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 28.40580% with 247 lines in your changes missing coverage. Please review.
✅ Project coverage is 45.55%. Comparing base (4e87d9c) to head (a1f1cab).

Files with missing lines	Patch %	Lines
python/sdist/amici/jax/nn.py	12.06%	102 Missing ⚠️
python/sdist/amici/jax/petab.py	45.98%	74 Missing ⚠️
python/sdist/amici/de_model.py	5.35%	53 Missing ⚠️
python/sdist/amici/petab/petab_import.py	20.00%	8 Missing ⚠️
python/sdist/amici/petab/parameter_mapping.py	30.00%	7 Missing ⚠️
python/sdist/amici/jax/jaxcodeprinter.py	75.00%	1 Missing ⚠️
python/sdist/amici/jax/ode_export.py	80.00%	1 Missing ⚠️
python/sdist/amici/sbml_import.py	50.00%	1 Missing ⚠️

❗ There is a different number of reports uploaded between BASE (4e87d9c) and HEAD (a1f1cab). Click for more details.

HEAD has 9 uploads less than BASE

Flag	BASE (4e87d9c)	HEAD (a1f1cab)
petab	2	1
python	9	4
cpp	2	0
cpp_python	2	1

Additional details and impacted files

@@             Coverage Diff             @@
##             main    #2614       +/-   ##
===========================================
- Coverage   76.51%   45.55%   -30.97%     
===========================================
  Files         308      309        +1     
  Lines       19548    19881      +333     
  Branches     1500     1499        -1     
===========================================
- Hits        14958     9057     -5901     
- Misses       4577    10793     +6216     
- Partials       13       31       +18     

Flag	Coverage Δ
cpp	?
cpp_python	37.72% <7.24%> (-0.54%)	⬇️
petab	38.59% <27.82%> (-0.28%)	⬇️
python	38.61% <28.40%> (-31.05%)	⬇️
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	94.35% <100.00%> (-2.54%)	⬇️
python/sdist/amici/jax/__init__.py	100.00% <ø> (ø)
python/sdist/amici/jax/model.py	85.14% <100.00%> (-1.41%)	⬇️
python/sdist/amici/petab/sbml_import.py	74.60% <ø> (ø)
python/sdist/amici/petab/util.py	86.66% <ø> (ø)
python/sdist/amici/jax/jaxcodeprinter.py	87.09% <75.00%> (-1.80%)	⬇️
python/sdist/amici/jax/ode_export.py	83.33% <80.00%> (-3.94%)	⬇️
python/sdist/amici/sbml_import.py	92.50% <50.00%> (-1.45%)	⬇️
python/sdist/amici/petab/parameter_mapping.py	76.88% <30.00%> (-7.85%)	⬇️
python/sdist/amici/petab/petab_import.py	38.46% <20.00%> (-61.54%)	⬇️
... and 3 more

... and 206 files with indirect coverage changes

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[FFroehlich]

SciML tests pass locally with SBML validation disabled, tests failing due to sebapersson/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)

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