Support for PEtab SciML in jax

[FFroehlich]

CI

• turn testcase runner into proper pytest
• add github workflow

neural nets

• fix non-passing networks tests involving convolutional layers (004-008, 021, 022, 046 - 048, 050)

amici core

• separate symbolic processing for jax modules (separate PR) (Decouple JAX & C++ code generation #2615)
• remove workaround for initial condition initialization (State reinitialisation in JAX #2619)
• add support for timeseries in v2.0 (Separate pre-equilibration and dynamic simulation in jax #2617 + XXX)
• add nn placeholders for neural network elements
• maker better use of petab methods where appropriate

tests

• fix testcases (PEtab YAML formatting PEtab-dev/petab_sciml#4)
• remove temporary fixes to testcases

[codecov]

Codecov Report

❌ Patch coverage is 91.30435% with 30 lines in your changes missing coverage. Please review.
✅ Project coverage is 76.73%. Comparing base (4e87d9c) to head (675cee9).
⚠️ Report is 99 commits behind head on main.

Files with missing lines	Patch %	Lines
python/sdist/amici/jax/petab.py	86.86%	18 Missing ⚠️
python/sdist/amici/de_model.py	89.28%	6 Missing ⚠️
python/sdist/amici/jax/nn.py	94.82%	6 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2614      +/-   ##
==========================================
+ Coverage   76.51%   76.73%   +0.21%     
==========================================
  Files         308      309       +1     
  Lines       19548    19884     +336     
  Branches     1500     1498       -2     
==========================================
+ Hits        14958    15258     +300     
- Misses       4577     4613      +36     
  Partials       13       13              

Flag	Coverage Δ
cpp	72.55% <54.49%> (-0.37%)	⬇️
cpp_python	37.72% <7.24%> (-0.54%)	⬇️
petab	38.59% <27.82%> (-0.28%)	⬇️
petab_sciml	14.15% <85.21%> (?)
python	69.37% <56.23%> (-0.28%)	⬇️
sbmlsuite-jax	33.01% <14.78%> (-0.92%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
python/sdist/amici/de_export.py	96.89% <100.00%> (+<0.01%)	⬆️
python/sdist/amici/jax/__init__.py	100.00% <ø> (ø)
python/sdist/amici/jax/jaxcodeprinter.py	90.32% <100.00%> (+1.43%)	⬆️
python/sdist/amici/jax/model.py	86.85% <100.00%> (+0.30%)	⬆️
python/sdist/amici/jax/ode_export.py	88.33% <100.00%> (+1.06%)	⬆️
python/sdist/amici/petab/parameter_mapping.py	85.37% <100.00%> (+0.64%)	⬆️
python/sdist/amici/petab/petab_import.py	100.00% <100.00%> (ø)
python/sdist/amici/petab/sbml_import.py	74.60% <ø> (ø)
python/sdist/amici/petab/util.py	86.66% <ø> (ø)
python/sdist/amici/sbml_import.py	93.95% <100.00%> (+0.01%)	⬆️
... and 3 more

... and 2 files with indirect coverage changes

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[FFroehlich]

SciML tests pass locally with SBML validation disabled, tests failing due to PEtab-dev/petab_sciml_testsuite#14

[dweindl]

Thanks, looks good. Please run pre-commit run --all-files before merging.

[sonarqubecloud]

Quality Gate failed

Failed conditions
1 Security Hotspot
C Reliability Rating on New Code (required ≥ A)

See analysis details on SonarQube Cloud

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