skpkg: codespell src/

Author: TingwenZhang

.codespell/ignore_words.txt

@@ -4,8 +4,21 @@
 ;; abbreviation for "materials" often used in a journal title
 mater
 
-;; alternative use of socioeconomic
-socio-economic
-
 ;; Frobenius norm used in np.linalg.norm
 fro
+
+;; "discus" is the name of a software package
+discus
+DISCUS
+
+;; chemical elements
+Te
+Nd
+
+;; /src/diffpy/structure/parsers/p_pdb.py:100
+;; pdb identifier
+CONECT
+
+;; /src/diffpy/structure/parsers/p_xcfg.py:452
+;; used in a function
+BU

src/diffpy/structure/expansion/shapeutils.py

@@ -32,7 +32,7 @@ def findCenter(S):
     """
     best = -1
     bestd = len(S)
-    center = [0.5, 0.5, 0.5]  # the cannonical center
+    center = [0.5, 0.5, 0.5]  # the canonical center
 
     for i in range(len(S)):
         d = S.lattice.dist(S[i].xyz, center)

src/diffpy/structure/parsers/p_auto.py

@@ -148,7 +148,7 @@ def parseFile(self, filename):
     def _wrapParseMethod(self, method, *args, **kwargs):
         """A helper evaluator method that try the specified parse method
         with each registered structure parser and return the first
-        successful resul.
+        successful result.
 
         Structure parsers that match structure file extension are
         tried first.

src/diffpy/structure/parsers/p_discus.py

@@ -272,7 +272,7 @@ def _parse_unknown_record(self, words):
         Raises
         ------
         StructureFormatError
-            Unkown record.
+            Unknown record.
         """
         self.ignored_lines.append(self.line)
         return

src/diffpy/structure/parsers/p_xcfg.py

@@ -424,7 +424,7 @@ def getParser():
 
 
 def _assign_auxiliaries(a, fields, auxiliaries, no_velocity):
-    """Assing auxiliary properties for `Atom` object when reading CFG
+    """Assign auxiliary properties for `Atom` object when reading CFG
     format.
 
     Parameters

src/diffpy/structure/spacegroupmod.py

@@ -7,7 +7,7 @@
 
 import numpy
 
-# 64 unique rotation matricies
+# 64 unique rotation matrices
 Rot_Z_mY_X = numpy.array([[0.0, 0.0, 1.0], [0.0, -1.0, 0.0], [1.0, 0.0, 0.0]], float)
 Rot_Y_mX_mZ = numpy.array([[0.0, 1.0, 0.0], [-1.0, 0.0, 0.0], [0.0, 0.0, -1.0]], float)
 Rot_XmY_X_mZ = numpy.array([[1.0, -1.0, 0.0], [1.0, 0.0, 0.0], [0.0, 0.0, -1.0]], float)

src/diffpy/structure/structure.py

@@ -453,7 +453,7 @@ def __getitem__(self, idx):
 
         Parameters
         ----------
-        idx : int ot str ot Iterable
+        idx : int or str or Iterable
             `Atom` identifier. When integer use standard list lookup.
             For iterables use numpy lookup, this supports integer or
             boolean flag arrays. For string or string-containing iterables
@@ -566,7 +566,7 @@ def _fixlat(a):
                 keep = set(super(Structure, self).__getitem__(idx))
                 v1 = (a if a in keep else Atom(a) for a in value)
             vfinal = filter(_fixlat, v1)
-        # handle scalar assingment
+        # handle scalar assignment
         else:
             vfinal = Atom(value) if copy else value
             vfinal.lattice = self.lattice

src/diffpy/structure/symmetryutilities.py

@@ -147,7 +147,7 @@ class _Position2Tuple(object):
     Attributes
     ----------
     eps : float
-        Cutoff for equivalent coordinates. When two coordiantes map to the
+        Cutoff for equivalent coordinates. When two coordinates map to the
         same tuple, they are closer than `eps`.
     """