fix(bash/env): when rebuilt env, had issue with not using the environment's jupyter - add line to get jupyter path, and add jupyter to environment (plus renamed environment)

Author: amyheather

environment.yaml

@@ -1,10 +1,11 @@
-name: template-des
+name: pydesrapmms
 channels:
   - conda-forge
 dependencies:
   - ipykernel=6.29.5
   - jinja2=3.1.5
   - joblib=1.4.2
+  - jupyter=1.1.1
   - nbconvert=7.16.6
   - nbformat=5.10.4
   - nbqa=1.9.0

run_notebooks.sh

@@ -1,12 +1,15 @@
 #!/usr/bin/env bash
 
+# Get the conda environment's jupyter path
+CONDA_JUPYTER=$(dirname "$(which python)")/jupyter
+
 # Loop through all notebooks in the specified directory
 for nb in notebooks/*.ipynb; do
     echo "🏃 Running notebook: $nb"
 
     # Execute and update the notebook in-place
     # With some processing to remove metadata created by nbconvert
-    if python -m jupyter nbconvert --to notebook --inplace --execute \
+    if "${CONDA_JUPYTER}" nbconvert --to notebook --inplace --execute \
         --ClearMetadataPreprocessor.enabled=True \
         --ClearMetadataPreprocessor.clear_notebook_metadata=False \
         --ClearMetadataPreprocessor.preserve_cell_metadata_mask="kernelspec" \