used sorted for tests and edited input function to include file list only if user specifies it

Author: yucongalicechen

src/diffpy/labpdfproc/tests/test_tools.py

@@ -27,9 +27,6 @@
     (  # glob input directory
         ["./input_dir"],
         [
-            "./good_data.chi",
-            "./good_data.xy",
-            "./good_data.txt",
             "input_dir/good_data.chi",
             "input_dir/good_data.xy",
             "input_dir/good_data.txt",
@@ -72,7 +69,7 @@ def test_set_input_lists(inputs, expected, user_filesystem):
     cli_inputs = ["2.5"] + inputs
     actual_args = get_args(cli_inputs)
     actual_args = set_input_lists(actual_args)
-    assert set(actual_args.input_paths) == set(expected_paths)
+    assert sorted(actual_args.input_paths) == sorted(expected_paths)
 
 
 # This test covers non-existing single input file or directory, in this case we raise an error with message

src/diffpy/labpdfproc/tools.py

@@ -35,17 +35,6 @@ def _parse_file_list_file(input_path):
         return input_files
 
 
-def _parse_input_paths(input_path):
-    # Takes a path to return either a list of files paths if it is a file list,
-    # a list of single file path if it is a data file, or nothing
-    if "file_list" in input_path.name:
-        return _parse_file_list_file(input_path)
-    elif input_path.is_file():
-        return [input_path]
-    else:
-        return []
-
-
 def set_input_lists(args):
     """
     Set input directory and files.
@@ -69,11 +58,16 @@ def set_input_lists(args):
         input_path = Path(input).resolve()
         if input_path.exists():
             if input_path.is_file():
-                input_paths.extend(_parse_input_paths(input_path))
+                if "file_list" in input_path.name:
+                    input_paths.extend(_parse_file_list_file(input_path))
+                else:
+                    input_paths.append(input_path)
             elif input_path.is_dir():
                 input_files = input_path.glob("*")
-                for file in input_files:
-                    input_paths.extend(_parse_input_paths(file))
+                input_files = [
+                    file.resolve() for file in input_files if file.is_file() and "file_list" not in file.name
+                ]
+                input_paths.extend(input_files)
             else:
                 raise FileNotFoundError(f"Cannot find {input}. Please specify valid input file(s) or directories.")
         else: