Update conda environment if its outdated compared to the environment.yml

Author: JohT

scripts/activateCondaEnvironment.sh

@@ -17,25 +17,34 @@ set -o errexit -o pipefail
 # CDPATH reduces the scope of the cd command to potentially prevent unintended directory changes.
 # This way non-standard tools like readlink aren't needed.
 SCRIPTS_DIR=${SCRIPTS_DIR:-$( CDPATH=. cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd -P )} # Repository directory containing the shell scripts
-echo "activateCondaEnvironment: SCRIPTS_DIR=$SCRIPTS_DIR"
+echo "activateCondaEnvironment: SCRIPTS_DIR=${SCRIPTS_DIR}"
 
 # Get the "jupyter" directory by taking the path of this script and going two directory up and then to "jupyter".
 JUPYTER_NOTEBOOK_DIRECTORY=${JUPYTER_NOTEBOOK_DIRECTORY:-"${SCRIPTS_DIR}/../jupyter"} # Repository directory containing the Jupyter Notebooks
-echo "activateCondaEnvironment: JUPYTER_NOTEBOOK_DIRECTORY=$JUPYTER_NOTEBOOK_DIRECTORY"
+echo "activateCondaEnvironment: JUPYTER_NOTEBOOK_DIRECTORY=${JUPYTER_NOTEBOOK_DIRECTORY}"
+
+# Get the file name of the environment description file for the conda package and environment manager 
+# that contains all dependencies and their versions.
+CONDA_ENVIRONMENT_FILE=${CONDA_ENVIRONMENT_FILE:-"${JUPYTER_NOTEBOOK_DIRECTORY}/environment.yml"} # Conda (package manager for Python) environment file path
+if [ ! -f "${CONDA_ENVIRONMENT_FILE}" ] ; then
+    echo "activateCondaEnvironment: Couldn't find environment file ${CONDA_ENVIRONMENT_FILE}."
+    exit 2
+fi
 
 # Define conda environment to use for code structure analysis. Default "codegraph"
 CODEGRAPH_CONDA_ENVIRONMENT=${CODEGRAPH_CONDA_ENVIRONMENT:-"codegraph"} # Name of the conda environment to use for code graph analysis
 echo "activateCondaEnvironment: CONDA_PREFIX=${CONDA_PREFIX}"
 echo "activateCondaEnvironment: Current conda environment=${CONDA_DEFAULT_ENV}"
 echo "activateCondaEnvironment: Target conda environment=${CODEGRAPH_CONDA_ENVIRONMENT}"
 
-if [ "${CONDA_DEFAULT_ENV}" = "${CODEGRAPH_CONDA_ENVIRONMENT}" ] ; then
-    echo "activateCondaEnvironment: Skipping activation. Target conda environment ${CODEGRAPH_CONDA_ENVIRONMENT} is already activated."
-    # "return" needs to be used here instead of "exit".
-    # This script is included in another script by using "source". 
-    # "exit" would end the main script, "return" just ends this sub script.
-    return 0
-fi
+# TODO Find out, if conda updates (when needed) should also be done here instead of just returning 0.
+# if [ "${CONDA_DEFAULT_ENV}" = "${CODEGRAPH_CONDA_ENVIRONMENT}" ] ; then
+#     echo "activateCondaEnvironment: Skipping activation. Target conda environment ${CODEGRAPH_CONDA_ENVIRONMENT} is already activated."
+#     # "return" needs to be used here instead of "exit".
+#     # This script is included in another script by using "source". 
+#     # "exit" would end the main script, "return" just ends this sub script.
+#     return 0
+# fi 
 
 # Include operation system function to for example detect Windows.
 source "${SCRIPTS_DIR}/operatingSystemFunctions.sh"
@@ -60,18 +69,24 @@ echo "activateCondaEnvironment: scriptExtension=${scriptExtension}"
 eval "$(${pathToConda}conda${scriptExtension} shell.bash hook)"
 echo "activateCondaEnvironment: Current conda environment after shell hook=${CONDA_DEFAULT_ENV}"
 
-# Create (if missing) and activate Conda environment for code structure graph analysis
-if { "${pathToConda}conda" env list | grep "${CODEGRAPH_CONDA_ENVIRONMENT} "; } >/dev/null 2>&1; then
-    echo "activateCondaEnvironment: Conda environment ${CODEGRAPH_CONDA_ENVIRONMENT} already created"
-else
-    if [ ! -f "${JUPYTER_NOTEBOOK_DIRECTORY}/environment.yml" ] ; then
-        echo "activateCondaEnvironment: Couldn't find environment file ${JUPYTER_NOTEBOOK_DIRECTORY}/environment.yml."
-        exit 2
+# If missing, create Conda environment for code graph analysis
+# Note: The curly braces are grouping the outputs of both (piped) operations together to suppress them later (dev/null).
+if "${pathToConda}conda" env list | grep "${CODEGRAPH_CONDA_ENVIRONMENT} " >/dev/null 2>&1; then
+    echo "activateCondaEnvironment: Conda environment ${CODEGRAPH_CONDA_ENVIRONMENT} has already been created."
+    
+    # Check if the declaration in the environment file matches the actual environment to find out if it needs to be updated.
+    if "${pathToConda}conda" compare --name "${CODEGRAPH_CONDA_ENVIRONMENT}" "${CONDA_ENVIRONMENT_FILE}" >/dev/null 2>&1; then
+        echo "activateCondaEnvironment: Conda environment ${CODEGRAPH_CONDA_ENVIRONMENT} is up-to-date."
+    else
+        echo "activateCondaEnvironment: Conda environment ${CODEGRAPH_CONDA_ENVIRONMENT} needs to be updated."
+        "${pathToConda}conda" env update --file "${CONDA_ENVIRONMENT_FILE}" --name ${CODEGRAPH_CONDA_ENVIRONMENT} --prune
     fi
-    echo "activateCondaEnvironment: Creating Conda environment ${CODEGRAPH_CONDA_ENVIRONMENT}"
-    "${pathToConda}conda" env create --file "${JUPYTER_NOTEBOOK_DIRECTORY}/environment.yml" --name "${CODEGRAPH_CONDA_ENVIRONMENT}"
+else
+    echo "activateCondaEnvironment: Creating Conda environment ${CODEGRAPH_CONDA_ENVIRONMENT}..."
+    "${pathToConda}conda" env create --file "${CONDA_ENVIRONMENT_FILE}" --name "${CODEGRAPH_CONDA_ENVIRONMENT}"
 fi
 
+# Activate code graph Conda environment
 echo "activateCondaEnvironment: Activating Conda environment ${CODEGRAPH_CONDA_ENVIRONMENT}"
 "${pathToConda}conda" activate ${CODEGRAPH_CONDA_ENVIRONMENT}