Feature: cleanup script (#184)

Simple interactive utility script for cleanup of IMI output. Currently set up to delete:

- OutputDir files for jacobian simulations except for prior and background simulation
- data_sensitivities files in either normal or KF mode
I also include a dry-run mode that prints all the directories that will have recursive deletions without performing the removals.

Usage is:
./cleanup_script.sh <optional_config_file_path.yml>

src/components/inversion_component/inversion.sh

@@ -29,6 +29,7 @@ setup_inversion() {
     cp ${InversionPath}/src/inversion_scripts/utils.py inversion/
     cp ${InversionPath}/src/inversion_scripts/run_inversion.sh inversion/
     cp ${InversionPath}/src/notebooks/visualization_notebook.ipynb inversion/
+    cp ${InversionPath}/src/utilities/cleanup_script.sh .
     sed -i -e "s:{INVERSION_PATH}:${InversionPath}:g" \
            -e "s:{CONFIG_FILE}:${ConfigFile}:g" \
            -e "s:{STATE_VECTOR_ELEMENTS}:${nElements}:g" \

src/utilities/cleanup_script.sh

@@ -0,0 +1,98 @@
+#!/bin/bash
+
+# Description:
+#   This script will cleanup the directories and files created by 
+#   the imi inversion workflow. Note that some files, like the 
+#   calculated sensitivities may be necessary for adding additional 
+#   observation operators, so be careful when deleting files.
+# Usage:
+#   cleanup_script.sh [config.yml]
+#  If no config file is provided, the script will assume the current
+#  directory is the IMI run directory.
+
+printf "\n###########################################"
+printf "\n#            IMI Cleanup Script           #"
+printf "\n###########################################\n\n"
+
+# check if config file is provided
+if [[ $# == 1 ]] ; then
+    ConfigFile=$1
+    # parse config file
+    source parse_yaml.sh
+    eval $(parse_yaml $1)
+
+else
+    printf "\n No config file provided. Using current directory as IMI run directory: $(pwd)\n"
+    RunName=$(basename "$PWD")
+    OutputPath=../
+fi
+
+# Path for IMI rundir based on config file
+RunDir="${OutputPath}/${RunName}"
+
+# check to see if user wants to do a dry run
+printf "\nDo you want to do a dry-run (y/n)?" 
+printf "\nThis will print out all files to be deleted but not any deletions.\n"
+read response
+if [[ "x${response}" == "xy" ]]; then
+    printf "\nEntering dry-run mode. No deletions will take place.\n"
+    rm_command="echo rm"
+else
+    printf "\nEntering deletion mode. Caution: All deletions permanent.\n"
+    rm_command=rm
+fi
+
+# Ask user if they want to remove data_sensitivities directory
+printf "\nDo you want to remove the data_sensitivity directories and files (y/n)?\n"
+printf "\nNote: removing these files means you will need to recalculate sensitivities for jacobian perturbations."
+printf " This data is generally no longer needed if you do not plan on adding additional observation operators.\n"
+read response
+
+# Remove data_sensitivities directories
+if [[ "x${response}" == "xy" ]]; then
+    # Check if directory exists before removing them
+    kf_inversion_dirs="${RunDir}/kf_inversions/"
+    inversion_sensi_dir="${RunDir}/inversion/data_sensitivities"
+    # look for KF sensitivities
+    if [ -d "${kf_inversion_dirs}" ]; then
+        printf "\nRemoving data_sensitivity directories: ${kf_inversion_dirs}period*/data_sensitivities\n"
+        find ${kf_inversion_dirs} -type f -path '*period*/data_sensitivities/*' -exec ${rm_command} -r {} \;
+    # look for inversion sensitivities
+    elif [ -d "${inversion_sensi_dir}" ]; then
+        printf "\nRemoving data_sensitivity directories: ${inversion_sensi_dir}\n"
+        ${rm_command} -rf ${inversion_sensi_dir}
+    else
+        printf "\nNo data_sensitivities directories found in ${RunDir}\n"
+    fi
+else 
+    printf "\nSkipping removal of data_sensitivities directories.\n"
+fi
+
+# Ask user if they want to remove the jacobian output directories
+printf "\nDo you want to remove the jacobian simulation output directories and files (y/n)?\n"
+printf "\nNote: removing these files means you will be unable to recalculate sensitivities " 
+printf "without rerunning all simulations."
+printf "This is recommended if you have already calculated the sensitivities.\n"
+read response
+
+# Remove jacobian run output directories
+if [[ "x${response}" == "xy" ]]; then
+    # Check if directory exists before removing them
+    jacobian_dir="${RunDir}/jacobian_runs"
+    if [ -d "${jacobian_dir}/${RunName}_0001" ]; then
+        printf "\nRemoving jacobian run outputs (except for the prior and background sim): ${jacobian_dir}/{RunName}_****/OutputDir\n"
+        jacobian_dirs_array=($(find jacobian_runs -maxdepth 2 -type d -name "${RunName}_*" ! -name "${RunName}_background" ! -name "${RunName}_0000"))
+        for dir in "${jacobian_dirs_array[@]}"; do
+            echo "Removing files from dir: ${dir}/OutputDir/"
+            find ${dir}/OutputDir/ -type f -name "*" -exec ${rm_command} {} \;
+        done
+    else
+        printf "\nNo jacobian_run OutputDirs found in ${jacobian_dir}\n"
+    fi
+else 
+    printf "\nSkipping removal of jacobian simulation output directories\n"
+fi
+
+# Finish cleanup
+printf "\nCleanup complete\n"
+exit 0