simplify JAX API

[FFroehlich]

remove user facing instantiations of JaxModel in favour of directly instantiating JaxProblem.

[Copilot]

Pull Request Overview

This PR refactors the import_petab_problem function to directly return a JAXProblem instance when jax=True, instead of returning a JAXModel that users must manually wrap. This simplifies the API by eliminating the need for users to explicitly create JAXProblem(jax_model, petab_problem).

Key changes:

• Modified import_petab_problem to return JAXProblem instead of JAXModel when jax=True
• Updated all test files and examples to use the simplified API by removing manual JAXProblem instantiation
• Removed unused JAXProblem import from test files where it's no longer needed

Reviewed Changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated no comments.

File	Description
python/sdist/amici/petab/petab_import.py	Updated return type annotation and implementation to create and return JAXProblem directly when jax=True
tests/benchmark_models/test_petab_benchmark_jax.py	Removed manual JAXProblem instantiation and unused import
python/tests/test_jax.py	Updated multiple test functions to use the simplified API without manual JAXProblem creation
doc/examples/example_jax_petab/ExampleJaxPEtab.ipynb	Updated tutorial to reflect new API, including documentation and variable references

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 76.05%. Comparing base (4360d5e) to head (19518d3).
⚠️ Report is 97 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2998      +/-   ##
==========================================
- Coverage   76.73%   76.05%   -0.68%     
==========================================
  Files         309      309              
  Lines       19884    19884              
  Branches     1498     1498              
==========================================
- Hits        15258    15123     -135     
- Misses       4613     4748     +135     
  Partials       13       13              

Flag	Coverage Δ
cpp	72.55% <ø> (ø)
cpp_python	37.72% <ø> (ø)
petab	38.59% <ø> (ø)
petab_sciml	14.15% <ø> (ø)
python	69.37% <ø> (ø)
sbmlsuite-jax	?

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Files with missing lines	Coverage Δ
python/sdist/amici/petab/petab_import.py	100.00% <ø> (ø)

... and 6 files with indirect coverage changes

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[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud