fixed all codespell issues; fixed all line length issues

Author: TingwenZhang

.codespell/ignore_words.txt

@@ -9,3 +9,11 @@ socio-economic
 
 ;; Frobenius norm used in np.linalg.norm
 fro
+
+DISCUS
+discus
+CONECT
+Discus
+Te
+Nd
+BU

.pre-commit-config.yaml

@@ -50,6 +50,7 @@ repos:
       - id: codespell
         additional_dependencies:
           - tomli
+        args: [--ignore-words=.codespell/ignore_words.txt]
   # prettier - multi formatter for .json, .yml, and .md files
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: f12edd9c7be1c20cfa42420fd0e6df71e42b51ea # frozen: v4.0.0-alpha.8

CHANGELOG.rst

@@ -28,7 +28,7 @@ Release Notes
 **Fixed:**
 
 * Add getting started section and re-arrange install success check instructions
-* Added termial script for transtru app in pyproject.toml
+* Added terminal script for transtru app in pyproject.toml
 * Changed requires-python to align with classifiers
 
 

devutils/sgtbx_extra_groups.py

@@ -1,10 +1,11 @@
 #!/usr/bin/env python
 
-"""Quick and extremely dirty script for generating code for SpaceGroup that
-are defined in cctbx, but not in mmLib.  It was used to generate module
+"""Quick and extremely dirty script for generating code for SpaceGroup that are
+defined in cctbx, but not in mmLib.  It was used to generate module
 sgtbxspacegroups.
 
-This is a utility script that should not be included with code distribution.
+This is a utility script that should not be included with code
+distribution.
 
 Not to be included with code distributions.
 """
@@ -16,7 +17,12 @@
 import numpy
 from cctbx import sgtbx
 
-from diffpy.structure.spacegroups import IsSpaceGroupIdentifier, SpaceGroup, SymOp, mmLibSpaceGroupList
+from diffpy.structure.spacegroups import (
+    IsSpaceGroupIdentifier,
+    SpaceGroup,
+    SymOp,
+    mmLibSpaceGroupList,
+)
 
 
 def tupleToSGArray(tpl):

src/diffpy/structure/__init__.py

@@ -12,9 +12,7 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-
-"""
-Crystal structure container and parsers for structure formats.
+"""Crystal structure container and parsers for structure formats.
 
 Classes related to the structure of materials:
     * Atom
@@ -42,7 +40,11 @@
 from diffpy.structure.parsers import getParser
 from diffpy.structure.pdffitstructure import PDFFitStructure
 from diffpy.structure.structure import Structure
-from diffpy.structure.structureerrors import LatticeError, StructureFormatError, SymmetryError
+from diffpy.structure.structureerrors import (
+    LatticeError,
+    StructureFormatError,
+    SymmetryError,
+)
 
 # package version
 from diffpy.structure.version import __version__

src/diffpy/structure/_legacy_importer.py

@@ -12,9 +12,7 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-
-"""
-Support import of old camel-case module names with DeprecationWarning.
+"""Support import of old camel-case module names with DeprecationWarning.
 
 The imported camel-case modules are aliases for the current module
 instances. Their `__name__` attributes are thus all in lower-case.
@@ -61,6 +59,7 @@ def find_spec(self, fullname, path=None, target=None):
 
 class MapRenamedStructureModule(importlib.abc.Loader):
     """Loader for old camel-case module names.
+
     Import the current module and alias it under the old name.
     """
 
@@ -80,7 +79,11 @@ def exec_module(self, module):
 # ----------------------------------------------------------------------------
 
 # show deprecation warning for diffpy.Structure
-warn(WMSG.format("diffpy.Structure", "diffpy.structure"), DeprecationWarning, stacklevel=2)
+warn(
+    WMSG.format("diffpy.Structure", "diffpy.structure"),
+    DeprecationWarning,
+    stacklevel=2,
+)
 
 # install meta path finder for diffpy.Structure submodules
 sys.meta_path.append(FindRenamedStructureModule())

src/diffpy/structure/apps/__init__.py

@@ -12,5 +12,4 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
 """Script applications that use the `diffpy.structure` package."""

src/diffpy/structure/apps/anyeye.py

@@ -12,14 +12,13 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
-"""
-Anyeye view structure file in atomeye.
+"""Anyeye view structure file in atomeye.
 
