CODE: update pre-commit hooks

.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
@@ -21,45 +21,45 @@ 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:
           - tomli
   # prettier - multi formatter for .json, .yml, and .md files
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: f12edd9c7be1c20cfa42420fd0e6df71e42b51ea # frozen: v4.0.0-alpha.8
+    rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
         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-hook-update.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/__init__.py

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

src/diffpy/pdfgui/applications/pdfgui.py

@@ -12,9 +12,8 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-"""
-PDFgui Graphical User Interface for Pair Distribution Function fitting
-Usage: pdfgui [project.dpp]
+"""PDFgui Graphical User Interface for Pair Distribution Function
+fitting Usage: pdfgui [project.dpp]
 
 PDFgui is graphical user interface to PDFfit2 - a Python library for PDF
 simulation and structure refinement.  PDFgui has many nice features such

src/diffpy/pdfgui/control/calculation.py

@@ -291,11 +291,12 @@ def save(self, z, subpath):
         return
 
     def copy(self, other=None):
-        """Copy self to other. if other is None, create new instance.
+        """Copy self to other.
 
-        other -- reference to other object
+        if other is None, create new instance.
+                other -- reference to other object
 
-        returns reference to copied object
+                returns reference to copied object
         """
         if other is None:
             other = Calculation(self.name)

src/diffpy/pdfgui/control/constraint.py

@@ -67,8 +67,9 @@ def evalFormula(self, parvalues):
         return result
 
     def lambdaFormula(self):
-        """Build lambda function from constraint formula. Lambda
-        function expects dictionary argument.
+        """Build lambda function from constraint formula.
+
+        Lambda function expects dictionary argument.
 
         returns lambda function
         """

src/diffpy/pdfgui/control/fitdataset.py

@@ -243,8 +243,9 @@ def readObsStr(self, datastring):
         return self
 
     def write(self, filename):
-        """Same as writeCalc().  Use writeObs() to save experimental PDF
-        data.
+        """Same as writeCalc().
+
+        Use writeObs() to save experimental PDF data.
 
         filename -- name of file to write to
 
@@ -267,8 +268,9 @@ def writeCalc(self, filename):
         return
 
     def writeStr(self):
-        """Same as writeCalcStr.  Use writeObsStr() for experimental
-        PDF.
+        """Same as writeCalcStr.
+
+        Use writeObsStr() for experimental PDF.
 
         Return data string.
         """
@@ -379,9 +381,11 @@ def writeResampledObsStr(self):
         return s
 
     def findParameters(self):
-        """Obtain dictionary of parameters used by self.constraints. The
-        keys of returned dictionary are integer parameter indices, and
-        their values Parameter instances, with guessed initial values.
+        """Obtain dictionary of parameters used by self.constraints.
+
+        The keys of returned dictionary are integer parameter indices,
+        and their values Parameter instances, with guessed initial
+        values.
 
         returns dictionary of indices and Parameter instances
         """
@@ -434,11 +438,12 @@ def changeParameterIndex(self, oldidx, newidx):
         return
 
     def copy(self, other=None):
-        """Copy self to other. if other is None, create new instance.
+        """Copy self to other.
 
-        other -- ref to other object
+        if other is None, create new instance.
+                other -- ref to other object
 
-        returns reference to copied object
+                returns reference to copied object
         """
         # check arguments
         if other is None:
@@ -529,9 +534,10 @@ def save(self, z, subpath):
     # interface for data sampling
 
     def getFitSamplingType(self):
-        """Description of r-sampling used in the fit.  This method
-        compares self.fitrstep with r-sampling in the observed data and
-        with Nyquist r step.
+        """Description of r-sampling used in the fit.
+
+        This method compares self.fitrstep with r-sampling in the
+        observed data and with Nyquist r step.
 
         Return a string, possible values are "data", "Nyquist" or
         "custom".
@@ -683,7 +689,8 @@ def _set_rcalc(self, value):
         _get_rcalc,
         _set_rcalc,
         doc="""R-grid for refined data, read-only.
-        Use fitrmin, fitrmax, fitrstep to change it""",
+        Use fitrmin, fitrmax, fitrstep to change it"""
+                                                      ,
     )
 
     # Gcalc

src/diffpy/pdfgui/control/fitstructure.py

@@ -170,9 +170,11 @@ def obtainRefined(self, server, iphase):
         return
 
     def findParameters(self):
-        """Obtain dictionary of parameters used by self.constraints. The
-        keys of returned dictionary are integer parameter indices, and
-        the values are Parameter instances, with guessed initial values.
+        """Obtain dictionary of parameters used by self.constraints.
+
+        The keys of returned dictionary are integer parameter indices,
+        and the values are Parameter instances, with guessed initial
+        values.
 
         returns dictionary of indices and Parameter instances
         """
@@ -677,11 +679,13 @@ def _parseAtomSelectionString(self, s):
         # delayed initialization of the class variable
         if self._rxatomselection is None:
             FitStructure._rxatomselection = re.compile(
-                r"""
-            (?P<negate>!?)                      # exclamation point
-            (?:(?P<element>[a-zA-Z]+)$|         # element|all   or
-               (?P<start>\d+)(?P<stop>:\d+)?$   # number range
-            )""",
+                r"""(?P<negate>!?)                      # exclamation
+                point (?:(?P<element>[a-zA-Z]+)$|         # element|all
+                or.
+
+                (?P<start>\d+)(?P<stop>:\d+)?$   # number range )
+                """
+                   ,
                 re.VERBOSE,
             )
         assert self._rxatomselection
@@ -724,11 +728,12 @@ def _parseAtomSelectionString(self, s):
         return rv
 
     def copy(self, other=None):
-        """Copy self to other. if other is None, create new instance.
+        """Copy self to other.
 
-        other -- reference to other object
+        if other is None, create new instance.
+                other -- reference to other object
 
-        returns reference to copied object
+                returns reference to copied object
         """
         # check arguments
         if other is None:

src/diffpy/pdfgui/control/fitting.py

@@ -178,10 +178,11 @@ def _getStrId(self):
         return "f_" + self.name
 
     def copy(self, other=None):
-        """Copy self to other. if other is None, create an instance.
+        """Copy self to other.
 
-        other -- ref to other object
-        return value: reference to copied object
+        if other is None, create an instance.
+                other -- ref to other object
+                return value: reference to copied object
         """
         if other is None:
             other = Fitting(self.name)
@@ -448,8 +449,9 @@ def _configureBondCalculation(self, struc):
         return
 
     def outputBondAngle(self, struc, i, j, k):
-        """Output bond angle defined by atoms i, j, k. The angle is
-        calculated using the shortest lengths ji and jk with respect to
+        """Output bond angle defined by atoms i, j, k.
+
+        The angle is calculated using the shortest lengths ji and jk with respect to
         periodic boundary conditions.
 
         struc   -- instance of PDFStructure
@@ -472,8 +474,9 @@ def outputBondAngle(self, struc, i, j, k):
         return
 
     def outputBondLengthAtoms(self, struc, i, j):
-        """Output shortest bond between atoms i, j. Periodic boundary
-        conditions are applied to find the shortest bond.
+        """Output shortest bond between atoms i, j.
+
+        Periodic boundary conditions are applied to find the shortest bond.
 
         struc   -- instance of PDFStructure
         i, j    -- atom indices starting at 1

src/diffpy/pdfgui/control/organizer.py

@@ -30,8 +30,9 @@ def spd_constrained(ds):
 
 
 class Organizer(PDFComponent):
-    """Base class for Fitting. It holds separate lists of datasets,
-    strucs and calculations.
+    """Base class for Fitting.
+
+    It holds separate lists of datasets, strucs and calculations.
 
     datasets:     dataset list
     strucs:       structure list
@@ -204,10 +205,11 @@ def save(self, z, subpath):
         return
 
     def copy(self, other=None):
-        """Copy self to other. if other is None, create an instance.
+        """Copy self to other.
 
-        other -- ref to other object
-        returns reference to copied object
+        if other is None, create an instance.
+                other -- ref to other object
+                returns reference to copied object
         """
         if other is None:
             other = Organizer(self.name)

src/diffpy/pdfgui/control/pdfdataset.py

@@ -99,8 +99,9 @@ def clear(self):
         return
 
     def setvar(self, var, value):
-        """Assign data member using PdfFit-style variable. Used by
-        applyParameters().
+        """Assign data member using PdfFit-style variable.
+
+        Used by applyParameters().
 
         var   -- string representation of dataset PdfFit variable.
                  Possible values: qdamp, qbroad, dscale
@@ -116,8 +117,9 @@ def setvar(self, var, value):
         return
 
     def getvar(self, var):
-        """Obtain value corresponding to PdfFit dataset variable. Used
-        by findParameters().
+        """Obtain value corresponding to PdfFit dataset variable.
+
+        Used by findParameters().
 
         var   -- string representation of dataset PdfFit variable.
                  Possible values: qdamp, qbroad, dscale
@@ -334,10 +336,11 @@ def writeStr(self):
         return datastring
 
     def copy(self, other=None):
-        """Copy self to other. if other is None, create new instance.
+        """Copy self to other.
 
-        other -- ref to other object
-        returns reference to copied object
+        if other is None, create new instance.
+                other -- ref to other object
+                returns reference to copied object
         """
         if other is None:
             other = PDFDataSet(self.name)