From ed26a93cff839abd3aa739fa3ad57ccf84c44c46 Mon Sep 17 00:00:00 2001
From: Ravnoor Gill <ravnoor@gmail.com>
Date: Fri, 13 Dec 2024 14:50:00 -0500
Subject: [PATCH] feat(preproc): replace conda with mamba calls

---
 app/preprocess.sh | 18 +++++++-----------
 1 file changed, 7 insertions(+), 11 deletions(-)

diff --git a/app/preprocess.sh b/app/preprocess.sh
index 5aa827e..50725da 100755
--- a/app/preprocess.sh
+++ b/app/preprocess.sh
@@ -25,19 +25,15 @@ OUTDIR=${BASEDIR}/${ID}/        # args.outdir = os.path.join(args.dir, args.id)
 
 PWD=$(dirname "$0")
 
-conda=${CONDA_EXE}
-eval "$(conda shell.bash hook)"
-conda activate preprocess
-# echo $CONDA_PREFIX
+eval "$(micromamba shell hook --shell posix)"
+micromamba activate
 
 if [ ${PREPROCESSING} -eq 1 ] && [ ${USE_GPU} -eq 0 ]; then
-	python3 $PWD/preprocess.py -i ${ID} -t1 ${T1_FNAME} -t2 ${T2_FNAME} -d ${BASEDIR} --preprocess
+	micromamba run -n preprocess python3 $PWD/preprocess.py -i ${ID} -t1 ${T1_FNAME} -t2 ${T2_FNAME} -d ${BASEDIR} --preprocess
 elif [ ${PREPROCESSING} -eq 0 ] && [ ${USE_GPU} -eq 1 ]; then	
-	python3 $PWD/preprocess.py -i ${ID} -t1 ${T1_FNAME} -t2 ${T2_FNAME} -d ${BASEDIR} --use_gpu
+	micromamba run -n preprocess python3 $PWD/preprocess.py -i ${ID} -t1 ${T1_FNAME} -t2 ${T2_FNAME} -d ${BASEDIR} --use_gpu
 elif [ ${PREPROCESSING} -eq 1 ] && [ ${USE_GPU} -eq 1 ]; then
-	python3 $PWD/preprocess.py -i ${ID} -t1 ${T1_FNAME} -t2 ${T2_FNAME} -d ${BASEDIR} --preprocess --use_gpu
+	micromamba run -n preprocess python3 $PWD/preprocess.py -i ${ID} -t1 ${T1_FNAME} -t2 ${T2_FNAME} -d ${BASEDIR} --preprocess --use_gpu
 else
-    python3 $PWD/preprocess.py -i ${ID} -t1 ${T1_FNAME} -t2 ${T2_FNAME} -d ${BASEDIR}
-fi
-
-conda deactivate
\ No newline at end of file
+  micromamba run -n preprocess python3 $PWD/preprocess.py -i ${ID} -t1 ${T1_FNAME} -t2 ${T2_FNAME} -d ${BASEDIR}
+fi
\ No newline at end of file