diffpy.structure 3.3.0__py3-none-any.whl → 3.3.1__py3-none-any.whl

diffpy/__init__.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (c) 2024 The Trustees of Columbia University in the City of New York.
+# (c) 2024-2025 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
 # File coded by: Billinge Group members and community contributors.
@@ -12,12 +12,3 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-
-"""Blank namespace package for module diffpy."""
-
-
-from pkgutil import extend_path
-
-__path__ = extend_path(__path__, __name__)
-
-# End of file

diffpy/structure/__init__.py

@@ -1,10 +1,10 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (c) 2024 The Trustees of Columbia University in the City of New York.
+# (c) 2024-2025 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
-# File coded by: Billinge Group members and community contributors.
+# File coded by: Chris Farrow, Pavol Juhas,  Simon Billinge, Billinge Group members.
 #
 # See GitHub contributions for a more detailed list of contributors.
 # https://github.com/diffpy/diffpy.structure/graphs/contributors
@@ -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

diffpy/structure/_legacy_importer.py

@@ -12,9 +12,8 @@
 # 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 +60,7 @@ class FindRenamedStructureModule(importlib.abc.MetaPathFinder):
 
 class MapRenamedStructureModule(importlib.abc.Loader):
     """Loader for old camel-case module names.
+
     Import the current module and alias it under the old name.
     """
 

diffpy/structure/apps/__init__.py

@@ -12,6 +12,4 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
-"""Script applications that use the `diffpy.structure` package.
-"""
+"""Script applications that use the `diffpy.structure` package."""

diffpy/structure/apps/anyeye.py

@@ -12,9 +12,7 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
-"""
-Anyeye view structure file in atomeye.
+"""Anyeye view structure file in atomeye.
 
 Usage: ``anyeye [options] strufile``
 
@@ -65,7 +63,8 @@ pd = {
 
 
 def usage(style=None):
-    """Show usage info, for ``style=="brief"`` show only first 2 lines."""
+    """Show usage info, for ``style=="brief"`` show only first 2
+    lines."""
     import os.path
 
     myname = os.path.basename(sys.argv[0])
@@ -175,7 +174,7 @@ 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):

diffpy/structure/apps/transtru.py

@@ -12,7 +12,6 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
 """Translate structure file to different format.
 
 Usage: ``transtru INFMT..OUTFMT strufile``
@@ -44,7 +43,8 @@ from diffpy.structure.structureerrors import StructureFormatError
 
 
 def usage(style=None):
-    """Show usage info, for ``style=="brief"`` show only first 2 lines."""
+    """Show usage info, for ``style=="brief"`` show only first 2
+    lines."""
     import os.path
 
     myname = os.path.basename(sys.argv[0])

diffpy/structure/atom.py

@@ -12,10 +12,8 @@
 # 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
 
@@ -176,7 +174,8 @@ class Atom(object):
         return msd
 
     def msdCart(self, vc):
-        """Calculate mean square displacement along the Cartesian vector.
+        """Calculate mean square displacement along the Cartesian
+        vector.
 
         Parameters
         ----------
@@ -252,7 +251,8 @@ class Atom(object):
 
     @property
     def xyz_cartn(self):
-        """numpy.ndarray: Atom position in absolute Cartesian coordinates.
+        """numpy.ndarray: Atom position in absolute Cartesian
+        coordinates.
 
         This is computed from fractional coordinates `xyz` and the
         current `lattice` setup. Assignment to *xyz_cartn* or
@@ -301,7 +301,8 @@ class Atom(object):
 
     @property
     def U(self):
-        """numpy.ndarray : The 3x3 matrix of anisotropic atomic displacements.
+        """numpy.ndarray : The 3x3 matrix of anisotropic atomic
+        displacements.
 
         For isotropic displacements (when `anisotropy` is ``False``)
         assignment to *U* uses only the first ``Unew[0, 0]`` element
@@ -537,7 +538,8 @@ class _AtomCartesianCoordinates(numpy.ndarray):
         return
 
     def __array_wrap__(self, out_arr, context=None, return_scalar=None):
-        """Ensure math operations on this type yield standard numpy array."""
+        """Ensure math operations on this type yield standard numpy
+        array."""
         return out_arr.view(numpy.ndarray)
 
 

diffpy/structure/expansion/__init__.py

@@ -12,7 +12,6 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
 """Methods and classes for manipulating `Structure` instances.
 
 Package content:

diffpy/structure/expansion/makeellipsoid.py

@@ -12,7 +12,6 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
 """Make a spheroid nanoparticle from a template structure."""
 
 from math import ceil
@@ -42,8 +41,7 @@ def makeSphere(S, radius):
 
 
 def makeEllipsoid(S, a, b=None, c=None):
-    """
-    Cut a `Structure` out of another one.
+    """Cut a `Structure` out of another one.
 
     Parameters
     ----------

diffpy/structure/expansion/shapeutils.py

@@ -12,7 +12,6 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
 """Utilities for making shapes."""
 
 
@@ -33,7 +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)

diffpy/structure/expansion/supercell_mod.py

@@ -12,9 +12,8 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
-"""This module contains functions for simple `Structure` manipulation.
-"""
+"""This module contains functions for simple `Structure`
+manipulation."""
 
 import numpy
 
@@ -22,8 +21,7 @@ from diffpy.structure import Atom, Structure
 
 
 def supercell(S, mno):
-    """
-    Perform supercell expansion for a `Structure`.
+    """Perform supercell expansion for a `Structure`.
 
     New `lattice` parameters are multiplied and fractional coordinates
     divided by corresponding multiplier. New `Atoms` are grouped with

diffpy/structure/lattice.py

@@ -12,9 +12,8 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
-"""Class Lattice stores properties and provides simple operations in lattice
-coordinate system.
+"""Class Lattice stores properties and provides simple operations in
+lattice coordinate system.
 
 Attributes
 ----------
@@ -442,6 +441,7 @@ class Lattice(object):
 
     def abcABG(self):
         """Return the cell parameters in the standard setting.
+
         Returns
         -------
         tuple :
@@ -452,6 +452,7 @@ class Lattice(object):
 
     def reciprocal(self):
         """Return the reciprocal lattice of the current lattice.
+
         Returns
         -------
         Lattice

diffpy/structure/mmlibspacegroups.py

@@ -3,8 +3,7 @@
 # This code is part of the PyMMLib distribution and governed by
 # its license.Please see the LICENSE_pymmlib file that should have been
 # included as part of this package.
-"""Space groups defined as a part of the pymmlib.
-"""
+"""Space groups defined as a part of the pymmlib."""
 
 from diffpy.structure.spacegroupmod import (
     Rot_mX_mXY_mZ,

diffpy/structure/parsers/__init__.py

@@ -12,7 +12,6 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
 """Conversion plugins for various structure formats.
 
 The recognized structure formats are defined by subclassing `StructureParser`,

diffpy/structure/parsers/p_auto.py

@@ -12,7 +12,6 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
 """Parser for automatic file format detection.
 
 This Parser does not provide the the `toLines()` method.
@@ -54,6 +53,7 @@ class P_auto(StructureParser):
     # parseLines helpers
     def _getOrderedFormats(self):
         """Build a list of relevance ordered structure formats.
+
         This only works when `self.filename` has a known extension.
         """
         from diffpy.structure.parsers import inputFormats
@@ -77,7 +77,8 @@ class P_auto(StructureParser):
         return ofmts
 
     def parseLines(self, lines):
-        """Detect format and create `Structure` instance from a list of lines.
+        """Detect format and create `Structure` instance from a list of
+        lines.
 
         Set format attribute to the detected file format.
 
@@ -119,7 +120,8 @@ class P_auto(StructureParser):
         return self._wrapParseMethod("parse", s)
 
     def parseFile(self, filename):
-        """Detect format and create Structure instance from an existing file.
+        """Detect format and create Structure instance from an existing
+        file.
 
         Set format attribute to the detected file format.
 
@@ -144,9 +146,9 @@ class P_auto(StructureParser):
         return self._wrapParseMethod("parseFile", 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.
+        """A helper evaluator method that try the specified parse method
+        with each registered structure parser and return the first
+        successful result.
 
         Structure parsers that match structure file extension are
         tried first.

diffpy/structure/parsers/p_cif.py

@@ -12,7 +12,6 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
 """Parser for basic CIF file format.
 
 Attributes
@@ -33,6 +32,7 @@ import sys
 from contextlib import contextmanager
 
 import numpy
+from CifFile.yapps3_compiled_rt import YappsSyntaxError
 
 from diffpy.structure import Atom, Lattice, Structure
 from diffpy.structure.parsers import StructureParser
@@ -267,7 +267,8 @@ class P_cif(StructureParser):
     _tr_atom_site_aniso_B_23 = staticmethod(_tr_atom_site_aniso_B_23)
 
     def _get_atom_setters(cifloop):
-        """Static method for finding translators of CifLoop items to data in `Atom` instance.
+        """Static method for finding translators of CifLoop items to
+        data in `Atom` instance.
 
         Parameters
         ----------
@@ -408,7 +409,7 @@ class P_cif(StructureParser):
                     # stop after reading the first structure
                     if self.stru is not None:
                         break
-        except (StarError, ValueError, IndexError) as err:
+        except (YappsSyntaxError, StarError, ValueError, IndexError) as err:
             exc_type, exc_value, exc_traceback = sys.exc_info()
             emsg = str(err).strip()
             e = StructureFormatError(emsg)
@@ -416,8 +417,8 @@ class P_cif(StructureParser):
         return self.stru
 
     def _parseCifBlock(self, blockname):
-        """Translate CIF file block, skip blocks without `_atom_site_label`.
-        Updates data members `stru`, `eau`.
+        """Translate CIF file block, skip blocks without
+        `_atom_site_label`. Updates data members `stru`, `eau`.
 
         Parameters
         ----------
@@ -505,7 +506,8 @@ class P_cif(StructureParser):
         return
 
     def _parse_atom_site_aniso_label(self, block):
-        """Obtain value of anisotropic thermal displacements from a `CifBlock`.
+        """Obtain value of anisotropic thermal displacements from a
+        `CifBlock`.
 
         This method updates `U` members of `Atom` instances in `self.stru`.
         The `labelindex` dictionary has to be defined beforehand.
@@ -599,7 +601,8 @@ class P_cif(StructureParser):
         return
 
     def _expandAsymmetricUnit(self, block):
-        """Perform symmetry expansion of `self.stru` using `self.spacegroup`.
+        """Perform symmetry expansion of `self.stru` using
+        `self.spacegroup`.
 
         This method updates data in `stru` and `eau`.
 
@@ -763,7 +766,8 @@ rx_float = re.compile(r"[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?")
 
 
 def leading_float(s, d=0.0):
-    """Extract the first float from a string and ignore trailing characters.
+    """Extract the first float from a string and ignore trailing
+    characters.
 
     Useful for extracting values from "value(std)" syntax.
 
@@ -863,7 +867,8 @@ def getParser(eps=None):
 
 @contextmanager
 def _suppressCifParserOutput():
-    """Context manager which suppresses diagnostic messages from CIF parser."""
+    """Context manager which suppresses diagnostic messages from CIF
+    parser."""
     from CifFile import yapps3_compiled_rt
 
     print_error = yapps3_compiled_rt.print_error

diffpy/structure/parsers/p_discus.py

@@ -12,9 +12,7 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
-"""Parser for DISCUS structure format
-"""
+"""Parser for DISCUS structure format."""
 
 import sys
 from functools import reduce
@@ -25,8 +23,8 @@ from diffpy.structure.structureerrors import StructureFormatError
 
 
 class P_discus(StructureParser):
-    """Parser for DISCUS structure format. The parser chokes
-    on molecule and generator records.
+    """Parser for DISCUS structure format. The parser chokes on molecule
+    and generator records.
 
     Attributes
     ----------
@@ -274,7 +272,7 @@ class P_discus(StructureParser):
         Raises
         ------
         StructureFormatError
-            Unkown record.
+            Unknown record.
         """
         self.ignored_lines.append(self.line)
         return

diffpy/structure/parsers/p_pdb.py

@@ -12,7 +12,6 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
 """Basic parser for PDB structure format.
 
 Note
@@ -281,9 +280,8 @@ class P_pdb(StructureParser):
         return lines
 
     def atomLines(self, stru, idx):
-        """Build `ATOM` records and possibly `SIGATM`, `ANISOU` or `SIGUIJ` records
-        for `structure` stru `atom` number aidx.
-        """
+        """Build `ATOM` records and possibly `SIGATM`, `ANISOU` or
+        `SIGUIJ` records for `structure` stru `atom` number aidx."""
         lines = []
         a = stru[idx]
         ad = a.__dict__

diffpy/structure/parsers/p_pdffit.py

@@ -12,9 +12,7 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
-"""Parser for PDFfit structure format
-"""
+"""Parser for PDFfit structure format."""
 
 import sys
 from functools import reduce

diffpy/structure/parsers/p_rawxyz.py

@@ -12,11 +12,10 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
 """Parser for raw XYZ file format.
 
-Raw XYZ is a 3 or 4 column text file with cartesian coordinates
-of atoms and an optional first column for atom types.
+Raw XYZ is a 3 or 4 column text file with cartesian coordinates of atoms
+and an optional first column for atom types.
 """
 
 import sys

diffpy/structure/parsers/p_xcfg.py

@@ -12,7 +12,6 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
 """Parser for extended CFG format used by atomeye.
 
 Attributes
@@ -287,7 +286,8 @@ class P_xcfg(StructureParser):
         return stru
 
     def toLines(self, stru):
-        """Convert Structure stru to a list of lines in XCFG atomeye format.
+        """Convert Structure stru to a list of lines in XCFG atomeye
+        format.
 
         Parameters
         ----------
@@ -424,7 +424,8 @@ def getParser():
 
 
 def _assign_auxiliaries(a, fields, auxiliaries, no_velocity):
-    """Assing auxiliary properties for `Atom` object when reading CFG format.
+    """Assign auxiliary properties for `Atom` object when reading CFG
+    format.
 
     Parameters
     ----------

diffpy/structure/parsers/p_xyz.py

@@ -12,12 +12,11 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
+"""Parser for XYZ file format, where.
 
-"""Parser for XYZ file format, where
-
-    * First line gives number of atoms.
-    * Second line has optional title.
-    * Remaining lines contain element, `x, y, z`.
+* First line gives number of atoms.
+* Second line has optional title.
+* Remaining lines contain element, `x, y, z`.
 """
 
 import sys

diffpy/structure/parsers/parser_index_mod.py

@@ -12,7 +12,6 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
 """Index of recognized structure formats, their IO capabilities and
 associated modules where they are defined.
 

diffpy/structure/parsers/structureparser.py

@@ -12,9 +12,7 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
-"""Definition of StructureParser, a base class for specific parsers.
-"""
+"""Definition of StructureParser, a base class for specific parsers."""
 
 
 class StructureParser(object):

diffpy/structure/pdffitstructure.py

@@ -12,9 +12,7 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
-"""Definition of PDFFitStructure class derived from Structure
-"""
+"""Definition of PDFFitStructure class derived from Structure."""
 
 
 from diffpy.structure.structure import Structure

diffpy/structure/sgtbxspacegroups.py

@@ -12,9 +12,9 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
-"""Extra space group representations generated using `sgtbx` module from `cctbx`.
-Import of this module extends the `SpaceGroupList` in the `SpaceGroups` module.
+"""Extra space group representations generated using `sgtbx` module from
+`cctbx`. Import of this module extends the `SpaceGroupList` in the
+`SpaceGroups` module.
 
 Attributes
 ----------

diffpy/structure/spacegroupmod.py

@@ -3,12 +3,11 @@
 # This code is part of the PyMMLib distribution and governed by
 # its license. Please see the LICENSE_pymmlib file that should have been
 # included as part of this package.
-"""Symmetry operations as functions on vectors or arrays.
-"""
+"""Symmetry operations as functions on vectors or arrays."""
 
 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)
@@ -144,7 +143,8 @@ class SymOp(object):
         return x
 
     def __call__(self, vec):
-        """Return symmetry-related position for the specified coordinates.
+        """Return symmetry-related position for the specified
+        coordinates.
 
         Parameters
         ----------
@@ -302,7 +302,8 @@ class SpaceGroup(object):
         return False
 
     def iter_equivalent_positions(self, vec):
-        """Generate symmetry equivalent positions for the specified position.
+        """Generate symmetry equivalent positions for the specified
+        position.
 
