PEtab-dev / PEtab-dev/libpetab-python
Improve model abstractions
Open
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 18
- Forks
- 9
- PR merge metrics
- No merged PRs in 30d
Description
The current model abstraction in petab.v1.models.model.Model isn't great. Non-exhaustive list of problems:
- We don't have proper handling of derived parameters (#517 / https://github.com/PEtab-dev/libpetab-python/pull/517#issuecomment-5566488336)
is_state_variableconflates different questions. The simulator decides what's treated as a state variable - that's none of PEtab's business.- Ideally, the library would more closely adopt the specs' taxonomy regarding constant, differential, and algebraic entities.
Improve that. This will probably impact quite a number of places and needs to be addressed carefully.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reading petab.v1.models.model.Model and the discussion in #517, including the linked pull request comment. Map how derived parameters and is_state_variable are used across the package before proposing changes. Done means the model abstraction reflects the constant, differential, and algebraic taxonomy without conflating simulator decisions.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- tooling
- Issue type
- Refactor
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Active
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100