Move sundials-related functionality to amici.sim.sundials.*

[dweindl]

Related to #3041.

[codecov]

Codecov Report

❌ Patch coverage is 62.66667% with 28 lines in your changes missing coverage. Please review.
✅ Project coverage is 78.16%. Comparing base (20b07e9) to head (0bad2c4).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
python/sdist/amici/__main__.py	0.00%	9 Missing ⚠️
...dist/amici/importers/petab/v1/parameter_mapping.py	33.33%	4 Missing ⚠️
...ython/sdist/amici/_installation/custom_commands.py	0.00%	2 Missing ⚠️
python/sdist/amici/sim/sundials/__init__.py	83.33%	2 Missing ⚠️
python/sdist/amici/sim/sundials/plotting.py	0.00%	2 Missing ⚠️
models/model_calvetti_py/model_calvetti_py.h	0.00%	1 Missing ⚠️
models/model_dirac_py/model_dirac_py.h	0.00%	1 Missing ⚠️
models/model_events_py/model_events_py.h	0.00%	1 Missing ⚠️
...odel_jakstat_adjoint_py/model_jakstat_adjoint_py.h	0.00%	1 Missing ⚠️
...ls/model_nested_events_py/model_nested_events_py.h	0.00%	1 Missing ⚠️
... and 4 more

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #3060   +/-   ##
=======================================
  Coverage   78.15%   78.16%           
=======================================
  Files         312      313    +1     
  Lines       20643    20656   +13     
  Branches     1499     1499           
=======================================
+ Hits        16133    16145   +12     
- Misses       4500     4502    +2     
+ Partials       10        9    -1     

Flag	Coverage Δ
cpp	71.61% <55.55%> (+0.81%)	⬆️
cpp_python	37.25% <41.66%> (+0.01%)	⬆️
petab	45.86% <58.20%> (+<0.01%)	⬆️
petab_sciml	13.82% <26.56%> (+0.04%)	⬆️
python	70.21% <61.11%> (+0.76%)	⬆️
sbmlsuite-jax	32.77% <31.25%> (+0.05%)	⬆️

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

Files with missing lines	Coverage Δ
python/sdist/amici/__init__.py	95.16% <100.00%> (+1.41%)	⬆️
python/sdist/amici/adapters/fiddy.py	78.51% <100.00%> (ø)
python/sdist/amici/debugging/__init__.py	78.57% <100.00%> (ø)
...hon/sdist/amici/importers/petab/_petab_importer.py	89.69% <100.00%> (ø)
...ython/sdist/amici/importers/petab/v1/conditions.py	98.33% <100.00%> (ø)
...n/sdist/amici/importers/petab/v1/import_helpers.py	85.71% <ø> (ø)
...on/sdist/amici/importers/petab/v1/petab_problem.py	89.23% <ø> (ø)
...thon/sdist/amici/importers/petab/v1/simulations.py	94.73% <100.00%> (ø)
python/sdist/amici/importers/petab/v1/simulator.py	96.66% <ø> (ø)
python/sdist/amici/importers/pysb/__init__.py	94.54% <ø> (ø)
... and 21 more

... and 3 files with indirect coverage changes

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[FFroehlich]

Leave in amici.plotting? Doesn‘t have to be sundial specific.

[dweindl]

Currently, all of it relies on ExpData, amici::Model, ReturnData. We can make them more generic, but I'd find it cleaner to have separate implementations, as the involved objects are quite different.

[FFroehlich]

Are trhese still useful? :( I had hoped we could just silently get rid of them.

[dweindl]

Half of the functionality is available through the ReturnData xarray interface, but that doesn't encode the experimental conditions. Not sure how relevant.
Serialization of ExpData is meanwhile available elsewhere.

I just searched on GitHub and got 0 hits outside of amici. For this PR, I'd leave it in, but we can remove it afterwards.

-> #3063