Merge pull request #99 from sbillinge/black

black

Author: sbillinge

pyproject.toml

@@ -52,3 +52,28 @@ where = ["src"]  # list of folders that contain the packages (["."] by default)
 include = ["diffpy*"]  # package names should match these glob patterns (["*"] by default)
 exclude = ["diffpy.pdfmorph.tests*"]  # exclude packages matching these glob patterns (empty by default)
 namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
+
+[tool.black]
+line-length = 115
+include = '\.pyi?$'
+exclude = '''
+/(
+    \.git
+  | \.hg
+  | \.mypy_cache
+  | \.tox
+  | \.venv
+  | _build
+  | buck-out
+  | build
+  | dist
+
+  # The following are specific to Black, you probably don't want those.
+  | blib2to3
+  | tests/data
+)/
+'''
+
+[tool.flake8]
+max-line-length = 115
+per-file-ignores="__init__.py:F401"

src/diffpy/pdfmorph/__init__.py

@@ -16,12 +16,12 @@
 """Tools for manipulating and comparing PDFs.
 """
 
+# top-level import
+from diffpy.pdfmorph.pdfmorph_api import (morph_default_config, pdfmorph,
+                                          plot_morph)
 # obtain version information
 from diffpy.pdfmorph.version import __version__
 
-# top-level import
-from diffpy.pdfmorph.pdfmorph_api import pdfmorph, morph_default_config, plot_morph
-
 # key used when saving multiple morphs
 __save_morph_as__ = "save_morph_as"
 

src/diffpy/pdfmorph/log.py

@@ -23,11 +23,11 @@
 import logging
 
 # logging configuration
-plog = logging.getLogger('diffpy.pdfmorph')
+plog = logging.getLogger("diffpy.pdfmorph")
 
 
 def set_verbosity(vb):
-    '''Set verbosity of the pdfmorph logger.
+    """Set verbosity of the pdfmorph logger.
 
     Parameters
     ----------
@@ -37,7 +37,7 @@ def set_verbosity(vb):
     Returns
     -------
     No return value.
-    '''
+    """
     try:
         if type(vb) is str:
             level = int(getattr(logging, vb.upper(), vb))

src/diffpy/pdfmorph/morph_helpers/__init__.py

@@ -13,13 +13,13 @@
 
 """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 = [
     TransformXtalPDFtoRDF,
     TransformXtalRDFtoPDF,
 ]
-
-

src/diffpy/pdfmorph/morph_helpers/transformpdftordf.py

@@ -22,7 +22,7 @@
 
 
 class TransformXtalPDFtoRDF(Morph):
-    '''Transform crystal PDFs to RDFs.
+    """Transform crystal PDFs to RDFs.
 
     Converts both morph data and target data PDFs to RDFs.
 
@@ -35,10 +35,10 @@ class TransformXtalPDFtoRDF(Morph):
     With s = baselineslope,
     R(r) = r * (G(r) - r * s)
 
-    '''
+    """
 
     # Define input output types
-    summary = 'Turn the PDF into the RDF for both the morph and target'
+    summary = "Turn the PDF into the RDF for both the morph and target"
     xinlabel = LABEL_RA
     yinlabel = LABEL_GR
     xoutlabel = LABEL_RA

src/diffpy/pdfmorph/morph_helpers/transformrdftopdf.py

@@ -19,11 +19,12 @@
 
 
 import numpy
+
 from diffpy.pdfmorph.morphs.morph import *
 
 
 class TransformXtalRDFtoPDF(Morph):
-    '''Transform crystal RDFs to PDFs.
+    """Transform crystal RDFs to PDFs.
 
     Converts both morph data and target data RDFs to PDFs.
 
@@ -36,10 +37,10 @@ class TransformXtalRDFtoPDF(Morph):
     With s = baselineslope,
     G(r) = R(r) / r + r * s
 
-    '''
+    """
 
     # Define input output types
-    summary = 'Turn the PDF into the RDF for both the morph and target'
+    summary = "Turn the PDF into the RDF for both the morph and target"
     xinlabel = LABEL_RA
     yinlabel = LABEL_RR
     xoutlabel = LABEL_RA
@@ -51,10 +52,10 @@ def morph(self, x_morph, y_morph, x_target, y_target):
         Morph.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'):
+        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.x_target_in == 0] = 0
-        with numpy.errstate(divide='ignore', invalid='ignore'):
+        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.x_target_in == 0] = 0
         return self.xyallout

src/diffpy/pdfmorph/morphs/__init__.py

@@ -19,11 +19,11 @@
 
 from diffpy.pdfmorph.morphs.morph import Morph
 from diffpy.pdfmorph.morphs.morphchain import MorphChain
+from diffpy.pdfmorph.morphs.morphishape import MorphISphere, MorphISpheroid
 from diffpy.pdfmorph.morphs.morphresolution import MorphResolutionDamping
 from diffpy.pdfmorph.morphs.morphrgrid import MorphRGrid
 from diffpy.pdfmorph.morphs.morphscale import MorphScale
 from diffpy.pdfmorph.morphs.morphshape import MorphSphere, MorphSpheroid
-from diffpy.pdfmorph.morphs.morphishape import MorphISphere, MorphISpheroid
 from diffpy.pdfmorph.morphs.morphshift import MorphShift
 from diffpy.pdfmorph.morphs.morphsmear import MorphSmear
 from diffpy.pdfmorph.morphs.morphstretch import MorphStretch

src/diffpy/pdfmorph/morphs/morph.py

@@ -18,13 +18,13 @@
 """
 
 
-LABEL_RA = 'r (A)'  # r-grid
-LABEL_GR = 'G (1/A^2)'  # PDF G(r)
-LABEL_RR = 'R (1/A)'  # RDF R(r)
+LABEL_RA = "r (A)"  # r-grid
+LABEL_GR = "G (1/A^2)"  # PDF G(r)
+LABEL_RR = "R (1/A)"  # RDF R(r)
 
 
 class Morph(object):
-    '''Base class for implementing a morph given a target.
+    """Base class for implementing a morph given a target.
 
