Add documentation

Author: Sparks29032

docs/source/morphpy.rst

@@ -38,7 +38,7 @@ Python Morphing Functions
 
        * ``morph_info`` contains all morphs as keys (e.g. ``"scale"``, ``"stretch"``, ``"smear"``) with
          the optimized morphing parameters found by ``diffpy.morph`` as values. ``morph_info`` also contains
-         the Rw and Pearson correlation coefficients found post-morphing. Try printing ``print(morph_info)``
+         the Rw and Pearson correlation coefficients found post-morphing. Try printing ``print(morph_info)``
          and compare the values stored in this dictionary to those given by the CLI output!
        * ``morph_table`` is a two-column array of the morphed function interpolated onto the grid of the
          target function (e.g. in our example, it returns the contents of `darkSub_rh20_C_01.gr` after
@@ -74,6 +74,10 @@ General Parameters
 
 save: str or path
     Save the morphed function to a the file passed to save. Use '-' for stdout.
+get_diff: bool
+    Return the difference function (morphed function minus target function) instead of
+    the morphed function (default). When save is enabled, the difference function
+    is saved instead of the morphed function.
 verbose: bool
     Print additional header details to saved files. These include details about the morph
     inputs and outputs.
@@ -240,4 +244,4 @@ As you can see, the fitted scale and offset values match the ones used
 to generate the target (scale=20 & offset=0.8). This example shows how
 ``MorphFuncy`` can be used to fit and apply custom transformations. Now
 it's your turn to experiment with other custom functions that may be useful
-for analyzing your data.
+for analyzing your data.

src/diffpy/morph/morphapp.py

@@ -93,7 +93,7 @@ def custom_error(self, msg):
     parser.add_option(
         "--diff",
         "--get-diff",
-        dest="diff",
+        dest="get_diff",
         action="store_true",
         help=(
             "Save the difference curve rather than the manipulated function.\n"
@@ -719,7 +719,7 @@ def single_morph(
 
     # Print summary to terminal and save morph to file if requested
     xy_save = [chain.x_morph_out, chain.y_morph_out]
-    if opts.diff is not None:
+    if opts.get_diff is not None:
         diff_chain = morphs.MorphChain(
             {"rmin": None, "rmax": None, "rstep": None}
         )

tests/test_morphpy.py

@@ -97,7 +97,7 @@ def test_morph_opts(self, setup_morph):
             "addpearson": True,
             "apply": True,
             "reverse": True,
-            "diff": True,
+            "get_diff": True,
             "multiple_morphs": True,
             "multiple_targets": True,
         }