Standardize lower-case for all dictionary keys

Author: Sparks29032

news/capitalization.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* All dictionary keys and column headers are lower-cased. This includes Rw->rw, Pearson->pearson, and the user-given --field-sort quantity is made lower-case.
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/morph/morph_io.py

@@ -129,7 +129,7 @@ def get_terminal_morph_output(mr_copy, uncertainties):
     # Handle special inputs (numerical)
     if "squeeze" in mr_copy:
         sq_dict = mr_copy.pop("squeeze")
-        rw_pos = list(mr_copy.keys()).index("Rw")
+        rw_pos = list(mr_copy.keys()).index("rw")
         morph_results_list = list(mr_copy.items())
         for idx, _ in enumerate(sq_dict):
             morph_results_list.insert(
@@ -148,22 +148,28 @@ def get_terminal_morph_output(mr_copy, uncertainties):
             func_dicts[func][0] = mr_copy.pop(f"{func}_function")
         if func in mr_copy:
             func_dicts[func][1] = mr_copy.pop(func)
-            rw_pos = list(mr_copy.keys()).index("Rw")
+            rw_pos = list(mr_copy.keys()).index("rw")
             morph_results_list = list(mr_copy.items())
             for idx, key in enumerate(func_dicts[func][1]):
                 morph_results_list.insert(
                     rw_pos + idx, (f"{func} {key}", func_dicts[func][1][key])
                 )
             mr_copy = dict(morph_results_list)
 
-    # Get uncertainties
+    # Keywords that should be capitalized in the saved files
+    special_keywords = ["rw", "pearson"]
+
+    # Print outputs including uncertainties when applicable
     if uncertainties is None:
         morphs_out += "\n".join(
-            f"# {key} = {mr_copy[key]:.6f}" for key in mr_copy.keys()
+            f"# {key.capitalize() if key in special_keywords else key} = "
+            f"{mr_copy[key]:.6f}"
+            for key in mr_copy.keys()
         )
     else:
         morphs_out += "\n".join(
-            f"# {key} = {mr_copy[key]:.6f}"
+            f"# {key.capitalize() if key in special_keywords else key} = "
+            f"{mr_copy[key]:.6f}"
             + (
                 f" +/- {uncertainties[key]:.6f}"
                 if key in uncertainties
@@ -431,11 +437,11 @@ def multiple_morph_output(
 
     # Table labels
     if not mm:
-        labels = "\n# Labels: [Target]"
+        labels = "\n# Labels: [target]"
     else:
-        labels = "\n# Labels: [Morph]"
+        labels = "\n# Labels: [morph]"
     if field is not None:
-        labels += f" [{field}]"
+        labels += f" [{field.lower()}]"
     for param in tabulated_results.keys():
         if len(tabulated_results[param]) > 0:
             labels += f" [{param}]"
@@ -501,7 +507,7 @@ def tabulate_results(multiple_morph_results):
         corresponding value is a list of data for that column.
     """
     # We only care about the following parameters in our data tables
-    relevant_parameters = ["Scale", "Smear", "Stretch", "Pearson", "Rw"]
+    relevant_parameters = ["scale", "smear", "stretch", "pearson", "rw"]
 
     # Keys in this table represent column names and the value will be a list
     # of column data

src/diffpy/morph/morphapp.py

@@ -854,8 +854,8 @@ def single_morph(
     # Output morph parameters
     morph_results = dict(config.items())
     # Ensure Rw, Pearson last two outputs
-    morph_results.update({"Rw": rw})
-    morph_results.update({"Pearson": pcc})
+    morph_results.update({"rw": rw})
+    morph_results.update({"pearson": pcc})
 
     # Print summary to terminal and save morph to file if requested
     xy_save = [chain.x_morph_out, chain.y_morph_out]
@@ -921,7 +921,7 @@ def single_morph(
     if python_wrap:
         morph_info = morph_results
         if opts.estimate_uncertainty is not None and unc is not None:
-            morph_info.update({"Uncertainties": unc})
+            morph_info.update({"uncertainties": unc})
         morph_table = numpy.array(xy_save).T
         return morph_info, morph_table
     else:
@@ -1089,7 +1089,7 @@ def multiple_targets(parser, opts, pargs, stdout_flag=True, python_wrap=False):
         plot_results = io.tabulate_results(morph_results)
         # Default parameter is Rw
         param_name = r"$R_w$"
-        param_list = plot_results["Rw"]
+        param_list = plot_results["rw"]
         # Find parameter if specified
         if opts.plotparam is not None:
             param_name = opts.plotparam
@@ -1284,7 +1284,7 @@ def multiple_morphs(parser, opts, pargs, stdout_flag=True, python_wrap=False):
         plot_results = io.tabulate_results(morph_results)
         # Default parameter is Rw
         param_name = r"$R_w$"
-        param_list = plot_results["Rw"]
+        param_list = plot_results["rw"]
         # Find parameter if specified
         if opts.plotparam is not None:
             param_name = opts.plotparam

