Flake8 fixes pt1

src/diffpy/pdfgui/doc/manual/fixHTMLCode.py

@@ -1,4 +1,7 @@
 #!/usr/bin/python
+import os
+import re
+import sys
 
 """Replace all equation marks in HTML file with <img> tag to display
 corresponding PNG file.  This assumes PNG files are in correct sequence.
@@ -16,10 +19,6 @@
 ##############################################################################
 # business
 
-import os
-import re
-import sys
-
 eqcnt = 0
 
 

src/diffpy/pdfgui/gui/aboutdialog.py

@@ -40,7 +40,7 @@
     computer programs for studying nanostructure in crystals,
     J. Phys.: Condens. Matter 19, 335219 (2007)."""
 
-_copyright = "(c) 2005-{year},".format(year=__date__[:4])
+_copyright = "(c) 2005-2024-{year},".format(year=__date__[:4])
 
 _homepage = "https://www.diffpy.org"
 
@@ -233,7 +233,7 @@ def onColumbiaLogo(self, event):  # wxGlade: DialogAbout.<event_handler>
 
 # end of class DialogAbout
 
-##### testing code ###########################################################
+# testing code ###########################################################
 
 if __name__ == "__main__":
     app = wx.App()

src/diffpy/pdfgui/gui/mainframe.py

@@ -4,7 +4,7 @@
 #
 # PDFgui            by DANSE Diffraction group
 #                   Simon J. L. Billinge
-#                   (c) 2006 trustees of the Michigan State University.
+#                   (c) 2006-2024 trustees of the Michigan State University.
 #                   All rights reserved.
 #
 # File coded by:    Chris Farrow
@@ -758,31 +758,31 @@ def __menuBindings(self):
         # For recent items
         self.Bind(wx.EVT_MENU_RANGE, self.onMRUFile, id=wx.ID_FILE1, id2=wx.ID_FILE5)
 
-        ## Edit Menu
+        # Edit Menu
         self.Bind(wx.EVT_MENU, self.onDelete, id=self.deleteId)
         self.Bind(wx.EVT_MENU, self.onCopy, id=self.copyId)
         self.Bind(wx.EVT_MENU, self.onPaste, id=self.pasteId)
         self.Bind(wx.EVT_MENU, self.onPasteLink, id=self.pasteLinkId)
         self.Bind(wx.EVT_MENU, self.onPreferences, self.prefItem)
 
-        ## View menu
+        # View menu
         self.Bind(wx.EVT_MENU, self.onDefaultLayout, self.defaultLayoutItem)
         self.Bind(wx.EVT_MENU, self.onShowFit, self.showFitItem)
         self.Bind(wx.EVT_MENU, self.onShowPlot, self.showPlotItem)
         self.Bind(wx.EVT_MENU, self.onShowOutput, self.showOutputItem)
         self.Bind(wx.EVT_MENU, self.onShowJournal, self.showJournalItem)
 
-        ## Fits Menu
+        # Fits Menu
         self.Bind(wx.EVT_MENU, self.onNewFit, id=self.newFitId)
         self.Bind(wx.EVT_MENU, self.onRun, id=self.runFitId)
         self.Bind(wx.EVT_MENU, self.onStop, id=self.stopFitId)
         self.Bind(wx.EVT_MENU, self.onExportRes, id=self.exportResId)
         self.Bind(wx.EVT_MENU, self.onRSeries, self.rseriesItem)
         self.Bind(wx.EVT_MENU, self.onTSeries, self.tseriesItem)
         self.Bind(wx.EVT_MENU, self.onDSeries, self.dseriesItem)
-        ## Macros are inserted individually
+        # Macros are inserted individually
 
-        ## Phases Menu
+        # Phases Menu
         self.Bind(wx.EVT_MENU, self.onInsPhase, id=self.newPhaseId)
         self.Bind(wx.EVT_MENU, self.onPrintBL, id=self.printBLId)
         self.Bind(wx.EVT_MENU, self.onPrintBA, id=self.printBAId)
@@ -791,16 +791,16 @@ def __menuBindings(self):
         self.Bind(wx.EVT_MENU, self.onPlotIStruct, id=self.plotIStructId)
         self.Bind(wx.EVT_MENU, self.onPlotFStruct, id=self.plotFStructId)
 
