docs: add docs for tools, update readme for --mud

Author: yucongalicechen

README.rst

@@ -110,14 +110,14 @@ Example
 Navigate to the directory that contains 1D diffraction patterns that you would like to process.
 Activate the conda environment (`conda activate diffpy.labpdfproc_env`) that contains the package and run the following command ::
 
-        labpdfproc <muD> <path/to/inputfile.txt>
+        labpdfproc <path/to/inputfile.txt> --mud <muD>
 
 Here replace <muD> with the value of muD for your sample
 and <path/to/inputfile.txt> with the path and filename of your input file.
 For example, if the uncorrected data case is called zro2_mo.xy and is in the current directory
 and it has a muD of 2.5 then the command would be ::
 
-        labpdfproc 2.5 zro2_mo.xy
+        labpdfproc zro2_mo.xy --mud 2.5
 
 Please type ::
 

news/tools-doc.rst

@@ -1,10 +1,10 @@
 **Added:**
 
-* <news item>
+* Utility and example documentation for ``tools`` module.
 
 **Changed:**
 
-* <news item>
+* Readme: muD now requires the ``--mud`` flag instead of a required argument.
 
 **Deprecated:**
 

src/diffpy/labpdfproc/tools.py

@@ -457,13 +457,13 @@ def preprocessing_args(args):
         The updated argparse Namespace with arguments preprocessed.
     """
     args = set_mud(args)
-    args = load_package_info(args)
-    args = load_user_info(args)
     args = set_input_lists(args)
     args = set_output_directory(args)
     args = set_wavelength(args)
     args = set_xtype(args)
     args = load_user_metadata(args)
+    args = load_user_info(args)
+    args = load_package_info(args)
     return args