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 3.19149% with 182 lines in your changes missing coverage. Please review.

Project coverage is 34.59%. Comparing base (c385f81) to head (7f5c3ad).
Report is 1 commits behind head on develop.

Files with missing lines	Patch %	Lines
python/sdist/amici/jax/nn.py	0.00%	73 Missing ⚠️
python/sdist/amici/jax/petab.py	0.00%	65 Missing ⚠️
python/sdist/amici/de_model.py	7.89%	35 Missing ⚠️
python/sdist/amici/jax/ode_export.py	0.00%	5 Missing ⚠️
python/sdist/amici/jax/jaxcodeprinter.py	0.00%	2 Missing ⚠️
python/sdist/amici/jax/model.py	0.00%	1 Missing ⚠️
python/sdist/amici/sbml_import.py	50.00%	1 Missing ⚠️

❗ There is a different number of reports uploaded between BASE (c385f81) and HEAD (7f5c3ad). Click for more details.

HEAD has 4 uploads less than BASE

Flag	BASE (c385f81)	HEAD (7f5c3ad)
petab	1	0
python	4	2
cpp	1	0

Additional details and impacted files

@@             Coverage Diff              @@
##           develop    #2614       +/-   ##
============================================
- Coverage    78.00%   34.59%   -43.42%     
============================================
  Files          329      324        -5     
  Lines        23252    23184       -68     
  Branches      1512     1840      +328     
============================================
- Hits         18138     8020    -10118     
- Misses        5105    15133    +10028     
- Partials         9       31       +22     

Flag	Coverage Δ
cpp	?
cpp_python	34.59% <3.19%> (+0.70%)	⬆️
petab	?
python	31.68% <3.19%> (-41.24%)	⬇️

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	94.01% <100.00%> (-1.28%)	⬇️
python/sdist/amici/jax/__init__.py	0.00% <ø> (-100.00%)	⬇️
python/sdist/amici/petab/parameter_mapping.py	45.32% <100.00%> (-36.69%)	⬇️
python/sdist/amici/petab/petab_import.py	66.66% <ø> (-9.61%)	⬇️
python/sdist/amici/petab/sbml_import.py	35.20% <ø> (-42.08%)	⬇️
python/sdist/amici/petab/util.py	30.00% <ø> (-50.96%)	⬇️
python/sdist/amici/jax/model.py	0.00% <0.00%> (-87.75%)	⬇️
python/sdist/amici/sbml_import.py	61.03% <50.00%> (-17.57%)	⬇️
python/sdist/amici/jax/jaxcodeprinter.py	0.00% <0.00%> (-84.62%)	⬇️
python/sdist/amici/jax/ode_export.py	0.00% <0.00%> (-96.88%)	⬇️
... and 3 more

... and 269 files with indirect coverage changes

🚀 New features to boost your workflow:

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

[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

[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

[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

[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