define per-model regions in PolyclonalCollection (for averaging) (#186

)

* add `PolyclonalCollection.mut_escape_df_replicates_by_region`

* fix to plotting to work w numpy 2

* start adding regions as param to `PolyclonalCollection`

* finish adding regions as param to `PolyclonalCollection`

* add region averaging to `RBD_average` notebook

* fix bug in `PolyclonalCollection` code (typo in variable name)

* update CHANGELOG

* increment version to 6.13

* catch edge case of `PolyclonalCollection` of just one model

CHANGELOG.rst

@@ -6,6 +6,11 @@ All notable changes to this project will be documented in this file.
 
 The format is based on `Keep a Changelog <https://keepachangelog.com>`_.
 
+6.13
+----
+- Fixed ``altair`` plots to work with ``numpy`` version 2, which caused problems in some cases apparently due to a data type conversion issue.
+- Add ability to specify specific regions for each model in ``PolyclonalCollection``. This adds the ``region_col`` parameter and the ``PolyclonalCollection.regions`` and ``PolyclonalCollection.n_models_by_site`` attributes. Related to adding functionality to address `this issue <https://github.com/dms-vep/dms-vep-pipeline-3/issues/160>`_.
+
 6.12
 ----
 - Switch to using ``scipy.sparse`` arrays rather than matrices to keep up with `this <https://github.com/jbloomlab/binarymap/issues/6>`_ `change <https://github.com/jbloomlab/binarymap/pull/7>`_ to ``binarymap`` (now require ``binarymap`` >= 0.7).