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

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Merged
jbloom merged 9 commits into from
Dec 14, 2024
Merged

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

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9ffa120
add `PolyclonalCollection.mut_escape_df_replicates_by_region`
jbloom Dec 3, 2024
e9a9764
fix to plotting to work w numpy 2
jbloom Dec 4, 2024
81fd83a
start adding regions as param to `PolyclonalCollection`
jbloom Dec 5, 2024
6296e34
finish adding regions as param to `PolyclonalCollection`
jbloom Dec 13, 2024
19bd384
add region averaging to `RBD_average` notebook
jbloom Dec 14, 2024
859f03e
fix bug in `PolyclonalCollection` code (typo in variable name)
jbloom Dec 14, 2024
996d4e5
update CHANGELOG
jbloom Dec 14, 2024
d93ad00
increment version to 6.13
jbloom Dec 14, 2024
b639fca
catch edge case of `PolyclonalCollection` of just one model
jbloom Dec 14, 2024
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5 changes: 5 additions & 0 deletions CHANGELOG.rst
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Expand Up @@ -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).
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