chore: update pre-commit

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ ci:
   submodules: false
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v6.0.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
@@ -21,31 +21,31 @@ repos:
       - id: check-toml
       - id: check-added-large-files
   - repo: https://github.com/psf/black
-    rev: 24.4.2
+    rev: 26.5.1
     hooks:
       - id: black
   - repo: https://github.com/pycqa/flake8
-    rev: 7.0.0
+    rev: 7.3.0
     hooks:
       - id: flake8
   - repo: https://github.com/pycqa/isort
-    rev: 5.13.2
+    rev: 9.0.0a3
     hooks:
       - id: isort
         args: ["--profile", "black"]
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
+    rev: 0.9.1
     hooks:
       - id: nbstripout
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v6.0.0
     hooks:
       - id: no-commit-to-branch
         name: Prevent Commit to Main Branch
         args: ["--branch", "main"]
         stages: [pre-commit]
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.2
     hooks:
       - id: codespell
         additional_dependencies:
@@ -58,8 +58,8 @@ repos:
         additional_dependencies:
           - "prettier@^3.2.4"
   # docformatter - PEP 257 compliant docstring formatter
-  - repo: https://github.com/s-weigand/docformatter
-    rev: 5757c5190d95e5449f102ace83df92e7d3b06c6c
+  - repo: https://github.com/PyCQA/docformatter
+    rev: v1.7.8
     hooks:
       - id: docformatter
         additional_dependencies: [tomli]

devutils/sgtbx_extra_groups.py

@@ -10,7 +10,6 @@
 Not to be included with code distributions.
 """
 
-
 import math
 import re
 

news/CI-badge-fix.rst

@@ -2,6 +2,7 @@
 
 * No News Added: fix CI badge and target in README.rst
 
+
 **Changed:**
 
 * <news item>

news/pre-commit_edits.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* No news needed: updating docformatter not user facing
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -63,6 +63,7 @@ skip = "*.cif,*.dat"
 recursive = true
 wrap-summaries = 72
 wrap-descriptions = 72
+non-cap = ["str", "int", "float", "bool", "list", "dict", "tuple", "set", "none", "ndarray"]
 
 [tool.black]
 line-length = 115

src/diffpy/structure/__init__.py

@@ -33,7 +33,6 @@
     * SymmetryError
 """
 
-
 import os
 import sys
 

src/diffpy/structure/_legacy_importer.py

@@ -27,7 +27,6 @@
 This module is deprecated and will be removed in the future.
 """
 
-
 import importlib.abc
 import sys
 from warnings import warn

src/diffpy/structure/apps/vesta_viewer.py

@@ -72,12 +72,13 @@
 
 
 def usage(style=None):
-    """Show usage info. for ``style=="brief"`` show only first 2 lines.
+    """Show usage info.
 
-    Parameters
-    ----------
-    style : str, optional
-        The usage display style.
+    for ``style=="brief"`` show only first 2 lines.
+        Parameters
+        ----------
+        style : str, optional
+            The usage display style.
     """
     myname = Path(sys.argv[0]).name
     msg = __doc__.replace("vestaview", myname)

src/diffpy/structure/atom.py

@@ -82,19 +82,19 @@ class Atom(object):
     Attributes
     ----------
     element : str
-        The string type of the atom. An element or ion symbol.
+        The string type of the atom. An element or ion symbol, default "".
     xyz : numpy.ndarray
         The fractional coordinates in the associated `lattice`.
     label : str
-        A unique string label referring to this atom, for example, "C_1".
+        The unique string label referring to this atom, for example, "C_1".
         The *label* can be used to reference this atom when contained in
-        a `Structure` object.
+        a `Structure` object, default "".
     occupancy : float
-        The fractional occupancy of this atom.
+        The fractional occupancy of this atom, default 1.0.
     lattice : Lattice
-        Coordinate system for the fractional coordinates `xyz` and
+        The coordinate system for the fractional coordinates `xyz` and
         the tensor of atomic displacement parameters `U`.
-        Use the absolute Cartesian coordinates when ``None``.
+        Use the absolute Cartesian coordinates when ``None`` as the default.
 
     Note
     ----
@@ -104,21 +104,17 @@ class Atom(object):
     # Private attributes
     #
     #   _U : 3-by-3 ndarray
-    #       Internal storage of the displacement parameters.
+    #       The internal storage of the displacement parameters.
 
     # instance attributes that have immutable default values
     element = ""
-    """str: Default values of `element`."""
 
     label = ""
-    """str: Default values of `label`."""
 
     occupancy = 1.0
-    """float: Default values of `occupancy`."""
 
     _anisotropy = False
     lattice = None
-    """None: Default values of `lattice`."""
 
     def __init__(
         self,
@@ -294,8 +290,8 @@ def xyz_cartn(self):
         coordinates.
 
         This is computed from fractional coordinates `xyz` and the
-        current `lattice` setup. Assignment to *xyz_cartn* or
-        its components is applied on fractional coordinates `xyz`.
+        current `lattice` setup. Assignment to *xyz_cartn* or its
+        components is applied on fractional coordinates `xyz`.
         """
         if not self.lattice:
             rv = self.xyz
@@ -439,7 +435,8 @@ def _set_uij(self, i, j, value):
 
     @property
     def Uisoequiv(self):
-        """float : The isotropic displacement parameter or an equivalent value.
+        """float : The isotropic displacement parameter or an equivalent
+        value.
 
         Setting a new value rescales tensor `U` so it yields equivalent
         direction-averaged displacements.
@@ -533,7 +530,8 @@ 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

src/diffpy/structure/expansion/shapeutils.py

@@ -24,6 +24,8 @@
 )
 """Utilities for making shapes."""
 
+# FIXME: remove this line when `docformatter` fixes the blank line bug
+
 
 @deprecated(findCenter_deprecation_msg)
 def findCenter(S):

src/diffpy/structure/lattice.py

@@ -18,7 +18,7 @@
 Attributes
 ----------
 cartesian : Lattice
-    Constant instance of Lattice, default Cartesian system.
+    The constant instance of Lattice, default Cartesian system.
 """
 
 import math

src/diffpy/structure/parsers/p_auto.py

@@ -55,10 +55,10 @@ class P_auto(StructureParser):
     Attributes
     ----------
     format : str
-        Detected structure format. Initially set to "auto" and updated
+        The detected structure format. Initially set to "auto" and updated
         after successful detection of the structure format.
     pkw : dict
-        Keyword arguments passed to the parser.
+        The keyword arguments passed to the parser.
     """
 
     def __init__(self, **kw):

src/diffpy/structure/parsers/p_cif.py

@@ -17,9 +17,9 @@
 Attributes
 ----------
 rx_float : re.Pattern
-    Constant regular expression for `leading_float()`.
+    The constant regular expression for `leading_float()`.
 symvec : dict
-    Helper dictionary for `getSymOp()`.
+    The helper dictionary for `getSymOp()`.
 
 Note
 ----
@@ -79,26 +79,26 @@ class P_cif(StructureParser):
     Attributes
     ----------
     format : str
-        Structure format name.
+        The structure format name.
     ciffile : CifFile
-        Instance of `CifFile` from `PyCifRW`.
+        The instance of `CifFile` from `PyCifRW`.
     stru : Structure
-        `Structure` instance used for CIF input or output.
+        The `Structure` instance used for CIF input or output.
     spacegroup : SpaceGroup
-        Instance of `SpaceGroup` used for symmetry expansion.
+        The instance of `SpaceGroup` used for symmetry expansion.
     eps : float
-        Resolution in fractional coordinates for non-equal positions.
+        The resolution in fractional coordinates for non-equal positions.
         Used for expansion of asymmetric unit.
     eau : ExpandAsymmetricUnit
-        Instance of `ExpandAsymmetricUnit` from `SymmetryUtilities`.
+        The instance of `ExpandAsymmetricUnit` from `SymmetryUtilities`.
     asymmetric_unit : list
-        List of `Atom` instances for the original asymmetric unit in the CIF file.
+        The list of `Atom` instances for the original asymmetric unit in the CIF file.
     labelindex : dict
-        Dictionary mapping unique atom label to index of `Atom` in `self.asymmetric_unit`.
+        The dictionary mapping unique atom label to index of `Atom` in `self.asymmetric_unit`.
     anisotropy : dict
-        Dictionary mapping unique atom label to displacement anisotropy resolved at that site.
+        The dictionary mapping unique atom label to displacement anisotropy resolved at that site.
     cif_sgname : str or None
-        Space group name obtained by looking up the value of
+        The space group name obtained by looking up the value of
         `_space_group_name_Hall`,
         `_symmetry_space_group_name_Hall`,
         `_space_group_name_H-M_alt`,
@@ -151,8 +151,8 @@ class P_cif(StructureParser):
         _atom_setters[k] = _atom_setters[k.lower()] = k
     del k
 
+    # Conversion factor from B values to U values, as a float
     BtoU = 1.0 / (8 * numpy.pi**2)
-    """float: Conversion factor from B values to U values."""
 
     def _tr_ignore(a, value):
         return

src/diffpy/structure/parsers/p_discus.py

@@ -39,23 +39,24 @@
 
 
 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
     ----------
     format : str
-        File format name, default "discus".
+        The file format name, default "discus".
     nl : int
-        Line number of the current line being parsed.
+        The line number of the current line being parsed.
     lines : list of str
-        List of lines from the input file.
+        The list of lines from the input file.
     line : str
-        Current line being parsed.
+        The current line being parsed.
     stru : PDFFitStructure
-        Structure being parsed.
+        The structure being parsed.
     ignored_lines : list of str
-        List of lines that were ignored during parsing.
+        The list of lines that were ignored during parsing.
     cell_read : bool
         ``True`` if cell record processed.
     ncell_read : bool

src/diffpy/structure/parsers/p_pdb.py

@@ -74,7 +74,11 @@ class P_pdb(StructureParser):
     Attributes
     ----------
     format : str
-        Format name, default "pdb".
+        The format name, default "pdb".
+    orderOfRecords : list
+        The ordered list of PDB record labels.
+    validRecords : dict
+        The set of valid PDB record labels.
     """
 
     # Static data members
@@ -135,10 +139,8 @@ class P_pdb(StructureParser):
         "MASTER",
         "END",
     ]
-    """list: Ordered list of PDB record labels."""
 
     validRecords = dict.fromkeys(orderOfRecords)
-    """dict: Dictionary of PDB record labels."""
 
     def __init__(self):
         StructureParser.__init__(self)

src/diffpy/structure/parsers/p_pdffit.py

@@ -40,11 +40,11 @@ class P_pdffit(StructureParser):
     Attributes
     ----------
     format : str
-        Format name, default "pdffit".
+        The format name, default "pdffit".
     ignored_lines : list
-        List of lines ignored during parsing.
+        The list of lines ignored during parsing.
     stru : PDFFitStructure
-        Structure instance used for cif input or output.
+        The structure instance used for cif input or output.
     """
 
     def __init__(self):

src/diffpy/structure/parsers/p_rawxyz.py

@@ -48,7 +48,7 @@ class P_rawxyz(StructureParser):
     Attributes
     ----------
     format : str
-        Format name, default "rawxyz".
+        The format name, default "rawxyz".
     """
 
     def __init__(self):