Merge pull request #138 from TingwenZhang/level-5

Level 5

Author: sbillinge

.flake8

@@ -1,3 +1,5 @@
+# As of now, flake8 does not natively support configuration via pyproject.toml
+# https://github.com/microsoft/vscode-flake8/issues/135
 [flake8]
 exclude =
     .git,

.isort.cfg

@@ -1,4 +1,5 @@
 [settings]
+# Keep import statement below line_length character limit
 line_length = 115
 multi_line_output = 3
 include_trailing_comma = True

pyproject.toml

@@ -6,13 +6,13 @@ build-backend = "setuptools.build_meta"
 name = "diffpy.structure"
 dynamic=['version', 'dependencies']
 authors = [
-  { name="Simon J.L. Billinge group", email="[email protected]" },
+  { name="Simon Billinge", email="[email protected]" },
 ]
 maintainers = [
-  { name="Simon J.L. Billinge group", email="[email protected]" },
+  { name="Simon Billinge", email="[email protected]" },
 ]
 description = "Crystal structure container and parsers for structure formats."
-keywords = ['diffpy', 'crystal structure data storage CIF PDB']
+keywords = ['diffpy', 'crystal structure data storage', 'CIF', 'PDB']
 readme = "README.rst"
 requires-python = ">=3.11, <3.14"
 classifiers = [
@@ -32,13 +32,13 @@ classifiers = [
         'Topic :: Scientific/Engineering :: Chemistry',
 ]
 
+[project.scripts]
+transtru = "diffpy.structure.apps.transtru:main"
+
 [project.urls]
 Homepage = "https://github.com/diffpy/diffpy.structure/"
 Issues = "https://github.com/diffpy/diffpy.structure/issues/"
 
-[project.scripts]
-transtru = "diffpy.structure.apps.transtru:main"
-
 [tool.setuptools-git-versioning]
 enabled = true
 template = "{tag}"
@@ -54,6 +54,16 @@ namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements/pip.txt"]}
 
+[tool.codespell]
+exclude-file = ".codespell/ignore_lines.txt"
+ignore-words = ".codespell/ignore_words.txt"
+skip = "*.cif,*.dat"
+
+[tool.docformatter]
+recursive = true
+wrap-summaries = 72
+wrap-descriptions = 72
+
 [tool.black]
 line-length = 115
 include = '\.pyi?$'

src/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

src/diffpy/structure/__init__.py

@@ -1,20 +1,18 @@
 #!/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
 #
 # 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

src/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 @@ 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.
     """
 

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

@@ -12,9 +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 @@
 
 
 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):

src/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 @@
 
 
 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])

src/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 @@ def msdLat(self, vl):
         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 @@ def __copy__(self, target=None):
 
     @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 @@ def anisotropy(self, value):
 
     @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 @@ def __setitem__(self, idx, value):
         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)
 
 

src/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:

src/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
     ----------

src/diffpy/structure/expansion/shapeutils.py

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

src/diffpy/structure/expansion/supercell_mod.py

@@ -12,17 +12,16 @@
 # 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
 
 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

src/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 @@ def setLatBase(self, base):
 
     def abcABG(self):
         """Return the cell parameters in the standard setting.
+
         Returns
         -------
         tuple :
@@ -452,6 +452,7 @@ def abcABG(self):
 
     def reciprocal(self):
         """Return the reciprocal lattice of the current lattice.
+
         Returns
         -------
         Lattice

src/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`,

src/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 @@ def __init__(self, **kw):
     # 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 @@ def _getOrderedFormats(self):
         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 @@ def parse(self, s):
         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 @@ def parseFile(self, filename):
         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 resul.
 
         Structure parsers that match structure file extension are
         tried first.