Release XpongeCPP 0.2.8

.github/workflows/build-packages.yml

@@ -16,7 +16,7 @@ env:
   CIBW_TEST_COMMAND: >-
     python -c "import importlib.util, XpongeCPP, Xponge,
     XpongeCPP.io_bundle, XpongeCPP.metal_assignment;
-    assert XpongeCPP.__version__ == '0.2.7';
+    assert XpongeCPP.__version__ == '0.2.8';
     assert not hasattr(XpongeCPP, 'MC' + 'PB');
     assert importlib.util.find_spec('XpongeCPP.' + ('MC' + 'PB').lower()) is None"
   CIBW_BEFORE_ALL_LINUX: >-

.github/workflows/publish-pypi.yml

@@ -12,7 +12,7 @@ env:
   CIBW_TEST_COMMAND: >-
     python -c "import importlib.util, XpongeCPP, Xponge,
     XpongeCPP.io_bundle, XpongeCPP.metal_assignment;
-    assert XpongeCPP.__version__ == '0.2.7';
+    assert XpongeCPP.__version__ == '0.2.8';
     assert not hasattr(XpongeCPP, 'MC' + 'PB');
     assert importlib.util.find_spec('XpongeCPP.' + ('MC' + 'PB').lower()) is None"
   CIBW_BEFORE_ALL_LINUX: >-

RELEASE_NOTES.md

@@ -1,3 +1,18 @@
+# XpongeCPP 0.2.8
+
+Compatibility target: Xponge-origin 1.7.1.
+
+This patch release restores the Python instance-attribute behavior required
+by the Xponge RESP diagnostics contract. The pybind-backed `Assign` type now
+supports compatibility attributes, allowing `calculate_charge(...,
+return_diagnostics=True)` and `return_metadata=True` to retain
+`charge_fit_diagnostics` and `charge_fit_metadata` after fitting.
+
+Regression coverage verifies diagnostics, metadata, and general legacy
+extension attributes without requiring a QM backend. Release validation also
+includes a real PySCF RESP calculation and the complete compatibility suite
+against the official Xponge 1.7.1 package.
+
 # XpongeCPP 0.2.7
 
 Compatibility target: Xponge-origin 1.7b11.

cpp/python/bindings_assign.cpp

@@ -50,7 +50,7 @@ void save_assignment_pdb_object(const Assign& assignment, const std::string& fil
 }  // namespace
 
 void bind_assign_module(py::module_& m) {
-    py::class_<Assign, std::shared_ptr<Assign>>(m, "Assign")
+    py::class_<Assign, std::shared_ptr<Assign>>(m, "Assign", py::dynamic_attr())
         .def(py::init<std::string>(), py::arg("name") = "ASN")
         .def_readwrite("name", &Assign::name)
         .def_property_readonly("atom_count", &Assign::atom_count)

pyproject.toml

@@ -4,13 +4,13 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "XpongeCPP"
-version = "0.2.7"
-description = "C++ core rewrite of Xponge workflows, compatible with Xponge-origin 1.7b11"
+version = "0.2.8"
+description = "C++ core rewrite of Xponge workflows, compatible with Xponge-origin 1.7.1"
 readme = "README.md"
 requires-python = ">=3.10,<3.13"
 authors = [{ name = "The XpongeCPP contributors" }]
 license = { text = "Apache License 2.0" }
-keywords = ["molecular-dynamics", "molecular-mechanics", "Xponge-origin-1.7b11"]
+keywords = ["molecular-dynamics", "molecular-mechanics", "Xponge-origin-1.7.1"]
 classifiers = [
     "Development Status :: 4 - Beta",
     "Intended Audience :: Science/Research",

src/XpongeCPP/__init__.py

@@ -194,7 +194,7 @@ def _get_molecule_charge(molecule):
 from .legacy_types import _LegacyResidueTypeHandle
 from .template_ops import load_mol2
 
-__version__ = "0.2.7"
+__version__ = "0.2.8"
 __mokda_backend__ = "xpongecpp"
 __implementation_version__ = __version__
 pi = np.pi

tests/test_compat_assign.py

@@ -210,3 +210,36 @@ def test_assign_legacy_atom_numbers_and_residuetype_aliases_match_old_mokda_usag
 
     assert residue_type.name == "TES"
     assert len(residue_type.atoms) == 1
+
+
+def test_assign_resp_preserves_diagnostics_and_metadata_attributes(monkeypatch):
+    import Xponge
+    from XpongeCPP.assign import resp
+
+    assign = Xponge.Assign("RESP_ATTRIBUTES")
+    assign.add_atom("O", 0.0, 0.0, 0.0, name="O1")
+    diagnostics = {"max_constraint_residual": 0.0}
+    metadata = {"backend": "mock"}
+
+    def fake_resp_fit(*_args, **kwargs):
+        assert kwargs["return_diagnostics"] is True
+        assert kwargs["return_metadata"] is True
+        return {
+            "charges": [0.0],
+            "diagnostics": diagnostics,
+            "metadata": metadata,
+        }
+
+    monkeypatch.setattr(resp, "resp_fit", fake_resp_fit)
+
+    assign.calculate_charge(
+        "resp",
+        return_diagnostics=True,
+        return_metadata=True,
+    )
+
+    assert assign.charges == [0.0]
+    assert assign.charge_fit_diagnostics == diagnostics
+    assert assign.charge_fit_metadata == metadata
+    assign.legacy_extension = "available"
+    assert assign.legacy_extension == "available"

tests/test_release_025.py

@@ -1,4 +1,4 @@
-"""Release-contract checks for the Xponge-origin 1.7b11 alignment."""
+"""Release-contract checks for the Xponge-origin 1.7.1 alignment."""
 
 from __future__ import annotations
 
@@ -18,8 +18,8 @@ def test_release_version_and_compatibility_target():
     metadata = tomllib.loads(
         (ROOT / "pyproject.toml").read_text(encoding="utf-8")
     )["project"]
-    assert metadata["version"] == XpongeCPP.__version__ == "0.2.7"
-    assert "Xponge-origin 1.7b11" in metadata["description"]
+    assert metadata["version"] == XpongeCPP.__version__ == "0.2.8"
+    assert "Xponge-origin 1.7.1" in metadata["description"]
     assert metadata["requires-python"] == ">=3.10,<3.13"