python: fix Model.subchains() and Chain.subchains()

uses recently added nb::call_policy to keep model/chain alive
as long as the returned values are alive.

requires nanobind 2.4.0

finally fixes #317

pyproject.toml

@@ -1,7 +1,7 @@
 [build-system]
 requires = [
     "scikit-build-core ~=0.10.7",
-    "nanobind >=2.2",
+    "nanobind >=2.4",
     "typing-extensions >=4.0; python_version < '3.11'"
 ]
 build-backend = "scikit_build_core.build"

python/mol.cpp

@@ -25,6 +25,18 @@ NB_MAKE_OPAQUE(info_map_type)
 
 namespace {
 
+// cf. returns_references_to in nanobind docs
+struct returns_references {
+  static void precall(PyObject **, size_t, nb::detail::cleanup_list *) {}
+
+  static void postcall(PyObject **args, size_t, nb::handle ret) {
+    if (!nb::isinstance<nb::sequence>(ret))
+      throw std::runtime_error("return value should be a sequence");
+    for (nb::handle nurse : ret)
+      nb::detail::keep_alive(nurse.ptr(), args[0]);
+  }
+};
+
 template<typename T, typename C>
 C& add_item(T& container, C child, int pos) {
   if ((size_t) pos > container.size()) // true also for negative pos
@@ -223,7 +235,7 @@ void add_mol(nb::module_& m) {
          (ResidueSpan (Model::*)(const std::string&)) &Model::get_subchain,
          nb::arg("name"), nb::rv_policy::reference_internal)
     .def("subchains", (std::vector<ResidueSpan> (Model::*)()) &Model::subchains,
-         nb::rv_policy::reference_internal)
+         nb::call_policy<returns_references>())
     .def("find_residue_group", &Model::find_residue_group,
          nb::arg("chain"), nb::arg("seqid"),
          nb::keep_alive<0, 1>())
@@ -316,7 +328,8 @@ void add_mol(nb::module_& m) {
     .def("add_residue", add_child<Chain, Residue>,
          nb::arg("residue"), nb::arg("pos")=-1,
          nb::rv_policy::reference_internal)
-    .def("subchains", (std::vector<ResidueSpan> (Chain::*)()) &Chain::subchains)
+    .def("subchains", (std::vector<ResidueSpan> (Chain::*)()) &Chain::subchains,
+         nb::call_policy<returns_references>())
     .def("whole", (ResidueSpan (Chain::*)()) &Chain::whole,
          nb::keep_alive<0, 1>())
     .def("get_polymer", (ResidueSpan (Chain::*)()) &Chain::get_polymer,

tools/upstream-check.py

@@ -8,7 +8,7 @@
 from urllib.request import urlopen
 
 TAGGED_REPOS = {
-    'wjakob/nanobind': 'v2.2.0',
+    'wjakob/nanobind': 'v2.4.0',
     'scikit-build/scikit-build-core': 'v0.10.7',
     'taocpp/PEGTL': '2.8.3',
     'cxong/tinydir': '1.2.6',