Merge pull request #164 from ycexiao/line_width

style: set the line width limit to 79

Author: sbillinge

Diff for: .flake8

@@ -5,7 +5,7 @@ exclude =
     build,
     dist,
     doc/source/conf.py
-max-line-length = 115
+max-line-length = 79
 # Ignore some style 'errors' produced while formatting by 'black'
 # https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#labels-why-pycodestyle-warnings
 extend-ignore = E203

Diff for: .isort.cfg

@@ -1,4 +1,4 @@
 [settings]
-line_length = 115
+line_length = 79
 multi_line_output = 3
 include_trailing_comma = True

Diff for: doc/source/conf.py

@@ -223,7 +223,13 @@
 # (source start file, target name, title,
 # author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    ("index", "diffpy.pdfmorph.tex", "diffpy.pdfmorph Documentation", ab_authors, "manual"),
+    (
+        "index",
+        "diffpy.pdfmorph.tex",
+        "diffpy.pdfmorph Documentation",
+        ab_authors,
+        "manual",
+    ),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -251,7 +257,15 @@
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [("index", "diffpy.pdfmorph", "diffpy.pdfmorph Documentation", ab_authors, 1)]
+man_pages = [
+    (
+        "index",
+        "diffpy.pdfmorph",
+        "diffpy.pdfmorph Documentation",
+        ab_authors,
+        1,
+    )
+]
 
 # If true, show URL addresses after external links.
 # man_show_urls = False

Diff for: news/line79.rst

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

Diff for: pyproject.toml

@@ -60,7 +60,7 @@ ignore-words = ".codespell/ignore_words.txt"
 skip = "*.cif,*.dat,*agr"
 
 [tool.black]
-line-length = 115
+line-length = 79
 include = '\.pyi?$'
 exclude = '''
 /(

Diff for: src/diffpy/pdfmorph/morph_helpers/__init__.py

@@ -11,10 +11,15 @@
 #
 ##############################################################################
 
-"""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
-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 = [

Diff for: src/diffpy/pdfmorph/morph_helpers/transformpdftordf.py

@@ -51,7 +51,9 @@ def morph(self, x_morph, y_morph, x_target, y_target):
         morph_baseline = self.baselineslope * self.x_morph_in
         self.y_morph_out = self.x_morph_in * (self.y_morph_in - morph_baseline)
         target_baseline = self.baselineslope * self.x_target_in
-        self.y_target_out = self.x_target_in * (self.y_target_in - target_baseline)
+        self.y_target_out = self.x_target_in * (
+            self.y_target_in - target_baseline
+        )
         return self.xyallout
 
 

Diff for: src/diffpy/pdfmorph/morph_helpers/transformrdftopdf.py

@@ -53,10 +53,14 @@ def morph(self, x_morph, y_morph, x_target, y_target):
         morph_baseline = self.baselineslope * self.x_morph_in
         target_baseline = self.baselineslope * self.x_target_in
         with numpy.errstate(divide="ignore", invalid="ignore"):
-            self.y_target_out = self.y_target_in / self.x_target_in + target_baseline
+            self.y_target_out = (
+                self.y_target_in / self.x_target_in + target_baseline
+            )
         self.y_target_out[self.x_target_in == 0] = 0
         with numpy.errstate(divide="ignore", invalid="ignore"):
-            self.y_morph_out = self.y_morph_in / self.x_morph_in + morph_baseline
+            self.y_morph_out = (
+                self.y_morph_in / self.x_morph_in + morph_baseline
+            )
         self.y_morph_out[self.x_target_in == 0] = 0
         return self.xyallout
 

Diff for: 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
         -------
@@ -234,7 +239,9 @@ def plotOutputs(self, xylabels=True, **plotargs):
 
         pargs = dict(plotargs)
         pargs.pop("label", None)
-        rv = plot(self.x_target_out, self.y_target_out, label="target", **pargs)
+        rv = plot(
+            self.x_target_out, self.y_target_out, label="target", **pargs
+        )
         rv = plot(self.x_morph_out, self.y_morph_out, label="morph", **pargs)
         if xylabels:
             xlabel(self.xoutlabel)

Diff for: 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).
 
@@ -66,19 +68,47 @@ class MorphChain(list):
         The properties return tuples of None if there are no morphs.
     """
 
-    x_morph_in = property(lambda self: None if len(self) == 0 else self[0].x_morph_in)
-    y_morph_in = property(lambda self: None if len(self) == 0 else self[0].y_morph_in)
-    x_target_in = property(lambda self: None if len(self) == 0 else self[0].x_target_in)
-    y_target_in = property(lambda self: None if len(self) == 0 else self[0].y_target_in)
-    x_morph_out = property(lambda self: None if len(self) == 0 else self[-1].x_morph_out)
-    y_morph_out = property(lambda self: None if len(self) == 0 else self[-1].y_morph_out)
-    x_target_out = property(lambda self: None if len(self) == 0 else self[-1].x_target_out)
-    y_target_out = property(lambda self: None if len(self) == 0 else self[-1].y_target_out)
-    xy_morph_in = property(lambda self: (None, None) if len(self) == 0 else self[0].xy_morph_in)
-    xy_morph_out = property(lambda self: (None, None) if len(self) == 0 else self[-1].xy_morph_out)
-    xy_target_in = property(lambda self: (None, None) if len(self) == 0 else self[0].xy_target_in)
-    xy_target_out = property(lambda self: (None, None) if len(self) == 0 else self[-1].xy_target_out)
-    xyallout = property(lambda self: (None, None, None, None) if len(self) == 0 else self[-1].xyallout)
+    x_morph_in = property(
+        lambda self: None if len(self) == 0 else self[0].x_morph_in
+    )
+    y_morph_in = property(
+        lambda self: None if len(self) == 0 else self[0].y_morph_in
+    )
+    x_target_in = property(
+        lambda self: None if len(self) == 0 else self[0].x_target_in
+    )
+    y_target_in = property(
+        lambda self: None if len(self) == 0 else self[0].y_target_in
+    )
+    x_morph_out = property(
+        lambda self: None if len(self) == 0 else self[-1].x_morph_out
+    )
+    y_morph_out = property(
+        lambda self: None if len(self) == 0 else self[-1].y_morph_out
+    )
+    x_target_out = property(
+        lambda self: None if len(self) == 0 else self[-1].x_target_out
+    )
+    y_target_out = property(
+        lambda self: None if len(self) == 0 else self[-1].y_target_out
+    )
+    xy_morph_in = property(
+        lambda self: (None, None) if len(self) == 0 else self[0].xy_morph_in
+    )
+    xy_morph_out = property(
+        lambda self: (None, None) if len(self) == 0 else self[-1].xy_morph_out
+    )
+    xy_target_in = property(
+        lambda self: (None, None) if len(self) == 0 else self[0].xy_target_in
+    )
+    xy_target_out = property(
+        lambda self: (None, None) if len(self) == 0 else self[-1].xy_target_out
+    )
+    xyallout = property(
+        lambda self: (
+            (None, None, None, None) if len(self) == 0 else self[-1].xyallout
+        )
+    )
     parnames = property(lambda self: set(p for m in self for p in m.parnames))
 
     def __init__(self, config, *args):
@@ -89,7 +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)
@@ -108,7 +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
         -----

Diff for: 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
@@ -63,18 +64,27 @@ def morph(self, x_morph, y_morph, x_target, y_target):
         r_step_target = self.x_target_in[1] - self.x_target_in[0]
         r_step_morph = self.x_morph_in[1] - self.x_morph_in[0]
         rstepinc = max(r_step_target, r_step_morph)
-        rmaxinc = min(self.x_target_in[-1] + r_step_target, self.x_morph_in[-1] + r_step_morph)
+        rmaxinc = min(
+            self.x_target_in[-1] + r_step_target,
+            self.x_morph_in[-1] + r_step_morph,
+        )
         if self.rmin is None or self.rmin < rmininc:
             self.rmin = rmininc
         if self.rmax is None or self.rmax > rmaxinc:
             self.rmax = rmaxinc
         if self.rstep is None or self.rstep < rstepinc:
             self.rstep = rstepinc
         # Make sure that rmax is exclusive
-        self.x_morph_out = numpy.arange(self.rmin, self.rmax - epsilon, self.rstep)
-        self.y_morph_out = numpy.interp(self.x_morph_out, self.x_morph_in, self.y_morph_in)
+        self.x_morph_out = numpy.arange(
+            self.rmin, self.rmax - epsilon, self.rstep
+        )
+        self.y_morph_out = numpy.interp(
+            self.x_morph_out, self.x_morph_in, self.y_morph_in
+        )
         self.x_target_out = self.x_morph_out.copy()
-        self.y_target_out = numpy.interp(self.x_target_out, self.x_target_in, self.y_target_in)
+        self.y_target_out = numpy.interp(
+            self.x_target_out, self.x_target_in, self.y_target_in
+        )
         return self.xyallout
 
 

Diff for: 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
     ----------
@@ -163,21 +164,19 @@ def _spheroidalCF2(r, psize, axrat):
         r = rx[rx <= v * psize]
         r2 = r * r
         f1 = (
-            1
-            - 3 * r / (4 * d * v) * (1 - r2 / (4 * d2) * (1 + 2.0 / (3 * v2)))
-            - 3 * r / (4 * d) * (1 - r2 / (4 * d2)) * v / sqrt(1 - v2) * atanh(sqrt(1 - v2))
+            1 - 3*r/(4*d*v)*(1-r2/(4*d2)*(1+2.0/(3*v2))) - 3*r/(4*d)*(1-r2/(4*d2))*v/sqrt(1-v2)*atanh(sqrt(1-v2))  # fmt: skip # noqa: E501
         )
 
         r = rx[numpy.logical_and(rx > v * psize, rx <= psize)]
         r2 = r * r
+        # fmt: off
         f2 = (
             (
-                3 * d / (8 * r) * (1 + r2 / (2 * d2)) * sqrt(1 - r2 / d2)
-                - 3 * r / (4 * d) * (1 - r2 / (4 * d2)) * atanh(sqrt(1 - r2 / d2))
+                3*d/(8*r)*(1+r2/(2*d2))*sqrt(1-r2/d2) - 3*r/(4*d)*(1-r2/(4*d2))*atanh(sqrt(1-r2/d2))  # noqa: E501
             )
-            * v
-            / sqrt(1 - v2)
+            * v / sqrt(1-v2)
         )
+        # fmt: on
 
         r = rx[rx > psize]
         f3 = numpy.zeros_like(r)
@@ -188,24 +187,13 @@ def _spheroidalCF2(r, psize, axrat):
         r = rx[rx <= psize]
         r2 = r * r
         f1 = (
-            1
-            - 3 * r / (4 * d * v) * (1 - r2 / (4 * d2) * (1 + 2.0 / (3 * v2)))
-            - 3 * r / (4 * d) * (1 - r2 / (4 * d2)) * v / sqrt(v2 - 1) * atan(sqrt(v2 - 1))
+            1 - 3*r/(4*d*v)*(1-r2/(4*d2)*(1+2.0/(3*v2))) - 3*r/(4*d)*(1-r2/(4*d2))*v/sqrt(v2-1)*atan(sqrt(v2-1))  # fmt: skip # noqa: E501
         )
 
         r = rx[numpy.logical_and(rx > psize, rx <= v * psize)]
         r2 = r * r
         f2 = (
-            1
-            - 3 * r / (4 * d * v) * (1 - r2 / (4 * d2) * (1 + 2.0 / (3 * v2)))
-            - 3.0 / 8 * (1 + r2 / (2 * d2)) * sqrt(1 - d2 / r2) * v / sqrt(v2 - 1)
-            - 3
-            * r
-            / (4 * d)
-            * (1 - r2 / (4 * d2))
-            * v
-            / sqrt(v2 - 1)
-            * (atan(sqrt(v2 - 1)) - atan(sqrt(r2 / d2 - 1)))
+            1 - 3*r/(4*d*v)*(1-r2/(4*d2)*(1+2.0/(3*v2))) - 3.0/8*(1+r2/(2*d2))*sqrt(1-d2/r2)*v/sqrt(v2-1) - 3*r/(4*d)*(1-r2/(4*d2))*v/sqrt(v2-1)*(atan(sqrt(v2-1))-atan(sqrt(r2/d2-1)))  # fmt: skip # noqa:E501
         )
 
         r = rx[rx > v * psize]