Copyright updates

src/diffpy/pdfgui/applications/__init__.py

@@ -3,7 +3,7 @@
 #
 # diffpy.pdfgui     by DANSE Diffraction group
 #                   Simon J. L. Billinge
-#                   (c) 2009 Trustees of the Columbia University
+#                   (c) 2009-2024 Trustees of the Columbia University
 #                   in the City of New York.  All rights reserved.
 #
 # File coded by:    Pavol Juhas

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

src/diffpy/pdfgui/control/organizer.py

@@ -230,44 +230,50 @@ 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"]
         elif assigned_datas:
             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
 
 

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"""

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)

src/diffpy/pdfgui/control/structureviewer.py

@@ -3,7 +3,7 @@
 #
 # diffpy.pdfgui     by DANSE Diffraction group
 #                   Simon J. L. Billinge
-#                   (c) 2009 Trustees of the Columbia University
+#                   (c) 2009-2024 Trustees of the Columbia University
 #                   in the City of New York.  All rights reserved.
 #
 # File coded by:    Pavol Juhas

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.

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)

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.
 

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 #####################################################

src/diffpy/pdfgui/gui/errorreportdialog_control_fix.py

@@ -17,14 +17,15 @@
 # generated by wxGlade 0.9.3 on Fri Jul 19 16:01:37 2019
 
 import re
-import webbrowser
 
 #
 # "Bug report" Dialog
 #
 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 #####################################################

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,

src/diffpy/pdfgui/tests/__init__.py

@@ -3,7 +3,7 @@
 #
 # diffpy.pdfgui     by DANSE Diffraction group
 #                   Simon J. L. Billinge
-#                   (c) 2012 Trustees of the Columbia University
+#                   (c) 2012-2024 Trustees of the Columbia University
 #                   in the City of New York.  All rights reserved.
 #
 # File coded by:    Pavol Juhas

src/diffpy/pdfgui/tests/run.py

@@ -3,7 +3,7 @@
 #
 # diffpy.pdfgui     by DANSE Diffraction group
 #                   Simon J. L. Billinge
-#                   (c) 2012 Trustees of the Columbia University
+#                   (c) 2012-2024 Trustees of the Columbia University
 #                   in the City of New York.  All rights reserved.
 #
 # File coded by:    Pavol Juhas

src/diffpy/pdfgui/tests/rundeps.py

@@ -3,7 +3,7 @@
 #
 # diffpy.pdfgui     by DANSE Diffraction group
 #                   Simon J. L. Billinge
-#                   (c) 2012 Trustees of the Columbia University
+#                   (c) 2012-2024 Trustees of the Columbia University
 #                   in the City of New York.  All rights reserved.
 #
 # File coded by:    Pavol Juhas

src/diffpy/pdfgui/tests/showphasenotebookpanel.py

@@ -3,7 +3,7 @@
 #
 # diffpy.pdfgui     by DANSE Diffraction group
 #                   Simon J. L. Billinge
-#                   (c) 2016 Trustees of the Columbia University
+#                   (c) 2016-2024 Trustees of the Columbia University
 #                   in the City of New York.  All rights reserved.
 #
 # File coded by:    Pavol Juhas

src/diffpy/pdfgui/tests/testutils.py

@@ -3,7 +3,7 @@
 #
 # diffpy.pdfgui     by DANSE Diffraction group
 #                   Simon J. L. Billinge
-#                   (c) 2016 Trustees of the Columbia University
+#                   (c) 2016-2024 Trustees of the Columbia University
 #                   in the City of New York.  All rights reserved.
 #
 # File coded by:    Pavol Juhas