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Added tutorial for handling evaporation and updated GH actions #44

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merged 10 commits into from
Nov 27, 2024

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viktorht
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@viktorht viktorht commented Nov 27, 2024

Candidate for release 1.0.1.

The primary addition of this PR mainly considers evaporation from bioreactors and how to handle this using the Pseudo batch transformation. The additions are the following

  • A validation dataset of a simulated fed-batch where water evaporates at a constant rate.
  • An integration test, which validates that the pseudo batch transformation can handle scenarios when water evaporates from the bioreactor.
  • A tutorial that discuss how to deal with evaporation when using the pseudo batch transformation

Additionally, this PR holds some updates to the Github actions. The primary focus is to avoid unnecessary workflow executions.

This version should be released to make the new test dataset available to the users.

Setup a simulation where volume evaporated from the bioreactor at a constant rate. This data set was added to the datasets module and validated in a evaporation notebook.
Still require proof reading.

This draft validates that the pseudo batch method works when water evaporates and show how to handle biassed volume data.
This is done to save computational resources.
@viktorht viktorht marked this pull request as draft November 27, 2024 12:08
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Converted to a draft because I will include security fixes flag by Github.

@viktorht viktorht marked this pull request as ready for review November 27, 2024 15:11
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Previously noted security issues were only found in the exact packages used to reproduce the work presented in the paper (i.e. locked dependencies in article/requirements.txt). Thus, these security issues are not relevant for the up-to-date version of the pseudobatch package and therefore this version is ready to be merged and released.

@viktorht viktorht merged commit ae4ffb7 into main Nov 27, 2024
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