removal of whitespace excluding .txt and .rst

.coveragerc

@@ -1,5 +1,5 @@
 [run]
-source = 
+source =
     src/diffpy/pdfmorph/
 [report]
 omit =

.github/workflows/docs.yml

@@ -25,7 +25,7 @@ jobs:
 
       - name: install requirements
         run: >-
-          conda install -n build -c conda-forge 
+          conda install -n build -c conda-forge
           --file requirements/build.txt
           --file requirements/run.txt
           --file requirements/docs.txt
@@ -42,4 +42,3 @@ jobs:
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: ./doc/manual/build/html
-

doc/manual/source/conf.py

@@ -11,12 +11,12 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 import sys
-from pathlib import Path
 from importlib.metadata import version
+from pathlib import Path
+
 import sphinx_rtd_theme
 from jinja2 import Environment, FileSystemLoader, Template
 
-
 sys.path.insert(0, str(Path("../../..").resolve()))
 sys.path.insert(0, str(Path("../../../src").resolve()))
 

run_tests.py

@@ -1,15 +1,16 @@
 #!/usr/bin/env python
 
 import sys
+
 import pytest
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     # show output results from every test function
-    args = ['-v']
+    args = ["-v"]
     # show the message output for skipped and expected failure tests
     if len(sys.argv) > 1:
         args.extend(sys.argv[1:])
-    print('pytest arguments: {}'.format(args))
+    print("pytest arguments: {}".format(args))
     # # compute coverage stats for xpdAcq
     # call pytest and exit with the return code from pytest so that
     # travis will fail correctly if tests fail

src/diffpy/pdfmorph/__init__.py

@@ -17,8 +17,8 @@
 """
 
 # top-level import
-from diffpy.pdfmorph.pdfmorph_api import (morph_default_config, pdfmorph,
-                                          plot_morph)
+from diffpy.pdfmorph.pdfmorph_api import morph_default_config, pdfmorph, plot_morph
+
 # obtain version information
 from diffpy.pdfmorph.version import __version__
 

src/diffpy/pdfmorph/morph_helpers/__init__.py

@@ -13,10 +13,8 @@
 
 """List of helpers for certain morphing operations (currently only used for smear)."""
 
-from diffpy.pdfmorph.morph_helpers.transformpdftordf import \
-    TransformXtalPDFtoRDF
-from diffpy.pdfmorph.morph_helpers.transformrdftopdf import \
-    TransformXtalRDFtoPDF
+from diffpy.pdfmorph.morph_helpers.transformpdftordf import TransformXtalPDFtoRDF
+from diffpy.pdfmorph.morph_helpers.transformrdftopdf import TransformXtalRDFtoPDF
 
 # List of helpers
 morph_helpers = [

src/diffpy/pdfmorph/morphs/morphishape.py

@@ -15,7 +15,7 @@
 
 
 """class MorphISphere -- apply inverse spherical shape function
-class MorphISpheroid -- apply inverse spheroidal shape function 
+class MorphISpheroid -- apply inverse spheroidal shape function
 """
 
 

src/diffpy/pdfmorph/pdfmorph_io.py

@@ -48,7 +48,7 @@ def single_morph_output(
     morph_file
         Name of the morphed PDF file. Required when printing to a non-terminal file.
     param xy_out: list
-        List of the form [x_morph_out, y_morph_out]. x_morph_out is a List of r values 
+        List of the form [x_morph_out, y_morph_out]. x_morph_out is a List of r values
          and y_morph_out is a List of gr values.
     verbose: bool
         Print additional details about the morph when True (default False).

src/diffpy/pdfmorph/pdfmorphapp.py

@@ -206,31 +206,31 @@ def custom_error(self, msg):
         type="float",
         metavar="RADIUS",
         help="""Apply characteristic function of sphere with radius RADIUS.
-         If PRADIUS is also specified, instead apply characteristic function of spheroid with equatorial radius RADIUS 
+         If PRADIUS is also specified, instead apply characteristic function of spheroid with equatorial radius RADIUS
          and polar radius PRADIUS.""",
     )
     group.add_option(
         "--pradius",
         type="float",
         metavar="PRADIUS",
         help="""Apply characteristic function of spheroid with equatorial
-         radius RADIUS and polar radius PRADIUS. If only PRADIUS is specified, instead apply characteristic 
+         radius RADIUS and polar radius PRADIUS. If only PRADIUS is specified, instead apply characteristic
          function of sphere with radius PRADIUS.""",
     )
     group.add_option(
         "--iradius",
         type="float",
         metavar="IRADIUS",
-        help="""Apply inverse characteristic function of sphere with radius IRADIUS.  If IPRADIUS is 
-         also specified, instead apply inverse characteristic function of spheroid with equatorial 
+        help="""Apply inverse characteristic function of sphere with radius IRADIUS.  If IPRADIUS is
+         also specified, instead apply inverse characteristic function of spheroid with equatorial
          radius IRADIUS and polar radius IPRADIUS.""",
     )
     group.add_option(
         "--ipradius",
         type="float",
         metavar="IPRADIUS",
-        help="""Apply inverse characteristic function of spheroid with equatorial radius IRADIUS and 
-         polar radius IPRADIUS. If only IPRADIUS is specified, instead apply inverse characteristic function 
+        help="""Apply inverse characteristic function of spheroid with equatorial radius IRADIUS and
+         polar radius IPRADIUS. If only IPRADIUS is specified, instead apply inverse characteristic function
          of sphere with radius IPRADIUS.""",
     )
 