         The initial position must be in fractional coordinates and so
         are the symmetry equivalent positions yielded by iteration.

diffpy/structure/spacegroups.py

@@ -12,7 +12,6 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
 """Space group classes and definitions from mmLib and sgtbx.
 
 Attributes
@@ -693,7 +692,8 @@ def GetSpaceGroup(sgid):
 
 
 def IsSpaceGroupIdentifier(sgid):
-    """Check if identifier can be used as an argument to `GetSpaceGroup`.
+    """Check if identifier can be used as an argument to
+    `GetSpaceGroup`.
 
     Returns
     -------
@@ -768,6 +768,7 @@ def _hashSymOpList(symops):
 
 def _buildSGLookupTable():
     """Rebuild space group lookup table from the `SpaceGroupList` data.
+
     This routine updates the global `_sg_lookup_table` dictionary.
     """
     _sg_lookup_table.clear()
@@ -809,7 +810,8 @@ _sg_lookup_table = {}
 
 
 def _getSGHashLookupTable():
-    """Return lookup table of symop hashes to standard `SpaceGroup` objects."""
+    """Return lookup table of symop hashes to standard `SpaceGroup`
+    objects."""
     if _sg_hash_lookup_table:
         return _sg_hash_lookup_table
     for sg in SpaceGroupList:

diffpy/structure/structure.py

@@ -12,9 +12,7 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
-"""This module defines class `Structure`.
-"""
+"""This module defines class `Structure`."""
 
 import codecs
 import copy as copymod
@@ -29,7 +27,8 @@ from diffpy.structure.utils import _linkAtomAttribute, atomBareSymbol, isiterabl
 
 
 class Structure(list):
-    """Define group of atoms in a specified lattice. Structure --> group of atoms.
+    """Define group of atoms in a specified lattice. Structure --> group
+    of atoms.
 
     `Structure` class is inherited from Python `list`. It contains
     a list of `Atom` instances. `Structure` overloads `setitem` and `setslice`
@@ -184,7 +183,8 @@ class Structure(list):
         return
 
     def distance(self, aid0, aid1):
-        """Calculate distance between 2 `Atoms`, no periodic boundary conditions.
+        """Calculate distance between 2 `Atoms`, no periodic boundary
+        conditions.
 
         Parameters
         ----------
@@ -208,8 +208,7 @@ class Structure(list):
         return self.lattice.dist(a0.xyz, a1.xyz)
 
     def angle(self, aid0, aid1, aid2):
-        """
-        The bond angle at the second of three `Atoms` in degrees.
+        """The bond angle at the second of three `Atoms` in degrees.
 
         Parameters
         ----------
@@ -236,7 +235,7 @@ class Structure(list):
         return self.lattice.angle(u10, u12)
 
     def placeInLattice(self, new_lattice):
-        """place structure into `new_lattice` coordinate system.
+        """Place structure into `new_lattice` coordinate system.
 
         Sets `lattice` to `new_lattice` and recalculate fractional coordinates
         of all `Atoms` so their absolute positions remain the same.
@@ -353,7 +352,8 @@ class Structure(list):
         return
 
     def writeStr(self, format):
-        """return string representation of the structure in specified format.
+        """Return string representation of the structure in specified
+        format.
 
         Note
         ----
@@ -368,14 +368,16 @@ class Structure(list):
         return s
 
     def tolist(self):
-        """Return `Atoms` in this `Structure` as a standard Python list."""
+        """Return `Atoms` in this `Structure` as a standard Python
+        list."""
         rv = [a for a in self]
         return rv
 
     # Overloaded list Methods and Operators ----------------------------------
 
     def append(self, a, copy=True):
-        """Append `Atom` to a structure and update its `lattice` attribute.
+        """Append `Atom` to a structure and update its `lattice`
+        attribute.
 
         Parameters
         ----------
@@ -451,7 +453,7 @@ class Structure(list):
 
         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
@@ -564,7 +566,7 @@ class Structure(list):
                 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
@@ -572,7 +574,8 @@ class Structure(list):
         return
 
     def __add__(self, other):
-        """Return new `Structure` object with appended `Atoms` from other.
+        """Return new `Structure` object with appended `Atoms` from
+        other.
 
