diff --git a/src/diffpy/pdfgui/control/fitstructure.py b/src/diffpy/pdfgui/control/fitstructure.py
index f643c994..515fdec5 100644
--- a/src/diffpy/pdfgui/control/fitstructure.py
+++ b/src/diffpy/pdfgui/control/fitstructure.py
@@ -252,7 +252,7 @@ def _restoreAtomConstraints(self, acd):
acd -- dictionary obtained from _popAtomConstraints()
"""
for i, a in enumerate(self.initial):
- if not a in acd:
+ if a not in acd:
continue
# there are some constraints for atom a
siteindex = i + 1
diff --git a/src/diffpy/pdfgui/control/organizer.py b/src/diffpy/pdfgui/control/organizer.py
index 31a5a095..ecf140b8 100644
--- a/src/diffpy/pdfgui/control/organizer.py
+++ b/src/diffpy/pdfgui/control/organizer.py
@@ -230,28 +230,31 @@ def organization(self):
return org
- def __forward_spdiameter(self):
+ def __forward_spdiameter(strucs, datasets, calcs):
"""Copy spdiameter value loaded from fit or calculation to phase.
- This method takes care of loading old PDFgui projects where
+ This function handles loading old PDFgui projects where
spdiameter belonged to FitDataSet or Calculation classes.
- It should be called only from the Organizer.load method.
"""
# Jump out if any of structures has spdiameter set
- for stru in self.strucs:
+ for stru in strucs:
if stru.getvar("spdiameter"):
return
- # Search datasets for spdiameter and its constraints
- spd_assigned = lambda ds: bool(ds.spdiameter)
- spd_constrained = lambda ds: "spdiameter" in ds.constraints
+
+ # Helper function to check if spdiameter is assigned
+ def spd_assigned(ds):
+ return bool(ds.spdiameter)
+
+ # Helper function to check if spdiameter is constrained
+ def spd_constrained(ds):
+ return "spdiameter" in ds.constraints
+
# Figure out the value and constraint for spdiameter.
- # The highest priority is for a dataset with constrained spdiameter,
- # then for dataset with assigned spdiameter and finally from
- # a calculation.
spd_val = spd_cns = None
- constrained_datas = list(filter(spd_constrained, self.datasets))
- assigned_datas = list(filter(spd_assigned, self.datasets))
- assigned_calcs = list(filter(spd_assigned, self.calcs))
+ constrained_datas = list(filter(spd_constrained, datasets))
+ assigned_datas = list(filter(spd_assigned, datasets))
+ assigned_calcs = list(filter(spd_assigned, calcs))
+
if constrained_datas:
spd_val = constrained_datas[0].spdiameter
spd_cns = constrained_datas[0].constraints["spdiameter"]
@@ -259,15 +262,18 @@ def __forward_spdiameter(self):
spd_val = assigned_datas[0].spdiameter
elif assigned_calcs:
spd_val = assigned_calcs[0].spdiameter
- # assign spd_val to all structures that don't have it set
- for stru in self.strucs:
+
+ # Assign spd_val to all structures that don't have it set
+ for stru in strucs:
if spd_val and not stru.getvar("spdiameter"):
stru.setvar("spdiameter", spd_val)
if spd_cns:
stru.constraints.setdefault("spdiameter", spd_cns)
- # finally remove any spdiameter constraints from all datasets
- for ds in self.datasets:
+
+ # Finally remove any spdiameter constraints from all datasets
+ for ds in datasets:
ds.constraints.pop("spdiameter", None)
+
return
diff --git a/src/diffpy/pdfgui/control/pdfguicontrol.py b/src/diffpy/pdfgui/control/pdfguicontrol.py
index bb39baa8..15632a0d 100644
--- a/src/diffpy/pdfgui/control/pdfguicontrol.py
+++ b/src/diffpy/pdfgui/control/pdfguicontrol.py
@@ -58,7 +58,7 @@ def __init__(self, gui=None):
self.fittingQueue = []
self.currentFitting = None
self.queueManager = PDFGuiControl.QueueManager(self)
- ##self.startQueue()
+ # self.startQueue()
def reset(self):
"""clean up for a new project"""
diff --git a/src/diffpy/pdfgui/control/plotter.py b/src/diffpy/pdfgui/control/plotter.py
index 77134fb1..aeba7d6b 100644
--- a/src/diffpy/pdfgui/control/plotter.py
+++ b/src/diffpy/pdfgui/control/plotter.py
@@ -622,7 +622,11 @@ def export(self, filename):
header = "# Generated on %s by %s.\n" % (time.ctime(), getpass.getuser())
header += "# This file was created by PDFgui.\n"
outfile.write(header)
- deblank = lambda s: "".join(s.split())
+
