wrap up preprocessing steps (set inputs, wavelengths, etc) as a public function in tools

Author: yucongalicechen

src/diffpy/labpdfproc/labpdfprocapp.py

@@ -2,16 +2,7 @@
 from argparse import ArgumentParser
 
 from diffpy.labpdfproc.functions import apply_corr, compute_cve
-from diffpy.labpdfproc.tools import (
-    known_sources,
-    load_metadata,
-    load_package_info,
-    load_user_info,
-    load_user_metadata,
-    set_input_lists,
-    set_output_directory,
-    set_wavelength,
-)
+from diffpy.labpdfproc.tools import known_sources, load_metadata, preprocessing_args
 from diffpy.utils.parsers.loaddata import loadData
 from diffpy.utils.scattering_objects.diffraction_objects import XQUANTITIES, Diffraction_object
 
@@ -113,12 +104,7 @@ def get_args(override_cli_inputs=None):
 
 def main():
     args = get_args()
-    args = load_package_info(args)
-    args = load_user_info(args)
-    args = set_input_lists(args)
-    args.output_directory = set_output_directory(args)
-    args = set_wavelength(args)
-    args = load_user_metadata(args)
+    args = preprocessing_args(args)
 
     for filepath in args.input_paths:
         outfilestem = filepath.stem + "_corrected"

src/diffpy/labpdfproc/tests/test_tools.py

@@ -11,6 +11,7 @@
     load_package_info,
     load_user_info,
     load_user_metadata,
+    preprocessing_args,
     set_input_lists,
     set_output_directory,
     set_wavelength,
@@ -281,7 +282,7 @@ def test_load_package_info(mocker):
     assert actual_args.package_info == {"diffpy.labpdfproc": "1.2.3", "diffpy.utils": "3.3.0"}
 
 
-def _setup(mocker, user_filesystem):
+def test_load_metadata(mocker, user_filesystem):
     cwd = Path(user_filesystem)
     home_dir = cwd / "home_dir"
     mocker.patch("pathlib.Path.home", lambda _: home_dir)
@@ -290,20 +291,6 @@ def _setup(mocker, user_filesystem):
         "importlib.metadata.version",
         side_effect=lambda package_name: "3.3.0" if package_name == "diffpy.utils" else "1.2.3",
     )
-
-
-def _preprocess_args(args):
-    args = load_package_info(args)
-    args = load_user_info(args)
-    args = set_input_lists(args)
-    args.output_directory = set_output_directory(args)
-    args = set_wavelength(args)
-    args = load_user_metadata(args)
-    return args
-
-
-def test_load_metadata(mocker, user_filesystem):
-    _setup(mocker, user_filesystem)
     cli_inputs = [
         "2.5",
         ".",
@@ -315,7 +302,7 @@ def test_load_metadata(mocker, user_filesystem):
         "[email protected]",
     ]
     actual_args = get_args(cli_inputs)
-    actual_args = _preprocess_args(actual_args)
+    actual_args = preprocessing_args(actual_args)
     for filepath in actual_args.input_paths:
         actual_metadata = load_metadata(actual_args, filepath)
         expected_metadata = {

src/diffpy/labpdfproc/tools.py

@@ -218,6 +218,28 @@ def load_package_info(args):
     return args
 
 
+def preprocessing_args(args):
+    """
+    Perform preprocessing on the provided argparse Namespace
+
+    Parameters
+    ----------
+    args argparse.Namespace
+        the arguments from the parser, default is None
+
+    Returns
+    -------
+    the updated argparse Namespace with arguments preprocessed
+    """
+    args = load_package_info(args)
+    args = load_user_info(args)
+    args = set_input_lists(args)
+    args.output_directory = set_output_directory(args)
+    args = set_wavelength(args)
+    args = load_user_metadata(args)
+    return args
+
+
 def load_metadata(args, filepath):
     """
     Load relevant metadata from args