Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Inverse problem doc remake and new petab tutorial #701

Merged
merged 33 commits into from
Nov 7, 2023
Merged

Conversation

TorkelE
Copy link
Member

@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
@TorkelE
Copy link
Member Author

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.

Copy link
Contributor

@sebapersson sebapersson left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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

docs/src/inverse_problems/petab_ode_param_fitting.md Outdated Show resolved Hide resolved
docs/src/inverse_problems/petab_ode_param_fitting.md Outdated Show resolved Hide resolved
docs/src/inverse_problems/petab_ode_param_fitting.md Outdated Show resolved Hide resolved
docs/src/inverse_problems/petab_ode_param_fitting.md Outdated Show resolved Hide resolved
docs/src/inverse_problems/petab_ode_param_fitting.md Outdated Show resolved Hide resolved
docs/src/inverse_problems/petab_ode_param_fitting.md Outdated Show resolved Hide resolved
docs/src/inverse_problems/petab_ode_param_fitting.md Outdated Show resolved Hide resolved
TorkelE and others added 5 commits October 28, 2023 09:44
Co-authored-by: sebapersson <46872750+sebapersson@users.noreply.github.com>
Co-authored-by: sebapersson <46872750+sebapersson@users.noreply.github.com>
@TorkelE
Copy link
Member Author

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
docs/src/inverse_problems/petab_ode_param_fitting.md Outdated Show resolved Hide resolved
kD, SE --> S + E
kP, SE --> P + E
end
```
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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.

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

What do you mean by the scope?

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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

docs/src/inverse_problems/petab_ode_param_fitting.md Outdated Show resolved Hide resolved
docs/src/inverse_problems/petab_ode_param_fitting.md Outdated Show resolved Hide resolved
docs/src/inverse_problems/petab_ode_param_fitting.md Outdated Show resolved Hide resolved
TorkelE and others added 5 commits November 2, 2023 17:42
Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
TorkelE and others added 10 commits November 2, 2023 17:47
Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
@TorkelE
Copy link
Member Author

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 and others added 3 commits November 3, 2023 09:54
Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
@TorkelE TorkelE merged commit 507ae86 into master Nov 7, 2023
7 of 9 checks passed
@TorkelE TorkelE deleted the PEtab_tutorial_2 branch June 8, 2024 18:31
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants