chore: updated pre-commit hook dependencies

.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: 26.3.1
     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"]
   - 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]

news/precommit-deps-update.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* No news needed: updating pre-commit hooks, black, flake8, isort, nbstripout, codespell and docformatter. Not user facing.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/__init__.py

@@ -14,7 +14,6 @@
 ##############################################################################
 """Blank namespace package for module diffpy."""
 
-
 from pkgutil import extend_path
 
 __path__ = extend_path(__path__, __name__)

src/diffpy/srreal/_cleanup.py

@@ -24,7 +24,6 @@ class prototypes is implemented in libdiffpy.  Any Python-extended classes
 a call of _registerThisType.
 """
 
-
 import atexit
 import weakref
 

src/diffpy/srreal/_final_imports.py

@@ -15,14 +15,16 @@
 """Finalize tweak of classes from the extension module srreal_ext.
 
 This private module handles loading of Python-level tweaks of the
-extension-defined classes.  Any client that imports this module
-must call the `import_now` function.  If this module is not loaded
-by the time of srreal_ext initialization, `import_now` is executed
-from srreal_ext.
+extension-defined classes.  Any client that imports this module must
+call the `import_now` function.  If this module is not loaded by the
+time of srreal_ext initialization, `import_now` is executed from
+srreal_ext.
 
 This avoids unresolvable import dependencies for any order of imports.
 """
 
+_import_now_called = False
+
 
 def import_now():
     """Import all Python modules that tweak extension-defined
@@ -46,6 +48,3 @@ def import_now():
     import_module("diffpy.srreal.pdfcalculator")
     import_module("diffpy.srreal.structureconverters")
     return
-
-
-_import_now_called = False

src/diffpy/srreal/atomradiitable.py

@@ -14,7 +14,6 @@
 ##############################################################################
 """Class AtomRadiiTable -- storage of empirical atom radii."""
 
-
 # exported items, these also makes them show in pydoc.
 __all__ = ["AtomRadiiTable", "ConstantRadiiTable", "CovalentRadiiTable"]
 
@@ -66,8 +65,9 @@ def clone(self):
         return copy.copy(self)
 
     def type(self):
-        """Unique string identifier of the CovalentRadiiTable type. This
-        is used for class registration and as an argument for the
+        """Unique string identifier of the CovalentRadiiTable type.
+
+        This is used for class registration and as an argument for the
         createByType function.
 
         Return string.

src/diffpy/srreal/attributes.py

@@ -13,7 +13,7 @@
 #
 ##############################################################################
 """class Attributes  -- wrapper to C++ class diffpy::Attributes
-    A base to PairQuantity and quite a few other classes.
+A base to PairQuantity and quite a few other classes.
 """
 
 __all__ = ["Attributes"]

src/diffpy/srreal/bondcalculator.py

@@ -14,7 +14,6 @@
 ##############################################################################
 """Class BondCalculator -- distances between atoms in the structure."""
 
-
 # exported items, these also makes them show in pydoc.
 __all__ = ["BondCalculator"]
 
@@ -28,14 +27,12 @@
 
 BondCalculator.rmin = propertyFromExtDoubleAttr(
     "rmin",
-    """Lower bound for the bond distances.
-        [0 A]""",
+    "Lower bound for the bond distances. [0 A]",
 )
 
 BondCalculator.rmax = propertyFromExtDoubleAttr(
     "rmax",
-    """Upper bound for the bond distances.
-        [5 A]""",
+    "Upper bound for the bond distances. [5 A]",
 )
 
 

src/diffpy/srreal/bvparameterstable.py

@@ -15,7 +15,6 @@
 """Class BVParametersTable -- storage of bond valence parameters class BVParam
 -- bond valence data associated with specific cation-anion pair."""
 
-
 # exported items, these also makes them show in pydoc.
 __all__ = ["BVParam", "BVParametersTable"]
 

src/diffpy/srreal/bvscalculator.py

@@ -14,7 +14,6 @@
 ##############################################################################
 """Class BVSCalculator -- bond valence sums calculator."""
 
-
 # exported items
 __all__ = ["BVSCalculator"]
 
@@ -28,30 +27,32 @@
 
 BVSCalculator.valenceprecision = propertyFromExtDoubleAttr(
     "valenceprecision",
-    """Cutoff value for valence contributions at long distances.
-        [1e-5]""",
+    "Cutoff value for valence contributions at long distances. [1e-5]",
 )
 
 BVSCalculator.rmaxused = propertyFromExtDoubleAttr(
     "rmaxused",
-    """Effective bound for bond lengths, where valence contributions
-        become smaller than valenceprecission, read-only.  Always smaller or
-        equal to rmax.  The value depends on ions present in the structure.
-        """,
+    (
+        "Effective bound for bond lengths, where valence contributions"
+        " become smaller than valenceprecission, read-only."
+        "  Always smaller or equal to rmax."
+        "  The value depends on ions present in the structure."
+    ),
 )
 
 BVSCalculator.rmin = propertyFromExtDoubleAttr(
     "rmin",
-    """Lower bound for the summed bond lengths.
-        [0 A]""",
+    "Lower bound for the summed bond lengths. [0 A]",
 )
 
 BVSCalculator.rmax = propertyFromExtDoubleAttr(
     "rmax",
-    """Upper bound for the summed bond lengths.  The calculation is
-        actually cut off much earlier when valence contributions get below
-        valenceprecission.  See also rmaxused and valenceprecission.
-        [1e6 A]""",
+    (
+        "Upper bound for the summed bond lengths."
+        "  The calculation is actually cut off much earlier when"
+        " valence contributions get below valenceprecission."
+        "  See also rmaxused and valenceprecission. [1e6 A]"
+    ),
 )
 
 

src/diffpy/srreal/eventticker.py

@@ -15,7 +15,6 @@
 """Class EventTicker -- storage of modification times of dependent
 objects."""
 
-
 # exported items
 __all__ = ["EventTicker"]
 

src/diffpy/srreal/overlapcalculator.py

@@ -15,7 +15,6 @@
 """Class OverlapCalculator -- calculator of atom overlaps in a
 structure."""
 
-
 # exported items, these also makes them show in pydoc.
 __all__ = ["OverlapCalculator"]
 
@@ -29,22 +28,21 @@
 
 OverlapCalculator.rmin = propertyFromExtDoubleAttr(
     "rmin",
-    """Lower bound for the bond distances.
-        [0 A]""",
+    "Lower bound for the bond distances. [0 A]",
 )
 
 OverlapCalculator.rmax = propertyFromExtDoubleAttr(
     "rmax",
-    """Upper bound for the bond distances.
-        [5 A]""",
+    "Upper bound for the bond distances. [5 A]",
 )
 
 OverlapCalculator.rmaxused = propertyFromExtDoubleAttr(
     "rmaxused",
-    """Effective upper bound for the bond distances.
-        rmaxused equals either a double of the maximum atom radius
-        in the structure or rmax.
-        """,
+    (
+        "Effective upper bound for the bond distances."
+        " rmaxused equals either a double of the maximum"
+        " atom radius in the structure or rmax."
+    ),
 )
 
 # method overrides that support keyword arguments

src/diffpy/srreal/pairquantity.py

@@ -15,7 +15,6 @@
 """Class PairQuantity    -- base class for Python defined
 calculators."""
 
-
 # exported items
 __all__ = ["PairQuantity"]
 

src/diffpy/srreal/parallel.py

@@ -16,7 +16,6 @@
 into parallel calculators.
 """
 
-
 # exported items
 __all__ = ["createParallelCalculator"]
 
@@ -48,8 +47,10 @@ def createParallelCalculator(pqobj, ncpu, pmap):
     """
 
     class ParallelPairQuantity(Attributes):
-        """Class for running parallel calculations.  This is a proxy
-        class to the wrapper PairQuantity type with the same interface.
+        """Class for running parallel calculations.
+
+        This is a proxy class to the wrapper PairQuantity type
+        with the same interface.
 
         Instance data:
 
@@ -144,7 +145,7 @@ def parallel_eval(stru):
 
         @property
         def evaluatortype(self):
-            """str : Type of evaluation procedure.
+            """Str : Type of evaluation procedure.
 
             Parallel calculations allow only the 'BASIC' type.
             """
@@ -166,11 +167,9 @@ def evaluatortype(self, value):
 
     # create proxy methods to all public methods and some protected methods
 
-    proxy_forced = set(
-        """_getDoubleAttr _setDoubleAttr _hasDoubleAttr
+    proxy_forced = set("""_getDoubleAttr _setDoubleAttr _hasDoubleAttr
         _namesOfDoubleAttributes _namesOfWritableDoubleAttributes
-        """.split()
-    )
+        """.split())
 
     def _make_proxymethod(name, f):
         def proxymethod(self, *args, **kwargs):

src/diffpy/srreal/pdfbaseline.py

@@ -17,7 +17,6 @@
     PDFBaseline, ZeroBaseline, LinearBaseline
 """
 
-
 # exported items
 __all__ = """
     PDFBaseline makePDFBaseline
@@ -40,8 +39,10 @@
 
 LinearBaseline.slope = propertyFromExtDoubleAttr(
     "slope",
-    """Slope of an unscaled linear baseline.  For crystal structures it
-    is preset to (-4 * pi * rho0).""",
+    (
+        "Slope of an unscaled linear baseline.  For crystal structures it"
+        " is preset to (-4 * pi * rho0)."
+    ),
 )
 
 # Python functions wrapper