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allow non-specific currents not starting with 'i' #145

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merged 7 commits into from
Jun 24, 2024

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AurelienJaquier
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@AurelienJaquier AurelienJaquier commented Jun 17, 2024

reason: we can have non-specific currents starting with another letter, e.g. 'lk'.

Also only return unique currents and ionic concentrations in get_ion_currents_concentrations().

Use latest nexus metadata standards to get currents and ionic concentration data in nexus access_point.

Use cross_bucket=False in the fetch of available_mechanisms. Reason: some mechanisms in other projects do not conform to latest metadata standards and having cross_bucket=True can lead to resources from other projects with missing metadata to be picked over the actual resource from our project with full metadata.

Change-Id: I5bbc6a583b1afec2d23a0c86fb464808958b5467
@AurelienJaquier AurelienJaquier self-assigned this Jun 17, 2024
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codecov-commenter commented Jun 17, 2024

Codecov Report

Attention: Patch coverage is 21.73913% with 18 lines in your changes missing coverage. Please review.

Project coverage is 53.44%. Comparing base (8d5b0ab) to head (8a0c42f).
Report is 23 commits behind head on main.

Files Patch % Lines
bluepyemodel/access_point/nexus.py 0.00% 15 Missing ⚠️
bluepyemodel/access_point/forge_access_point.py 33.33% 2 Missing ⚠️
bluepyemodel/evaluation/evaluator.py 0.00% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #145      +/-   ##
==========================================
- Coverage   60.07%   53.44%   -6.64%     
==========================================
  Files         109      122      +13     
  Lines        7838     9665    +1827     
==========================================
+ Hits         4709     5165     +456     
- Misses       3129     4500    +1371     

☔ View full report in Codecov by Sentry.
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@ilkilic/ @AurelienJaquier could you test this PR to see if currentscape plots are correct for one of the models?

Jaquier Aurélien Tristan added 6 commits June 21, 2024 09:46
Change-Id: I724132c47f063b536a732f2a8866f88a3e1edc3c
Change-Id: I64a6695e273f228e8cee28f12af967e60e026fb5
Change-Id: I91765433d901453d6544dc66af8112f3d4b72ebf
…andards

Change-Id: I1cd73f3b77297b5815015dfbe1b6598c45529e20
Change-Id: Ib2e97450eb5ea5415d025f2deaf75e50c7e18a8e
@AurelienJaquier
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@ilkilic/ @AurelienJaquier could you test this PR to see if currentscape plots are correct for one of the models?

Tested with nexus access point for resource using lk current and currentscape looked as expected, with all currents, including lk

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Looks good! Thanks

@AurelienJaquier AurelienJaquier merged commit 730166e into main Jun 24, 2024
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@AurelienJaquier AurelienJaquier deleted the fix-ion-current branch June 24, 2024 14:19
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4 participants