fix(ci): source env before running tests #40
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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)" | |
| micromamba create -n deepFCD -f ./app/conda-lock.yml --yes | |
| - 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 deepFCD | |
| ./app/inference.py ${CI_TESTING_PATIENT_ID} t1.nii.gz flair.nii.gz ~/io cuda 1 1 | |
| env: | |
| CI_TESTING_PATIENT_ID: "sub-00055" | |
| CI_TESTING_GT: "./tests/segmentations/sub-00055/sub-00055_label_dilated_final.nii.gz" | |
| CI_TESTING_PRED_DIR: "/home/ga/io" | |
| - name: Run tests to compare outputs with previous validated runs | |
| run: | | |
| eval "$(micromamba shell hook -s posix)" | |
| micromamba activate deepFCD | |
| bash ./tests/run_tests.sh | |
| env: | |
| CI_TESTING_PATIENT_ID: "sub-00055" | |
| CI_TESTING_PRED_DIR: "/home/ga/io" |