Add PEtab SciML benchmarks

[BSnelling]

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 77.82%. Comparing base (266e23f) to head (c600bc4).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3203      +/-   ##
==========================================
- Coverage   78.46%   77.82%   -0.64%     
==========================================
  Files         317      317              
  Lines       20968    20968              
  Branches     1483     1482       -1     
==========================================
- Hits        16452    16318     -134     
- Misses       4508     4642     +134     
  Partials        8        8              

Flag	Coverage Δ
cpp	72.07% <100.00%> (-0.01%)	⬇️
cpp_python	36.66% <0.00%> (-0.01%)	⬇️
petab	47.15% <0.00%> (-0.02%)	⬇️
petab_sciml	16.22% <100.00%> (+<0.01%)	⬆️
petab_sciml_benchmarks	14.77% <100.00%> (?)
python	70.30% <100.00%> (-0.01%)	⬇️
sbmlsuite-jax	?

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Files with missing lines	Coverage Δ
python/sdist/amici/sim/jax/petab.py	91.34% <100.00%> (+0.03%)	⬆️

... and 7 files with indirect coverage changes

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[FFroehlich]

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[FFroehlich]

@claude review once

[Copilot]

Pull request overview

Adds a new CI workflow and test coverage for running the PEtab SciML benchmark suite, and updates the JAX/PEtab SciML HDF5 array-loading logic to support the benchmark models.

Changes:

• Added a new pytest module to execute PEtab SciML benchmarks and compare expected LLH values.
• Updated HDF5 array loading in the JAX PEtab SciML integration to load parameters/inputs by configured neural-network IDs.
• Added a dedicated GitHub Actions workflow to download the benchmark suite and run the new tests with coverage upload.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 6 comments.

File	Description
tests/sciml_benchmarks/test_sciml_benchmarks.py	New benchmark-driven pytest verifying JAX simulation LLH against expected YAML solutions.
python/sdist/amici/sim/jax/petab.py	Adjusts loading of neural-network parameter/input arrays from SciML HDF5 files.
.github/workflows/test_petab_sciml_benchmarks.yml	New CI workflow to fetch the benchmark suite, install dependencies, and run the benchmark tests.

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[claude]

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