | |
| run: | | |
| eval "$(micromamba shell hook -s posix)" | |
| micromamba create -n preprocess python=3.8 --yes | |
| micromamba activate preprocess | |
| python -m pip install -r ./app/deepMask/app/requirements.txt | |
| - name: Install dependencies for deepFCD | |
| run: | | |
| eval "$(micromamba shell hook -s posix)" | |
| mamba activate | |
| python -m pip install -r ./app/requirements.txt | |
| micromamba install -c conda-forge pygpu==0.7.6 --yes | |
| pip cache purge | |
| - name: Download openneuro.org dataset to test the inference pipeline # https://openneuro.org/datasets/ds004199/versions/1.0.5 | |
| run: | | |
| PATIENT_ID=sub-00055 | |
| BASE_URL=https://s3.amazonaws.com/openneuro.org/ds004199/${PATIENT_ID}/anat | |
| mkdir -p ~/io/${PATIENT_ID} | |
| echo "retrieving single-patient multimodal dataset.." | |
| wget ${BASE_URL}/${PATIENT_ID}_acq-sag111_T1w.nii.gz\?versionId\=IKGWDiLR7B7ls2yPVyycJo.6R1Sqhujf -O ~/io/sub-00055/t1.nii.gz | |
| wget ${BASE_URL}/${PATIENT_ID}_acq-tse3dvfl_FLAIR.nii.gz\?versionId\=HmzYoUuYkdbyd8jkpdJjVkZydRHNSqUX -O ~/io/sub-00055/flair.nii.gz | |
| wget ${BASE_URL}/${PATIENT_ID}_acq-tse3dvfl_FLAIR_roi.nii.gz\?versionId\=ulmEU3nb8WCvGwcwTbkcdNSVr07PMPQN -O ~/io/sub-00055/label.nii.gz | |
| - name: Run inference for deepFCD | |
| run: | | |
| eval "$(micromamba shell hook -s posix)" | |
| micromamba activate | |
| ./app/inference.py ${CI_TESTING_PATIENT_ID} t1.nii.gz flair.nii.gz ~/io cuda 1 1 | |
| env: | |
| CI_TESTING_PATIENT_ID: "sub-00055" | |
| CI_TESTING_GT: "./tests/segmentations/sub-00055/sub-00055_label_dilated_final.nii.gz" | |
| CI_TESTING_PRED_DIR: "/home/ga/io" | |
| - name: Run tests to compare outputs with previous validated runs | |
| run: bash ./tests/run_tests.sh | |
| env: | |
| CI_TESTING_PATIENT_ID: "sub-00055" | |
| CI_TESTING_PRED_DIR: "/home/ga/io" |