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[MRG] Add name parameter to tonic bias and add tonic biases to different sections #922

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asoplata merged 28 commits into jonescompneurolab:master from katduecker:tonic_bias_sections

Jan 10, 2025

+66 −21

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katduecker commented Oct 27, 2024

This issue was opened by @gtdang as #768. I have added the option to name a tonic bias and define the section where the tonic bias should be applied.

I need this feature for some of the tuning that I want to do based on literature on patch clamp recordings. In my case, I want the L5 pyramidal neuron to behave differently for somatic and apical stimulation (and stimulating both at the same time).

I hope this is useful!

katduecker changed the title ~~[MRG] Add name parameter to tonic bias and add tonic biases to different sections~~ Add name parameter to tonic bias and add tonic biases to different sections

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jasmainak commented Oct 28, 2024

@katduecker can you add some unit tests?

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katduecker commented Oct 30, 2024

@katduecker can you add some unit tests?

Yep, done! User now receives a warning when they don't define a section, and there will be an error if they define a section that's not part of the cell. I used a DeprecationWarning because Userwarnings don't seem to be raised on my computer so the test would fail. I mentioned this before that UserWarnings aren't raised by default on all systems.

Somehow connection to NEURON timed out? Apart from that I'm ready for code review

katduecker changed the title ~~Add name parameter to tonic bias and add tonic biases to different sections~~ [MRG] Add name parameter to tonic bias and add tonic biases to different sections

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gtdang left a comment

Added some questions and suggestions.

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gtdang requested a review from asoplata

October 30, 2024 14:59

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gtdang mentioned this pull request

Rename the io module #926

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jasmainak left a comment

Just a few more tweaks @katduecker ...

Also don't forget to update whats_new.rst !

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katduecker commented Nov 7, 2024

Thanks Mainak, done!

jasmainak enabled auto-merge (squash)

November 7, 2024 19:15

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jasmainak commented Nov 7, 2024

I enabled auto-merge once CIs pass. Thanks @katduecker ! 🥳

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katduecker commented Jan 9, 2025 •

edited

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I didn't realize this wasn't merged yet. Just pulled changes from here and pushed again, but automerge seems to be disabled now?

auto-merge was automatically disabled

January 9, 2025 22:30

Head branch was pushed to by a user without write access

katduecker force-pushed the tonic_bias_sections branch from 766cc06 to 0e0edf7 Compare

January 10, 2025 15:51

katduecker added 9 commits

January 10, 2025 10:52


          tonic bias options

502b1ed


          update defaults

1f5c435


          describe new parameters

105d650


          stop tracking arm64

6aeb75e


          flake8

8bac8a1


          unit tests

2680d26


          change sect_name to section for consistency

6220c78


          change sect_name to section for consistency test_gui

fa323ad


          workaround backwards compatibility

477317d

katduecker and others added 19 commits

January 10, 2025 10:52


          change CSD back

855cd70


          add deprecation warning

e80b86d


          fix typos

ddddcb3


          unit tests

9b25c3d


          clean up section warning

fbe25bc


          refactor: changed the default value from None to 'soma'

097a96b


          chore: updated test asset with section attributes in external_biases

6972d22


          chore: removed 'section' from ignore_keys in test_gui.check_equal_net…

751c462

…works


          fix test

bc6322c


          add bias_name test

0c75278


          update value error

e890f83


          fix regex test

321ff3f


          Update hnn_core/tests/test_network.py

d74bb87

Co-authored-by: Mainak Jas <[email protected]>


          Update hnn_core/tests/test_network.py

4ec2a3a

Co-authored-by: Mainak Jas <[email protected]>


          Update hnn_core/tests/test_network.py

d8556ed

Co-authored-by: Mainak Jas <[email protected]>


          Update hnn_core/network.py

d358188

Co-authored-by: Mainak Jas <[email protected]>


          Update hnn_core/network.py

aadf0d7

Co-authored-by: Mainak Jas <[email protected]>


          update whats_new and fix flake8

277cdbb


          update whats_new

cf08aba

katduecker force-pushed the tonic_bias_sections branch from 0e0edf7 to cf08aba Compare

January 10, 2025 15:54

gtdang approved these changes

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gtdang left a comment

Approved

asoplata approved these changes

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asoplata left a comment

LGTM; see my comment here #922 (comment)

asoplata merged commit 2a82933 into jonescompneurolab:master

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jasmainak commented Jan 10, 2025

Sorry, maybe auto-merge was disabled because the reviewers had not approved the PR yet ... glad it's merged now! 🥳

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