chore: remove customPQConfig and deprecate NoMetaStructureAdapter

news/remove-custompqconfig.rst

@@ -0,0 +1,18 @@
+**Changed:**
+
+* Structure conversion now returns ordinary atomic or periodic adapters,
+  without reading ``pdffit`` metadata. Configure PDF parameters explicitly
+  through the existing calculator interfaces.
+* ``nometa()`` returns or converts the source adapter without a proxy.
+  ``None`` returns the empty adapter.
+
+**Deprecated:**
+
+* ``NoMetaStructureAdapter``, retained for saved objects and subclasses.
+  Its Python constructor now emits ``DeprecationWarning``. Historical
+  metadata adapter classes remain importable for pickle compatibility.
+
+**Removed:**
+
+* The ``_customPQConfig`` bindings and Python callback dispatch, including
+  automatic application of structure metadata to PDF calculators.

src/diffpy/srreal/pdfcalculator.py

@@ -163,8 +163,8 @@ def _defineCommonInterface(cls):
     def _call_kwargs(self, structure=None, **kwargs):
         """Calculate PDF for the given structure as an (r, G) tuple.
         Keyword arguments can be used to configure calculator
-        attributes, these override any properties that may be passed
-        from the structure, such as spdiameter.
+        attributes. Structure pdffit metadata is ignored; pass any
+        desired settings explicitly.
 
         Attributes
         ----------
@@ -180,9 +180,6 @@ def _call_kwargs(self, structure=None, **kwargs):
         """
         setattrFromKeywordArguments(self, **kwargs)
         self.eval(structure)
-        # apply kwargs again if structure contained any attribute
-        # that may affect the result.
-        setattrFromKeywordArguments(self, **kwargs)
         rv = (self.rgrid, self.pdf)
         return rv
 

src/diffpy/srreal/structureadapter.py

@@ -18,9 +18,8 @@
 Routines:
 
 createStructureAdapter -- create StructureAdapter from a Python object
-nometa       -- create StructureAdapter with disabled _customPQConfig method
-                this prevents copying of diffpy.structure pdffit metadata
-                to PDFCalculator object
+nometa       -- return or convert a StructureAdapter without a proxy;
+                structure metadata no longer configures calculators
 nosymmetry   -- create StructureAdapter with disabled symmetry expansion.
 
 Constants:

src/diffpy/srreal/structureconverters.py

@@ -43,107 +43,24 @@ def convertDiffPyStructure(stru):
     """Adapt Structure class from diffpy.structure package."""
     haslattice = (1, 1, 1, 90, 90, 90) != stru.lattice.abcABG()
     isperiodic = haslattice
-    hasmeta = _DiffPyStructureMetadata.hasMetadata(stru)
-    if hasmeta:
-        if isperiodic:
-            adpt = DiffPyStructurePeriodicAdapter()
-        else:
-            adpt = DiffPyStructureAtomicAdapter()
-        adpt._fetchMetadata(stru)
-    else:
-        if isperiodic:
-            adpt = PeriodicStructureAdapter()
-        else:
-            adpt = AtomicStructureAdapter()
+    adpt = (
+        PeriodicStructureAdapter() if isperiodic else AtomicStructureAdapter()
+    )
     _fetchDiffPyStructureData(adpt, stru)
     return adpt
 
