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 sebapersson/petab_sciml#4)
• remove temporary fixes to testcases

[codecov]

Codecov Report

Attention: Patch coverage is 26.11111% with 133 lines in your changes missing coverage. Please review.

Project coverage is 73.74%. Comparing base (1716181) to head (bd103db).

Files with missing lines	Patch %	Lines
python/sdist/amici/jax/nn.py	13.69%	63 Missing ⚠️
python/sdist/amici/de_model.py	7.89%	35 Missing ⚠️
python/sdist/amici/jax/petab.py	44.64%	31 Missing ⚠️
python/sdist/amici/jax/ode_export.py	66.66%	2 Missing ⚠️
python/sdist/amici/jax/jaxcodeprinter.py	50.00%	1 Missing ⚠️
python/sdist/amici/sbml_import.py	50.00%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #2614      +/-   ##
===========================================
- Coverage    77.03%   73.74%   -3.30%     
===========================================
  Files          332      326       -6     
  Lines        22970    21958    -1012     
  Branches      1478     1457      -21     
===========================================
- Hits         17695    16192    -1503     
- Misses        5264     5757     +493     
+ Partials        11        9       -2     

Flag	Coverage Δ
cpp	73.74% <26.11%> (-0.41%)	⬇️
cpp_python	?
petab	?
python	70.17% <26.11%> (-1.95%)	⬇️

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	89.05% <100.00%> (-6.29%)	⬇️
python/sdist/amici/jax/__init__.py	100.00% <ø> (ø)
python/sdist/amici/jax/model.py	82.60% <100.00%> (-4.56%)	⬇️
python/sdist/amici/petab/parameter_mapping.py	48.01% <100.00%> (-33.92%)	⬇️
python/sdist/amici/petab/petab_import.py	66.66% <ø> (-9.61%)	⬇️
python/sdist/amici/petab/sbml_import.py	37.19% <ø> (-38.84%)	⬇️
python/sdist/amici/petab/util.py	43.33% <ø> (-37.62%)	⬇️
python/sdist/amici/jax/jaxcodeprinter.py	81.81% <50.00%> (-2.80%)	⬇️
python/sdist/amici/sbml_import.py	77.52% <50.00%> (-1.95%)	⬇️
python/sdist/amici/jax/ode_export.py	94.54% <66.66%> (-2.33%)	⬇️
... and 3 more

... and 55 files with indirect coverage changes

[sonarqubecloud]

Quality Gate passed

Issues
7 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