Implemented clean.sh script generation (#39)

* implemented clean.sh script generation

* removed README.md typo mistake

FileGenerator.py

@@ -96,7 +96,34 @@ def generate_run(self) -> None:
 
     def generate_clean(self) -> None:
         """Generates the clean.sh file."""
-        #TODO
+        try:
+            tempalte_clean_sh = Path(__file__).parent / "templates" / "template_clean.sh"
+            self.logger.info("Reading in the template file for clean.sh")
+
+            # Check if the template file exists
+            if not tempalte_clean_sh.exists():
+                raise FileNotFoundError(f"Template file not found: {tempalte_clean_sh}")
+
+            # Read the template content
+            template_content = tempalte_clean_sh.read_text(encoding="utf-8")
+
+            # Set the target for the clean.sh
+            target = self.structure.clean
+
+            self.logger.info(f"Writing the template to the target: {str(target)}")
+
+            # Write content to the target file
+            with open(target, 'w', encoding="utf-8") as README:
+                README.write(template_content)
+
+            self.logger.success(f"Successfully written clean.sh content to: {str(target)}")
+
+        except FileNotFoundError as fileNotFoundException:
+            self.logger.error(f"File not found: {fileNotFoundException}")
+        except PermissionError as premissionErrorException:
+            self.logger.error(f"Permission error: {premissionErrorException}")
+        except Exception as generalExcpetion:
+            self.logger.error(f"An unexpected error occurred: {generalExcpetion}")
         pass
 
     def generate_adapter_config(self, target_participant: str) -> None:
@@ -128,4 +155,5 @@ def generate_adapter_config(self, target_participant: str) -> None:
     fileGenerator = FileGenerator(args.input_file, args.output_path)
     fileGenerator.generate_precice_config()
     fileGenerator.generate_README()
+    fileGenerator.generate_clean()
     fileGenerator.generate_adapter_config(target_participant="Calculix")

