diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst index 536bc50..e5138f5 100644 --- 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 `_. -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 `_. +* 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. `PR#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. `PR#107 `_. +* Added ``FEMap.get_cycle_closure_edge_statistics_dataframe`` to report per-edge cycle closure statistics. `PR#107 `_. +* Added ``plotting.plot_cycle_closure`` to visualize the cycle closure error distribution as a histogram. `PR#107 `_. +* Documentation and tutorials for the ECDF plotting functionality `PR#206 `_. +* Added error estimates to ECDF plots via bootstrapping `PR#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 `_. +* Exposed stats calculation functions in the ``cinnabar.stats`` module to the public API and added docs allowing users to use them directly `PR#186 `_. +* Added the ``compute_fraction_best_ligands`` function to compute the fraction of best ligands metric `PR#164 `_. +* Added ``highlight_edges`` argument to the ``draw_graph`` function, allowing the user to highlight edges in the network graph `PR#203 `_. +* Guidelines on scatter plots can now be set manually, the values are also annotated on the plots `PR#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 `_. +* 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 `_. +* All scatter and ECDF plotting functions can now plot as ``pIC50``. This is controlled by passing ``observable_type="pic50"`` `PR#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 `_. + +**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 `_. +* 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 `_. +* ``cinnabar.arsenic`` has been renamed to ``cinnabar.cli``, other references to arsenic have also been removed. `PR#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 `_. +* 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 `_. + +**Deprecated:** + +* ``plotting._master_plot`` is deprecated and will be removed in a future version. Use ``plotting.pair_plot`` instead `PR#204 `_. +* ``FEMap.to_legacy_graph`` method is now deprecated and will be removed in a future release `PR#212 `_. + +**Fixed:** + +* Fixed bug in ``FEMap.get_relative_dataframe()`` which gave the wrong values if absolute values were generated first using ``FEMap.generate_absolute_values()`` `PR#206 `_. +* The ``plot_all_DDGs`` function now correctly uses the covariance matrix when available to compute error bars for the predicted values `PR#212 `_. + + +v0.5.0 +==================== **Added:** @@ -24,8 +68,8 @@ The full release history can be viewed `at the GitHub cinnabar releases page `_). -0.2.1 - Release ---------------- +v0.2.1 - Release +==================== Bugfixes ^^^^^^^^ diff --git a/news/add_pi.rst b/news/add_pi.rst deleted file mode 100644 index 3fdc720..0000000 --- a/news/add_pi.rst +++ /dev/null @@ -1,23 +0,0 @@ -**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 `_. - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/align_dataframes.rst b/news/align_dataframes.rst deleted file mode 100644 index 2fe2b1a..0000000 --- a/news/align_dataframes.rst +++ /dev/null @@ -1,24 +0,0 @@ -**Added:** - -* - -**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 `_. -* 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 `_. - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/arsenic_update.rst b/news/arsenic_update.rst deleted file mode 100644 index f1ea217..0000000 --- a/news/arsenic_update.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* - -**Changed:** - -* ``cinnabar.arsenic`` has been renamed to ``cinnabar.cli``, other references to arsenic have also been removed `PR#158 `_ - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/custom_estimators.rst b/news/custom_estimators.rst deleted file mode 100644 index 1f8c420..0000000 --- a/news/custom_estimators.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* 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 `_. - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/cycle_closure.rst b/news/cycle_closure.rst deleted file mode 100644 index db4f3ad..0000000 --- a/news/cycle_closure.rst +++ /dev/null @@ -1,26 +0,0 @@ -**Added:** - -* 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. - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/ecdf_docs.rst b/news/ecdf_docs.rst deleted file mode 100644 index 0a925f1..0000000 --- a/news/ecdf_docs.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* Documentation and tutorials for the ECDF plotting functionality `PR#206 `_. - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**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 `_. - -**Security:** - -* diff --git a/news/ecdf_error.rst b/news/ecdf_error.rst deleted file mode 100644 index 7683dbb..0000000 --- a/news/ecdf_error.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* added error estimates to ECDF plots via bootstrapping `PR#201 `_. - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/ecdf_plots.rst b/news/ecdf_plots.rst deleted file mode 100644 index da4a5a4..0000000 --- a/news/ecdf_plots.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* 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 `_. - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/expose_stats.rst b/news/expose_stats.rst deleted file mode 100644 index c2cb794..0000000 --- a/news/expose_stats.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* Exposed stats calculation functions in the ``cinnabar.stats`` module to the public API and added docs allowing users to use them directly `PR#186 `_. - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/fraction_of_best.rst b/news/fraction_of_best.rst deleted file mode 100644 index 7c4c865..0000000 --- a/news/fraction_of_best.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* add the ``compute_fraction_best_ligands`` function to compute the fraction of best ligands metric `PR#164 `_. - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/highlight_edges.rst b/news/highlight_edges.rst deleted file mode 100644 index 4e2636b..0000000 --- a/news/highlight_edges.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* A `highlight_edges` argument was added to the `draw_graph` function, allowing the user to highlight edges in the network graph `PR#203 `_. - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/master_plotdep.rst b/news/master_plotdep.rst deleted file mode 100644 index 75a0bc7..0000000 --- a/news/master_plotdep.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* Guidelines on scatter plots can now be set manually, the values are also annotated on the plots `PR#204 `_. - -**Changed:** - -* - -**Deprecated:** - -* ``plotting._master_plot`` is deprecated and will be removed in a future version. Use ``plotting.pair_plot`` instead `PR#204 `_. - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/pairwise_df.rst b/news/pairwise_df.rst deleted file mode 100644 index 2fd3a32..0000000 --- a/news/pairwise_df.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* 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 `_. - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/pic50_dataframes.rst b/news/pic50_dataframes.rst deleted file mode 100644 index cf0b8d4..0000000 --- a/news/pic50_dataframes.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* 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 `_. - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/pic50_plots.rst b/news/pic50_plots.rst deleted file mode 100644 index 4010bba..0000000 --- a/news/pic50_plots.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* All scatter and ECDF plotting functions can now plot as ``pIC50``. This is controlled by passing ``observable_type="pic50"`` `PR#213 `_. - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/plotting_api_update.rst b/news/plotting_api_update.rst deleted file mode 100644 index 5194862..0000000 --- a/news/plotting_api_update.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* - -**Changed:** - -* 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 `_. - -**Deprecated:** - -* ``FEMap.to_legacy_graph`` method is now deprecated and will be removed in a future release `PR#212 `_. - -**Removed:** - -* - -**Fixed:** - -* The ``plot_all_DDGs`` function now correctly uses the covariance matrix when available to compute error bars for the predicted values `PR#212 `_. - -**Security:** - -* diff --git a/news/svd_error.rst b/news/svd_error.rst deleted file mode 100644 index 73e97f5..0000000 --- a/news/svd_error.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* - -**Changed:** - -* 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 `_. - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/unit_conversions.rst b/news/unit_conversions.rst deleted file mode 100644 index 7ee7112..0000000 --- a/news/unit_conversions.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* 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 `_. - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -*