From c8976dcbf7ceb182543f0a5506a5927b0bad4d98 Mon Sep 17 00:00:00 2001
From: Ravnoor Gill <ravnoor@gmail.com>
Date: Sun, 15 Dec 2024 17:44:51 -0500
Subject: [PATCH] feat(ci): switch to micromamba from conda

---
 .github/workflows/test-inference-pipeline.yml | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/test-inference-pipeline.yml b/.github/workflows/test-inference-pipeline.yml
index 43fce31..3157105 100644
--- a/.github/workflows/test-inference-pipeline.yml
+++ b/.github/workflows/test-inference-pipeline.yml
@@ -19,21 +19,18 @@ 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 "$(conda shell.bash hook)"
-          conda create -n deepFCD python=3.8
-          conda activate deepFCD
+          eval "$(micromamba shell hook -s posix)"
+          mamba activate
           python -m pip install -r ./app/requirements.txt
-          conda install -c conda-forge pygpu==0.7.6
+          micromamba install -c conda-forge pygpu==0.7.6 --yes
           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: |
@@ -47,6 +44,8 @@ jobs:
 
       - name: Run inference for deepFCD
         run: |
+          eval "$(micromamba shell hook -s posix)"
+          mamba 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"