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Feat: Add a uniform diameter model and deprecate the 'radius' parameter #85

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merged 3 commits into from Sep 21, 2023

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Description

The 'radius' parameter is used as default diameter value when we add sections but it's supposed to overwritten by the NeuronGrower._diametrize method, so we can just use an internal default value. Nevertheless, in some specific cases the diametrizer does nothing (that's actually the case in many tests), which I think is a bit weird. But to reproduce this behavior if someone needs it I added a uniform model which can take a diameter value and apply it to the entire neurites.

Checklist

This pull request is:

  • A documentation / typographical error fix
    • Good to go, no issue or tests are needed
  • A short code fix
    • Please include: Fixes: #<issue number> in the description if it solves an existing issue
      (which must include a complete example of the issue).
    • Please include tests that fail with the main branch and pass with the provided fix.
  • A new feature implementation or update an existing feature
    • Please include: Fixes: #<issue number> in the description if it solves an existing issue
      (which must include a complete example of the feature).
    • Please include tests that cover every lines of the new/updated feature.
    • Please update the documentation to describe the new/updated feature.

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codecov bot commented Sep 20, 2023

Codecov Report

Merging #85 (1f25229) into main (ed9f4f0) will decrease coverage by 0.08%.
The diff coverage is 89.47%.

Additional details and impacted files
@@            Coverage Diff             @@
##             main      #85      +/-   ##
==========================================
- Coverage   97.69%   97.62%   -0.08%     
==========================================
  Files          39       39              
  Lines        2172     2191      +19     
  Branches      375      381       +6     
==========================================
+ Hits         2122     2139      +17     
- Misses         30       31       +1     
- Partials       20       21       +1     
Flag Coverage Δ
pytest 97.62% <89.47%> (-0.08%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files Changed Coverage Δ
neurots/generate/diametrizer.py 98.74% <75.00%> (-1.26%) ⬇️
neurots/generate/tree.py 99.00% <100.00%> (+0.03%) ⬆️
neurots/preprocess/validity_checkers.py 100.00% <100.00%> (ø)

@arnaudon arnaudon merged commit c0c7720 into main Sep 21, 2023
7 of 9 checks passed
@arnaudon arnaudon deleted the deprecate_radius branch September 21, 2023 08:23
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2 participants