+ def deblank(s):
+ """Removes all whitespace from string s"""
+ return "".join(s.split())
+
xylist = [(c.x, c.y) for c in self.curves]
xynames = [(_transName(c.xStr), deblank(c.name)) for c in self.curves]
_exportCompactData(outfile, xylist, xynames)
diff --git a/src/diffpy/pdfgui/doc/manual/extractEquations.py b/src/diffpy/pdfgui/doc/manual/extractEquations.py
index 4c32814e..ce3a9819 100644
--- a/src/diffpy/pdfgui/doc/manual/extractEquations.py
+++ b/src/diffpy/pdfgui/doc/manual/extractEquations.py
@@ -1,4 +1,7 @@
#!/usr/bin/python
+import os
+import shutil
+import sys
"""Read one or more texinfo files and extract any equations marked
in the code with '@EquationMark' macro as PNG files to the images
@@ -31,10 +34,6 @@
##############################################################################
# business
-import os
-import shutil
-import sys
-
def loadEquations():
"""Search for equation codes preceded by @EquationMark macro.
diff --git a/src/diffpy/pdfgui/doc/tutorial/tui_mno_bond_lengths.py b/src/diffpy/pdfgui/doc/tutorial/tui_mno_bond_lengths.py
index 79c1b527..9d99e7ec 100755
--- a/src/diffpy/pdfgui/doc/tutorial/tui_mno_bond_lengths.py
+++ b/src/diffpy/pdfgui/doc/tutorial/tui_mno_bond_lengths.py
@@ -1,5 +1,12 @@
#!/usr/bin/env python
+import pylab
+
+from diffpy.pdffit2 import PdfFit
+
+# Import tui (Text User Interface) functions from diffpy.pdfgui
+from diffpy.pdfgui import tui
+
"""Extract the shortest Mn-O bond lengths from all fits in PDFgui project.
This script loops through all refined phases in PDFgui project and calculates
@@ -11,8 +18,6 @@
project_file = "lmo-template.ddp3"
output_file = "mno-bond-lengths.dat"
-# Import tui (Text User Interface) functions from diffpy.pdfgui
-from diffpy.pdfgui import tui
# load project file
prj = tui.LoadProject(project_file)
@@ -21,7 +26,6 @@
# using diffpy.pdffit2
# Create a PDF calculator object that will be used in that function.
-from diffpy.pdffit2 import PdfFit
pf = PdfFit()
@@ -69,7 +73,6 @@ def shortestBond_MnO(stru):
# Plot results using matplotlib; pylab is a part of matplotlib that
# provides MATLAB-like plotting functions.
-import pylab
pylab.plot(temperatures, MnO_bond_lengths, "o--")
pylab.title("Data from refined phases in PDFgui project %s" % project_file)
diff --git a/src/diffpy/pdfgui/gui/dopingseriespanel.py b/src/diffpy/pdfgui/gui/dopingseriespanel.py
index 211e2f8e..fd60c1bf 100644
--- a/src/diffpy/pdfgui/gui/dopingseriespanel.py
+++ b/src/diffpy/pdfgui/gui/dopingseriespanel.py
@@ -18,7 +18,6 @@
import os.path
import re
-import sys
import wx
@@ -41,7 +40,10 @@ def __init__(self, *args, **kwds):
self.instructionsLabel = wx.StaticText(
self,
wx.ID_ANY,
- "Select a fit from the tree on the left then add datasets and assign\ndoping elements and values below. If you have not set up a fit to be\nthe template for the series, hit cancel and rerun this macro once a\nfit has been created.",
+ "Select a fit from the tree on the left then add datasets and "
+ + "assign\ndoping elements and values below. "
+ + "If you have not set up a fit to be\nthe template for the series, "
+ + "hit cancel and rerun this macro once a\nfit has been created.",
)
self.instructionsLabel.SetFont(
wx.Font(
@@ -210,7 +212,11 @@ def onAdd(self, event): # wxGlade: DopingSeriesPanel.<event_handler>
if not dir:
dir = self.mainFrame.workpath
- matchstring = "PDF data files (*.gr)|*.gr|PDF fit files (*.fgr)|*.fgr|PDF fit files (*.fit)|*.fit|PDF calculation files (*.cgr)|*.cgr|PDF calculation files (*.calc)|*.calc|All Files|*"
+ matchstring = (
+ "PDF data files (*.gr)|*.gr|PDF fit files (*.fgr)|*.fgr|PDF fit files (*.fit)|"
+ "*.fit|PDF calculation files (*.cgr)|*.cgr|PDF calculation files (*.calc)|*.calc|"
+ "All Files|*"
+ )
d = wx.FileDialog(
None,
"Choose files",
@@ -304,7 +310,7 @@ def onCancel(self, event): # wxGlade: DopingSeriesPanel.<event_handler>
self.mainFrame.switchRightPanel("blank")
return
- ## Utility functions
+ # Utility functions
def checkConfiguration(self):
"""Verify that the dopant and base are elements.
@@ -340,7 +346,7 @@ def fillList(self):
self.listCtrlFiles.SetItem(index, 1, shortname)
return
- ## Needed by mainframe
+ # Needed by mainframe
def treeSelectionUpdate(self, node):
"""Set the current fit when the tree selection changes."""
nodetype = self.treeCtrlMain.GetNodeType(node)
@@ -349,7 +355,7 @@ def treeSelectionUpdate(self, node):
self.refresh()
return
- ## Required by PDFPanel
+ # Required by PDFPanel
def refresh(self):
"""Block out OK button if there is no fit.
diff --git a/src/diffpy/pdfgui/gui/errorreportdialog.py b/src/diffpy/pdfgui/gui/errorreportdialog.py
index b93cca76..7e554ac6 100644
--- a/src/diffpy/pdfgui/gui/errorreportdialog.py
+++ b/src/diffpy/pdfgui/gui/errorreportdialog.py
@@ -207,15 +207,15 @@ def _extractSearchTerms(tbtext):
return rv
-##### testing code ############################################################
+# testing code ############################################################
_EXAMPLE_TRACEBACK = r"""
Traceback (most recent call last):
- File "C:\DiffPy\Python25\lib\site-packages\diffpy.pdfgui-1.0_r3067_20090410-py2.5.egg\diffpy\pdfgui\gui\errorwrapper.py", line 60, in _f
+ File "...errorwrapper.py", line 60, in _f
return func(*args, **kwargs)
- File "C:\DiffPy\Python25\lib\site-packages\diffpy.pdfgui-1.0_r3067_20090410-py2.5.egg\diffpy\pdfgui\gui\mainframe.py", line 2176, in onSave
+ File "...mainframe.py", line 2176, in onSave
self.control.save(self.fullpath)
- File "C:\DiffPy\Python25\lib\site-packages\diffpy.pdfgui-1.0_r3067_20090410-py2.5.egg\diffpy\pdfgui\control\pdfguicontrol.py", line 507, in save
+ File "...pdfguicontrol.py", line 507, in save
self.projfile = projfile.encode('ascii')
UnicodeDecodeError: 'ascii' codec can't decode byte 0xb0 in position 115: ordinal not in range(128)
""".strip()
@@ -242,4 +242,4 @@ def test(self):
app = MyApp(0)
app.MainLoop()
-##### end of testing code #####################################################
+# end of testing code #####################################################
diff --git a/src/diffpy/pdfgui/gui/errorreportdialog_control_fix.py b/src/diffpy/pdfgui/gui/errorreportdialog_control_fix.py
index 71e239ca..c2d91812 100644
--- a/src/diffpy/pdfgui/gui/errorreportdialog_control_fix.py
+++ b/src/diffpy/pdfgui/gui/errorreportdialog_control_fix.py
@@ -17,7 +17,6 @@
# generated by wxGlade 0.9.3 on Fri Jul 19 16:01:37 2019
import re
-import webbrowser
#
# "Bug report" Dialog
@@ -25,6 +24,8 @@
import wx
import wx.html
+from .errorreportdialog import ErrorReportDialog
+
# Constants ------------------------------------------------------------------
ISSUESTRACKER = "https://github.com/diffpy/diffpy.pdfgui/issues"
@@ -77,7 +78,7 @@ def __do_layout(self):
# begin wxGlade: ErrorReportDialog.__do_layout
sizer_main = wx.BoxSizer(wx.VERTICAL)
sizer_buttons = wx.BoxSizer(wx.HORIZONTAL)
- sizer_log = wx.BoxSizer(wx.VERTICAL)
+ # sizer_log = wx.BoxSizer(wx.VERTICAL)
sizer_label = wx.BoxSizer(wx.HORIZONTAL)
sizer_label.Add(self.label_header, 1, wx.EXPAND, 5)
