From c7ae975b2567dcaa944cb07701dd451136e490d1 Mon Sep 17 00:00:00 2001
From: grallewellyn <grace.llewellyn@jpl.nasa.gov>
Date: Thu, 18 Jun 2026 15:10:19 -0700
Subject: [PATCH 1/3] renamed default conda env and no longer using positional
 args

---
 convert_to_grayscale/run_grayscale.sh | 16 ++++++++++++++--
 gdal_wrapper/environment.yml          |  2 +-
 gdal_wrapper/run_gdal.sh              | 20 +++++++++++++++++---
 3 files changed, 32 insertions(+), 6 deletions(-)

diff --git a/convert_to_grayscale/run_grayscale.sh b/convert_to_grayscale/run_grayscale.sh
index 1fac55a..6102902 100755
--- a/convert_to_grayscale/run_grayscale.sh
+++ b/convert_to_grayscale/run_grayscale.sh
@@ -32,8 +32,20 @@ INPUT_DIR=input
 # Since we only have one input we can list it as below
 INPUT_IMAGE_PATH=$(ls input/*)
 
-# Read the positional argument as defined in the algorithm registration here
-OUTPUT_IMAGE_NAME=$1
+# Parse named arguments instead of positional arguments
+while [[ $# -gt 0 ]]; do
+  case $1 in
+    --output_image_name)
+      OUTPUT_IMAGE_NAME="$2"
+      shift 2
+      ;;
+    *)
+      echo "Unknown argument: $1"
+      exit 1
+      ;;
+  esac
+done
+
 OUTPUT_IMAGE_PATH="output/${OUTPUT_IMAGE_NAME}"
 
 # Call the script using the absolute path
diff --git a/gdal_wrapper/environment.yml b/gdal_wrapper/environment.yml
index eaf4034..d057e47 100644
--- a/gdal_wrapper/environment.yml
+++ b/gdal_wrapper/environment.yml
@@ -1,4 +1,4 @@
-name: python
+name: notebook
 channels:
   - conda-forge
   - defaults
diff --git a/gdal_wrapper/run_gdal.sh b/gdal_wrapper/run_gdal.sh
index a5d9585..eb1c308 100755
--- a/gdal_wrapper/run_gdal.sh
+++ b/gdal_wrapper/run_gdal.sh
@@ -25,9 +25,23 @@ INPUT_DIR=input
 # Since we only have one input we can list it as below
 input_filename=$(ls -d input/*)
 
-# Read the positional argument as defined in the algorithm registration here
-output_filename=$1
-reduction_size=$2
+# Parse named arguments instead of positional arguments
+while [[ $# -gt 0 ]]; do
+  case $1 in
+    --output_filename)
+      output_filename="$2"
+      shift 2
+      ;;
+    --reduction_size)
+      reduction_size="$2"
+      shift 2
+      ;;
+    *)
+      echo "Unknown argument: $1"
+      exit 1
+      ;;
+  esac
+done
 
 # Call the script using the absolute paths
 # Use the updated environment when calling 'conda run'

From f54470b9003f3accf61b33fd4f7ab564b835156f Mon Sep 17 00:00:00 2001
From: grallewellyn <grace.llewellyn@jpl.nasa.gov>
Date: Thu, 18 Jun 2026 15:45:19 -0700
Subject: [PATCH 2/3] removed input assumption and all named args

---
 gdal_wrapper/run_gdal.sh | 19 +++++++------------
 1 file changed, 7 insertions(+), 12 deletions(-)

diff --git a/gdal_wrapper/run_gdal.sh b/gdal_wrapper/run_gdal.sh
index eb1c308..198708c 100755
--- a/gdal_wrapper/run_gdal.sh
+++ b/gdal_wrapper/run_gdal.sh
@@ -16,23 +16,18 @@ basedir=$(dirname "$(readlink -f "$0")")
 
 mkdir -p output
 
-
-# DPS downloads all files provided as inputs to
-# this directory called input.
-# In our example the image will be downloaded here.
-INPUT_DIR=input
-
-# Since we only have one input we can list it as below
-input_filename=$(ls -d input/*)
-
-# Parse named arguments instead of positional arguments
+# Parse named arguments as defined in the CWL file
 while [[ $# -gt 0 ]]; do
   case $1 in
-    --output_filename)
+    --input_file)
+      input_filename="$2"
+      shift 2
+      ;;
+    --output_file)
       output_filename="$2"
       shift 2
       ;;
-    --reduction_size)
+    --outsize)
       reduction_size="$2"
       shift 2
       ;;

From 19047ac96468eaab228492eb68d359c1d508979d Mon Sep 17 00:00:00 2001
From: grallewellyn <grace.llewellyn@jpl.nasa.gov>
Date: Thu, 18 Jun 2026 16:48:26 -0700
Subject: [PATCH 3/3] updated conda env name in run command

---
 gdal_wrapper/run_gdal.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gdal_wrapper/run_gdal.sh b/gdal_wrapper/run_gdal.sh
index 198708c..21a51fd 100755
--- a/gdal_wrapper/run_gdal.sh
+++ b/gdal_wrapper/run_gdal.sh
@@ -42,6 +42,6 @@ done
 # Use the updated environment when calling 'conda run'
 # This lets us run the same way in a Terminal as in DPS
 # Any output written to the stdout and stderr streams will be automatically captured and placed in the output dir
-# echo conda run --live-stream --name vanilla python ${basedir}/gdal_wrapper.py --input_file ${input_filename} --output_file output/${output_filename} --outsize ${reduction_size}
+# echo conda run --live-stream --name notebook python ${basedir}/gdal_wrapper.py --input_file ${input_filename} --output_file output/${output_filename} --outsize ${reduction_size}
 
-conda run --live-stream --name python python ${basedir}/gdal_wrapper.py --input_file ${input_filename} --output_file output/${output_filename} --outsize ${reduction_size}
+conda run --live-stream --name notebook python ${basedir}/gdal_wrapper.py --input_file ${input_filename} --output_file output/${output_filename} --outsize ${reduction_size}