tests/test_morphapp.py

@@ -344,7 +344,7 @@ def gaussian(x, mu, sigma):
         )[0]
         # Variances add, and 3^2+4^2=5^2
         assert pytest.approx(abs(smear_results["smear"])) == 4.0
-        assert pytest.approx(smear_results["Rw"]) == 0.0
+        assert pytest.approx(smear_results["rw"]) == 0.0
 
         # PDF-specific smear (should activate baseline slope)
         opts, _ = self.parser.parse_args(
@@ -361,4 +361,4 @@ def gaussian(x, mu, sigma):
             self.parser, opts, pargs, stdout_flag=False
         )[0]
         assert pytest.approx(abs(pdf_smear_results["smear"])) == 4.0
-        assert pytest.approx(pdf_smear_results["Rw"]) == 0.0
+        assert pytest.approx(pdf_smear_results["rw"]) == 0.0

tests/test_morphio.py

@@ -461,8 +461,8 @@ def fx(x, y, ax0, ax1):
             uncertainty=True,
         )
 
-        assert "Uncertainties" in morph_info.keys()
+        assert "uncertainties" in morph_info.keys()
         params = ["funcy ay0", "funcy ay1", "funcx ax0", "funcx ax1"]
-        for unc in morph_info["Uncertainties"].keys():
+        for unc in morph_info["uncertainties"].keys():
             assert unc in params
-            assert morph_info["Uncertainties"][unc] is not None
+            assert morph_info["uncertainties"][unc] is not None

tests/test_morphpy.py

@@ -186,7 +186,7 @@ class Chain:
             rw = get_rw(chain)
             del chain
             assert np.allclose(
-                [rw], [self.morphapp_results[target_file.name]["Rw"]]
+                [rw], [self.morphapp_results[target_file.name]["rw"]]
             )
         # Check values in dictionaries are approximately equal
         for file in morph_results.keys():
@@ -257,7 +257,7 @@ class Chain:
             rw = get_rw(chain)
             del chain
             assert np.allclose(
-                [rw], [self.morphapp_results[target_file.name]["Rw"]]
+                [rw], [self.morphapp_results[target_file.name]["rw"]]
             )
             # Check values in dictionaries are approximately equal
             for file in morph_results.keys():

tests/testdata/testsequence/testsaving/succinct/Morph_Reference_Table.txt

@@ -9,7 +9,7 @@
 # hshift = None
 # vshift = None
 
-# Labels: [Target] [Temperature] [Pearson] [Rw]
+# Labels: [target] [temperature] [pearson] [rw]
 f_180K.gr 180.0 0.999810 0.020141
 e_186K.gr 186.0 0.999424 0.034859
 d_192K.gr 192.0 0.998077 0.062392

tests/testdata/testsequence/testsaving/verbose/Morph_Reference_Table.txt

@@ -57,7 +57,7 @@
 # Rw = 0.127100
 # Pearson = 0.992111
 
-# Labels: [Target] [Temperature] [Pearson] [Rw]
+# Labels: [target] [temperature] [pearson] [rw]
 f_180K.gr 180.0 0.999810 0.020141
 e_186K.gr 186.0 0.999424 0.034859
 d_192K.gr 192.0 0.998077 0.062392

tests/testdata/testsequence/testsaving/verbose_unc/Morph_Reference_Table.txt

@@ -77,7 +77,7 @@
 # Rw = 0.117614
 # Pearson = 0.993059
 
-# Labels: [Target] [Temperature] [Scale] [Pearson] [Rw]
+# Labels: [target] [temperature] [scale] [pearson] [rw]
 f_180K.gr 180.0 0.994948 0.999842 0.017766
 e_186K.gr 186.0 0.992167 0.999549 0.030029
 d_192K.gr 192.0 0.993095 0.998318 0.057982