         Parameters
         ----------
@@ -605,7 +608,8 @@ class Structure(list):
         return self
 
     def __sub__(self, other):
-        """Return new `Structure` that has `Atoms` from the other removed.
+        """Return new `Structure` that has `Atoms` from the other
+        removed.
 
         Parameters
         ----------
@@ -640,8 +644,8 @@ class Structure(list):
         return self
 
     def __mul__(self, n):
-        """Return new `Structure` with n-times concatenated `Atoms` from self.
-        `Atoms` and `lattice` in the new structure are all copies.
+        """Return new `Structure` with n-times concatenated `Atoms` from
+        self. `Atoms` and `lattice` in the new structure are all copies.
 
         Parameters
         ----------
@@ -661,8 +665,8 @@ class Structure(list):
     __rmul__ = __mul__
 
     def __imul__(self, n):
-        """Concatenate this `Structure` to n-times more `Atoms`.
-        For positive multiple the current `Atom` objects remain at the
+        """Concatenate this `Structure` to n-times more `Atoms`. For
+        positive multiple the current `Atom` objects remain at the
         beginning of this `Structure`.
 
         Parameters
@@ -859,7 +863,8 @@ class Structure(list):
     # Private Methods --------------------------------------------------------
 
     def __emptySharedStructure(self):
-        """Return empty `Structure` with standard attributes same as in self."""
+        """Return empty `Structure` with standard attributes same as in
+        self."""
         rv = Structure()
         rv.__dict__.update([(k, getattr(self, k)) for k in rv.__dict__])
         return rv

diffpy/structure/structureerrors.py

@@ -12,9 +12,7 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
-"""Exceptions used in Structure package.
-"""
+"""Exceptions used in Structure package."""
 
 
 class StructureFormatError(Exception):

diffpy/structure/symmetryutilities.py

@@ -12,9 +12,8 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
-"""Symmetry utility functions such as expansion of asymmetric unit,
-and generation of positional constraints.
+"""Symmetry utility functions such as expansion of asymmetric unit, and
+generation of positional constraints.
 
 Attributes
 ----------
@@ -132,8 +131,8 @@ def isconstantFormula(s):
 
 
 class _Position2Tuple(object):
-    """Create callable object that converts fractional coordinates to
-    a tuple of integers with given precision. For presision close to zero
+    """Create callable object that converts fractional coordinates to a
+    tuple of integers with given precision. For presision close to zero
     it will return a tuples of double.
 
     Note
@@ -148,7 +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`.
     """
 
@@ -417,7 +416,8 @@ class GeneratorSite(object):
         ],
         dtype=float,
     )
-    """numpy.ndarray: 6x3x3 array of independent components of U matrices."""
+    """numpy.ndarray: 6x3x3 array of independent components of U
+    matrices."""
 
     idx2Usymbol = {0: "U11", 1: "U12", 2: "U13", 3: "U12", 4: "U22", 5: "U23", 6: "U13", 7: "U23", 8: "U33"}
     """dict: Mapping of index to standard U symbol."""
@@ -467,7 +467,8 @@ class GeneratorSite(object):
         return
 
     def signedRatStr(self, x):
-        """Convert floating point number to signed rational representation.
+        """Convert floating point number to signed rational
+        representation.
 
         Possible fractional are multiples of 1/3, 1/6, 1/7, 1/9, if these
         are not close, return `%+g` format.
@@ -495,6 +496,7 @@ class GeneratorSite(object):
 
     def _findNullSpace(self):
         """Calculate `self.null_space` from `self.invariants`.
+
         Try to represent `self.null_space` using small integers.
         """
         R0 = self.invariants[0].R
@@ -525,7 +527,8 @@ class GeneratorSite(object):
         return
 
     def _findPosParameters(self):
-        """Find pparameters and their values for expressing `self.xyz`."""
+        """Find pparameters and their values for expressing
+        `self.xyz`."""
         usedsymbol = {}
         # parameter values depend on offset of self.xyz
         txyz = self.xyz
@@ -542,8 +545,7 @@ class GeneratorSite(object):
 
     def _findUSpace(self):
         """Find independent U components with respect to invariant
-        rotations.
-        """
+        rotations."""
         n = len(self.invariants)
         R6zall = numpy.tile(-numpy.identity(6, dtype=float), (n, 1))
         R6zall_iter = numpy.split(R6zall, n, axis=0)
@@ -568,7 +570,8 @@ class GeneratorSite(object):
         return
 
     def _findUParameters(self):
-        """Find Uparameters and their values for expressing `self.Uij`."""
+        """Find Uparameters and their values for expressing
+        `self.Uij`."""
         # permute indices as     00 11 22 01 02 12 10 20 21
         diagorder = numpy.array((0, 4, 8, 1, 2, 5, 3, 6, 7))
         Uijflat = self.Uij.flatten()
@@ -583,7 +586,8 @@ class GeneratorSite(object):
         return
 
     def _findeqUij(self):
-        """Adjust `self.Uij` and `self.eqUij` to be consistent with spacegroup."""
+        """Adjust `self.Uij` and `self.eqUij` to be consistent with
+        spacegroup."""
         self.Uij = numpy.zeros((3, 3), dtype=float)
         for i in range(len(self.Uparameters)):
             Usp = self.Uspace[i]
@@ -598,7 +602,8 @@ class GeneratorSite(object):
         return
 
     def positionFormula(self, pos, xyzsymbols=("x", "y", "z")):
-        """Formula of equivalent position with respect to generator site.
+        """Formula of equivalent position with respect to generator
+        site.
 
         Parameters
         ----------
@@ -646,7 +651,8 @@ class GeneratorSite(object):
         return dict(zip(("x", "y", "z"), xyzformula))
 
     def UFormula(self, pos, Usymbols=stdUsymbols):
-        """List of atom displacement formulas with custom parameter symbols.
+        """List of atom displacement formulas with custom parameter
+        symbols.
 
         Parameters
         ----------
@@ -902,7 +908,8 @@ class SymmetryConstraints(object):
         return
 
     def _findConstraints(self):
-        """Find constraints for positions and anisotropic displacements `Uij`."""
+        """Find constraints for positions and anisotropic displacements
+        `Uij`."""
         numpos = len(self.positions)
         # canonical xyzsymbols and Usymbols
         xyzsymbols = [smbl + str(i) for i in range(numpos) for smbl in "xyz"]
@@ -994,7 +1001,8 @@ class SymmetryConstraints(object):
         return rv
 
     def positionFormulasPruned(self, xyzsymbols=None):
-        """List of position formula dictionaries with constant items removed.
+        """List of position formula dictionaries with constant items
+        removed.
 
         See also
         --------
@@ -1014,7 +1022,8 @@ class SymmetryConstraints(object):
         return rv
 
     def UparSymbols(self):
-        """Return list of standard atom displacement parameter symbols."""
+        """Return list of standard atom displacement parameter
+        symbols."""
         return [n for n, v in self.Upars]
 
     def UparValues(self):
@@ -1022,7 +1031,8 @@ class SymmetryConstraints(object):
         return [v for n, v in self.Upars]
 
     def UFormulas(self, Usymbols=None):
-        """List of atom displacement formulas with custom parameter symbols.
+        """List of atom displacement formulas with custom parameter
+        symbols.
 
         Parameters
         ----------
@@ -1059,8 +1069,8 @@ class SymmetryConstraints(object):
         return rv
 
     def UFormulasPruned(self, Usymbols=None):
-        """List of atom displacement formula dictionaries with constant items
-        removed.
+        """List of atom displacement formula dictionaries with constant
+        items removed.
 
         See Also
         --------

diffpy/structure/utils.py

@@ -12,9 +12,7 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
-"""Small shared functions.
-"""
+"""Small shared functions."""
 
 from collections.abc import Iterable as _Iterable
 
@@ -38,7 +36,8 @@ def isfloat(s):
 
 
 def atomBareSymbol(smbl):
-    """Remove atom type string stripped of isotope and ion charge symbols.
+    """Remove atom type string stripped of isotope and ion charge
+    symbols.
 
     This function removes any blank, isotope numbers (0-9), leading hyphens (-), and ion charge
     symbols (1-9)(+-) from the given atom type string, returning only the bare element symbol.

diffpy/structure/version.py

@@ -1,18 +1,17 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (c) 2024 The Trustees of Columbia University in the City of New York.
+# (c) 2024-2025 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
-# File coded by: Billinge Group members and community contributors.
+# File coded by: Chris Farrow, Pavol Juhas,  Simon Billinge, Billinge Group members.
 #
 # See GitHub contributions for a more detailed list of contributors.
-# https://github.com/diffpy/diffpy.structure/graphs/contributors
+# https://github.com/diffpy/diffpy.structure/graphs/contributors  # noqa: E501
 #
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-
 """Definition of __version__."""
 
 #  We do not use the other three variables, but can be added back if needed.

{diffpy.structure-3.3.0.dist-info → diffpy_structure-3.3.1.dist-info}/METADATA

@@ -1,12 +1,12 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: diffpy.structure
-Version: 3.3.0
+Version: 3.3.1
 Summary: Crystal structure container and parsers for structure formats.
-Author-email: "Simon J.L. Billinge group" <simon.billinge@gmail.com>
-Maintainer-email: "Simon J.L. Billinge group" <simon.billinge@gmail.com>
+Author-email: Simon Billinge <sb2896@columbia.edu>
+Maintainer-email: Simon Billinge <sb2896@columbia.edu>
 Project-URL: Homepage, https://github.com/diffpy/diffpy.structure/
 Project-URL: Issues, https://github.com/diffpy/diffpy.structure/issues/
-Keywords: diffpy,crystal structure data storage CIF PDB
+Keywords: diffpy,crystal structure data storage,CIF,PDB
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Developers
@@ -23,12 +23,13 @@ Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Scientific/Engineering :: Chemistry
 Requires-Python: <3.14,>=3.11
 Description-Content-Type: text/x-rst
+License-File: LICENSE-DANSE.rst
+License-File: LICENSE-pymmlib.rst
 License-File: LICENSE.rst
-License-File: LICENSE_DANSE.rst
-License-File: LICENSE_pymmlib.rst
 License-File: AUTHORS.rst
 Requires-Dist: numpy
 Requires-Dist: pycifrw
+Dynamic: license-file
 
 |Icon| |title|_
 ===============
@@ -40,7 +41,7 @@ Requires-Dist: pycifrw
         :target: https://diffpy.github.io/diffpy.structure
         :height: 100px
 
-|PyPi| |Forge| |PythonVersion| |PR|
+|PyPI| |Forge| |PythonVersion| |PR|
 
 |CI| |Codecov| |Black| |Tracking|
 
@@ -58,7 +59,7 @@ Requires-Dist: pycifrw
 
 .. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
 
-.. |PyPi| image:: https://img.shields.io/pypi/v/diffpy.structure
+.. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.structure
         :target: https://pypi.org/project/diffpy.structure/
 
 .. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.structure
@@ -164,7 +165,7 @@ trying to commit again.
 
 Improvements and fixes are always appreciated.
 
-Before contribuing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.structure/blob/main/CODE_OF_CONDUCT.rst>`_.
+Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.structure/blob/main/CODE-OF-CONDUCT.rst>`_.
 
 Acknowledgement
 ---------------
@@ -175,6 +176,8 @@ originate from the `pymmlib project <http://pymmlib.sourceforge.net>`_.
 Less common settings of space groups were generating using the
 `Computational Crystallography Toolbox <http://cctbx.sourceforge.net>`_.
 
+``diffpy.structure`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.
+
 Contact
 -------
 

diffpy_structure-3.3.1.dist-info/RECORD

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+diffpy_structure-3.3.1.dist-info/licenses/LICENSE.rst,sha256=80VidrcIGGKZSC-cL7Ru0BZ4ZEPHcYHyv_cXkkTJXFE,6011
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+diffpy_structure-3.3.1.dist-info/RECORD,,

{diffpy.structure-3.3.0.dist-info → diffpy_structure-3.3.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.2.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{diffpy.structure-3.3.0.dist-info → diffpy_structure-3.3.1.dist-info/licenses}/LICENSE.rst

@@ -15,7 +15,7 @@ Copyright (c) 2014, Australian Synchrotron Research Program Inc., ("ASRP")
 
 Copyright (c) 2014-2019, Brookhaven Science Associates, Brookhaven National Laboratory
 
-Copyright (c) 2024, The Trustees of Columbia University in the City of New York.
+Copyright (c) 2024-2025, The Trustees of Columbia University in the City of New York.
 All rights reserved.
 
 The "DiffPy-CMI" is distributed subject to the following license conditions:

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