arbor Arbor cable cell exporter and backend support in BluePyOpt

This is functionality to support Arbor simulations with cells optimized with Neuron in BluePyOpt as implemented in https://github.com/BlueBrain/BluePyOpt/pull/393 and related to https://github.com/arbor-sim/arbor/issues/1839.

It includes exported versions and example scripts for the simplecell and l5pc examples from BluePyOpt. The format is detailed in the referenced PR. The functionality added to Arbor includes pruning a particular tag from a morphology (going through a segment tree) and calculating an approximation for the radius of the axon replacement.

Closes #1839 Closes #1221

Aug 24 '22 11:08 lukasgd

I added the two related issues to be closed

Sep 02 '22 10:09 thorstenhater

All requests should be addressed, prune_tag and median_distal_radii are removed (see comments for details), split_at fixed, tests and documentation added.

Sep 15 '22 18:09 lukasgd

Changed the split_at implementation again to avoid redundant loops on large models. I've changed the node predicate as well to a segment id predicate - the node struct contains the parent ID in the new subtree, which seems not very useful to filter on.

Sep 15 '22 19:09 lukasgd

@lukasgd could you

Merge master
Write a nice commit message
Squash/merge

?

Sep 20 '22 09:09 thorstenhater

Thanks for the feedback. @brenthuisman, I've resolved all points I've addressed in 622f204. Feel free to reopen any if you'd like further changes.

Oct 18 '22 21:10 lukasgd

I've swapped the label-dict and decor arguments to the cable_cell constructor and in the returned values of read_acc. @brenthuisman, is there anything more from your review that needs to be addressed?

Oct 24 '22 14:10 lukasgd

@lukasgd would you like to write the commit message and merge the whole affair?

Oct 25 '22 10:10 thorstenhater

The test failure is not critical, it's our old friend; should be gone in master

Oct 25 '22 10:10 thorstenhater