style: apply manual editing to shorten the line width

Author: ycexiao

news/line79.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* reduce the line width limit to 79
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/pdfmorph/morph_helpers/__init__.py

@@ -11,7 +11,8 @@
 #
 ##############################################################################
 
-"""List of helpers for certain morphing operations (currently only used for smear)."""
+"""List of helpers for certain morphing operations
+(currently only used for smear)."""
 
 from diffpy.pdfmorph.morph_helpers.transformpdftordf import (
     TransformXtalPDFtoRDF,

src/diffpy/pdfmorph/morphs/morph.py

@@ -26,10 +26,12 @@
 class Morph(object):
     """Base class for implementing a morph given a target.
 
-    Adapted from diffpy.pdfgetx to include two sets of arrays that get passed through.
+    Adapted from diffpy.pdfgetx to include two sets of arrays that get passed
+    through.
 
-    Attributes are taken from config when not found locally. The morph may modify the config dictionary.
-    This is the means by which to communicate automatically modified attributes.
+    Attributes are taken from config when not found locally. The morph may
+    modify the config dictionary. This is the means by which to communicate
+    automatically modified attributes.
 
     Class Attributes
     ----------------
@@ -142,7 +144,8 @@ def __init__(self, config=None):
     def morph(self, x_morph, y_morph, x_target, y_target):
         """Morph arrays morphed or target.
 
-        Identity operation. This method should be overloaded in a derived class.
+        Identity operation.
+        This method should be overloaded in a derived class.
 
         Parameters
         ----------
@@ -154,7 +157,8 @@ def morph(self, x_morph, y_morph, x_target, y_target):
         Returns
         -------
         tuple
-            A tuple of numpy arrays (x_morph_out, y_morph_out, x_target_out, y_target_out)
+            A tuple of numpy arrays
+            (x_morph_out, y_morph_out, x_target_out, y_target_out)
         """
         self.x_morph_in = x_morph
         self.y_morph_in = y_morph
@@ -223,7 +227,8 @@ def plotOutputs(self, xylabels=True, **plotargs):
         xylabels: bool
             Flag for updating x and y axes labels.
         plotargs
-            Arguments passed to the pylab plot function. Note that "label" will be ignored.
+            Arguments passed to the pylab plot function.
+            Note that "label" will be ignored.
 
         Returns
         -------

src/diffpy/pdfmorph/morphs/morphchain.py

@@ -20,8 +20,9 @@
 class MorphChain(list):
     """Class for chaining morphs together.
 
-    This class is a queue of morphs that get executed in order via the 'morph' method.
-    This class derives from the built-in list, and list methods are used to modify the queue.
+    This class is a queue of morphs that get executed in order via the 'morph'
+    method. This class derives from the built-in list, and list methods are
+    used to modify the queue.
 
     This derives from list and relies on its methods where possible.
 
@@ -57,7 +58,8 @@ class MorphChain(list):
     xy_target_out
         Tuple of (x_target_out, y_target_out) from last morph.
     xyallout
-        Tuple of (x_morph_out, y_morph_out, x_target_out, y_target_out) from last morph.
+        Tuple of (x_morph_out, y_morph_out, x_target_out, y_target_out)
+        from last morph.
     parnames
         Names of parameters collected from morphs (Read only).
 
@@ -117,7 +119,8 @@ def __init__(self, config, *args):
 
         Notes
         -----
-            Additional arguments are morphs that will extend the queue of morphs.
+            Additional arguments are morphs that will extend the queue of
+            morphs.
         """
         self.config = config
         self.extend(args)
@@ -136,7 +139,8 @@ def morph(self, x_morph, y_morph, x_target, y_target):
         Returns
         -------
         tuple
-            A tuple of numpy arrays (x_morph_out, y_morph_out, x_target_out, y_target_out).
+            A tuple of numpy arrays
+            (x_morph_out, y_morph_out, x_target_out, y_target_out).
 
         Notes
         -----

src/diffpy/pdfmorph/morphs/morphrgrid.py

@@ -43,9 +43,10 @@ class MorphRGrid(Morph):
 
     Notes
     -----
-        If any of these is not defined or outside the bounds of the input arrays,
-        then it will be taken to be the most inclusive value from the input arrays.
-        These modified values will be stored as the above attributes.
+        If any of these is not defined or outside the bounds of the input
+        arrays, then it will be taken to be the most inclusive value from the
+        input arrays. These modified values will be stored as the above
+        attributes.
     """
 
     # Define input output types

src/diffpy/pdfmorph/morphs/morphshape.py

@@ -89,7 +89,8 @@ def morph(self, x_morph, y_morph, x_target, y_target):
 def _sphericalCF(r, psize):
     """Spherical nanoparticle characteristic function.
 
-    From Kodama et al., Acta Cryst. A, 62, 444-453 (converted from radius to diameter).
+    From Kodama et al., Acta Cryst. A, 62, 444-453
+    (converted from radius to diameter).
 
     Parameters
     ----------

src/diffpy/pdfmorph/pdfmorph_api.py

@@ -143,7 +143,8 @@ def pdfmorph(
 
         - morph_chain: diffpy.pdfmorph.morphs.morphchain.MorphChain
               The instance of processed morph chain.
-              Calling ``x_morph, y_morph, x_target, y_target = morph_chain.xyallout``
+              Calling
+              ``x_morph, y_morph, x_target, y_target = morph_chain.xyallout``
               will conveniently return morphed data and reference data
         - morphed_cfg: dict
               A dictionary of refined morphing parameters
@@ -156,8 +157,9 @@ def pdfmorph(
 
     Examples
     --------
-    # morphing (x_morph, y_morph) pair to (x_target, y_target) pair with scaling
-    from diffpy.pdfmorph.pdfmorph_api import pdfmorph, morph_default_config, plot_morph
+    # morphing (x_morph, y_morph) pair to (x_target, y_target) pair with
+    scaling from diffpy.pdfmorph.pdfmorph_api import pdfmorph,
+    morph_default_config, plot_morph
 
     morph_cfg = morph_default_config(scale=1.01)
     morph_rv_dict = pdfmorph(x_morph, y_morph, x_target, y_target, **morph_cfg)
@@ -258,14 +260,16 @@ def plot_morph(chain, ax=None, **kwargs):
         An instance of processed morph chain.
     ax: matplotlib.axes.Axes, optional
         An instance of Axes class to plot the morphing result.
-        If ax is None, instances of new Figure and Axes will be created. Default to None.
+        If ax is None, instances of new Figure and Axes will be created.
+        Default to None.
     kwargs:
         Additional keyword arguments will be passed to ``ax.plot(...**kwargs)``
 
     Returns
     -------
     l_list: list
-        A list of ``matplotlib.lines.Line2D`` objects representing the plotted data.
+        A list of ``matplotlib.lines.Line2D`` objects representing the
+        plotted data.
     """
     if ax is None:
         fig, ax = plt.subplots()

src/diffpy/pdfmorph/pdfmorph_io.py

@@ -46,10 +46,11 @@ def single_morph_output(
     save_file
         Name of file to print to. If None (default) print to terminal.
     morph_file
-        Name of the morphed PDF file. Required when printing to a non-terminal 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 and
-         y_morph_out is a List of gr 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).
     stdout_flag: bool
@@ -107,14 +108,16 @@ def single_morph_output(
 def create_morphs_directory(save_directory):
     """Create a directory for saving multiple morphed PDFs.
 
-    Takes in a user-given path to a directory save_directory and create a subdirectory named Morphs.
-    PDFmorph will save all morphs into the Morphs subdirectory while metadata about the morphs will
-    be stored in save_directory outside Morphs.
+    Takes in a user-given path to a directory save_directory and create a
+    subdirectory named Morphs. PDFmorph will save all morphs into the Morphs
+    subdirectory while metadata about the morphs will be stored in
+    save_directory outside Morphs.
 
     Parameters
     ----------
     save_directory
-        Path to a directory. PDFmorph will save all generated files within this directory.
+        Path to a directory. PDFmorph will save all generated files within
+        this directory.
 
