Adding extracellular features; phase analysis features description in docs #minor

[darshanmandge]

Description

• Adding Extracellular features used for microelectrode array (MEA) data:
  "peak_to_valley", "halfwidth", "peak_trough_ratio", "repolarization_slope", "recovery_slope", "neg_peak_relative", "pos_peak_relative", "neg_peak_diff", "pos_peak_diff", "neg_image", "pos_image"
  based on those used in Buccino et al., 2024. These features were originally added in BluePyOpt. I will create a new PR in BluePyOpt to import the features from eFEL so that we have only one source of truth (no duplication of code).

• Efeatures that can be used for phase analysis have been mentioned in their documentation description. Some phase analysis are: "AP_phaseslope" and "phaseslope_max" , "AP_fall_rate", "AP_fall_rate_change", "AP_peak_downstroke", "AP_peak_upstroke", "AP_rise_rate" and "AP_rise_rate_change".

Checklist:

• Unit tests are added to cover the changes (skip if not applicable).
• The changes are mentioned in the documentation (skip if not applicable).
• CHANGELOG file is updated (skip if not applicable).

[AurelienJaquier]

I don't think it is a good idea to have Phase analysis in the docs because currently the docs reproduce the code structure (each category is a .cpp file). If we move features from spikeshape into Phase analysis in the docs without changing it in the code, the docs no longer reflect the code structure

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 93.10345% with 16 lines in your changes missing coverage. Please review.

Project coverage is 92.27%. Comparing base (2cddd26) to head (4eddaf3).
Report is 22 commits behind head on master.

Files	Patch %	Lines
efel/pyfeatures/extrafeats.py	89.93%	16 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #401      +/-   ##
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+ Coverage   91.73%   92.27%   +0.53%     
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  Files          36       39       +3     
  Lines        6278     7348    +1070     
  Branches     2033     2280     +247     
==========================================
+ Hits         5759     6780    +1021     
- Misses        266      287      +21     
- Partials      253      281      +28     

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[darshanmandge]

I don't think it is a good idea to have Phase analysis in the docs because currently the docs reproduce the code structure (each category is a .cpp file). If we move features from spikeshape into Phase analysis in the docs without changing it in the code, the docs no longer reflect the code structure

Ok. I have removed the new category and instead added a line in phase related features: This feature can used for AP phase analysis. In this way, we preserve the code and docs structure.

[darshanmandge]

I have updated the files with most of your suggestions and have commented where I had some additional points to mention. I also checked the documentation html and it looks fine to me.

[ilkilic]

could you rename it to max_trough_idx ?

[ilkilic]

could you also move all the import statements to the top of the file?

[darshanmandge]

I moved the imports to top in the latest commit. I also addressed your other comments in the commit.

[ilkilic]

fyi, this line is not really necessary in a Jupyter notebook

[ilkilic]

Thanks @darshanmandge ! Well done!