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Inverse problem doc remake and new petab tutorial #701

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merged 33 commits into from
Nov 7, 2023
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@TorkelE TorkelE commented Oct 7, 2023

Supersedes:
#674
#695

Since the inverse problem doc remake PR had the same git mess as the petab tutorial one (with the latter probably inheriting from the former). I merged them into one, new one.

This was referenced Oct 7, 2023
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TorkelE commented Oct 7, 2023

Worth noting is this problem noted in the last PEtab tutorial PR:|

This tutorial is now in a good state where I am happy to receive feedback before merging.

A side note (and a problem) is that I am unable to update the Project.toml file in the docs environment to use the latest PEtab version (2+). I get this error:

(docs) pkg> update PEtab
Updating registry at ~/.julia/registries/General.toml
ERROR: Unsatisfiable requirements detected for package SuiteSparse_jll [bea87d4a]:
SuiteSparse_jll [bea87d4a] log:
├─possible versions are: 7.2.0 or uninstalled
├─restricted to versions * by an explicit requirement, leaving only versions: 7.2.0
└─found to have no compatible versions left with Sundials_jll [fb77eaff]
└─Sundials_jll [fb77eaff] log:
├─possible versions are: 3.1.1-6.6.0 or uninstalled
└─restricted to versions 5.2.1 by an explicit requirement, leaving only versions: 5.2.1

which does not directly seem to involve PEtab. Unsure how to interpret it, but I have had various weird package management errors relating to Sundials of late.

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Looks good! Just some minor comments, primarily on adding small things to the documentation

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TorkelE commented Oct 31, 2023

@isaacsas Did you have a look at whether we could merge this one? It passes everything, so should be good to go. There is a couple of stuff which depends on the new doc structure, so it would save me (and Sophie) a decent amount of git effort to have this one merged asap.
(I also indicated at ICSB that this tutorial would be up very soon, so really would like it to be available asap)

docs/src/inverse_problems/petab_ode_param_fitting.md Outdated Show resolved Hide resolved
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kD, SE --> S + E
kP, SE --> P + E
end
```
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Suggested change
```
rn = complete(rn)

We might as well start converting over to using `complete` and symbolic indexing everywhere with all PRs we merge going forward.

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I'd rather hold off on this for now, until I have figured out what the scope of these changes actually are.

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What do you mean by the scope?

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As in the scope of the changes to MTK and what they would mean for us.

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TorkelE commented Nov 3, 2023

I have not cut the identifiability thing (which I still prefer this way), and the symbolic usage (the same) I have made changes for everything. Still would need to go through to check that it builds properly and that I didn't miss any of your comments, but otherwise this should be good to go.

@TorkelE TorkelE merged commit 507ae86 into master Nov 7, 2023
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@TorkelE TorkelE deleted the PEtab_tutorial_2 branch June 8, 2024 18:31
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3 participants