     Returns
     -------
@@ -133,8 +136,9 @@ def create_morphs_directory(save_directory):
 
 def get_multisave_names(target_list: list, save_names_file=None, mm=False):
     """Create or import a dictionary that specifies names to save morphs as.
-    First attempt to import names from a specified file. If names for certain morphs not found,
-    use default naming scheme: 'Morph_with_Target_<target file name>.cgr'.
+    First attempt to import names from a specified file.
+    If names for certain morphs not found, use default naming scheme:
+    'Morph_with_Target_<target file name>.cgr'.
 
     Used when saving multiple morphs.
 
@@ -150,7 +154,8 @@ def get_multisave_names(target_list: list, save_names_file=None, mm=False):
     Returns
     -------
     dict
-        The names to save each morph as. Keys are the target PDF file names used to produce that morph.
+        The names to save each morph as. Keys are the target PDF file names
+        used to produce that morph.
     """
 
     # Dictionary storing save file names
@@ -167,15 +172,19 @@ def get_multisave_names(target_list: list, save_names_file=None, mm=False):
                 save_names.update(
                     {
                         target_file.name: {
-                            __save_morph_as__: f"Morph_with_Target_{target_file.stem}.cgr"
+                            __save_morph_as__: (
+                                f"Morph_with_Target_{target_file.stem}.cgr"
+                            )
                         }
                     }
                 )
             else:
                 save_names.update(
                     {
                         target_file.name: {
-                            __save_morph_as__: f"Morph_of_{target_file.stem}.cgr"
+                            __save_morph_as__: (
+                                f"Morph_of_{target_file.stem}.cgr"
+                            )
                         }
                     }
                 )
@@ -209,11 +218,14 @@ def multiple_morph_output(
     save_directory
         Name of directory to save morphs in.
     field
-        Name of field if data was sorted by a particular field. Otherwise, leave blank.
+        Name of field if data was sorted by a particular field.
+        Otherwise, leave blank.
     field_list: list
-        List of field values for each target PDF. Generated by diffpy.pdfmorph.tools.field_sort().
+        List of field values for each target PDF.
+        Generated by diffpy.pdfmorph.tools.field_sort().
     morph_file
-        Name of the morphed PDF file. Required to give summary data after saving to a directory.
+        Name of the morphed PDF file.
+        Required to give summary data after saving to a directory.
     target_directory
         Name of the directory containing the target PDF files.
         Required to give summary data after saving to a directory.
@@ -222,8 +234,8 @@ def multiple_morph_output(
     stdout_flag: bool
         Print to terminal when True (default False).
     mm: bool
-        Multiple morphs done with a single target rather than multiple targets for a single morphed file.
-        Swaps morph and target in the code.
+        Multiple morphs done with a single target rather than multiple
+        targets for a single morphed file. Swaps morph and target in the code.
     """
 
     # Input parameters used for every morph
@@ -235,7 +247,8 @@ def multiple_morph_output(
     # Verbose to get output for every morph
     verbose_outputs = ""
     if verbose:
-        # Output for every morph (information repeated in a succinct table below)
+        # Output for every morph
+        # (information repeated in a succinct table below)
         for target in morph_results.keys():
             if not mm:
                 output = f"\n# Target: {target}\n"
@@ -307,24 +320,27 @@ def multiple_morph_output(
 
 
 def tabulate_results(multiple_morph_results):
-    """Helper function to make a data table summarizing details about the results of multiple morphs.
+    """Helper function to make a data table summarizing details about the
+    results of multiple morphs.
 
     Parameters
     ----------
     multiple_morph_results
-        A collection of Dictionaries. Each Dictionary summarizes the resultsof a single morph.
+        A collection of Dictionaries. Each Dictionary summarizes the
+        resultsof a single morph.
 
     Returns
     -------
     tabulated_results: dict
-        Keys in tabulated_results are the table's column names and each corresponding value is a list
-        of data for that column.
+        Keys in tabulated_results are the table's column names and each
+        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"]
 
-    # Keys in this table represent column names and the value will be a list of column data
+    # Keys in this table represent column names and the value will be a list
+    # of column data
     tabulated_results = {}
     for param in relevant_parameters:
         tabulated_results.update(