chore: merge remaining main edits into v3.3.0

AUTHORS.rst

@@ -1,5 +1,5 @@
 Authors
-=======
+-------
 
 Christopher Farrow, Pavol Juhas, Caden Myers, Simon J. L. Billinge, and members of the Billinge Group
 

docs/source/conf.py

@@ -75,7 +75,7 @@
 napoleon_custom_sections = [
     ("Managed Parameters", "Attributes"),
     ("Usable Metadata", "Attributes"),
-    ("General Metadata", "Attributes"),
+    ("General Metadata", "params_style"),
     ("Metadata", "Attributes"),
     ("Properties", "Attributes"),
     ("Operator Attributes", "Attributes"),
@@ -334,4 +334,7 @@
 
 
 # Example configuration for intersphinx: refer to the Python standard library.
-# intersphinx_mapping = {'http://docs.python.org/': None}
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+}

news/clean-python-3.14.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* Support for Python 3.14
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* Support for Python 3.11
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

news/documentation-metadata.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* No News Added: rebuild the documentation with proper metadata handling
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

news/fix-qmax-update.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* Fixed load new parsed data with updated `Qmax` attribute
+
+**Security:**
+
+* <news item>

news/fix-test-package.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* Added `diffpy.structure` back to the requirements and run the test
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

news/sync-w-main-v2.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* No news needed: merge main into v3.3.0.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

news/update_pre-commit.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>

requirements/conda.txt

@@ -3,3 +3,4 @@ numpy
 scipy
 bg-mpl-stylesheets
 diffpy.utils
+diffpy.structure

requirements/pip.txt

@@ -3,3 +3,4 @@ numpy
 scipy
 bg-mpl-stylesheets
 diffpy.utils
+diffpy.structure

src/diffpy/__init__.py

@@ -15,3 +15,6 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
+from pkgutil import extend_path
+
+__path__ = extend_path(__path__, __name__)

src/diffpy/srfit/exceptions.py

@@ -12,9 +12,7 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-"""
-Exceptions used for SrFit - specific errors.
-"""
+"""Exceptions used for SrFit - specific errors."""
 
 # FIXME: remove this line when black and docformatter agree.
 

src/diffpy/srfit/fitbase/fitrecipe.py

@@ -489,10 +489,10 @@ def residual(self, p=[]):
         ----------
         p : list or numpy.ndarray
             The list of current variable values, provided in the same order
-            as the '_parameters' list. If p is an empty iterable (default),
-            then it is assumed that the parameters have already been
-            updated in some other way, and the explicit update within this
-            function is skipped.
+            as the ``_parameters`` list. If ``p`` is an empty iterable
+            (default), then it is assumed that the parameters have already
+            been updated in some other way, and the explicit update within
+            this function is skipped.
 
         Return
         ------
@@ -541,15 +541,17 @@ def scalar_residual(self, p=[]):
         ----------
         p : list or numpy.ndarray
             The list of current variable values, provided in the same order
-            as the '_parameters' list. If p is an empty iterable (default),
-            then it is assumed that the parameters have already been
-            updated in some other way, and the explicit update within this
-            function is skipped.
+            as the ``_parameters`` list. If ``p`` is an empty iterable
+            (default), then it is assumed that the parameters have already
+            been updated in some other way, and the explicit update within
+            this function is skipped.
 
+        Notes
+        -----
         The residual is by default the weighted concatenation of each
-        FitContribution's residual, plus the value of each restraint. The array
-        returned, denoted chiv, is such that
-        dot(chiv, chiv) = chi^2 + restraints.
+        :class:`FitContribution` residual, plus the value of each restraint.
+        The returned array, denoted ``chiv``, is such that
+        ``dot(chiv, chiv) = chi^2 + restraints``.
         """
         chiv = self.residual(p)
         return dot(chiv, chiv)

src/diffpy/srfit/fitbase/profile.py

@@ -186,11 +186,16 @@ def set_observed_profile(self, xobs, yobs, dyobs=None):
             Numpy array of the observed signal.
         dyobs
             Numpy array of the uncertainty in the observed signal. If
-            dyobs is None (default), it will be set to 1 at each
-            observed xobs.
+            `dyobs` is None (default), it will be set to 1 at each
+            observed `xobs`.
 
-        Raises ValueError if len(yobs) != len(xobs)
-        Raises ValueError if dyobs != None and len(dyobs) != len(xobs)
+
+        Raises
+        -----------
+        ValueError
+            if len(yobs) != len(xobs)
+        ValueError
+            if dyobs != None and len(dyobs) != len(xobs)
         """
         if len(yobs) != len(xobs):
             raise ValueError("xobs and yobs are different lengths")
@@ -247,8 +252,8 @@ def set_calculation_range(self, xmin=None, xmax=None, dx=None):
             The sample spacing in the independent variable.  When different
             from the data, resample the ``x`` as anchored at ``xmin``.
 