-        ## Data Menu
+        # Data Menu
         self.Bind(wx.EVT_MENU, self.onInsData, id=self.newDataId)
         self.Bind(wx.EVT_MENU, self.onExportPDF, id=self.exportFitPDFId)
 
-        ## Calculations Menu
+        # Calculations Menu
         self.Bind(wx.EVT_MENU, self.onInsCalc, id=self.newCalcId)
         self.Bind(wx.EVT_MENU, self.onRun, id=self.runCalcId)
         self.Bind(wx.EVT_MENU, self.onSaveCalc, id=self.exportCalcPDFId)
 
-        ## Help Menu
+        # Help Menu
         self.Bind(wx.EVT_MENU, self.onDocumentation, self.docItem)
         self.Bind(wx.EVT_MENU, self.onAbout, self.aboutItem)
         self.Bind(wx.EVT_MENU, self.onRequest, self.requestItem)
@@ -1529,11 +1529,11 @@ def disableSharedMenuItems(self, menu):
         noPhases = False
         if node:
             phases = self.treeCtrlMain.GetPhases(node)
-            ## No insert calculation if there are no phases
+            # No insert calculation if there are no phases
             if len(phases) == 0:
                 noPhases = True
 
-        ## No insert calculation if there are no phases
+        # No insert calculation if there are no phases
         if noPhases:
             menu.Enable(self.newCalcId, False)
 
@@ -1544,7 +1544,7 @@ def disableSharedMenuItems(self, menu):
         clipbranchtype = None
         cdata = self.treeCtrlMain.GetClipboard()
 
-        ## No paste if nothing in the clipboard
+        # No paste if nothing in the clipboard
         if cdata is None:
             menu.Enable(self.pasteId, False)
             menu.Enable(self.pasteLinkId, False)
@@ -1573,15 +1573,15 @@ def disableSharedMenuItems(self, menu):
             menu.SetLabel(self.pasteId, pastetext)
 
         # Disable certain entries based upon where we clicked.
-        ## No copy, paste, or insert on multiple items.
+        # No copy, paste, or insert on multiple items.
         if len(selections) > 1:
             menu.Enable(self.copyId, False)
             menu.Enable(self.pasteId, False)
             menu.Enable(self.pasteLinkId, False)
             menu.Enable(self.newDataId, False)
             menu.Enable(self.newPhaseId, False)
             menu.Enable(self.newCalcId, False)
-        ## Disallow paste of fit if no items selected
+        # Disallow paste of fit if no items selected
         elif not selections:
             menu.Enable(self.copyId, False)
             menu.Enable(self.deleteId, False)
@@ -1708,7 +1708,7 @@ def disableMainMenuItems(self):
             if not cdata.Gcalc:
                 menu.Enable(self.exportFitPDFId, False)
 
-        ## Check the run/stop status.
+        # Check the run/stop status.
         if self.runningDict:
             menu.Enable(self.newId, False)
             menu.Enable(self.runCalcId, False)
@@ -1756,7 +1756,7 @@ def disableMainMenuItems(self):
         return
 
     # Shared menu items
-    ## The bulk of the code for these methods is in the FitTree class.
+    # The bulk of the code for these methods is in the FitTree class.
     def onNewFit(self, event):
         """Start a new fit tree.
 
@@ -2377,7 +2377,14 @@ def onExportNewStruct(self, event):
         # branchname = self.treeCtrlMain.GetBranchName(node)
         name = self.treeCtrlMain.GetItemText(node)
         basename = ".".join(name.split(".")[:-1]) or name
-        matchstring = "PDFfit structure file (*.stru)|*.stru|Crystallographic Information File (*.cif)|*.cif|Protein Data Bank file (*.pdb)|*.pdb|Labeled coordinate file (*.xyz)|*.xyz|Raw corrdinate file (*.xyz)|*.xyz|AtomEye configuration file|*"
+        matchstring = (
+            "PDFfit structure file (*.stru)|*.stru|"
+            "Crystallographic Information File (*.cif)|*.cif|"
+            "Protein Data Bank file (*.pdb)|*.pdb|"
+            "Labeled coordinate file (*.xyz)|*.xyz|"
+            "Raw coordinate file (*.xyz)|*.xyz|"
+            "AtomEye configuration file|*"
+        )
         d = wx.FileDialog(
             None,
             "Save as...",
@@ -2416,7 +2423,14 @@ def onExportStruct(self, event):
         # branchname = self.treeCtrlMain.GetBranchName(node)
         name = self.treeCtrlMain.GetItemText(node)
         basename = ".".join(name.split(".")[:-1]) or name
-        matchstring = "PDFfit structure file (*.stru)|*.stru|Crystallographic Information File (*.cif)|*.cif|Protein Data Bank file (*.pdb)|*.pdb|Labeled coordinate file (*.xyz)|*.xyz|Raw corrdinate file (*.xyz)|*.xyz|AtomEye configuration file|*"
+        matchstring = (
+            "PDFfit structure file (*.stru)|*.stru|"
+            "Crystallographic Information File (*.cif)|*.cif|"
+            "Protein Data Bank file (*.pdb)|*.pdb|"
+            "Labeled coordinate file (*.xyz)|*.xyz|"
+            "Raw coordinate file (*.xyz)|*.xyz|"
+            "AtomEye configuration file|*"
+        )
         d = wx.FileDialog(
             None,
             "Save as...",

src/diffpy/pdfgui/gui/parameterspanel.py

@@ -4,7 +4,7 @@
 #
 # PDFgui            by DANSE Diffraction group
 #                   Simon J. L. Billinge
-#                   (c) 2006 trustees of the Michigan State University.
+#                   (c) 2006-2024 trustees of the Michigan State University.
 #                   All rights reserved.
 #
 # File coded by:    Dmitriy Bryndin, Chris Farrow
@@ -116,7 +116,7 @@ def refresh(self):
 
         nRows = len(self.parameters)
 
-        ### update the grid
+        # update the grid
         # remove all rows and create new ones
         self.grid_parameters.BeginBatch()
         gridrows = self.grid_parameters.GetNumberRows()
@@ -297,7 +297,7 @@ def popupMenu(self, window, x, y):
         menu.Destroy()
         return
 
-    ##### Popup menu events  ##################################################
+    # Popup menu events  ##################################################
     def onPopupFill(self, event):
         """Fills cells selected in the grid with a new value"""
 
@@ -402,7 +402,7 @@ def onPopupRenameParameters(self, event):
         event.Skip()
         return
 
-    ##### end of Popup menu events  ###########################################
+    # end of Popup menu events  ###########################################
 
     def onApplyParameters(self, event):  # wxGlade: ParametersPanel.<event_handler>
         self.fit.applyParameters()
@@ -439,7 +439,7 @@ def fillCells(self, indices, value):
 
 # end of class ParametersPanel
 
-##### testing code ############################################################
+# testing code ############################################################
 if __name__ == "__main__":
 
     class MyFrame(wx.Frame):
@@ -481,4 +481,4 @@ def onInit(self):
 
     app = MyApp(0)
     app.MainLoop()
-##### end of testing code #####################################################
+# end of testing code #####################################################

src/diffpy/pdfgui/gui/pdfguiglobals.py

@@ -3,7 +3,7 @@
 #
 # PDFgui            by DANSE Diffraction group
 #                   Simon J. L. Billinge
-#                   (c) 2006 trustees of the Michigan State University.
+#                   (c) 2006-2024 trustees of the Michigan State University.
 #                   All rights reserved.
 #
 # File coded by:    Pavol Juhas
@@ -19,6 +19,8 @@
 
 from pkg_resources import Requirement, resource_filename
 
+from diffpy.pdfgui.gui import debugoptions
+
 # Name of the program
 name = "PDFgui"
 # Maximum number of files to be remembered
@@ -76,7 +78,6 @@ def iconpath(iconfilename):
 cmdargs = []
 
 # debugging options:
-from diffpy.pdfgui.gui import debugoptions
 
 dbopts = debugoptions.DebugOptions()
 

src/diffpy/pdfgui/gui/tooltips.py

@@ -3,7 +3,7 @@
 #
 # PDFgui            by DANSE Diffraction group
 #                   Simon J. L. Billinge
-#                   (c) 2007 trustees of the Michigan State University.
+#                   (c) 2007-2024 trustees of the Michigan State University.
 #                   All rights reserved.
 #
 # File coded by:    Dmitriy Bryndin
@@ -17,9 +17,12 @@
 """
 
 
+def isalias(s):
+    return s[1:-1] and s[:: len(s) - 1] == "{}" and s[1:-1].replace("_", "").isalnum()
+
+
 def _expand_tooltip_aliases(ttps):
     "Replace aliased equivalent values {other} in tooltip strings."
-    isalias = lambda s: (s[1:-1] and s[:: len(s) - 1] == "{}" and s[1:-1].replace("_", "").isalnum())
     for n, t in list(ttps.items()):
         if not isalias(t):
             continue
@@ -79,7 +82,10 @@ def _expand_tooltip_aliases(ttps):
 
 
 dopingseriespanel = {
-    #    'instructionsLabel' : '', # StaticText "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."
+    #    'instructionsLabel' : '', # StaticText "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."
     #    'labelBaseElement' : '', # StaticText "Base element"
     #    'textCtrlBaseElement' : '', # TextCtrl
     #    'labelDopant' : '', # StaticText "Dopant"
@@ -175,7 +181,9 @@ def _expand_tooltip_aliases(ttps):
 
 
 temperatureseriespanel = {
-    #    'instructionsLabel' : '', # StaticText "Select a fit from the tree on the left then add datasets and assign\ntemperatues below. If you have not set up a fit to be the template\nfor the series, hit cancel and rerun this macro once a fit has been\ncreated."
+    #    'instructionsLabel' : '', # StaticText "Select a fit from the tree on the left
+    #     then add datasets and assign\ntemperatues below. If you have not set up a fit to
+    #     be the template\nfor the series, hit cancel and rerun this macro once a fit has been\ncreated."
     "listCtrlFiles": "Click header to sort by temperature",  # AutoWidthListCtrl
     #    'buttonUp' : '', # BitmapButton
     #    'buttonDown' : '', # BitmapButton

src/diffpy/pdfgui/gui/windowperspective.py

@@ -3,7 +3,7 @@
 #
 # PDFgui            by DANSE Diffraction group
 #                   Simon J. L. Billinge
-#                   (c) 2007 trustees of the Michigan State University.
+#                   (c) 2007-2024 trustees of the Michigan State University.
 #                   All rights reserved.
 #
 # File coded by:    Chris Farrow
@@ -15,4 +15,4 @@
 
 """This contains the default perspective for the gui window."""
 
