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@phumtutum phumtutum commented Feb 3, 2022

#1417 added MarkovJumpModels which can be used to add stochastic models more easily. This PR:

  • removes the old stochastic logistic model and adds implements it in the new way
  • will add the stochastic simulation of production and degradation model
  • Schlogl's model
  • remove MarkovJumpModel's return of a zero array if the starting population is empty

@phumtutum phumtutum changed the title Moving stochastic logistic model to pints.toy.stochastic Added additional stochastic models[Not finished] Feb 3, 2022
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codecov bot commented Feb 3, 2022

Codecov Report

Merging #1432 (13e8eae) into master (7142c9a) will not change coverage.
The diff coverage is 100.00%.

@@            Coverage Diff            @@
##            master     #1432   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           90        92    +2     
  Lines         8971      8968    -3     
=========================================
- Hits          8971      8968    -3     
Impacted Files Coverage Δ
pints/toy/__init__.py 100.00% <ø> (ø)
pints/toy/stochastic/__init__.py 100.00% <100.00%> (ø)
pints/toy/stochastic/_logistic_model.py 100.00% <100.00%> (ø)
pints/toy/stochastic/_markov_jump_model.py 100.00% <100.00%> (ø)
pints/toy/stochastic/_michaelis_menten_model.py 100.00% <100.00%> (ø)
...ts/toy/stochastic/_production_degradation_model.py 100.00% <100.00%> (ø)
pints/toy/stochastic/_schlogl_model.py 100.00% <100.00%> (ø)

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This PR is ready for a review. As in #1413, some unit tests are failing, however, I think this is not because of this PR.

@phumtutum phumtutum changed the title Added additional stochastic models[Not finished] Added additional stochastic models[finished] Feb 4, 2022
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Looks great! Thanks @phumtutum I've made a few cosmetic changes to the notebooks, but otherwise I'm happy for this to go in.

@phumtutum phumtutum merged commit ba6d5ce into master Mar 16, 2022
@MichaelClerx MichaelClerx deleted the additional-stochastic-models branch March 16, 2022 20:49
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4 participants