Port matlab test models to Python

[dweindl]

• Implements all current MATLAB test models in Python, except those for second-order sensitivities
  (the jakstat_adjoint example has a slightly different spline, because the old one is not exactly reproducible with the Python-AMICI spline-handling; the rest should be re-implemented pretty accurately). Model generation code is in amici.testing.models.
• Generates HDF5 files with expected test results via Python. This file is now stored on Git LFS.
• The model code is again added to the repository for faster testing and to quickly notice any changes in the generated code.
• The original MATLAB code is retained for testing the MATLAB interface until Drop MATLAB interface #2727.
• Some test code is partially duplicated to make it easier to remove the MATLAB-related code in Drop MATLAB interface #2727.

Closes #2822.
Closes #854.

[codecov]

Codecov Report

❌ Patch coverage is 58.83689% with 906 lines in your changes missing coverage. Please review.
✅ Project coverage is 78.96%. Comparing base (f83f92d) to head (d4eb8e2).
⚠️ Report is 60 commits behind head on main.

Files with missing lines	Patch %	Lines
models/model_calvetti_py/model_calvetti_py.h	56.05%	69 Missing ⚠️
models/model_dirac_py/model_dirac_py.h	57.61%	64 Missing ⚠️
...ls/model_nested_events_py/model_nested_events_py.h	61.68%	59 Missing ⚠️
models/model_events_py/model_events_py.h	65.26%	58 Missing ⚠️
...odel_jakstat_adjoint_py/model_jakstat_adjoint_py.h	70.51%	46 Missing ⚠️
models/model_calvetti_py/main.cpp	0.00%	45 Missing ⚠️
models/model_dirac_py/main.cpp	0.00%	45 Missing ⚠️
models/model_events_py/main.cpp	0.00%	45 Missing ⚠️
models/model_jakstat_adjoint_py/main.cpp	0.00%	45 Missing ⚠️
models/model_nested_events_py/main.cpp	0.00%	45 Missing ⚠️
... and 40 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2898      +/-   ##
==========================================
- Coverage   80.28%   78.96%   -1.32%     
==========================================
  Files         330      358      +28     
  Lines       22660    23007     +347     
  Branches     1531     1570      +39     
==========================================
- Hits        18192    18167      -25     
- Misses       4458     4829     +371     
- Partials       10       11       +1     

Flag	Coverage Δ
cpp	74.88% <58.83%> (-0.60%)	⬇️
cpp_python	33.19% <0.00%> (-0.54%)	⬇️
petab	39.00% <ø> (-0.15%)	⬇️
python	73.76% <58.83%> (-0.69%)	⬇️
sbmlsuite-jax	?

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

Files with missing lines	Coverage Δ
models/model_calvetti_py/create_splines.cpp	100.00% <100.00%> (ø)
models/model_calvetti_py/dwdw.cpp	100.00% <100.00%> (ø)
models/model_calvetti_py/dwdx.cpp	100.00% <100.00%> (ø)
models/model_calvetti_py/dxdotdw.cpp	100.00% <100.00%> (ø)
models/model_calvetti_py/dxdotdx_explicit.cpp	100.00% <100.00%> (ø)
models/model_calvetti_py/root.cpp	100.00% <100.00%> (ø)
models/model_calvetti_py/sigmay.cpp	100.00% <100.00%> (ø)
models/model_calvetti_py/w.cpp	100.00% <100.00%> (ø)
models/model_calvetti_py/wrapfunctions.cpp	100.00% <100.00%> (ø)
models/model_calvetti_py/x0.cpp	100.00% <100.00%> (ø)
... and 134 more

... and 235 files with indirect coverage changes

🚀 New features to boost your workflow:

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

[socket-security]

Review the following changes in direct dependencies. Learn more about Socket for GitHub.

Diff	Package	Supply Chain Security	Vulnerability	Quality	Maintenance	License
	amici@​0.33.0

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