 Usage: ``anyeye [options] strufile``
 
-Anyeye understands more `Structure` formats than atomeye. It converts `strufile`
-to a temporary XCFG file which is opened in atomeye. See supported file formats:
+Anyeye understands more `Structure` formats than atomeye. It converts
+`strufile` to a temporary XCFG file which is opened in atomeye. See supported
+file formats:
 ``inputFormats``
 
 Options:
@@ -71,7 +70,11 @@ def usage(style=None):
     myname = os.path.basename(sys.argv[0])
     msg = __doc__.replace("anyeye", myname)
     if style == "brief":
-        msg = msg.split("\n")[1] + "\n" + "Try `%s --help' for more information." % myname
+        msg = (
+            msg.split("\n")[1]
+            + "\n"
+            + "Try `%s --help' for more information." % myname
+        )
     else:
         from diffpy.structure.parsers import inputFormats
 
@@ -139,7 +142,10 @@ def convertStructureFile(pd):
     if pd["formula"]:
         formula = pd["formula"]
         if len(formula) != len(stru):
-            emsg = "Formula has %i atoms while structure %i" % (len(formula), len(stru))
+            emsg = "Formula has %i atoms while structure %i" % (
+                len(formula),
+                len(stru),
+            )
             raise RuntimeError(emsg)
         for a, el in zip(stru, formula):
             a.element = el
@@ -175,7 +181,7 @@ def cleanUp(pd):
 
 
 def parseFormula(formula):
-    """Parse chemical formula and return a list of elements"""
+    """Parse chemical formula and return a list of elements."""
     # remove all blanks
     formula = re.sub(r"\s", "", formula)
     if not re.match("^[A-Z]", formula):
@@ -218,7 +224,9 @@ def main():
     pd["watch"] = False
     try:
         opts, args = getopt.getopt(
-            sys.argv[1:], "f:whV", ["formula=", "watch", "viewer=", "formats=", "help", "version"]
+            sys.argv[1:],
+            "f:whV",
+            ["formula=", "watch", "viewer=", "formats=", "help", "version"],
         )
     except getopt.GetoptError as errmsg:
         print(errmsg, file=sys.stderr)

src/diffpy/structure/apps/transtru.py

@@ -12,14 +12,13 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
 """Translate structure file to different format.
 
 Usage: ``transtru INFMT..OUTFMT strufile``
 
-Translates structure file strufile from `INFMT` to `OUTFMT` format and prints it
-to the screen. Use "-" as `strufile` to read from standard input. To save the
-translated file, use
+Translates structure file strufile from `INFMT` to `OUTFMT` format and prints
+it to the screen. Use "-" as `strufile` to read from standard input. To save
+the translated file, use
 
     ``transtru INFMT..OUTFMT strufile > strufile.out``
 
@@ -50,7 +49,11 @@ def usage(style=None):
     myname = os.path.basename(sys.argv[0])
     msg = __doc__.replace("transtru", myname)
     if style == "brief":
-        msg = msg.split("\n")[1] + "\n" + "Try `%s --help' for more information." % myname
+        msg = (
+            msg.split("\n")[1]
+            + "\n"
+            + "Try `%s --help' for more information." % myname
+        )
     else:
         from diffpy.structure.parsers import inputFormats, outputFormats
 
@@ -99,7 +102,10 @@ def main():
             print("'%s' is not valid output format" % outfmt, file=sys.stderr)
             sys.exit(2)
     except ValueError:
-        print("invalid format specification '%s' does not contain .." % args[0], file=sys.stderr)
+        print(
+            "invalid format specification '%s' does not contain .." % args[0],
+            file=sys.stderr,
+        )
         sys.exit(2)
     # ready to do some real work
     try:

src/diffpy/structure/atom.py

@@ -12,10 +12,7 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
-"""
-Provide class Atom for managing properties of an atom in structure model.
-"""
+"""Provide class Atom for managing properties of an atom in structure model."""
 
