OpenFreeEnergy · atravitz · Jun 29, 2026 · Jun 29, 2026 · Jun 29, 2026 · Jun 29, 2026
diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst
@@ -4,6 +4,40 @@ Changelog
 
 .. current developments
 
+v1.12.0
+====================
+
+This release incorporates changes made to the OpenFE Ecosystem with the following releases:
+  * `cinnabar v0.6.0 <https://cinnabar.openfree.energy/en/latest/CHANGELOG.html#v0-6-0>`_
+  * `konnektor v0.4.0 <https://konnektor.openfree.energy/en/latest/CHANGELOG.html#v0-4-0>`_
+  * `kartograf v2.0 <https://kartograf.openfree.energy/en/latest/CHANGELOG.html#v2-0>`_
+  * `Lomap v3.3.0 <https://lomap.openfree.energy/en/latest/CHANGELOG.html#v3-3-0>`_
+  * `openfe_analysis v0.5.0 <https://openfe-analysis.readthedocs.io/en/latest/CHANGELOG.html#v0-5-0>`_
+
+**Added:**
+
+* Added CLI reference documentation for ``openfe test`` and ``openfe view-ligand-network`` (`PR #2017 <https://github.com/OpenFreeEnergy/openfe/pull/2017>`_).
+* Added structural analysis to the SepTop protocol. Results are saved as NPZ files and plots are generated automatically.
+  Analysis settings for SepTop are configurable via ``MultiStateAnalysisSettings`` (`PR #1982 <https://github.com/OpenFreeEnergy/openfe/pull/1982>`_).
+
+**Changed:**
+
+* AFE Protocols (``AbsoluteBindingProtocol`` and ``AbsoluteSolvationProtocol``) now assign a single uuid for all ``ProtocolUnits`` in a repeat rather than separating the uuid by legs of the transformation (`PR #1948 <https://github.com/OpenFreeEnergy/openfe/pull/1948>`_).
+* Absolute free energy predictions generated using the gather CLI command are now sorted by ligand name (`PR #1989 <https://github.com/OpenFreeEnergy/openfe/pull/1989>`_).
+* Improved alchemical charge correction to support explicitly solvated systems (``SolvatedPDBComponent`` and ``ProteinMembraneComponent``) by determining ion parameters from the forcefield if not present in the topology (`PR #1978 <https://github.com/OpenFreeEnergy/openfe/pull/1978>`_).
+* A warning is no longer raised by Hybrid Topology Protocols for mappings with element changes in core atoms (`Issue #1961 <https://github.com/OpenFreeEnergy/openfe/issues/1961>`_).
+* The ``RelativeHybridTopologyProtocol`` and ``SepTopProtocol`` now return an unbiased estimate of the standard deviation via the ``get_uncertainty`` method, reported uncertainties are expected to be larger than before (`PR #2000 <https://github.com/OpenFreeEnergy/openfe/pull/2000>`_).
+
+**Deprecated:**
+
+* ``LigandNetwork.to_rbfe_alchemical_network()`` has been deprecated and will be removed in gufe v1.13.0 (`PR #793 <https://github.com/OpenFreeEnergy/gufe/pull/793>`_).
+
+**Removed:**
+
+* Removed ``openfe.setup.atom_mapping.PersesAtomMapper`` and ``openfe.setup.atom_mapping.default_perses_scorer`` (`PR #1943 <https://github.com/OpenFreeEnergy/openfe/pull/1943>`_).
+
+
+
 v1.11.1
 ====================
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -194,7 +194,7 @@
     else:
         repo = git.Repo.clone_from(
             "https://github.com/OpenFreeEnergy/ExampleNotebooks.git",
-            branch="2026.04.28",
+            branch="2026.06.29",
             to_path=example_notebooks_path,
         )
 except Exception as e:

diff --git a/news/afe-uuid.rst b/news/afe-uuid.rst
diff --git a/news/cinnabar-update.rst b/news/cinnabar-update.rst
diff --git a/news/cli_docs.rst b/news/cli_docs.rst
diff --git a/news/membrane_charge_change.rst b/news/membrane_charge_change.rst
diff --git a/news/remove_element_change_warning.rst b/news/remove_element_change_warning.rst
diff --git a/news/remove_perses.rst b/news/remove_perses.rst
diff --git a/news/septop_structural_analysis.rst b/news/septop_structural_analysis.rst
diff --git a/news/uncertainty-update.rst b/news/uncertainty-update.rst
diff --git a/news/update_to_rbfe_deprecation.rst b/news/update_to_rbfe_deprecation.rst