feat(ci): switch to micromamba from conda

.github/workflows/test-inference-pipeline.yml

@@ -19,21 +19,16 @@ jobs:
 
       - name: Install dependencies for deepMask
         run: |
-          eval "$(conda shell.bash hook)"
-          conda create -n preprocess python=3.8
-          conda activate preprocess
+          eval "$(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
-          conda deactivate
 
       - name: Install dependencies for deepFCD
         run: |
-          eval "$(conda shell.bash hook)"
-          conda create -n deepFCD python=3.8
-          conda activate deepFCD
-          python -m pip install -r ./app/requirements.txt
-          conda install -c conda-forge pygpu==0.7.6
-          pip cache purge
-          conda deactivate
+          eval "$(micromamba shell hook -s posix)"
+          micromamba activate
+          micromamba create -n base -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: |
@@ -47,6 +42,8 @@ jobs:
 
       - 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"