removed nesting functions and the private function, moved file list test with missing file to errorous case

Author: yucongalicechen

src/diffpy/labpdfproc/labpdfprocapp.py

@@ -3,6 +3,7 @@
 
 from diffpy.labpdfproc.functions import apply_corr, compute_cve
 from diffpy.labpdfproc.tools import (
+    expand_list_file,
     known_sources,
     load_user_metadata,
     set_input_lists,
@@ -94,6 +95,7 @@ def get_args(override_cli_inputs=None):
 
 def main():
     args = get_args()
+    args = expand_list_file(args)
     args = set_input_lists(args)
     args.output_directory = set_output_directory(args)
     args.wavelength = set_wavelength(args)

src/diffpy/labpdfproc/tests/test_tools.py

@@ -6,6 +6,7 @@
 
 from diffpy.labpdfproc.labpdfprocapp import get_args
 from diffpy.labpdfproc.tools import (
+    expand_list_file,
     known_sources,
     load_user_metadata,
     set_input_lists,
@@ -49,10 +50,6 @@
             "input_dir/binary.pkl",
         ],
     ),
-    (  # file_list.txt list of files provided
-        ["input_dir/file_list.txt"],
-        ["good_data.chi", "good_data.xy", "good_data.txt"],
-    ),
     (  # file_list_example2.txt list of files provided in different directories
         ["input_dir/file_list_example2.txt"],
         ["input_dir/good_data.chi", "good_data.xy", "input_dir/good_data.txt"],
@@ -68,6 +65,7 @@ def test_set_input_lists(inputs, expected, user_filesystem):
 
     cli_inputs = ["2.5"] + inputs
     actual_args = get_args(cli_inputs)
+    actual_args = expand_list_file(actual_args)
     actual_args = set_input_lists(actual_args)
     assert sorted(actual_args.input_paths) == sorted(expected_paths)
 
@@ -87,6 +85,10 @@ def test_set_input_lists(inputs, expected, user_filesystem):
         ["good_data.chi", "good_data.xy", "unreadable_file.txt", "missing_file.txt"],
         "Cannot find missing_file.txt. Please specify valid input file(s) or directories.",
     ),
+    (  # file_list.txt list of files provided (with missing files)
+        ["input_dir/file_list.txt"],
+        "Cannot find missing_file.txt. Please specify valid input file(s) or directories.",
+    ),
 ]
 
 
@@ -96,6 +98,7 @@ def test_set_input_files_bad(inputs, msg, user_filesystem):
     os.chdir(base_dir)
     cli_inputs = ["2.5"] + inputs
     actual_args = get_args(cli_inputs)
+    actual_args = expand_list_file(actual_args)
     with pytest.raises(FileNotFoundError, match=msg[0]):
         actual_args = set_input_lists(actual_args)
 

src/diffpy/labpdfproc/tools.py

@@ -28,20 +28,27 @@ def set_output_directory(args):
     return output_dir
 
 
-def _parse_file_list_file(file_list_path):
-    with open(file_list_path, "r") as f:
-        # file_paths = [Path(file_path.strip()).resolve() for file_path in f.readlines()
-        # if Path(file_path.strip()).is_file()]
-        file_paths = [file_path.strip() for file_path in f.readlines()]
-        return file_paths
+def expand_list_file(args):
+    """
+    Expands the list of inputs by adding files from file lists and removing the file list.
 
+    Parameters
+    ----------
+    args argparse.Namespace
+        the arguments from the parser
 
-def expand_list_file(input):
-    file_list_inputs = [input_name for input_name in input if "file_list" in str(input_name)]
+    Returns
+    -------
+    the arguments with the modified input list
+
+    """
+    file_list_inputs = [input_name for input_name in args.input if "file_list" in input_name]
     for file_list_input in file_list_inputs:
-        input.remove(file_list_input)
-        input.extend(_parse_file_list_file(file_list_input))
-    return input
+        with open(file_list_input, "r") as f:
+            file_inputs = [input_name.strip() for input_name in f.readlines()]
+        args.input.extend(file_inputs)
+        args.input.remove(file_list_input)
+    return args
 
 
 def set_input_lists(args):
@@ -63,9 +70,8 @@ def set_input_lists(args):
     """
 
     input_paths = []
-    expanded_input = expand_list_file(args.input)
-    for input in expanded_input:
-        input_path = Path(input).resolve()
+    for input_name in args.input:
+        input_path = Path(input_name).resolve()
         if input_path.exists():
             if input_path.is_file():
                 input_paths.append(input_path)
@@ -76,9 +82,11 @@ def set_input_lists(args):
                 ]
                 input_paths.extend(input_files)
             else:
-                raise FileNotFoundError(f"Cannot find {input}. Please specify valid input file(s) or directories.")
+                raise FileNotFoundError(
+                    f"Cannot find {input_name}. Please specify valid input file(s) or directories."
+                )
         else:
-            raise FileNotFoundError(f"Cannot find {input}")
+            raise FileNotFoundError(f"Cannot find {input_name}")
     setattr(args, "input_paths", list(set(input_paths)))
     return args