update the base python image to 3.12-bookworm image

src/cirrocumulus/.devcontainer.json

@@ -12,15 +12,8 @@
     "${templateOption:login}"
   ],
   // re-mount bucket files on container start up
-  "postStartCommand": [
-    "./startupscript/remount-on-restart.sh",
-    "root",
-    "/root",
-    "${templateOption:cloud}",
-    "${templateOption:login}"
-  ],
+  "postStartCommand": "chmod +x /workspace/scripts/cirro_scanner.sh && nohup /workspace/scripts/cirro_scanner.sh > /root/.workbench/logs/cirro_scanner.log 2>&1 &",
   "features": {
-    "ghcr.io/devcontainers/features/aws-cli@sha256:bbc9fd513c22e331953126c75ad7b2ed1f9044f1cd5890b7073b634810459b18": {},
     "ghcr.io/dhoeric/features/google-cloud-cli@sha256:fa5d894718825c5ad8009ac8f2c9f0cea3d1661eb108a9d465cba9f3fc48965f": {},
     "ghcr.io/devcontainers/features/java@sha256:df67d6ff6e9cdd858207ae9e92a99ddb88384b789f79eecd6f873216e951d286": {}
   },

src/cirrocumulus/Dockerfile

@@ -1,8 +1,9 @@
 # Use an official Python runtime as a parent image
-FROM mcr.microsoft.com/vscode/devcontainers/python:3.10-buster
+FROM mcr.microsoft.com/vscode/devcontainers/python:3.12-bookworm
 
 ENV PYTHONDONTWRITEBYTECODE=1
 ENV PYTHONUNBUFFERED=1
 
 # Install any needed packages specified in requirements.txt
-RUN python -m pip install --upgrade pip && python -m pip install cirrocumulus
+RUN python -m pip install --upgrade pip && \
+    python -m pip install cirrocumulus

src/cirrocumulus/scripts/cirro_scanner.sh

@@ -29,7 +29,7 @@ readonly -f create_dataset
 # Define the function to perform the scanning
 function scan_folders_and_create_datasets() {
     # Search for folders with name *.zarr and create cirro dataset if it doesn't exist
-    find /root/workspace -type d -name '*.zarr' | while read -r folder; do
+    find /root/workspace \( -type d -name '*.zarr' -o -type f -name '*.h5ad' \) | while read -r folder; do
         if [[ "$(matching_dataset_count "${folder}")" -eq "0" ]]; then
             create_dataset "${folder}"
         else

startupscript/post-startup.sh

@@ -34,7 +34,7 @@ source "${SCRIPT_DIR}/emit.sh"
 
 source "${CLOUD_SCRIPT_DIR}/vm-metadata.sh"
 
-readonly RUN_AS_LOGIN_USER="sudo -u ${USER_NAME} bash -l -c"
+readonly RUN_AS_LOGIN_USER="sudo -u ${USER_NAME} bash -c"
 export RUN_AS_LOGIN_USER
 
 # Startup script status is propagated out to VM guest attributes