-default = "layout2|name=dseries;caption=;state=770;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=380;minw=190;minh=200;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=calculation;caption=;state=770;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=380;minw=190;minh=200;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=welcome;caption=;state=768;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=380;minw=190;minh=200;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=adddata;caption=;state=770;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=380;minw=190;minh=200;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=serverconfig;caption=;state=770;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=380;minw=190;minh=200;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=addphase;caption=;state=770;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=380;minw=190;minh=200;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=blank;caption=;state=770;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=380;minw=190;minh=200;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=phase;caption=;state=770;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=380;minw=190;minh=200;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=dataset;caption=;state=770;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=380;minw=190;minh=200;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=preferences;caption=;state=770;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=380;minw=190;minh=200;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=fit;caption=;state=770;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=380;minw=190;minh=200;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=rseries;caption=;state=770;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=380;minw=190;minh=200;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=tseries;caption=;state=770;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=380;minw=190;minh=200;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=outputPanel;caption=PDFfit2 Output;state=10487804;dir=3;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=40;minw=200;minh=40;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=treeCtrlMain;caption=Fit Tree;state=10487804;dir=4;layer=0;row=0;pos=0;prop=100000;bestw=200;besth=100;minw=200;minh=40;maxw=-1;maxh=-1;floatx=471;floaty=730;floatw=208;floath=124|name=plotPanel;caption=Plot Control;state=10487804;dir=4;layer=0;row=0;pos=1;prop=100000;bestw=200;besth=250;minw=200;minh=150;maxw=-1;maxh=-1;floatx=337;floaty=393;floatw=208;floath=274|name=journalPanel;caption=Project Journal;state=10487807;dir=4;layer=0;row=0;pos=0;prop=100000;bestw=450;besth=450;minw=200;minh=200;maxw=-1;maxh=-1;floatx=393;floaty=113;floatw=450;floath=450|dock_size(3,0,0)=59|dock_size(4,0,0)=202|dock_size(5,0,0)=362|"
+default = "layout2|name=dseries;caption=;state=770;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=380;minw=190;minh=200;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=calculation;caption=;state=770;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=380;minw=190;minh=200;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=welcome;caption=;state=768;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=380;minw=190;minh=200;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=adddata;caption=;state=770;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=380;minw=190;minh=200;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=serverconfig;caption=;state=770;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=380;minw=190;minh=200;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=addphase;caption=;state=770;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=380;minw=190;minh=200;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=blank;caption=;state=770;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=380;minw=190;minh=200;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=phase;caption=;state=770;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=380;minw=190;minh=200;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=dataset;caption=;state=770;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=380;minw=190;minh=200;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=preferences;caption=;state=770;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=380;minw=190;minh=200;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=fit;caption=;state=770;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=380;minw=190;minh=200;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=rseries;caption=;state=770;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=380;minw=190;minh=200;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=tseries;caption=;state=770;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=380;minw=190;minh=200;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=outputPanel;caption=PDFfit2 Output;state=10487804;dir=3;layer=0;row=0;pos=0;prop=100000;bestw=400;besth=40;minw=200;minh=40;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=treeCtrlMain;caption=Fit Tree;state=10487804;dir=4;layer=0;row=0;pos=0;prop=100000;bestw=200;besth=100;minw=200;minh=40;maxw=-1;maxh=-1;floatx=471;floaty=730;floatw=208;floath=124|name=plotPanel;caption=Plot Control;state=10487804;dir=4;layer=0;row=0;pos=1;prop=100000;bestw=200;besth=250;minw=200;minh=150;maxw=-1;maxh=-1;floatx=337;floaty=393;floatw=208;floath=274|name=journalPanel;caption=Project Journal;state=10487807;dir=4;layer=0;row=0;pos=0;prop=100000;bestw=450;besth=450;minw=200;minh=200;maxw=-1;maxh=-1;floatx=393;floaty=113;floatw=450;floath=450|dock_size(3,0,0)=59|dock_size(4,0,0)=202|dock_size(5,0,0)=362|"  # noqa: E501

src/diffpy/pdfgui/gui/wxextensions/validators.py

@@ -1,9 +1,14 @@
 #!/usr/bin/env python
+
+import string
+
+import wx
+
 ##############################################################################
 #
 # wxextensions      by DANSE Diffraction group
 #                   Simon J. L. Billinge
-#                   (c) 2006 trustees of the Michigan State University.
+#                   (c) 2006-2024 trustees of the Michigan State University.
 #                   All rights reserved.
 #
 # File coded by:    Chris Farrow
@@ -23,10 +28,6 @@
 DIGIT_ONLY = 2
 FLOAT_ONLY = 3
 
-import string
-
-import wx
-
 
 class TextValidator(wx.Validator):
     """This validator is designed to check text input for wxTextCtrls. (It might