[pre-commit.ci] auto fixes from pre-commit hooks

sbillinge · Sep 26, 2024 · Sep 25, 2024 · Sep 25, 2024 · Sep 25, 2024 · Sep 25, 2024
commit 5a44e70278c5313c46be343a01485d6e03dd959c
diff --git a/AUTHORS.rst b/AUTHORS.rst
@@ -15,17 +15,17 @@ This code was developed as part of the DiffPy project to create python
 modules for structure investigations from diffraction data.  The main
 contributors to this package were
 
-    Chris Farrow, 
-    Jiwu Liu, 
-    Pavol Juhas, 
+    Chris Farrow,
+    Jiwu Liu,
+    Pavol Juhas,
     Dmitriy Bryndin
 
 Other current and former contributors of the DiffPy project include
 
-    Simon Billinge, 
-    Chris Farrow, 
-    Emil Bozin, 
-    Wenduo Zhou, 
+    Simon Billinge,
+    Chris Farrow,
+    Emil Bozin,
+    Wenduo Zhou,
     Peng Tian
 
 The DiffPy team is part of the Billinge Group at Columbia University in New York,

diff --git a/README.rst b/README.rst
@@ -38,30 +38,30 @@
 Graphical user interface program for structure refinements to atomic
 pair distribution function.
 
-For users who do not have the expertise or necessity for command 
-line analysis, PDFgui is a convenient and easy to use graphical front 
-end for the PDFfit2 refinement program. It is capable of full-profile 
-fitting of the atomic pair distribution function (PDF) derived from x-ray 
-or neutron diffraction data and comes with built in graphical and structure 
+For users who do not have the expertise or necessity for command
+line analysis, PDFgui is a convenient and easy to use graphical front
+end for the PDFfit2 refinement program. It is capable of full-profile
+fitting of the atomic pair distribution function (PDF) derived from x-ray
+or neutron diffraction data and comes with built in graphical and structure
 visualization capabilities.
 
 PDFgui is a friendly interface to the PDFfit2 refinement engine, with many
 powerful extensions.  To get started, please open the manual from the
 help menu and follow the tutorial instructions. A detailed description
 is available in `this paper <http://dx.doi.org/10.1088/0953-8984/19/33/335219>`_.
 
-For more information about diffpy.pdfgui, please consult our 
+For more information about diffpy.pdfgui, please consult our
 `online documentation <https://diffpy.github.io/diffpy.pdfgui>`_.
 
 Citation
 --------
 
-If you use diffpy.pdfgui in a scientific publication, we would like you to 
+If you use diffpy.pdfgui in a scientific publication, we would like you to
 cite this package as
 
-        C L Farrow, P Juhas, J W Liu, D Bryndin, E S Božin, 
-        J Bloch, Th Proffen and S J L Billinge, PDFfit2 and PDFgui: 
-        computer programs for studying nanostructure in crystals, J. Phys.: 
+        C L Farrow, P Juhas, J W Liu, D Bryndin, E S Božin,
+        J Bloch, Th Proffen and S J L Billinge, PDFfit2 and PDFgui:
+        computer programs for studying nanostructure in crystals, J. Phys.:
         Condens. Matter 19 (2007) 335219. doi:10.1088/0953-8984/19/33/335219
 
 Installation
@@ -102,7 +102,7 @@ Support and Contribute
 
 `Diffpy user group <https://groups.google.com/g/diffpy-users>`_ is the discussion forum for general questions and discussions about the use of diffpy.pdfgui. Please join the diffpy.pdfgui users community by joining the Google group. The diffpy.pdfgui project welcomes your expertise and enthusiasm!
 
-If you see a bug or want to request a feature, please `report it as an issue <https://github.com/diffpy/diffpy.pdfgui/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.pdfgui/pulls>`_. You can also post it to the `Diffpy user group <https://groups.google.com/g/diffpy-users>`_. 
+If you see a bug or want to request a feature, please `report it as an issue <https://github.com/diffpy/diffpy.pdfgui/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.pdfgui/pulls>`_. You can also post it to the `Diffpy user group <https://groups.google.com/g/diffpy-users>`_.
 
 Feel free to fork the project and contribute. To install diffpy.pdfgui
 in a development mode, with its sources being directly used by Python

diff --git a/doc/source/api/diffpy.pdfgui.applications.rst b/doc/source/api/diffpy.pdfgui.applications.rst
@@ -18,4 +18,3 @@ diffpy.pdfgui.applications.pdfgui module
     :members:
     :undoc-members:
     :show-inheritance:
-
diff --git a/doc/source/api/diffpy.pdfgui.control.rst b/doc/source/api/diffpy.pdfgui.control.rst
@@ -138,4 +138,3 @@ diffpy.pdfgui.control.organizer module
     :members:
     :undoc-members:
     :show-inheritance:
-
diff --git a/doc/source/api/diffpy.pdfgui.gui.design.rst b/doc/source/api/diffpy.pdfgui.gui.design.rst
@@ -7,4 +7,3 @@ diffpy.pdfgui.gui.design package
     :members:
     :undoc-members:
     :show-inheritance:
-
diff --git a/doc/source/api/diffpy.pdfgui.gui.rst b/doc/source/api/diffpy.pdfgui.gui.rst
@@ -371,4 +371,3 @@ diffpy.pdfgui.gui.mainframe module
     :members:
     :undoc-members:
     :show-inheritance:
-
diff --git a/doc/source/api/diffpy.pdfgui.gui.wxextensions.rst b/doc/source/api/diffpy.pdfgui.gui.wxextensions.rst
@@ -58,4 +58,3 @@ diffpy.pdfgui.gui.wxextensions.paneldialog module
     :members:
     :undoc-members:
     :show-inheritance:
-
diff --git a/doc/source/api/diffpy.pdfgui.icons.rst b/doc/source/api/diffpy.pdfgui.icons.rst
@@ -7,4 +7,3 @@ diffpy.pdfgui.icons package
     :members:
     :undoc-members:
     :show-inheritance:
-
diff --git a/doc/source/api/diffpy.pdfgui.rst b/doc/source/api/diffpy.pdfgui.rst
@@ -37,4 +37,3 @@ diffpy.pdfgui.tui module
     :members:
     :undoc-members:
     :show-inheritance:
-
diff --git a/doc/source/index.rst b/doc/source/index.rst
@@ -9,11 +9,11 @@ diffpy.pdfgui - GUI for PDF simulation and structure refinement.
 | Software version |release|
 | Last updated |today|
 
-For users who do not have the expertise or necessity for command 
-line analysis, PDFgui is a convenient and easy to use graphical front 
-end for the PDFfit2 refinement program. It is capable of full-profile 
-fitting of the atomic pair distribution function (PDF) derived from x-ray 
-or neutron diffraction data and comes with built in graphical and structure 
+For users who do not have the expertise or necessity for command
+line analysis, PDFgui is a convenient and easy to use graphical front
+end for the PDFfit2 refinement program. It is capable of full-profile
+fitting of the atomic pair distribution function (PDF) derived from x-ray
+or neutron diffraction data and comes with built in graphical and structure
 visualization capabilities.
 
 PDFgui is a friendly interface to the PDFfit2 refinement engine, with many
@@ -32,17 +32,17 @@ and do not necessarily reflect the views of the NSF.
 
 The main contributors to this package were
 
-    Chris Farrow, 
-    Jiwu Liu, 
-    Pavol Juhas, 
+    Chris Farrow,
+    Jiwu Liu,
+    Pavol Juhas,
     Dmitriy Bryndin
 
 Other current and former contributors of the DiffPy project include
 
-    Simon Billinge, 
-    Chris Farrow, 
-    Emil Bozin, 
-    Wenduo Zhou, 
+    Simon Billinge,
+    Chris Farrow,
+    Emil Bozin,
+    Wenduo Zhou,
     Peng Tian
 
 The DiffPy team is part of the Billinge Group at Columbia University in New York,
@@ -55,13 +55,13 @@ https://github.com/diffpy/diffpy.pdfgui/graphs/contributors.
 Reference
 =========
 
-If you use this program for a scientific research that leads to publication, 
-we ask that you acknowledge use of the program by citing the following paper 
+If you use this program for a scientific research that leads to publication,
+we ask that you acknowledge use of the program by citing the following paper
 in your publication:
 
-   C L Farrow, P Juhas, J W Liu, D Bryndin, E S Božin, 
-   J Bloch, Th Proffen and S J L Billinge, `PDFfit2 and PDFgui: 
-   computer programs for studying nanostructure in crystals <https://doi.org/10.1088/0953-8984/19/33/335219>`_, 
+   C L Farrow, P Juhas, J W Liu, D Bryndin, E S Božin,
+   J Bloch, Th Proffen and S J L Billinge, `PDFfit2 and PDFgui:
+   computer programs for studying nanostructure in crystals <https://doi.org/10.1088/0953-8984/19/33/335219>`_,
    J. Phys.: Condens. Matter 19 (2007) 335219.
 
 ============
@@ -75,9 +75,9 @@ file included with the distribution.
 Tutorial
 ========
 
-The tutorial for the package can be found here: 
+The tutorial for the package can be found here:
 
-.. toctree:: 
+.. toctree::
 
    tutorial
 

diff --git a/tests/test_aboutdialog.py b/tests/test_aboutdialog.py
@@ -20,12 +20,13 @@
 import unittest
 
 import wx
-from diffpy.pdfgui.gui import aboutdialog
 from testutils import GUITestCase, overridewebbrowser
 
+from diffpy.pdfgui.gui import aboutdialog
 
 # ----------------------------------------------------------------------------
 
+
 class TestDialogAbout(GUITestCase):
     def setUp(self):
         self.app = wx.App()

diff --git a/tests/test_datasetpanels.py b/tests/test_datasetpanels.py
@@ -20,9 +20,9 @@
 import unittest
 
 import wx
+from testutils import GUITestCase, datafile, tooltiptext
 
 from diffpy.pdfgui.gui.mainframe import MainFrame
-from testutils import GUITestCase, datafile, tooltiptext
 
 # ----------------------------------------------------------------------------
 

diff --git a/tests/test_dopingseriespanel.py b/tests/test_dopingseriespanel.py
@@ -20,9 +20,9 @@
 import unittest
 
 import wx
+from testutils import GUITestCase, datafile, overridefiledialog
 
 from diffpy.pdfgui.gui.dopingseriespanel import DopingSeriesPanel
-from testutils import GUITestCase, datafile, overridefiledialog
 
 # ----------------------------------------------------------------------------
 

diff --git a/tests/test_extendedplotframe.py b/tests/test_extendedplotframe.py
@@ -21,11 +21,11 @@
 
 import numpy
 import wx
+from testutils import GUITestCase, overridefiledialog
 
 from diffpy.pdfgui.control.plotter import Plotter
 from diffpy.pdfgui.gui import extendedplotframe as epf
 from diffpy.pdfgui.gui.extendedplotframe import ExtendedPlotFrame
-from testutils import GUITestCase, overridefiledialog
 
 # ----------------------------------------------------------------------------
 

diff --git a/tests/test_fitdataset.py b/tests/test_fitdataset.py
@@ -20,10 +20,10 @@
 import unittest
 
 import numpy
+from testutils import datafile
 
 import diffpy.pdfgui.control.fitdataset as fds
 from diffpy.pdfgui.control.fitdataset import FitDataSet
-from testutils import datafile
 
 # ----------------------------------------------------------------------------
 

diff --git a/tests/test_fitstructure.py b/tests/test_fitstructure.py
@@ -6,11 +6,12 @@
 
 import unittest
 
+from testutils import datafile
+
 from diffpy.pdfgui.control.constraint import Constraint
 from diffpy.pdfgui.control.controlerrors import ControlTypeError
 from diffpy.pdfgui.control.fitstructure import FitStructure
 from diffpy.pdfgui.control.pdfstructure import PDFStructure
-from testutils import datafile
 from diffpy.structure import Structure
 
 # ----------------------------------------------------------------------------

diff --git a/tests/test_insertrowsdialog.py b/tests/test_insertrowsdialog.py
@@ -20,9 +20,9 @@
 import unittest
 
 import wx
+from testutils import GUITestCase
 
 from diffpy.pdfgui.gui.insertrowsdialog import InsertRowsDialog
-from testutils import GUITestCase
 
 # ----------------------------------------------------------------------------
 

diff --git a/tests/test_loadproject.py b/tests/test_loadproject.py
@@ -19,8 +19,9 @@
 
 import unittest
 
-from diffpy.pdfgui.control.controlerrors import ControlFileError
 from testutils import GUITestCase, datafile
+
+from diffpy.pdfgui.control.controlerrors import ControlFileError
 from diffpy.pdfgui.tui import LoadProject
 
 # ----------------------------------------------------------------------------

diff --git a/tests/test_mainframe.py b/tests/test_mainframe.py
@@ -20,9 +20,9 @@
 import unittest
 
 import wx
+from testutils import GUITestCase
 
 from diffpy.pdfgui.gui.mainframe import MainFrame
-from testutils import GUITestCase
 
 # ----------------------------------------------------------------------------
 

diff --git a/tests/test_parameter.py b/tests/test_parameter.py
@@ -20,11 +20,11 @@
 import unittest
 
 import wx
+from testutils import GUITestCase, datafile
 
 from diffpy.pdfgui.control.controlerrors import ControlKeyError, ControlTypeError
 from diffpy.pdfgui.control.parameter import Parameter
 from diffpy.pdfgui.gui.mainframe import MainFrame
-from testutils import GUITestCase, datafile
 
 # ----------------------------------------------------------------------------
 

diff --git a/tests/test_parameterspanel.py b/tests/test_parameterspanel.py
@@ -20,10 +20,10 @@
 import unittest
 
 import wx.grid
+from testutils import GUITestCase, clickcell
 
 from diffpy.pdfgui.control.parameter import Parameter
 from diffpy.pdfgui.gui.parameterspanel import ParametersPanel
-from testutils import GUITestCase, clickcell
 
 # ----------------------------------------------------------------------------
 

diff --git a/tests/test_pdfdataset.py b/tests/test_pdfdataset.py
@@ -19,9 +19,10 @@
 
 import unittest
 
-from diffpy.pdfgui.control.pdfdataset import PDFDataSet
 from testutils import datafile
 
+from diffpy.pdfgui.control.pdfdataset import PDFDataSet
+
 
 ##############################################################################
 class TestPDFDataSet(unittest.TestCase):

diff --git a/tests/test_pdfstructure.py b/tests/test_pdfstructure.py
@@ -6,9 +6,10 @@
 
 import unittest
 
+from testutils import datafile
+
 from diffpy.pdfgui.control.controlerrors import ControlFileError, ControlKeyError
 from diffpy.pdfgui.control.pdfstructure import PDFStructure
-from testutils import datafile
 
 # ----------------------------------------------------------------------------
 

diff --git a/tests/test_phaseconfigurepanel.py b/tests/test_phaseconfigurepanel.py
@@ -20,10 +20,10 @@
 import unittest
 
 import wx
+from testutils import GUITestCase, clickcell, datafile, overrideclipboard, tooltiptext
 
 from diffpy.pdfgui.gui.mainframe import MainFrame
 from diffpy.pdfgui.gui.phaseconfigurepanel import PhaseConfigurePanel
-from testutils import GUITestCase, clickcell, datafile, overrideclipboard, tooltiptext
 
 # ----------------------------------------------------------------------------
 

diff --git a/tests/test_structureviewer.py b/tests/test_structureviewer.py
@@ -7,9 +7,10 @@
 import os
 import unittest
 
+from testutils import datafile
+
 from diffpy.pdfgui.control.controlerrors import ControlConfigError
 from diffpy.pdfgui.control.structureviewer import StructureViewer, getStructureViewer
-from testutils import datafile
 
 
 ##############################################################################

diff --git a/tests/test_temperatureseriespanel.py b/tests/test_temperatureseriespanel.py
@@ -20,9 +20,9 @@
 import unittest
 
 import wx
+from testutils import GUITestCase, datafile, overridefiledialog
 
 from diffpy.pdfgui.gui.temperatureseriespanel import TemperatureSeriesPanel
-from testutils import GUITestCase, datafile, overridefiledialog
 
 # ----------------------------------------------------------------------------
 

diff --git a/tests/testutils.py b/tests/testutils.py
@@ -19,6 +19,7 @@
 import os
 from contextlib import contextmanager
 from unittest import TestCase
+
 import wx
 
 from diffpy.pdfgui.control import pdfguicontrol
@@ -29,7 +30,7 @@
 
 def datafile(filename):
     return "tests/testdata/" + filename
-    
+
 
 @contextmanager
 def overridewebbrowser(fnc_open):
Original file line number	Diff line number	Diff line change
Expand Up		@@ -18,4 +18,3 @@ diffpy.pdfgui.applications.pdfgui module
		:members:
		:undoc-members:
		:show-inheritance:
Original file line number	Diff line number	Diff line change
Expand Up		@@ -138,4 +138,3 @@ diffpy.pdfgui.control.organizer module
		:members:
		:undoc-members:
		:show-inheritance:
Original file line number	Diff line number	Diff line change
Expand Up		@@ -7,4 +7,3 @@ diffpy.pdfgui.gui.design package
		:members:
		:undoc-members:
		:show-inheritance:
Original file line number	Diff line number	Diff line change
Expand Up		@@ -371,4 +371,3 @@ diffpy.pdfgui.gui.mainframe module
		:members:
		:undoc-members:
		:show-inheritance:
Original file line number	Diff line number	Diff line change
Expand Up		@@ -58,4 +58,3 @@ diffpy.pdfgui.gui.wxextensions.paneldialog module
		:members:
		:undoc-members:
		:show-inheritance:
Original file line number	Diff line number	Diff line change
Expand Up		@@ -7,4 +7,3 @@ diffpy.pdfgui.icons package
		:members:
		:undoc-members:
		:show-inheritance:
Original file line number	Diff line number	Diff line change
Expand Up		@@ -37,4 +37,3 @@ diffpy.pdfgui.tui module
		:members:
		:undoc-members:
		:show-inheritance: