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>

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

@@ -108,13 +108,13 @@ class Atom(object):
 
     # instance attributes that have immutable default values
     element = ""
-    """str: Default values of `element`."""
+    """Str: Default values of `element`."""
 
     label = ""
-    """str: Default values of `label`."""
+    """Str: Default values of `label`."""
 
     occupancy = 1.0
-    """float: Default values of `occupancy`."""
+    """Float: Default values of `occupancy`."""
 
     _anisotropy = False
     lattice = None
@@ -294,8 +294,8 @@ 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
@@ -315,7 +315,7 @@ def xyz_cartn(self, value):
 
     @property
     def anisotropy(self):
-        """bool : Flag for allowing anisotropic displacement parameters.
+        """Bool : Flag for allowing anisotropic displacement parameters.
 
         When ``False`` the tensor of thermal displacement parameters `U`
         must be isotropic and only its diagonal elements are taken into
@@ -439,7 +439,8 @@ 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 +534,8 @@ 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
@@ -575,7 +577,7 @@ def __init__(self, atom):
 
     @property
     def asarray(self):
-        """ndarray : This array viewed as standard numpy array."""
+        """Ndarray : This array viewed as standard numpy array."""
         return self.view(numpy.ndarray)
 
     def __setitem__(self, idx, value):

src/diffpy/structure/expansion/shapeutils.py

@@ -24,7 +24,6 @@
 )
 """Utilities for making shapes."""
 
-
 @deprecated(findCenter_deprecation_msg)
 def findCenter(S):
     """This function has been deprecated and will be removed in version

src/diffpy/structure/parsers/p_cif.py

@@ -152,7 +152,7 @@ class P_cif(StructureParser):
     del k
 
     BtoU = 1.0 / (8 * numpy.pi**2)
-    """float: Conversion factor from B values to U values."""
+    """Float: Conversion factor from B values to U values."""
 
     def _tr_ignore(a, value):
         return

src/diffpy/structure/parsers/p_discus.py

@@ -39,8 +39,9 @@
 
 
 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
     ----------

src/diffpy/structure/parsers/p_pdb.py

@@ -135,10 +135,10 @@ class P_pdb(StructureParser):
         "MASTER",
         "END",
     ]
-    """list: Ordered list of PDB record labels."""
+    """List: Ordered list of PDB record labels."""
 
     validRecords = dict.fromkeys(orderOfRecords)
-    """dict: Dictionary of PDB record labels."""
+    """Dict: Dictionary of PDB record labels."""
 
     def __init__(self):
         StructureParser.__init__(self)

src/diffpy/structure/parsers/p_vesta.py

@@ -57,9 +57,11 @@ class P_vesta(StructureParser):
     """
 
     cluster_boundary = 2
-    """int: Width of boundary around corners of non-periodic cluster.
-    Retained from the original AtomEye/XCFG parser for API compatibility.
-    VESTA handles periodicity natively so this value has no effect on output.
+    """Int: Width of boundary around corners of non-periodic cluster.
+
+    Retained from the original AtomEye/XCFG parser for API
+    compatibility. VESTA handles periodicity natively so this value has
+    no effect on output.
     """
 
     def __init__(self):

src/diffpy/structure/parsers/p_xcfg.py

@@ -178,9 +178,8 @@ class P_xcfg(StructureParser):
     """
 
     cluster_boundary = 2
-    """int: Width of boundary around corners of non-periodic
-    cluster to avoid PBC effects in atomeye.
-    """
+    """Int: Width of boundary around corners of non-periodic cluster to
+    avoid PBC effects in atomeye."""
 
     def __init__(self):
         StructureParser.__init__(self)

src/diffpy/structure/pdffitstructure.py

@@ -14,7 +14,6 @@
 ##############################################################################
 """Definition of PDFFitStructure class derived from Structure."""
 
-
 from diffpy.structure.structure import Structure
 from diffpy.utils._deprecator import build_deprecation_message, deprecated
 

src/diffpy/structure/sgtbxspacegroups.py

@@ -22,7 +22,6 @@
     List of space group instances defined in this module.
 """
 
-
 from diffpy.structure.spacegroupmod import (
     Rot_mX_mY_mZ,
     Rot_mX_mY_Z,

src/diffpy/structure/spacegroupmod.py

@@ -305,7 +305,6 @@ def check_group_name(self, name):
             names of this space group or if it equals its `number`.
             Return ``False`` otherwise.
         """
-
         if name == self.short_name:
             return True
         if name == self.pdb_name:

src/diffpy/structure/spacegroups.py

@@ -789,7 +789,6 @@ def find_space_group(symops, shuffle=False):
     ValueError
         When `symops` do not match any known SpaceGroup.
     """
-
     tb = _get_sg_hash_lookup_table()
     hh = _hash_symop_list(symops)
     if hh not in tb: