Draft: Update pituitary gland ODE with better simulator, ODE class and dataframe

[WolfByttner]

This is an update to get better ODE parameters, add an ODE class (based on its behaviour) and integrate it more closely with Traja. The new setup generates dataframes to integrate with other Traja functions and work with the resampler, analysis functions.

[codecov[bot]]

Codecov Report

Merging #94 (42b948a) into master (f347c8c) will increase coverage by 0.46%. The diff coverage is 84.61%.

@@            Coverage Diff             @@
##           master      #94      +/-   ##
==========================================
+ Coverage   76.28%   76.75%   +0.46%     
==========================================
  Files          26       26              
  Lines        2703     2869     +166     
==========================================
+ Hits         2062     2202     +140     
- Misses        641      667      +26     

Flag	Coverage Δ
unittests	76.75% <84.61%> (+0.46%)	:arrow_up:

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

Impacted Files	Coverage Δ
traja/dataset/pituitary_gland.py	87.43% <84.61%> (-12.57%)	:arrow_down:

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[Saran-nns]

Hi Johan, the pytest fails on the windows due to the length of the function names, i assume. Months ago @justinshenk requested me to reduce the function names corresponding to ODE problems/models assuming the problem arises due to pep function/attribute naming style. However, we do not know the exact reason for the failure.

I also wish to have these ODE models as a general-purpose package at Traja. At the moment this PR seems to have examples of ODE models exclusively for forecasting the parameters of the pituitary gland. Is there any way we could extract these methods and develop them as a general-purpose package for ODE problems?

Thanks in advance ;)

[Saran-nns]

@WolfByttner I suggest this PR for traja-research since it is more or less application-specific at the moment. @justinshenk what do you think?

[JustinShenk]

I agree, we don’t have plans at the moment to add this to the basic functionality of the library so research makes more sense.

On Thu 2. Dec 2021 at 10:14 Saranraj Nambusubramaniyan < @.***> wrote:

@WolfByttner https://github.com/WolfByttner I suggest this PR for traja-research since it is more or less application-specific at the moment. @justinshenk https://github.com/justinshenk what do you think?

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