-        Note that xmin is always inclusive (unless clipped). xmax is inclusive
-        if it is within the bounds of the observed data.
+        Note that ``xmin`` is always inclusive (unless clipped).
+        ``xmax`` is inclusive if it is within the bounds of the observed data.
 
         Raises
         ------

src/diffpy/srfit/fitbase/profileparser.py

@@ -153,7 +153,9 @@ def parseString(self, patstring):
         patstring
             A string containing the pattern
 
-        Raises ParseError if the string cannot be parsed
+        Raises
+        ----------
+        ParseError if the string cannot be parsed
         """
         raise NotImplementedError()
 
@@ -170,8 +172,12 @@ def parseFile(self, filename):
         filename
             The name of the file to parse
 
-        Raises IOError if the file cannot be read
-        Raises ParseError if the file cannot be parsed
+        Raises
+        ----------
+        IOError
+            if the file cannot be read
+        ParseError
+            if the file cannot be parsed
         """
         infile = open(filename, "r")
         self._banks = []
@@ -339,7 +345,10 @@ def select_bank(self, index):
         index
             index of bank (integer, starting at 0).
 
-        Raises IndexError if requesting a bank that does not exist
+        Raises
+        ----------
+        IndexError
+            if requesting a bank that does not exist
         """
         if index is None:
             index = self._meta.get("bank", 0)
@@ -384,6 +393,8 @@ def get_data(self, index=None):
             index of bank (integer, starting at 0, default None). If
             index is None then the currently selected bank is used.
 
+        Returns
+        ----------
         This returns (x, y, dx, dy) tuple for the bank. dx is 0 if it cannot
         be determined from the data format.
         """

src/diffpy/srfit/fitbase/simplerecipe.py

@@ -195,9 +195,12 @@ def set_observed_profile(self, xobs, yobs, dyobs=None):
             dyobs is None (default), it will be set to 1 at each
             observed xobs.
 
-
-        Raises ValueError if len(yobs) != len(xobs)
-        Raises ValueError if dyobs != None and len(dyobs) != len(xobs)
+        Raises
+        ----------
+        ValueError
+            if len(yobs) != len(xobs)
+        ValueError
+            if dyobs != None and len(dyobs) != len(xobs)
         """
         return self.profile.set_observed_profile(xobs, yobs, dyobs)
 
@@ -222,20 +225,20 @@ def set_calculation_range(self, xmin=None, xmax=None, dx=None):
         Parameters
         ----------
 
-        xmin : float or "obs", optional
+        xmin : float or `obs`, optional
             The minimum value of the independent variable.  Keep the
             current minimum when not specified.  If specified as "obs"
             reset to the minimum observed value.
-        xmax : float or "obs", optional
+        xmax : float or `obs`, optional
             The maximum value of the independent variable.  Keep the
             current maximum when not specified.  If specified as "obs"
             reset to the maximum observed value.
-        dx : float or "obs", optional
+        dx : float or `obs`, optional
             The sample spacing in the independent variable.  When different
             from the data, resample the ``x`` as anchored at ``xmin``.
 
-        Note that xmin is always inclusive (unless clipped). xmax is inclusive
-        if it is within the bounds of the observed data.
+        Note that ``xmin`` is always inclusive (unless clipped).
+        ``xmax`` is inclusive if it is within the bounds of the observed data.
 
         Raises
         ------

src/diffpy/srfit/pdf/pdfcontribution.py

@@ -130,20 +130,20 @@ def setCalculationRange(self, xmin=None, xmax=None, dx=None):
         Parameters
         ----------
 
-        xmin : float or "obs", optional
+        xmin : float or `obs`, optional
             The minimum value of the independent variable.  Keep the
             current minimum when not specified.  If specified as "obs"
             reset to the minimum observed value.
-        xmax : float or "obs", optional
+        xmax : float or `obs`, optional
             The maximum value of the independent variable.  Keep the
             current maximum when not specified.  If specified as "obs"
             reset to the maximum observed value.
-        dx : float or "obs", optional
+        dx : float or `obs`, optional
             The sample spacing in the independent variable.  When different
             from the data, resample the ``x`` as anchored at ``xmin``.
 
-        Note that xmin is always inclusive (unless clipped). xmax is inclusive
-        if it is within the bounds of the observed data.
+        Note that ``xmin`` is always inclusive (unless clipped).
+        ``xmax`` is inclusive if it is within the bounds of the observed data.
 
         Raises
         ------

src/diffpy/srfit/pdf/pdfparser.py

@@ -137,7 +137,10 @@ def parseString(self, patstring):
         patstring
             A string containing the pattern
 
-        Raises ParseError if the string cannot be parsed
+        Raises
+        ----------
+        ParseError
+            if the string cannot be parsed
         """
         # useful regex patterns:
         rx = {"f": r"[-+]?(\d+(\.\d*)?|\d*\.\d+)([eE][-+]?\d+)?"}