Separate pre-equilibration and dynamic simulation in jax

[FFroehlich]

Prepares for timeseries implementation. Also fixes some issues with jax compilation that snuck into the develop branch.

TODO:

• repair symlink (thanks for nothing pycharm)
• update jax petab notebook
• properly separate jax & cpp modules

[codecov]

Codecov Report

Attention: Patch coverage is 53.84615% with 12 lines in your changes missing coverage. Please review.

Project coverage is 77.88%. Comparing base (d1c8250) to head (d972f3e).
Report is 1 commits behind head on develop.

Files with missing lines	Patch %	Lines
python/sdist/amici/jax/model.py	41.66%	7 Missing ⚠️
python/sdist/amici/jax/petab.py	20.00%	4 Missing ⚠️
python/sdist/amici/petab/sbml_import.py	66.66%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #2617      +/-   ##
===========================================
- Coverage    77.89%   77.88%   -0.01%     
===========================================
  Files          330      330              
  Lines        21834    21845      +11     
  Branches      1477     1477              
===========================================
+ Hits         17007    17014       +7     
- Misses        4816     4820       +4     
  Partials        11       11              

Flag	Coverage Δ
cpp	74.13% <42.30%> (-0.02%)	⬇️
cpp_python	33.64% <11.53%> (-0.01%)	⬇️
petab	36.45% <19.23%> (-0.01%)	⬇️
python	72.47% <46.15%> (-0.01%)	⬇️

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

Files with missing lines	Coverage Δ
python/sdist/amici/jax/ode_export.py	97.95% <100.00%> (-0.05%)	⬇️
python/sdist/amici/petab/import_helpers.py	86.95% <100.00%> (+1.01%)	⬆️
python/sdist/amici/petab/petab_import.py	66.66% <ø> (ø)
python/sdist/amici/petab/sbml_import.py	73.55% <66.66%> (+0.22%)	⬆️
python/sdist/amici/jax/petab.py	71.76% <20.00%> (-1.41%)	⬇️
python/sdist/amici/jax/model.py	75.00% <41.66%> (-1.35%)	⬇️

[dweindl]

Looks good to me.

[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