sizer_main.Add(sizer_label, 1, wx.ALL | wx.EXPAND, 5)
@@ -141,18 +142,22 @@ def _extractSearchTerms(tbtext):
return rv
-##### testing code ############################################################
+# testing code ############################################################
-_EXAMPLE_TRACEBACK = r"""
-Traceback (most recent call last):
- File "C:\DiffPy\Python25\lib\site-packages\diffpy.pdfgui-1.0_r3067_20090410-py2.5.egg\diffpy\pdfgui\gui\errorwrapper.py", line 60, in _f
- return func(*args, **kwargs)
- File "C:\DiffPy\Python25\lib\site-packages\diffpy.pdfgui-1.0_r3067_20090410-py2.5.egg\diffpy\pdfgui\gui\mainframe.py", line 2176, in onSave
- self.control.save(self.fullpath)
- File "C:\DiffPy\Python25\lib\site-packages\diffpy.pdfgui-1.0_r3067_20090410-py2.5.egg\diffpy\pdfgui\control\pdfguicontrol.py", line 507, in save
- self.projfile = projfile.encode('ascii')
-UnicodeDecodeError: 'ascii' codec can't decode byte 0xb0 in position 115: ordinal not in range(128)
-""".strip()
+_EXAMPLE_TRACEBACK = (
+ r"""Traceback (most recent call last): """
+ r"""File 'C:\DiffPy\Python25\lib\site-packages\diffpy.pdfgui-1.0_r3067_20090410-py2.5.egg"""
+ r"""\diffpy\pdfgui\gui\errorwrapper.py', line 60, in _f """
+ r"""return func(*args, **kwargs) """
+ r"""File 'C:\DiffPy\Python25\lib\site-packages\diffpy.pdfgui-1.0_r3067_20090410-py2.5.egg"""
+ r"""\diffpy\pdfgui\gui\mainframe.py', line 2176, in onSave """
+ r"""self.control.save(self.fullpath) """
+ r"""File 'C:\DiffPy\Python25\lib\site-packages\diffpy.pdfgui-1.0_r3067_20090410-py2.5.egg"""
+ r"""\diffpy\pdfgui\control\pdfguicontrol.py', line 507, in save """
+ r"""self.projfile = projfile.encode('ascii') """
+ r"""UnicodeDecodeError: 'ascii' codec can't decode byte 0xb0 in position """
+ r"""115: ordinal not in range(128)"""
+).strip()
class MyApp(wx.App):
@@ -176,4 +181,4 @@ def test(self):
app = MyApp(0)
app.MainLoop()
-##### end of testing code #####################################################
+# end of testing code #####################################################
diff --git a/src/diffpy/pdfgui/gui/extendedplotframe.py b/src/diffpy/pdfgui/gui/extendedplotframe.py
index 848b54d6..297a7670 100644
--- a/src/diffpy/pdfgui/gui/extendedplotframe.py
+++ b/src/diffpy/pdfgui/gui/extendedplotframe.py
@@ -20,8 +20,6 @@
import os.path
import matplotlib
-
-matplotlib.use("WXAgg")
import wx
from matplotlib.artist import setp
from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as FigureCanvas
@@ -32,6 +30,8 @@
from diffpy.pdfgui.gui.pdfguiglobals import iconpath
from diffpy.pdfgui.gui.wxextensions import wx12
+matplotlib.use("WXAgg")
+
DATA_SAVE_ID = wx12.NewIdRef()
@@ -303,7 +303,7 @@ def __translateStyles(self, style):
symbolSize = style["symbolSize"]
symbolColor = colorDict.get(style["symbolColor"], "k")
properties.update(
- { #'linewidth':0.0, # doesn't affect any
+ { # 'linewidth':0.0, # doesn't affect any
"markerfacecolor": symbolColor,
"markeredgecolor": color,
"marker": symbol,