     Adapted from diffpy.pdfgetx to include two sets of arrays that get passed through.
 
@@ -79,46 +79,51 @@ class Morph(object):
         Tuple of (x_target_out, y_target_out).
     xyallout
         Tuple of (x_morph_out, y_morph_out, x_target_out, y_target_out).
-    '''
+    """
 
     # Class variables
     # default array types are empty
-    summary = 'identity transformation'
-    xinlabel = 'x'
-    yinlabel = 'y'
-    xoutlabel = 'x'
-    youtlabel = 'y'
+    summary = "identity transformation"
+    xinlabel = "x"
+    yinlabel = "y"
+    xoutlabel = "x"
+    youtlabel = "y"
     parnames = []
 
     # Properties
 
     xy_morph_in = property(
         lambda self: (self.x_morph_in, self.y_morph_in),
-        doc='Return a tuple of morph input arrays',
+        doc="Return a tuple of morph input arrays",
     )
     xy_morph_out = property(
         lambda self: (self.x_morph_out, self.y_morph_out),
-        doc='Return a tuple of morph output arrays',
+        doc="Return a tuple of morph output arrays",
     )
     xy_target_in = property(
         lambda self: (self.x_target_in, self.y_target_in),
-        doc='Return a tuple of target input arrays',
+        doc="Return a tuple of target input arrays",
     )
     xy_target_out = property(
         lambda self: (self.x_target_out, self.y_target_out),
-        doc='Return a tuple of target output arrays',
+        doc="Return a tuple of target output arrays",
     )
     xyallout = property(
-        lambda self: (self.x_morph_out, self.y_morph_out, self.x_target_out, self.y_target_out),
-        doc='Return a tuple of all output arrays',
+        lambda self: (
+            self.x_morph_out,
+            self.y_morph_out,
+            self.x_target_out,
+            self.y_target_out,
+        ),
+        doc="Return a tuple of all output arrays",
     )
 
     def __init__(self, config=None):
-        '''Create a default Morph instance.
+        """Create a default Morph instance.
 
         config: dict
             All configuration variables.
-        '''
+        """
         # declare empty attributes
         if config is None:
             config = {}
@@ -135,7 +140,7 @@ def __init__(self, config=None):
         return
 
     def morph(self, x_morph, y_morph, x_target, y_target):
-        '''Morph arrays morphed or target.
+        """Morph arrays morphed or target.
 
         Identity operation. This method should be overloaded in a derived class.
 
@@ -150,7 +155,7 @@ def morph(self, x_morph, y_morph, x_target, y_target):
         -------
         tuple
             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
         self.x_target_in = x_target
@@ -163,11 +168,11 @@ def morph(self, x_morph, y_morph, x_target, y_target):
         return self.xyallout
 
     def __call__(self, x_morph, y_morph, x_target, y_target):
-        '''Alias for morph.'''
+        """Alias for morph."""
         return self.morph(x_morph, y_morph, x_target, y_target)
 
     def applyConfig(self, config):
-        '''Process any configuration data from a dictionary.
+        """Process any configuration data from a dictionary.
 
         Parameters
         ----------
@@ -177,19 +182,19 @@ def applyConfig(self, config):
         Returns
         -------
         No return value.
-        '''
+        """
         self.config = config
         return
 
     def checkConfig(self):
-        '''Verify data in self.config. No action by default.
+        """Verify data in self.config. No action by default.
 
         To be overridden in a derived class.
-        '''
+        """
         return
 
     def plotInputs(self, xylabels=True):
-        '''Plot input arrays using matplotlib.pyplot
+        """Plot input arrays using matplotlib.pyplot
 
         Parameters
         ----------
@@ -200,7 +205,7 @@ def plotInputs(self, xylabels=True):
         -------
         list:
             A list of matplotlib line objects.
-        '''
+        """
         from matplotlib.pyplot import plot, xlabel, ylabel
 
         rv = plot(self.x_target_in, self.y_target_in, label="target")
@@ -211,7 +216,7 @@ def plotInputs(self, xylabels=True):
         return rv
 
     def plotOutputs(self, xylabels=True, **plotargs):
-        '''Plot output arrays using matplotlib.pyplot
+        """Plot output arrays using matplotlib.pyplot
 
         Parameters
         ----------
@@ -224,7 +229,7 @@ def plotOutputs(self, xylabels=True, **plotargs):
         -------
         list
             A list of matplotlib line objects.
-        '''
+        """
         from matplotlib.pyplot import plot, xlabel, ylabel
 
         pargs = dict(plotargs)
@@ -237,7 +242,7 @@ def plotOutputs(self, xylabels=True, **plotargs):
         return rv
 
     def __getattr__(self, name):
-        '''Obtain the value from self.config, when normal lookup fails.
+        """Obtain the value from self.config, when normal lookup fails.
 
         Parameters
         ----------
@@ -252,23 +257,23 @@ def __getattr__(self, name):
         ------
         AttributeError
             Name is not available from self.config.
-        '''
+        """
         if name in self.config:
             return self.config[name]
         else:
-            emsg = 'Object has no attribute %r' % name
+            emsg = "Object has no attribute %r" % name
             raise AttributeError(emsg)
 
     def __setattr__(self, name, val):
-        '''Set configuration variables to config.
+        """Set configuration variables to config.
 
         Parameters
         ----------
         name
             Name of the attribute.
         val
             Value of the attribute.
-        '''
+        """
         if name in self.parnames:
             self.config[name] = val
         else: