OpenFreeEnergy · jthorton · Jun 8, 2026 · Jun 3, 2026 · Jun 3, 2026 · Jun 3, 2026
diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst
@@ -8,8 +8,52 @@ This section lists features and improvements of note in each release.
 
 The full release history can be viewed `at the GitHub cinnabar releases page <https://github.com/OpenFreeEnergy/cinnabar/releases>`_.
 
-0.5.0
-=====
+.. current developments
+
+v0.6.0
+====================
+
+**Added:**
+
+* Added the predictive index (PI) metric to compare ranking performance, this is also exposed in bootstrap statistics and can be used in plots `PR#194 <https://github.com/OpenFreeEnergy/cinnabar/pull/194>`_.
+* added the ability to define new estimators by subclassing the ``Estimator`` class and implementing the ``_estimate`` method, these can then be applied to the ``FEMap`` to generate absolute DG estimates. See `PR#193 <https://github.com/OpenFreeEnergy/cinnabar/pull/193>`_.
+* Added ``FEMap.get_cycle_closure_dataframe`` to calculate cycle closure errors for all cycles in the network,
+  reporting raw closure errors, per-edge contributions, and uncertainty-normalized cycle closures.
+* Added ``FEMap.get_cycle_closure_edge_statistics_dataframe`` to report per-edge cycle closure statistics.
+* Added ``plotting.plot_cycle_closure`` to visualize the cycle closure error distribution as a histogram.
+* Documentation and tutorials for the ECDF plotting functionality `PR#206 <https://github.com/OpenFreeEnergy/cinnabar/pull/206>`_.
+* added error estimates to ECDF plots via bootstrapping `PR#201 <https://github.com/OpenFreeEnergy/cinnabar/pull/201>`_.
+* added ECDF plotting functionality to visualize the empirical cumulative distribution function of predicted vs experimental absolute, relative and all-to-all pairwise binding free energies `PR#172 <https://github.com/OpenFreeEnergy/cinnabar/pull/172>`_.
+* Exposed stats calculation functions in the ``cinnabar.stats`` module to the public API and added docs allowing users to use them directly `PR#186 <https://github.com/OpenFreeEnergy/cinnabar/pull/186>`_.
+* add the ``compute_fraction_best_ligands`` function to compute the fraction of best ligands metric `PR#164 <https://github.com/OpenFreeEnergy/cinnabar/pull/164>`_.
+* A ``highlight_edges`` argument was added to the ``draw_graph`` function, allowing the user to highlight edges in the network graph `PR#203 <https://github.com/OpenFreeEnergy/cinnabar/pull/203>`_.
+* Guidelines on scatter plots can now be set manually, the values are also annotated on the plots `PR#204 <https://github.com/OpenFreeEnergy/cinnabar/pull/204>`_.
+* Added ``get_all_to_all_relative_dataframe()`` function the the ``FEMap`` class to compute pairwise relative free energy differences between all ligands in a dataset `PR#187 <https://github.com/OpenFreeEnergy/cinnabar/pull/187>`_.
+* The ``get_relative/absolute/all_to_all_relative_dataframe()`` functions can now return values as ``pIC50``. This is controlled by passing ``observable_type="pic50"`` `PR#208 <https://github.com/OpenFreeEnergy/cinnabar/pull/208>`_.
+* All scatter and ECDF plotting functions can now plot as ``pIC50``. This is controlled by passing ``observable_type="pic50"`` `PR#213 <https://github.com/OpenFreeEnergy/cinnabar/pull/213>`_.
+* Added an affinity conversion function ``convert_observable`` which provides value and uncertainty conversions to and from ``dg``, ``ki``, ``ic50`` and ``pic50`` with units `PR#182 <https://github.com/OpenFreeEnergy/cinnabar/pull/182>`_.
+
+**Changed:**
+
+* The ``FEMMap.get_absolute_dataframe`` and ``FEMap.get_relative_dataframe`` methods now return dataframes in a sorted order of node labels grouped by source flags to enable easier comparisons between sources and with experimental values `PR#192 <https://github.com/OpenFreeEnergy/cinnabar/pull/192>`_.
+* The ``FEMap.get_relative_dataframe`` now also includes experimental differences for the simulated legs in the dataframe to enable easier comparisons between predicted and experimental values `PR#192 <https://github.com/OpenFreeEnergy/cinnabar/pull/192>`_.
+* ``cinnabar.arsenic`` has been renamed to ``cinnabar.cli``, other references to arsenic have also been removed `PR#158 <https://github.com/OpenFreeEnergy/cinnabar/pull/158>`_
+* Plotting functions ``plot_DDGs``, ``plot_DGs`` and ``plot_all_DDGs`` now require an FEMap as input along with a computational source, see the api tutorial for more details `PR#212 <https://github.com/OpenFreeEnergy/cinnabar/pull/212>`_.
+* The MLE estimator will now raise an error on any uncertainties of exactly zero on calculated edges due to issues with SVD calculations `PR#177 <https://github.com/OpenFreeEnergy/cinnabar/pull/177>`_.
+
+**Deprecated:**
+
+* ``plotting._master_plot`` is deprecated and will be removed in a future version. Use ``plotting.pair_plot`` instead `PR#204 <https://github.com/OpenFreeEnergy/cinnabar/pull/204>`_.
+* ``FEMap.to_legacy_graph`` method is now deprecated and will be removed in a future release `PR#212 <https://github.com/OpenFreeEnergy/cinnabar/pull/212>`_.
+
+**Fixed:**
+
+* A bug in ``FEMap.get_relative_dataframe()`` which gave the wrong values if absolute values were generated first using ``FEMap.generate_absolute_values()`` `PR#206 <https://github.com/OpenFreeEnergy/cinnabar/pull/206>`_.
+* The ``plot_all_DDGs`` function now correctly uses the covariance matrix when available to compute error bars for the predicted values `PR#212 <https://github.com/OpenFreeEnergy/cinnabar/pull/212>`_.
+
+
+v0.5.0
+====================
 
 **Added:**
 
@@ -24,8 +68,8 @@ The full release history can be viewed `at the GitHub cinnabar releases page <ht
 * Scatter plots markers now have edge outlines for clearer visibility (PR `#113 <https://github.com/OpenFreeEnergy/cinnabar/pull/113>`_).
 
 
-0.2.1 - Release
----------------
+v0.2.1 - Release
+====================
 
 Bugfixes
 ^^^^^^^^

diff --git a/news/add_pi.rst b/news/add_pi.rst
diff --git a/news/align_dataframes.rst b/news/align_dataframes.rst
diff --git a/news/arsenic_update.rst b/news/arsenic_update.rst
diff --git a/news/custom_estimators.rst b/news/custom_estimators.rst
diff --git a/news/cycle_closure.rst b/news/cycle_closure.rst
diff --git a/news/ecdf_docs.rst b/news/ecdf_docs.rst
diff --git a/news/ecdf_error.rst b/news/ecdf_error.rst
diff --git a/news/ecdf_plots.rst b/news/ecdf_plots.rst
diff --git a/news/expose_stats.rst b/news/expose_stats.rst
diff --git a/news/fraction_of_best.rst b/news/fraction_of_best.rst
diff --git a/news/highlight_edges.rst b/news/highlight_edges.rst
diff --git a/news/master_plotdep.rst b/news/master_plotdep.rst
diff --git a/news/pairwise_df.rst b/news/pairwise_df.rst