 
 # Adapter classes and helpers for diffpy.structure class ---------------------
 
 
-class _DiffPyStructureMetadata(object):
-    """Base class for handling metadata information in the pdffit
-    attribute."""
-
-    pdffit = None
-
-    @staticmethod
-    def hasMetadata(stru):
-        """True if Structure object carries data in its pdffit
-        attribute."""
-        rv = hasattr(stru, "pdffit") and bool(stru.pdffit)
-        return rv
-
-    def _customPQConfig(self, pqobj):
-        """Apply PDF-related metadata if defined in PDFFit structure
-        format."""
-        pqname = type(pqobj).__name__
-        if pqname not in ("PDFCalculator", "DebyePDFCalculator"):
-            return
-        if not self.pdffit:
-            return
-        # scale
-        envtps = pqobj.usedenvelopetypes
-        if "scale" not in envtps:
-            pqobj.addEnvelope("scale")
-        pqobj.scale = self.pdffit["scale"]
-        # spdiameter
-        if "spdiameter" in self.pdffit:
-            if "sphericalshape" not in envtps:
-                pqobj.addEnvelope("sphericalshape")
-            pqobj.spdiameter = self.pdffit["spdiameter"]
-        # stepcut
-        if "stepcut" in self.pdffit:
-            if "stepcut" not in envtps:
-                pqobj.addEnvelope("stepcut")
-            pqobj.stepcut = self.pdffit["stepcut"]
-        # delta1, delta2 - set these only when using JeongPeakWidth model
-        if pqobj.peakwidthmodel.type() == "jeong":
-            pqobj.delta1 = self.pdffit["delta1"]
-            pqobj.delta2 = self.pdffit["delta2"]
-        return
-
-    def _fetchMetadata(self, stru):
-        """Copy data from the pdffit attribute of diffpy Structure
-        object.
-
-        Attributes
-        ----------
-        stru
-            instance of Structure class from diffpy.structure
-
-        No return value.
-        """
-        # get PDF-related metadata
-        self.pdffit = {}
-        if self.hasMetadata(stru):
-            self.pdffit.update(scale=1.0, delta1=0.0, delta2=0.0)
-            self.pdffit.update(stru.pdffit)
-        return
-
-
-# end of class _DiffPyStructureMetadata
-
-
-def _installDiffPyStructureMetadata(cls):
-    """Install diffpy.structure metadata hooks without multiple
-    inheritance."""
-    cls.pdffit = _DiffPyStructureMetadata.pdffit
-    cls.hasMetadata = staticmethod(_DiffPyStructureMetadata.hasMetadata)
-    cls._customPQConfig = _DiffPyStructureMetadata._customPQConfig
-    cls._fetchMetadata = _DiffPyStructureMetadata._fetchMetadata
-    return cls
-
-
-@_installDiffPyStructureMetadata
+# Keep the historical class paths so saved adapters can still be restored.
+# Their pdffit state, if present in a pickle, is inert.
 class DiffPyStructureAtomicAdapter(AtomicStructureAdapter):
-    pass
+    """Legacy adapter retained for pickle compatibility."""
 
 
-@_installDiffPyStructureMetadata
 class DiffPyStructurePeriodicAdapter(PeriodicStructureAdapter):
-    pass
+    """Legacy adapter retained for pickle compatibility."""
 
 
 def _fetchDiffPyStructureData(adpt, stru):

src/extensions/wrap_AtomicStructureAdapter.cpp

@@ -346,7 +346,7 @@ class AtomPickleSuite : public SerializationPickleSuite<Atom>
         }
 };
 
-// template wrapper class for overloading of clone and _customPQConfig
+// template wrapper class for overloading of clone and diff
 
 template <class T>
 class MakeWrapper :
@@ -368,17 +368,6 @@ class MakeWrapper :
         }
 
 
-        void customPQConfig(PairQuantity* pq) const override
-        {
-            NB_OVERRIDE_NAME("_customPQConfig", customPQConfig, pq);
-        }
-
-        void default_customPQConfig(PairQuantity* pq) const
-        {
-            this->T::customPQConfig(pq);
-        }
-
-
         StructureDifference diff(StructureAdapterConstPtr other) const override
         {
             nb::gil_scoped_acquire gil;
@@ -428,14 +417,6 @@ StructureAdapterPtr atomadapter_clone(const T& self)
     return wrapper ? wrapper->default_clone() : self.clone();
 }
 
-template <class T>
-void atomadapter_customPQConfig(const T& self, PairQuantity* pq)
-{
-    auto* wrapper = dynamic_cast<const MakeWrapper<T>*>(&self);
-    if (wrapper) wrapper->default_customPQConfig(pq);
-    else self.customPQConfig(pq);
-}
-
 // Wrapper helpers for class AtomicStructureAdapter
 
 typedef MakeWrapper<AtomicStructureAdapter> AtomicStructureAdapterWrap;
@@ -730,7 +711,6 @@ void prepare_structure_load(diffpy::srreal::StructureAdapter& adapter)
 // declare shared docstrings from wrap_StructureAdapter.cpp
 
 extern const char* doc_StructureAdapter___init__fromstring;
-extern const char* doc_StructureAdapter__customPQConfig;
 extern const char* doc_StructureAdapter_diff;
 
 // Wrapper definitions -------------------------------------------------------
@@ -823,10 +803,6 @@ void wrap_AtomicStructureAdapter(nb::module_& m)
         .def("clone",
                 atomadapter_clone<AtomicStructureAdapter>,
                 doc_AtomicStructureAdapter_clone)
-        .def("_customPQConfig",
-                atomadapter_customPQConfig<AtomicStructureAdapter>,
-                nb::arg("pqobj"),
-                doc_StructureAdapter__customPQConfig)
         .def("diff",
                 atomadapter_diff<AtomicStructureAdapter>,
                 nb::arg("other").none(),
@@ -873,10 +849,6 @@ void wrap_AtomicStructureAdapter(nb::module_& m)
         .def("clone",
                 atomadapter_clone<PeriodicStructureAdapter>,
                 doc_PeriodicStructureAdapter_clone)
-        .def("_customPQConfig",
-                atomadapter_customPQConfig<PeriodicStructureAdapter>,
-                nb::arg("pqobj"),
-                doc_StructureAdapter__customPQConfig)
         .def("diff",
                 atomadapter_diff<PeriodicStructureAdapter>,
                 nb::arg("other").none(),
@@ -916,10 +888,6 @@ void wrap_AtomicStructureAdapter(nb::module_& m)
         .def("clone",
                 atomadapter_clone<CrystalStructureAdapter>,
                 doc_CrystalStructureAdapter_clone)
-        .def("_customPQConfig",
-                atomadapter_customPQConfig<CrystalStructureAdapter>,
-                nb::arg("pqobj"),
-                doc_StructureAdapter__customPQConfig)
         .def("diff",
                 atomadapter_diff<CrystalStructureAdapter>,
                 nb::arg("other").none(),

src/extensions/wrap_StructureAdapter.cpp

@@ -19,6 +19,7 @@
 *****************************************************************************/
 
 #include <nanobind/nanobind.h>
+#include <new>
 #include "srreal_trampoline.hpp"
 #include <nanobind/stl/shared_ptr.h>
 
@@ -129,18 +130,6 @@ i    -- zero-based atom site index.\n\
 Return a 3 by 3 array.\n\
 ";
 
-const char* doc_StructureAdapter__customPQConfig = "\
-Support for optional custom configuration of the PairQuantity object.\n\
-This method is called from the setStructure and eval methods of the owner\n\
-PairQuantity object.\n\
-\n\
-pqobj    -- the owner PairQuantity object.  The function should check for the\n\
-            exact type of pqobj and apply configuration accordingly.\n\
-\n\
-No return value.  This method can be overloaded in a derived class.\n\
-No action by default.\n\
-";
-
 const char* doc_StructureAdapter_diff = "\
 Evaluate difference between this and other StructureAdapter.\n\
 \n\
@@ -153,14 +142,14 @@ This method can be overloaded in a derived class.\n\
 ";
 
 const char* doc_NoMetaStructureAdapter = "\
-StructureAdapter proxy which disables _customPQConfig method.\n\
+Deprecated structure proxy retained for compatibility with saved objects.\n\
+Structure metadata no longer configures calculators.\n\
 ";
 
 const char* doc_NoMetaStructureAdapter_init = "\
-Create proxy to StructureAdapter that disables _customPQConfig.\n\
+Create a deprecated proxy. Use the source adapter directly instead.\n\
 \n\
-adapter  -- StructureAdapter object to be proxied.  The new adapter\n\
-            will avoid calling of adapter._customPQConfig method.\n\
+adapter -- source StructureAdapter, or None for an empty structure.\n\
 ";
 
