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@asoplata asoplata commented Sep 2, 2025

cc: @Chetank99

This branch and PR should be the main place where we perform our refactoring of cells_default.py, in order to both better organize it, and, possibly, actually include Katharina's new celltypes. @Chetank99 and @katduecker are more than welcome to push commits directly to my branch for this PR, if desired (instead of having to do a PR on my personal fork to the branch).

I've added a working example of changing the L5 Pyramidal cell's creation functions into a self-contained "child class" of Cell, at the bottom of cells_default.py. This includes an example script at the top-level directory to show that the results output the same. Just to make it unambiguous that the script is not using the old pyramidal function of creating the L5 Pyramidal (or _cell_L5pyr), I have commented out some of its code.

Note: this will NOT currently pass testing for a number of reasons, including removing some functions, and changing an object's type.

This includes disabling of the existing way to create this
celltype (calling `pyramidal` which then calls `_cell_L5pyr`), and
includes an example script to show that the results output the same.
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