chore: update pre-commit hook with latest version

.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
@@ -21,15 +21,15 @@ repos:
       - id: check-toml
       - id: check-added-large-files
   - repo: https://github.com/psf/black
-    rev: 24.4.2
+    rev: 26.3.1
     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"]
@@ -39,14 +39,14 @@ repos:
   #   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
         exclude: '.*\.ipynb$'
@@ -83,8 +83,8 @@ 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]

CHANGELOG.rst

@@ -29,7 +29,7 @@ Version 2024.2.1
 **Changes:**
 
 * PowderPattern:
-  * Fix re-using a matplotlib figure when plotting
+  * Fix reusing a matplotlib figure when plotting
   * Add ``figure`` property
 
 Version 2024.2
@@ -125,7 +125,7 @@ Version 2.2.1 -- 2021-11-28
 * Fix blank line javascript output when updating the Crystal 3D view
 * Add ``RefinableObj.xml()`` to directly get the XMLOutput as a string
 * Add example notebooks to the sphinx-generated html documentation
-* Fix issue when using ``Crystal.XMLInput()`` for a non-empty structure. Existing scattering power will be re-used when possible, and otherwise not deleted anymore (which could lead to crashes)
+* Fix issue when using ``Crystal.XMLInput()`` for a non-empty structure. Existing scattering power will be reused when possible, and otherwise not deleted anymore (which could lead to crashes)
 
 Version 2.2.0 -- 2021-06-08
 ----------------------------

news/pre-commit-update.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* No News Added: Updated pre-commit hook to latest version
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/pyobjcryst/crystal.py

@@ -40,7 +40,9 @@
 
 import numpy as np
 
-from pyobjcryst._pyobjcryst import BumpMergePar
+from pyobjcryst._pyobjcryst import (
+    BumpMergePar,
+)
 from pyobjcryst._pyobjcryst import (
     CreateCrystalFromCIF as CreateCrystalFromCIF_orig,
 )
@@ -277,7 +279,6 @@ def _display_list(
             independent atoms, no symmetry or translation is applied
         :return : the list of atoms and bonds to be displayed for 3dmol
         """
-
         spg = self.GetSpaceGroup()
         vv = []
         idx = 0

src/pyobjcryst/diffractiondatasinglecrystal.py

@@ -36,9 +36,9 @@
 
 
 def create_singlecrystaldata_from_cif(file, crystal):
-    """
-    Create a DiffractionDataSingleCrystal object from a CIF file. Note that
-    this will use the last created Crystal as a reference structure.
+    """Create a DiffractionDataSingleCrystal object from a CIF file.
+
+    Note that this will use the last created Crystal as a reference structure.
     Example using the COD to load both crystal and data:
         c=create_crystal_from_cif('http://www.crystallography.net/cod/2201530.cif')
         d=create_singlecrystaldata_from_cif('http://www.crystallography.net/cod/2201530.hkl', c)

src/pyobjcryst/globaloptim.py

@@ -16,6 +16,7 @@
 Changes from ObjCryst::MonteCarloObj::
         In development !
 """
+
 __all__ = ["MonteCarlo", "AnnealingSchedule", "GlobalOptimType"]
 
 import warnings

src/pyobjcryst/molecule.py

@@ -126,8 +126,9 @@
 
 
 def ImportFenskeHallZMatrix(cryst, src, named=False):
-    """Create a Molecule from a Fenske-Hall z-matrix. This is cleaner
-    than importing the Z-matrix into a ZScatterer object and then using
+    """Create a Molecule from a Fenske-Hall z-matrix.
+
+    This is cleaner than importing the Z-matrix into a ZScatterer object and then using
     ZScatterer2Molecule, as it takes care of keeping only the created
     Molecule inside the Crystal.
 

src/pyobjcryst/powderpattern.py

@@ -32,7 +32,9 @@
     "SpaceGroupExplorer",
 ]
 
-from pyobjcryst._pyobjcryst import LSQ
+from pyobjcryst._pyobjcryst import (
+    LSQ,
+)
 from pyobjcryst._pyobjcryst import (
     CreatePowderPatternFromCIF as CreatePowderPatternFromCIF_orig,
 )
@@ -338,11 +340,11 @@ def _do_plot_hkl(self, nb_max=100, fontsize_hkl=None):
 
     @property
     def figure(self):
-        """
-        return: the figure used for plotting, or None. Note that
-            if you want to display it in a notebook using ipympl (aka
-            'matplotlib widget'), you should 'figure.canvas' to display
-            also the toolbar (zoom, etc...).
+        """Return: the figure used for plotting, or None.
+
+        Note that if you want to display it in a notebook using ipympl
+        (aka 'matplotlib widget'), you should 'figure.canvas' to display
+        also the toolbar (zoom, etc...).
         """
         return self._plot_fig
 

src/pyobjcryst/utils.py

@@ -14,7 +14,6 @@
 ##############################################################################
 """Utilities for crystals."""
 
-
 # FIXME: check if this function does any meaningful job.
 
 
@@ -95,7 +94,6 @@ def f(v):
 def _xyztostring(crystal):
     """Helper function to write xyz coordinates of a crystal to a
     string."""
-
     nsc = 0
     out = ""
     scl = crystal.GetScatteringComponentList()

tests/pyobjcryst_test_mem.py

@@ -12,8 +12,9 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-"""Small tests for pyobjcryst. Not run by pytest, for memory leak
-checks.
+"""Small tests for pyobjcryst.
+
+Not run by pytest, for memory leak checks.
 
 To check for memory leaks, run valgrind --tool=memcheck --leak-
 check=full python ./pyobjcrysttest.py

tests/test_crystal.py

@@ -141,7 +141,6 @@ def testDummyAtom(self):
 
     def testEmbedding(self):
         """Test integrity of mutually-embedded objects."""
-
         c = makeCrystal(*makeScatterer())
 
         class Level1(object):

tests/test_molecule.py

@@ -165,7 +165,6 @@ def testFindAtom(self):
 
     def testBonds(self):
         """Test the Bond methods."""
-
         a1 = self.m.GetAtom(0)
         a2 = self.m.GetAtom(1)
         a3 = self.m.GetAtom(2)
@@ -746,7 +745,6 @@ def tearDown(self):
 
     def testStretchModeBondLength(self):
         """Test the StretchModeBondLength class."""
-
         # Measure the distance
         ac = self.m[0]
         # The 0, 0, z atom
@@ -795,7 +793,6 @@ def tearDown(self):
 
     def testStretchModeBondAngle(self):
         """Test the StretchModeBondLength class."""
-
         a1 = self.m[1]
         ac = self.m[0]
         a2 = self.m[2]
@@ -839,7 +836,6 @@ def tearDown(self):
 
     def testStretchModeTorsion(self):
         """Test the StretchModeBondLength class."""
-
         a1 = self.m[1]
         ac0 = self.m[3]
         ac1 = self.m[0]

tests/test_spacegroup.py

@@ -14,7 +14,6 @@
 ##############################################################################
 """Unit tests for pyobjcryst.spacegroup."""
 
-
 import unittest
 
 from pyobjcryst.spacegroup import SpaceGroup