From b50343f7f79e68443e4c1ed6ac450b79a4214fd6 Mon Sep 17 00:00:00 2001
From: Greg Landrum <greg.landrum@gmail.com>
Date: Fri, 29 May 2026 10:19:17 +0200
Subject: [PATCH] Do deprecations for 2026.09 release (#9213)

* Do deprecations

* update release notes
---
 Code/GraphMol/Chirality.h        |  5 -----
 Code/GraphMol/Wrap/Chirality.cpp |  2 --
 Code/RDGeneral/hanoiSort.h       | 10 ----------
 ReleaseNotes.md                  |  4 ++++
 4 files changed, 4 insertions(+), 17 deletions(-)

diff --git a/Code/GraphMol/Chirality.h b/Code/GraphMol/Chirality.h
index c81ccc890..00f628293 100644
--- a/Code/GraphMol/Chirality.h
+++ b/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;
diff --git a/Code/GraphMol/Wrap/Chirality.cpp b/Code/GraphMol/Wrap/Chirality.cpp
index 98b350e53..0581875bd 100644
--- a/Code/GraphMol/Wrap/Chirality.cpp
+++ b/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,
diff --git a/Code/RDGeneral/hanoiSort.h b/Code/RDGeneral/hanoiSort.h
index 44fad460b..69182b49f 100644
--- a/Code/RDGeneral/hanoiSort.h
+++ b/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());
diff --git a/ReleaseNotes.md b/ReleaseNotes.md
index f683c82f0..c370126b6 100644
--- a/ReleaseNotes.md
+++ b/ReleaseNotes.md
@@ -14,6 +14,10 @@ definition is the one with the lowest index, and the second one is the neighbor
 to the first which also has the lowest index.
 
 ## Code removed in this release:
+- The version of hanoiSort() that takes raw pointers has been removed. Please use
+  the version that takes std::span and std::vector.
+- `Chirality::StereoInfo::NOATOM` (C++) and `Chem.StereoInfo.NOATOM` (Python) have
+  been removed. Please use `Atom::NOATOM` and `Chem.Atom.NOATOM`.
 
 ## Deprecated code (to be removed in a future release):