 import numpy
 
@@ -170,7 +167,9 @@ def msdLat(self, vl):
         lat = self.lattice or cartesian_lattice
         vln = numpy.array(vl, dtype=float) / lat.norm(vl)
         G = lat.metrics
-        rhs = numpy.array([G[0] * lat.ar, G[1] * lat.br, G[2] * lat.cr], dtype=float)
+        rhs = numpy.array(
+            [G[0] * lat.ar, G[1] * lat.br, G[2] * lat.cr], dtype=float
+        )
         rhs = numpy.dot(rhs, vln)
         msd = numpy.dot(rhs, numpy.dot(self.U, rhs))
         return msd
@@ -202,7 +201,13 @@ def msdCart(self, vc):
     def __repr__(self):
         """String representation of this Atom."""
         xyz = self.xyz
-        s = "%-4s %8.6f %8.6f %8.6f %6.4f" % (self.element, xyz[0], xyz[1], xyz[2], self.occupancy)
+        s = "%-4s %8.6f %8.6f %8.6f %6.4f" % (
+            self.element,
+            xyz[0],
+            xyz[1],
+            xyz[2],
+            self.occupancy,
+        )
         return s
 
     def __copy__(self, target=None):
@@ -354,13 +359,19 @@ def _set_Uij(self, i, j, value):
         """
 
     U11 = property(
-        lambda self: self._get_Uij(0, 0), lambda self, value: self._set_Uij(0, 0, value), doc=_doc_uii.format(0)
+        lambda self: self._get_Uij(0, 0),
+        lambda self, value: self._set_Uij(0, 0, value),
+        doc=_doc_uii.format(0),
     )
     U22 = property(
-        lambda self: self._get_Uij(1, 1), lambda self, value: self._set_Uij(1, 1, value), doc=_doc_uii.format(1)
+        lambda self: self._get_Uij(1, 1),
+        lambda self, value: self._set_Uij(1, 1, value),
+        doc=_doc_uii.format(1),
     )
     U33 = property(
-        lambda self: self._get_Uij(2, 2), lambda self, value: self._set_Uij(2, 2, value), doc=_doc_uii.format(2)
+        lambda self: self._get_Uij(2, 2),
+        lambda self, value: self._set_Uij(2, 2, value),
+        doc=_doc_uii.format(2),
     )
 
     _doc_uij = """
@@ -371,13 +382,19 @@ def _set_Uij(self, i, j, value):
         """
 
     U12 = property(
-        lambda self: self._get_Uij(0, 1), lambda self, value: self._set_Uij(0, 1, value), doc=_doc_uij.format(0, 1)
+        lambda self: self._get_Uij(0, 1),
+        lambda self, value: self._set_Uij(0, 1, value),
+        doc=_doc_uij.format(0, 1),
     )
     U13 = property(
-        lambda self: self._get_Uij(0, 2), lambda self, value: self._set_Uij(0, 2, value), doc=_doc_uij.format(0, 2)
+        lambda self: self._get_Uij(0, 2),
+        lambda self, value: self._set_Uij(0, 2, value),
+        doc=_doc_uij.format(0, 2),
     )
     U23 = property(
-        lambda self: self._get_Uij(1, 2), lambda self, value: self._set_Uij(1, 2, value), doc=_doc_uij.format(1, 2)
+        lambda self: self._get_Uij(1, 2),
+        lambda self, value: self._set_Uij(1, 2, value),
+        doc=_doc_uij.format(1, 2),
     )
 
     # clean local variables
@@ -481,7 +498,8 @@ def Uisoequiv(self, value):
 
     @property
     def Bisoequiv(self):
-        """float : The Debye-Waller isotropic displacement or an equivalent value.
+        """float : The Debye-Waller isotropic displacement or an equivalent
+        value.
 
         This equals ``8 * pi**2 * Uisoequiv``. Setting a new value
         rescales `U` tensor to yield equivalent direction-average of