Do deprecations for 2026.09 release (#9213)

* Do deprecations

* update release notes

Code/GraphMol/Chirality.h

@@ -117,11 +117,6 @@ enum class StereoSpecified {
 struct RDKIT_GRAPHMOL_EXPORT StereoInfo {
   // REVIEW: absolute stereo data member?
 
-  // used to mark missing atoms
-  [[deprecated(
-      "please use Atom::NOATOM")]] inline static constexpr unsigned int NOATOM =
-      Atom::NOATOM;
-
   StereoType type = StereoType::Unspecified;
   StereoSpecified specified = StereoSpecified::Unspecified;
   unsigned centeredOn = Atom::NOATOM;

Code/GraphMol/Wrap/Chirality.cpp

@@ -43,8 +43,6 @@ struct chirality_wrapper {
         .value("Bond_Trans", Chirality::StereoDescriptor::Bond_Trans);
     python::class_<Chirality::StereoInfo>("StereoInfo",
                                           "Class describing stereochemistry")
-        .def_readonly("NOATOM", &Atom::NOATOM,
-                      "marker for unspecified int values")
         .def_readwrite("type", &Chirality::StereoInfo::type,
                        "the type of stereo")
         .def_readwrite("specified", &Chirality::StereoInfo::specified,

Code/RDGeneral/hanoiSort.h

@@ -150,16 +150,6 @@ bool hanoi(int *base, int nel, int *temp, int *count, int *changed,
 }
 }  // namespace detail
 template <typename CompareFunc>
-[[deprecated("Use the overload that takes std::span and std::vector instead")]]
-void hanoisort(int *base, int nel, int *count, int *changed,
-               CompareFunc compar) {
-  assert(base);
-  std::vector<int> tempVec(nel);
-  if (detail::hanoi(base, nel, tempVec.data(), count, changed, compar)) {
-    memmove(base, tempVec.data(), nel * sizeof(int));
-  }
-}
-template <typename CompareFunc>
 void hanoisort(std::span<int> &base, std::vector<int> &count,
                std::vector<int> &changed, CompareFunc compar) {
   std::vector<int> tempVec(base.size());