@@ -492,7 +492,9 @@ def multiple_morphs(parser, opts, pargs, stdout_flag=True):
     # Sort files in directory by some field
     if field is not None:
         try:
-            target_list, field_list = tools.field_sort(target_list, field, opts.reverse, opts.serfile, get_field_values=True)
+            target_list, field_list = tools.field_sort(
+                target_list, field, opts.reverse, opts.serfile, get_field_values=True
+            )
         except KeyError:
             if opts.serfile is not None:
                 parser.custom_error("The requested field was not found in the metadata file.")
@@ -589,7 +591,10 @@ def multiple_morphs(parser, opts, pargs, stdout_flag=True):
             # Can occur for non-refined plotting parameters
             # i.e. --smear is not selected as an option, but smear is the plotting parameter
             except ValueError:
-                parser.custom_error("The plot parameter is missing values for at least one morph and target pair. " "No plot shown.")
+                parser.custom_error(
+                    "The plot parameter is missing values for at least one morph and target pair. "
+                    "No plot shown."
+                )
 
     return morph_results
 

src/diffpy/pdfmorph/tests/test_morphpdftordf.py

@@ -11,8 +11,7 @@
 tests_dir = os.path.dirname(os.path.abspath(thisfile))
 # testdata_dir = os.path.join(tests_dir, 'testdata')
 
-from diffpy.pdfmorph.morph_helpers.transformpdftordf import \
-    TransformXtalPDFtoRDF
+from diffpy.pdfmorph.morph_helpers.transformpdftordf import TransformXtalPDFtoRDF
 
 
 class TestTransformXtalPDFtoRDF:

src/diffpy/pdfmorph/tests/test_morphrdftopdf.py

@@ -11,8 +11,7 @@
 tests_dir = os.path.dirname(os.path.abspath(thisfile))
 # testdata_dir = os.path.join(tests_dir, 'testdata')
 
-from diffpy.pdfmorph.morph_helpers.transformrdftopdf import \
-    TransformXtalRDFtoPDF
+from diffpy.pdfmorph.morph_helpers.transformrdftopdf import TransformXtalRDFtoPDF
 
 
 class TestTransformXtalRDFtoPDF:

src/diffpy/pdfmorph/tests/test_morphshape.py

@@ -2,6 +2,7 @@
 
 
 import os
+
 import numpy
 import pytest
 

src/diffpy/pdfmorph/tests/test_pdfmorphapp.py

@@ -4,8 +4,7 @@
 
 import pytest
 
-from diffpy.pdfmorph.pdfmorphapp import (create_option_parser, multiple_morphs,
-                                         single_morph)
+from diffpy.pdfmorph.pdfmorphapp import create_option_parser, multiple_morphs, single_morph
 
 thisfile = locals().get("__file__", "file.py")
 tests_dir = Path(thisfile).parent.resolve()

src/diffpy/pdfmorph/tests/test_pdfmorphio.py

@@ -10,8 +10,7 @@
 except ImportError:
     pass
 
-from diffpy.pdfmorph.pdfmorphapp import (create_option_parser, multiple_morphs,
-                                         single_morph)
+from diffpy.pdfmorph.pdfmorphapp import create_option_parser, multiple_morphs, single_morph
 
 thisfile = locals().get("__file__", "file.py")
 tests_dir = Path(thisfile).parent.resolve()

src/diffpy/pdfmorph/tests/test_pdfplot.py

@@ -5,8 +5,7 @@
 import matplotlib.pyplot as plt
 import numpy as np
 
-from diffpy.pdfmorph.pdfmorph_api import (morph_default_config, pdfmorph,
-                                          plot_morph)
+from diffpy.pdfmorph.pdfmorph_api import morph_default_config, pdfmorph, plot_morph
 from diffpy.pdfmorph.tests.test_morphstretch import heaviside
 
 

src/diffpy/pdfmorph/tests/test_refine.py

@@ -11,10 +11,8 @@
 tests_dir = os.path.dirname(os.path.abspath(thisfile))
 testdata_dir = os.path.join(tests_dir, "testdata")
 
-from diffpy.pdfmorph.morph_helpers.transformpdftordf import \
-    TransformXtalPDFtoRDF
-from diffpy.pdfmorph.morph_helpers.transformrdftopdf import \
-    TransformXtalRDFtoPDF
+from diffpy.pdfmorph.morph_helpers.transformpdftordf import TransformXtalPDFtoRDF
+from diffpy.pdfmorph.morph_helpers.transformrdftopdf import TransformXtalRDFtoPDF
 from diffpy.pdfmorph.morphs.morphchain import MorphChain
 from diffpy.pdfmorph.morphs.morphscale import MorphScale
 from diffpy.pdfmorph.morphs.morphsmear import MorphSmear

src/diffpy/pdfmorph/tests/testdata/testsequence_serialfile.json

@@ -132,4 +132,4 @@
     "rstep": 0.01,
     "rpoly": 0.7
   }
-}
+}

tutorial/sample_namesfile.json

@@ -10,4 +10,4 @@
     "SaVe_MoRph_As": "this_also_works.extension",
     "note": "Capitalization does NOT matter. The program is case insensitive."
   }
-}
+}