Skip to content

Conversation

@dweindl
Copy link
Member

@dweindl dweindl commented Jul 28, 2025

I think it would often be convenient to have some ID for a given PEtab problem and I would like to add such a field to the yaml schema. Previously, we usually used the model ID in such situations. However, often we have multiple problems based on the same model but different datasets, and this doesn't work well in the case of multiple models.

Not sure whether it should be mandatory or optional. I think, I'd go for optional.

I think it would often be convenient to have some ID for a given PEtab problem and I would like to add such a field to the yaml schema.
Previously, we usually used the model ID in such situations. However, often we have multiple problems based on the same model but different datasets, and this doesn't work well in the case of multiple models.

Not sure whether it should be mandatory or optional. I think, I'd go for optional.
@dweindl dweindl marked this pull request as ready for review August 21, 2025 13:34
@dweindl dweindl requested a review from a team as a code owner August 21, 2025 13:34
Copy link
Contributor

@fbergmann fbergmann left a comment

Choose a reason for hiding this comment

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

I'm fine with an id field. I'd prefer to have it optional.

Copy link
Member

@dilpath dilpath left a comment

Choose a reason for hiding this comment

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

Fine for me as either optional or required. Some documentation for it should be added to the spec.

Copy link
Contributor

@matthiaskoenig matthiaskoenig left a comment

Choose a reason for hiding this comment

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

In favor of adding an id.

I will have many problems were I will have a multitude of PETab problems and subproblems. Having an id would make it much easier to work with these.

Personally I would like to have this required.

@dweindl
Copy link
Member Author

dweindl commented Aug 25, 2025

Thanks for the feedback. Let's briefly discuss optional/mandatory during the next editor's meeting. Maybe also whether we want some additional annotation fields in the yaml file, like description, ...

@dweindl
Copy link
Member Author

dweindl commented Sep 23, 2025

Let's briefly discuss optional/mandatory during the next editor's meeting. Maybe also whether we want some additional annotation fields in the yaml file, like description, ...

Outcome:

  • Add id, keep it optional
  • No other annotation fields for now. If users need to add additional metadata, this can be placed under extensions in the yaml file or be included in omex archives.

@dweindl dweindl merged commit c03825c into main Sep 24, 2025
2 checks passed
@dweindl dweindl deleted the problem_id branch September 24, 2025 07:50
dweindl added a commit to dweindl/libpetab-python that referenced this pull request Sep 24, 2025
* Update schema
* v2.Problem.id
* v2.ProblemConfig.id

Related to PEtab-dev/PEtab#646.
Closes PEtab-dev#441.
dweindl added a commit to dweindl/libpetab-python that referenced this pull request Sep 24, 2025
* Update schema
* v2.Problem.id
* v2.ProblemConfig.id

Related to PEtab-dev/PEtab#646.
Closes PEtab-dev#441.
dweindl added a commit to PEtab-dev/libpetab-python that referenced this pull request Oct 2, 2025
* Update schema
* v2.Problem.id
* v2.ProblemConfig.id

Related to PEtab-dev/PEtab#646.
Closes #441.
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.

5 participants