Fix spelling suggested by codespell

Author: bobleesj

.codespell/ignore_words.txt

@@ -9,3 +9,12 @@ socio-economic
 
 ;; Frobenius norm used in np.linalg.norm
 fro
+
+;; abbreviation for "structure"
+struc
+
+;; method name within JournalPanel class
+onText
+
+;; a method name within JournalPanel class
+delt

README.rst

@@ -132,7 +132,7 @@ trying to commit again.
 
 Improvements and fixes are always appreciated.
 
-Before contribuing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.pdfgui/blob/main/CODE_OF_CONDUCT.rst>`_.
+Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.pdfgui/blob/main/CODE_OF_CONDUCT.rst>`_.
 
 Contact
 -------

doc/manual/html/readme.txt

@@ -1,2 +1,2 @@
-This directory need to be relativly the same as doc/build/html/manual from
+This directory need to be relatively the same as doc/build/html/manual from
 doc/source/_static/images

doc/manual/pdfgui.texinfo

@@ -243,7 +243,7 @@ requirements. This can be done either for all atoms in the structure or for an
 arbitrary subset - for example when it is known that only a certain species
 show a local distortion. The code for space group definitions was provided by
 the Python Macromolecular Library (mmLib,
-@url{http://pymmlib.sourceforge.net}).  This was extened to include
+@url{http://pymmlib.sourceforge.net}).  This was extended to include
 non-standard space groups using the Computational Crystallography Toolbox
 (cctbx, @uref{https://cctbx.github.io}).  PDFgui also supports supercell
 expansion of a normal unit cell.

pyproject.toml

@@ -56,7 +56,7 @@ dependencies = {file = ["requirements/pip.txt"]}
 [tool.codespell]
 exclude-file = ".codespell/ignore_lines.txt"
 ignore-words = ".codespell/ignore_words.txt"
-skip = "*.cif,*.dat"
+skip = "*.cif,*.dat,*.html,*.m,*.textinfo"
 
 [tool.black]
 line-length = 115

src/diffpy/pdfgui/control/calculation.py

@@ -252,7 +252,7 @@ def load(self, z, subpath):
         z       -- zipped project file
         subpath -- path to its own storage within project file
 
-        returns a tree of internal hierachy
+        returns a tree of internal hierarchy
         """
         config = pickle.loads(z.read(subpath + "config"), encoding="latin1")
         self.rmin = config["rmin"]

src/diffpy/pdfgui/control/fitstructure.py

@@ -35,7 +35,7 @@ class FitStructure(PDFStructure):
     Class data members:
         symposeps   -- tolerance for recognizing site as symmetry position
 
-    Data members (in adition to those in PDFStructure):
+    Data members (in addition to those in PDFStructure):
         owner       -- instance of parent Fitting (set in Organizer.add())
         initial     -- initial structure, same as self
         refined     -- refined structure when available or None

src/diffpy/pdfgui/control/fitting.py

@@ -73,7 +73,7 @@ class Fitting(Organizer):
     Fitting will start a new thread to interact with the PdfFit server.
 
     rw:         fitness parameter
-    tolerancy:  accurancy requirement
+    tolerancy:  accuracy requirement
     step:       current refinement step
     res:        fitting result string
     parameters: parameter dictionary
@@ -200,7 +200,7 @@ def load(self, z, subpath):
         z -- zipped project file
         subpath -- path to its own storage within project file
 
-        returns a tree of internal hierachy
+        returns a tree of internal hierarchy
         """
         # subpath = projName/fitName/
         subs = subpath.split("/")
@@ -349,7 +349,7 @@ def configure(self):
             for key, var in struc.constraints.items():
                 self.server.constrain(key, var.formula)
 
-        # phase paramters configured
+        # phase parameters configured
 
         for dataset in self.datasets:
             dataset.clearRefined()
@@ -493,7 +493,7 @@ def outputBondLengthAtoms(self, struc, i, j):
         return
 
     def outputBondLengthTypes(self, struc, a1, a2, lb, ub):
-        """Output all a1-a2 bond lenghts within specified range.
+        """Output all a1-a2 bond lengths within specified range.
 
         struc  -- instance of PDFStructure
         a1     -- symbol of the first element in pair or "ALL"
@@ -589,7 +589,7 @@ def buildNameDict(self):
         """build up a data name dictionary, which will map data name to a
         unique index
 
-        The private dataNameDict has such strcture:
+        The private dataNameDict has such structure:
         { 'd_data1':{'Gobs':12, 'Gcalc':11, ....},
           'd_data2':{'Gobs':10, 'Gcalc':9, ....},
           ...
@@ -660,7 +660,7 @@ def appendStep(self, source):
             snapshot[nameDict["crw"]] = dataset.crw
             seq += 1
 
-        # udpate strucs
+        # update strucs
         seq = 1
         for struc in self.strucs:
             id = struc._getStrId()

src/diffpy/pdfgui/control/organizer.py

@@ -157,7 +157,7 @@ def load(self, z, subpath):
         z -- zipped project file
         subpath -- path to its own storage within project file
 
-        returns a tree of internal hierachy
+        returns a tree of internal hierarchy
         """
         # subpath = projName/myName/
         from urllib.parse import unquote_plus
@@ -223,7 +223,7 @@ def copy(self, other=None):
     def organization(self):
         """get internal organization
 
-        returns a tree of internal hierachy
+        returns a tree of internal hierarchy
         """
         org = [None] * 4
         org[0] = self

src/diffpy/pdfgui/control/parameter.py

@@ -137,7 +137,7 @@ def __getLinkedValue(self):
         srcfit = self.__findLinkedFitting()
         if srcfit is None:
             raise ControlKeyError("Fitting '%s' does not exist" % fitname)
-        # Check to see if srcfit has paramter srcidx
+        # Check to see if srcfit has parameter srcidx
         try:
             srcpar = srcfit.parameters[srcidx]
         except KeyError: