PEtab-dev / PEtab-dev/petab_select

Manage state information more cleanly

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Dominant language
Python
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14
Forks
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Description

Currently, the method state information is mostly stored in the candidate space object. All state information could be moved into a separate state object, such that the candidate space is no longer stateful. e.g. there are a few objects (Problem, ModelSubspace, ModelSpace, CandidateSpace) that each contain some logic to manage exclusions -- this could all be moved to the state object.

State information (some of which is only used by the FAMoS method currently):

  • each iteration:
    • the identified models
    • the calibrated models
    • the method
  • exclusions (accumulative over iterations)

Partially resolved by #128 , where all calibrated models from all iterations are now stored in Problem.state.

Use this in plotting code too, e.g.:

  • add method information from each iteration to graph_iteration_layers, to make FAMoS method switches clear

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First steps

  1. Read the whole issue, then the project's contributing guide.
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  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by tracing state and exclusion logic across Problem, ModelSubspace, ModelSpace, and CandidateSpace, including the state changes from #128. Then inspect graph_iteration_layers and Problem.state to determine how iteration methods should be represented. Done means state is managed separately from CandidateSpace and plotting makes FAMoS method switches clear.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend
Issue type
Refactor
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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