diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst index 3aa2a4cdc..b6492e2b3 100644 --- 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 `_ + * `konnektor v0.4.0 `_ + * `kartograf v2.0 `_ + * `Lomap v3.3.0 `_ + * `openfe_analysis v0.5.0 `_ + +**Added:** + +* Added CLI reference documentation for ``openfe test`` and ``openfe view-ligand-network`` (`PR #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 `_). + +**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 `_). +* Absolute free energy predictions generated using the gather CLI command are now sorted by ligand name (`PR #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 `_). +* A warning is no longer raised by Hybrid Topology Protocols for mappings with element changes in core atoms (`Issue #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 `_). + +**Deprecated:** + +* ``LigandNetwork.to_rbfe_alchemical_network()`` has been deprecated and will be removed in gufe v1.13.0 (`PR #793 `_). + +**Removed:** + +* Removed ``openfe.setup.atom_mapping.PersesAtomMapper`` and ``openfe.setup.atom_mapping.default_perses_scorer`` (`PR #1943 `_). + + + v1.11.1 ==================== diff --git a/docs/conf.py b/docs/conf.py index e16176552..c20381251 100644 --- 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 deleted file mode 100644 index 976d8a6e6..000000000 --- a/news/afe-uuid.rst +++ /dev/null @@ -1,25 +0,0 @@ -**Added:** - -* - -**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 - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/cinnabar-update.rst b/news/cinnabar-update.rst deleted file mode 100644 index 69e289d3d..000000000 --- a/news/cinnabar-update.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* - -**Changed:** - -* Absolute free energy predictions generated using the gather CLI command are now sorted by ligand name. #PR1989 - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/cli_docs.rst b/news/cli_docs.rst deleted file mode 100644 index 41da052a7..000000000 --- a/news/cli_docs.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* Added CLI reference documentation for ``openfe test`` and ``openfe view-ligand-network`` (`PR #2017 `_). - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/membrane_charge_change.rst b/news/membrane_charge_change.rst deleted file mode 100644 index d9ce89710..000000000 --- a/news/membrane_charge_change.rst +++ /dev/null @@ -1,24 +0,0 @@ -**Added:** - -* - -**Changed:** - -* Improved alchemical charge correction to support explicitly solvated systems -(:class:`SolvatedPDBComponent`) by determining ion parameters from the forcefield if not present in the topology. PR #1978 - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/remove_element_change_warning.rst b/news/remove_element_change_warning.rst deleted file mode 100644 index 10a13fc67..000000000 --- a/news/remove_element_change_warning.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* - -**Changed:** - -* A warning is no longer raised by Hybrid Topology Protocols for mappings with element changes in core atoms (`Issue #1961 `_) - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/remove_perses.rst b/news/remove_perses.rst deleted file mode 100644 index 303af7b58..000000000 --- a/news/remove_perses.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* Removed ``openfe.setup.atom_mapping.PersesAtomMapper`` and ``openfe.setup.atom_mapping.default_perses_scorer`` (`PR #1943 `_). - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/septop_structural_analysis.rst b/news/septop_structural_analysis.rst deleted file mode 100644 index 96b05be5c..000000000 --- a/news/septop_structural_analysis.rst +++ /dev/null @@ -1,24 +0,0 @@ -**Added:** - -* Added structural analysis to the SepTop protocol. Results are saved as NPZ files and plots are generated -automatically. Analysis settings are configurable via ``MultiStateAnalysisSettings``. PR #1982 - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/uncertainty-update.rst b/news/uncertainty-update.rst deleted file mode 100644 index 89251e527..000000000 --- a/news/uncertainty-update.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* - -**Changed:** - -* 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 - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/update_to_rbfe_deprecation.rst b/news/update_to_rbfe_deprecation.rst deleted file mode 100644 index d6833ecbb..000000000 --- a/news/update_to_rbfe_deprecation.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* - -**Changed:** - -* - -**Deprecated:** - -* ``LigandNetwork.to_rbfe_alchemical_network()`` has been deprecated and will be removed in gufe v1.13.0 (`PR #793 `_). - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -*