fix: fix iter-pars behavior

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/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/iteratepars-behavior.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* Changed `iterPars` method to match all equal-type atoms to have same ADPs
+
+**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/fitbase/fitrecipe.py

@@ -489,16 +489,17 @@ 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
-        ------
-        chiv : numpy.ndarray
-            The array of residuals to be optimized. The array is such that
-            dot(chiv, chiv) = chi^2 + restraints.
+        Notes
+        -----
+        The residual is by default the weighted concatenation of each
+        :class:`FitContribution` residual, plus the value of each restraint.
+        The returned array ``chiv`` satisfies
+        ``dot(chiv, chiv) = chi^2 + restraints``.
         """
 
         # Prepare, if necessary
@@ -541,15 +542,17 @@ 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/profilegenerator.py

@@ -163,15 +163,18 @@ def set_profile(self, profile):
             will store the calculated signal.
         """
         if self.profile is not None:
-            self.profile.removeObserver(self._flush)
+            self.profile.removeObserver(self._on_profile_update)
 
         self.profile = profile
-        self.profile.addObserver(self._flush)
-        self._flush(other=(self,))
+        self.profile.addObserver(self._on_profile_update)
+        self._on_profile_update(other=(self,))
+        return
 
-        # Merge the profiles metadata with our own
-        self.meta.update(self.profile.meta)
-        self._process_metadata()
+    def _on_profile_update(self, other=()):
+        if self.profile is not None:
+            self.meta.update(self.profile.meta)
+            self.processMetaData()
+        self._flush(other=other)
         return
 
     def _process_metadata(self):

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/recipeorganizer.py

@@ -240,48 +240,70 @@ def _iter_managed(self):
         """Get iterator over managed objects."""
         return chain(*(d.values() for d in self.__managed))
 
-    def iterate_over_parameters(self, pattern="", recurse=True):
+    def iterPars(self, pattern="", recurse=True, fullnames=False):
         """Iterate over the Parameters contained in this object.
 
         Parameters
         ----------
-        pattern : str, optional
-            The regular expression pattern to match parameter
-            names against. Only parameters with names matching
-            this pattern will be returned. Default is an empty
-            string, which matches all parameter names.
-        recurse : bool, optional
-            The flag indicating whether to recurse into managed
-            objects when iterating over parameters. If True
-            (default), the method will also iterate over
-            parameters in managed sub-objects. If False, only
-            top-level parameters will be iterated over.
-
-        Example
-        -------
-
-        ..
-            for param in recipe.iterate_over_parameters(pattern="scale_"):
-                # print the name and value of parameters containing "scale_"
-                print(f"{param.name}={param.value}")
+        pattern : str
+            Iterate over parameters with names matching this regular expression
+            (all parameters by default).
+
+            When `fullnames` is True, the regular expression is matched against
+            dotted parameter names relative to this object, e.g. ``Ni0.Biso``.
+        recurse : bool
+            Recurse into managed objects when True (default).
+        fullnames : bool
+            Match against hierarchical dotted names relative to this object
+            when True. Match only leaf parameter names when False (default).
         """
         regexp = re.compile(pattern)
-        for parameter in list(self._parameters.values()):
-            if regexp.search(parameter.name):
-                yield parameter
+        if not fullnames:
+            for par in list(self._parameters.values()):
+                if regexp.search(par.name):
+                    yield par
+            if not recurse:
+                return
+            managed = self.__managed[:]
+            managed.remove(self._parameters)
+            for m in managed:
+                for obj in m.values():
+                    if hasattr(obj, "iterPars"):
+                        for par in obj.iterPars(pattern=pattern, recurse=True):
+                            yield par
+            return
+        for par in self._iterpars_fullnames(
+            regexp, recurse=recurse, prefix=""
+        ):
+            yield par
+
+    def _iterpars_fullnames(self, regexp, recurse=True, prefix=""):
+        """Internal helper for iterPars(fullnames=True)."""
+        for par in list(self._parameters.values()):
+            name = f"{prefix}{par.name}"
+            if regexp.search(name):
+                yield par
+
         if not recurse:
             return
-        # Iterate over objects within the managed dictionaries.
+
         managed = self.__managed[:]
         managed.remove(self._parameters)
         for m in managed:
             for obj in m.values():
-                if hasattr(obj, "iterate_over_parameters"):
-                    for parameter in obj.iterate_over_parameters(
-                        pattern=pattern
+                if hasattr(obj, "_iterpars_fullnames"):
+                    childprefix = f"{prefix}{obj.name}."
+                    for par in obj._iterpars_fullnames(
+                        regexp,
+                        recurse=True,
+                        prefix=childprefix,
                     ):
-                        yield parameter
-        return
+                        yield par
+                elif hasattr(obj, "iterPars"):
+                    for par in obj.iterPars(
+                        pattern=regexp.pattern, recurse=True
+                    ):
+                        yield par
 
     @deprecated(iterPars_deprecation_msg)
     def iterPars(self, pattern="", recurse=True):