fix: add cleanup function for temporary files after apply and add csv files

Author: alastairtree

src/imap_mag/cli/apply.py

@@ -338,6 +338,21 @@ def _apply_for_date(
         l2_handler.version = 1  # set version to 0 for the output file naming
         outputManager.add_file(L2_file, l2_handler)
 
+    cleanup_workfolder_after_apply(
+        app_settings,
+        workScienceFile,
+        workLayers,
+        workRotationFile,
+        L2_files,
+        offset_file,
+    )
+
+    logger.info(f"Apply complete for date {date}. Temporary files cleaned up.")
+
+
+def cleanup_workfolder_after_apply(
+    app_settings, workScienceFile, workLayers, workRotationFile, L2_files, offset_file
+):
     files_to_cleanup: list[Path] = [
         offset_file,
         *L2_files,
@@ -347,10 +362,17 @@ def _apply_for_date(
     if workRotationFile:
         files_to_cleanup.append(workRotationFile)
 
+    # add the .csv version of all layer files to the cleanup list as well
+    for layer_file in workLayers:
+        if layer_file.suffix == ".json":
+            corresponding_csv = layer_file.with_suffix(".csv")
+            if corresponding_csv.exists():
+                files_to_cleanup.append(corresponding_csv)
+
     work_folder_resolved = app_settings.work_folder.resolve()
     for temp_file in files_to_cleanup:
         temp_file_resolved = temp_file.resolve()
-        if (
+        if temp_file_resolved.exists() and (
             temp_file_resolved == work_folder_resolved
             or work_folder_resolved in temp_file_resolved.parents
         ):
@@ -361,8 +383,6 @@ def _apply_for_date(
                 f"Skipping deletion of file outside work folder '{app_settings.work_folder}': {temp_file}"
             )
 
-    logger.info(f"Apply complete for date {date}. Temporary files cleaned up.")
-
 
 def _setup_zero_calibration_layer(
     work_folder: Path, workScienceFile: Path, content_date: datetime