templates/template_clean.sh

@@ -0,0 +1,199 @@
+#!/bin/bash
+
+# -------------------------------------------------------------------
+# Script Name: cleanup.sh
+# Description: Deletes all files and directories in the current directory
+#              except for the hardcoded preserved files.
+#              Preserved files:
+#                - clean.sh
+#                - README.md
+#                - run.sh
+#                - config/adapter-config.json
+#                - config/precice-config.xml
+# Usage: ./cleanup.sh [--dry-run]
+# -------------------------------------------------------------------
+
+# Exit immediately if a command exits with a non-zero status
+set -e
+
+# Define the root directory as the current directory
+ROOT_DIR="$(pwd)"
+
+# Define the preserved files with their relative paths from ROOT_DIR
+PRESERVE_FILES=(
+    "clean.sh"
+    "README.md"
+    "run.sh"
+    "config/adapter-config.json"
+    "config/precice-config.xml"
+)
+
+# Define backup directory (optional)
+BACKUP_DIR="$ROOT_DIR/backup_$(date '+%Y%m%d_%H%M%S')"
+
+# Default behavior is to perform actual deletion
+DRY_RUN=0
+
+# Define log file
+LOG_FILE="cleanup.log"
+
+# Function to display a message
+log() {
+    echo "$(date '+%Y-%m-%d %H:%M:%S') - $1" | tee -a "$LOG_FILE"
+}
+
+# Function to check if a relative path is in the preserved list
+is_preserved() {
+    local rel_path="$1"
+    for preserve in "${PRESERVE_FILES[@]}"; do
+        if [ "$rel_path" == "$preserve" ]; then
+            return 0  # true
+        fi
+    done
+    return 1  # false
+}
+
+# Function to delete or backup unpreserved files and directories
+cleanup() {
+    log "Starting cleanup in directory: $ROOT_DIR"
+
+    # Enable dotglob to include hidden files and directories
+    shopt -s dotglob
+
+    # Iterate over all items in the root directory, including hidden ones
+    for item in "$ROOT_DIR"/* "$ROOT_DIR"/.*; do
+        # Get the relative path from ROOT_DIR
+        rel_path="${item#$ROOT_DIR/}"
+
+        # Handle the case when item is ROOT_DIR itself
+        if [ "$rel_path" == "$ROOT_DIR" ]; then
+            continue
+        fi
+
+        # Skip '.' and '..'
+        if [ "$rel_path" == "." ] || [ "$rel_path" == ".." ]; then
+            continue
+        fi
+
+        # Check if the item is in the preserved list
+        if is_preserved "$rel_path"; then
+            log "Preserving: $rel_path"
+            continue
+        fi
+
+        # Check if the item is a preserved directory (e.g., 'config')
+        PRESERVED_DIRS=()
+        for preserve in "${PRESERVE_FILES[@]}"; do
+            dir=$(dirname "$preserve")
+            if [ "$dir" != "." ] && [[ ! " ${PRESERVED_DIRS[@]} " =~ " ${dir} " ]]; then
+                PRESERVED_DIRS+=("$dir")
+            fi
+        done
+
+        preserve_dir=false
+        for dir in "${PRESERVED_DIRS[@]}"; do
+            if [[ "$rel_path" == "$dir" && -d "$item" ]]; then
+                preserve_dir=true
+                break
+            fi
+        done
+
+        if [ "$preserve_dir" = true ]; then
+            log "Preserving directory: $rel_path"
+
+            # Iterate over items inside the preserved directory
+            for subitem in "$item"/* "$item"/.*; do
+                # Get the relative path of the subitem
+                sub_rel_path="${subitem#$ROOT_DIR/}"
+
+                # Skip '.' and '..' inside the directory
+                sub_basename="$(basename "$subitem")"
+                if [ "$sub_basename" == "." ] || [ "$sub_basename" == ".." ]; then
+                    continue
+                fi
+
+                # Check if the subitem is in the preserved list
+                if is_preserved "$sub_rel_path"; then
+                    log "Preserving: $sub_rel_path"
+                    continue
+                fi
+
+                # Decide to delete or backup
+                if [ "$DRY_RUN" -eq 1 ]; then
+                    log "Would delete file: $sub_rel_path"
+                else
+                    # Create backup directory if not already
+                    mkdir -p "$BACKUP_DIR"
+
+                    if [ -f "$subitem" ] || [ -L "$subitem" ]; then
+                        mv "$subitem" "$BACKUP_DIR/"
+                        log "Moved file to backup: $sub_rel_path"
+                    elif [ -d "$subitem" ]; then
+                        mv "$subitem" "$BACKUP_DIR/"
+                        log "Moved directory to backup: $sub_rel_path"
+                    fi
+                fi
+            done
+            continue  # Move to the next item in the root directory
+        fi
+
+        # If not preserved and not a preserved directory, delete or backup the item
+        if [ -f "$item" ] || [ -L "$item" ]; then
+            if [ "$DRY_RUN" -eq 1 ]; then
+                log "Would delete file: $rel_path"
+            else
+                # Create backup directory if not already
+                mkdir -p "$BACKUP_DIR"
+
+                mv "$item" "$BACKUP_DIR/"
+                log "Moved file to backup: $rel_path"
+            fi
+        elif [ -d "$item" ]; then
+            if [ "$DRY_RUN" -eq 1 ]; then
+                log "Would delete directory: $rel_path"
+            else
+                # Create backup directory if not already
+                mkdir -p "$BACKUP_DIR"
+
+                mv "$item" "$BACKUP_DIR/"
+                log "Moved directory to backup: $rel_path"
+            fi
+        fi
+    done
+
+    # Disable dotglob after processing
+    shopt -u dotglob
+
+    if [ "$DRY_RUN" -eq 1 ]; then
+        log "Dry run completed. No files were deleted or moved."
+    else
+        log "Cleanup completed successfully. Deleted files are backed up in '$BACKUP_DIR'."
+    fi
+}
+
+# Parse optional flags
+while [[ "$#" -gt 0 ]]; do
+    case $1 in
+        --dry-run) DRY_RUN=1 ;;
+        *) echo "Unknown parameter passed: $1"; exit 1 ;;
+    esac
+    shift
+done
+
+# Safety: Prompt the user before proceeding
+if [ "$DRY_RUN" -eq 1 ]; then
+    log "Dry run mode enabled. No files will be deleted or moved."
+else
+    read -p "This will delete all files and directories except the preserved ones. Are you sure you want to proceed? [y/N]: " confirm
+    case "$confirm" in
+        [yY][eE][sS]|[yY])
+            ;;
+        *)
+            log "Cleanup aborted by user."
+            exit 0
+            ;;
+    esac
+fi
+
+# Perform cleanup
+cleanup