 const char* doc_NoSymmetryStructureAdapter = "\
@@ -176,13 +165,10 @@ adapter  -- StructureAdapter object to be proxied.  Any iteration over\n\
 ";
 
 const char* doc_nometa = "\
-Return a proxy to StructureAdapter with _customPQConfig method disabled.\n\
-This creates a thin wrapper over a source StructureAdapter object that\n\
-disables _customPQConfig.\n\
+Return the structure adapter without creating a metadata proxy.\n\
 \n\
-stru -- StructureAdapter object or an object convertible to StructureAdapter.\n\
-\n\
-Return a proxy StructureAdapter with disabled _customPQConfig.\n\
+Existing adapters are returned unchanged. Other supported structures are\n\
+converted normally; None returns EMPTY. Structure metadata is not applied.\n\
 ";
 
 const char* doc_nosymmetry = "\
@@ -482,19 +468,6 @@ class StructureAdapterWrap :
         }
 
 
-        void customPQConfig(PairQuantity* pq) const override
-        {
-            if (mserialized) return mserialized->customPQConfig(pq);
-            NB_OVERRIDE_NAME("_customPQConfig", customPQConfig, pq);
-        }
-
-        void default_customPQConfig(PairQuantity* pq) const
-        {
-            if (mserialized) return mserialized->customPQConfig(pq);
-            this->StructureAdapter::customPQConfig(pq);
-        }
-
-
         StructureDifference diff(StructureAdapterConstPtr other) const override
         {
             nb::gil_scoped_acquire gil;
@@ -573,13 +546,6 @@ BaseBondGeneratorPtr createBondGenerator_shared(StructureAdapterPtr adpt)
     return adpt->createBondGenerator();
 }
 
-void customPQConfig_dispatch(const StructureAdapter& adpt, PairQuantity* pq)
-{
-    auto* wrap = dynamic_cast<const StructureAdapterWrap*>(&adpt);
-    if (wrap) wrap->default_customPQConfig(pq);
-    else adpt.customPQConfig(pq);
-}
-
 
 template <class T>
 class StructureProxyPickleSuite
@@ -681,10 +647,6 @@ void wrap_StructureAdapter(nb::module_& m)
         .def("siteCartesianUij",
                 siteCartesianUij_safe,
                 doc_StructureAdapter_siteCartesianUij)
-        .def("_customPQConfig",
-                customPQConfig_dispatch,
-                nb::arg("pqobj"),
-                doc_StructureAdapter__customPQConfig)
         .def("diff",
                 structure_diff_shared,
                 nb::arg("other").none(),
@@ -698,8 +660,14 @@ void wrap_StructureAdapter(nb::module_& m)
     nb::class_<NoMetaStructureAdapter, StructureAdapter> nometastructureadapter(m,
             "NoMetaStructureAdapter", doc_NoMetaStructureAdapter);
     nometastructureadapter
-        .def(nb::init<StructureAdapterPtr>(), nb::arg("adapter").none(),
-                    doc_NoMetaStructureAdapter_init)
+        .def("__init__", [](NoMetaStructureAdapter* self, StructureAdapterPtr source) {
+                    if (PyErr_WarnEx(PyExc_DeprecationWarning,
+                            "NoMetaStructureAdapter is deprecated; use the source "
+                            "adapter directly. Structure metadata no longer "
+                            "configures calculators.", 1) < 0)
+                        nb::raise_python_error();
+                    new (self) NoMetaStructureAdapter(source);
+                }, nb::arg("adapter").none(), doc_NoMetaStructureAdapter_init)
         ;
         StructureProxyPickleSuite<NoMetaStructureAdapter>::bind(nometastructureadapter);
 
@@ -734,8 +702,6 @@ void wrap_StructureAdapter(nb::module_& m)
 
 const char* doc_StructureAdapter___init__fromstring =
     nswrap_StructureAdapter::doc_StructureAdapter___init__fromstring;
-const char* doc_StructureAdapter__customPQConfig =
-    nswrap_StructureAdapter::doc_StructureAdapter__customPQConfig;
 const char* doc_StructureAdapter_diff =
     nswrap_StructureAdapter::doc_StructureAdapter_diff;