Fix for multiple subdirectories

Author: Sparks29032

src/diffpy/pdfmorph/pdfmorphapp.py

@@ -487,14 +487,14 @@ def single_morph(parser, opts, pargs, stdout_flag=True):
         parser.custom_error(save_fail_message)
 
     if opts.plot:
-        pairlist = [chain.xy_morph_out, chain.xy_target_out]
-        labels = [pargs[0], pargs[1]]  # Default is to use file names
+        pairlist = [chain.xy_target_out, chain.xy_morph_out]
+        labels = [pargs[1], pargs[0]]  # Default is to use file names
 
         # If user chooses labels
         if opts.mlabel is not None:
-            labels[0] = opts.mlabel
+            labels[1] = opts.mlabel
         if opts.tlabel is not None:
-            labels[1] = opts.tlabel
+            labels[0] = opts.tlabel
 
         # Plot extent defaults to calculation extent
         pmin = opts.pmin if opts.pmin is not None else opts.rmin
@@ -536,6 +536,8 @@ def multiple_targets(parser, opts, pargs, stdout_flag=True):
     for target in target_list:
         if target.is_dir():
             target_list.remove(target)
+    for morph in to_remove:
+        morph_list.remove(morph)
 
     # Do not morph morph_file against itself if it is in the same directory
     if morph_file in target_list:
@@ -678,9 +680,12 @@ def multiple_morphs(parser, opts, pargs, stdout_flag=True):
 
     # Get list of files from morph directory
     morph_list = list(morph_directory.iterdir())
+    to_remove = []
     for morph in morph_list:
         if morph.is_dir():
-            morph_list.remove(morph)
+            to_remove.append(morph)
+    for morph in to_remove:
+        morph_list.remove(morph)
 
     # Do not morph target_file against itself if it is in the same directory
     if target_file in morph_list: