[MRG] ENH: Add function to search for specific connections

[ntolley]

This PR turned into a gauntlet of if/else statements so I'd definitely love some input if you guys see a place to simplify. In any case I am quite happy with the functionality and to my eyes everything seems to be working correctly. The API works as follows:

net.pick_connection(src_gids='L2_pyramidal', target_gids=[0, 1, 2])

Will return the index of any connections in net.connectivity that both contain L2 pyramidal cells as src_gids, and [0, 1, 2] in the set of target_gids.

net.pick_connection(receptor=['nmda', 'ampa'])

Will return all connections that have either NMDA or AMPA synapses.

More succinctly, supplying a list to a single parameter corresponds to a logical_or, whereas supplying multiple parameters corresponds to a logical_and across the parameters. While it's wordy to explain, I find this setup to be the most intuitive with what I expect in a search function.

Let me know what you guys think!

[codecov-commenter]

Codecov Report

Merging #367 (fb99c9c) into master (78ce7cf) will decrease coverage by 0.27%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #367      +/-   ##
==========================================
- Coverage   90.54%   90.26%   -0.28%     
==========================================
  Files          16       17       +1     
  Lines        3013     3072      +59     
==========================================
+ Hits         2728     2773      +45     
- Misses        285      299      +14     

Impacted Files	Coverage Δ
hnn_core/network_builder.py	92.63% <ø> (ø)
hnn_core/check.py	100.00% <100.00%> (ø)
hnn_core/network.py	92.14% <100.00%> (+0.52%)	⬆️
hnn_core/viz.py	83.29% <100.00%> (ø)
hnn_core/parallel_backends.py	82.85% <0.00%> (-4.00%)	⬇️

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[jasmainak]

More succinctly, supplying a list to a single parameter corresponds to a logical_or, whereas supplying multiple parameters corresponds to a logical_and across the parameters. While it's wordy to explain, I find this setup to be the most intuitive with what I expect in a search function.

I think this makes sense to me!

[jasmainak]

I like this @ntolley !!!

[jasmainak]

@ntolley I recommend changing the title back to [WIP] when you are not actively seeking reviews or waiting for the PR to be merged. These prefixes allow us to filter the PRs that need attention: https://github.com/jonescompneurolab/hnn-core/pulls?q=is%3Apr+is%3Aopen+MRG. Probably not a biggie here but more important in larger projects that you may want to contribute to in the future :)

[ntolley]

Ready for more reviews here. The major change is the addition of check.py which cleans up a lot of redundant code in both net.add_connection, and net.pick_connection. I'll have to do a sweep to see if there's anything else that can benefit from the existing functions, or can be simplified by moving generic input checking to this file.

[jasmainak]

much better! now only thing is that you shouldn't have to do this:

Suggested change

conn_idx = conn_indices[0]

so plot_connectivity_matrix accepts a list. Can be a separate PR though. Are there other functions which benefit from pick_connection ?

[ntolley]

I agree that'd be a bit nicer, but what do you think the alternate behavior should be with a list? Returning multiple plots or subplots?

[jasmainak]

umm ... either is fine. Maybe subplots is better so user is not overwhelmed by plot windows. Each row is one connectivity matrix if multiple subplots. And you can even implement a scrollbar if there are too many subplots

[jasmainak]

Just some minor comments. Looks fine otherwise!

[jasmainak]

PR is good by me

@rythorpe @cjayb do you guys want to take a look?

[rythorpe]

Sorry for the delay, I'll try to look look through this tomorrow!

[jasmainak]

I went ahead and merged @rythorpe so we can keep the ball rolling. I hope it's okay. Thanks a lot @ntolley for the PR !

[rythorpe]

Sounds good, sorry @ntolley for taking so long! This will help a lot with unifying drive and local network connectivity.