From 63baeacf825fea78c5700264829fd5c3eb39b2ed Mon Sep 17 00:00:00 2001 From: Ravnoor Gill Date: Sun, 15 Dec 2024 02:20:43 -0500 Subject: [PATCH] feat(ci): migrate from base to dedicated env for deepFCD --- .github/workflows/test-inference-pipeline.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/test-inference-pipeline.yml b/.github/workflows/test-inference-pipeline.yml index 062ed09..06c050d 100644 --- a/.github/workflows/test-inference-pipeline.yml +++ b/.github/workflows/test-inference-pipeline.yml @@ -27,9 +27,12 @@ jobs: - name: Install dependencies for deepFCD run: | + eval "$(conda shell.bash hook)" + conda create -n deepFCD python=3.8 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: | @@ -43,7 +46,7 @@ jobs: - name: Run inference for deepFCD run: | - ./app/inference.py ${CI_TESTING_PATIENT_ID} t1.nii.gz flair.nii.gz ~/io cuda 1 1 + conda run -n 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"