test-inference-pipeline.yml

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 "$(conda shell.bash hook)"
          conda create -n preprocess python=3.8
          conda activate preprocess
          python -m pip install -r ./app/deepMask/app/requirements.txt
          conda deactivate

      - name: Install dependencies for deepFCD
        run: |
          eval "$(conda shell.bash hook)"
          conda create -n deepFCD python=3.8
          conda activate deepFCD
          python -m pip install -r ./app/requirements.txt
          conda install -c conda-forge pygpu==0.7.6
          pip cache purge
          conda deactivate

      - 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: |
          ./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"