doc: Exclude private API

[dweindl]

Set __all__, and remove some modules from the API doc completely.

Closes #3008.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 77.53%. Comparing base (c64ec7a) to head (bbf356e).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3095      +/-   ##
==========================================
- Coverage   78.17%   77.53%   -0.65%     
==========================================
  Files         313      313              
  Lines       20469    20477       +8     
  Branches     1500     1500              
==========================================
- Hits        16002    15876     -126     
- Misses       4458     4592     +134     
  Partials        9        9              

Flag	Coverage Δ
cpp	71.66% <100.00%> (+0.01%)	⬆️
cpp_python	37.67% <62.50%> (+<0.01%)	⬆️
petab	46.38% <75.00%> (+0.01%)	⬆️
petab_sciml	13.75% <37.50%> (+0.01%)	⬆️
python	70.30% <100.00%> (+0.01%)	⬆️
sbmlsuite-jax	?

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Files with missing lines	Coverage Δ
python/sdist/amici/__init__.py	95.16% <ø> (ø)
python/sdist/amici/adapters/fiddy.py	78.51% <ø> (ø)
python/sdist/amici/importers/antimony/__init__.py	83.33% <100.00%> (+0.98%)	⬆️
python/sdist/amici/importers/bngl/__init__.py	100.00% <100.00%> (ø)
python/sdist/amici/importers/pysb/__init__.py	94.64% <100.00%> (+0.01%)	⬆️
python/sdist/amici/importers/sbml/__init__.py	82.31% <100.00%> (-11.98%)	⬇️
...i/importers/sbml/conserved_quantities_demartino.py	65.75% <100.00%> (+0.06%)	⬆️
.../amici/importers/sbml/conserved_quantities_rref.py	96.49% <100.00%> (+0.06%)	⬆️
python/sdist/amici/importers/sbml/splines.py	80.62% <100.00%> (+0.03%)	⬆️
python/sdist/amici/sim/sundials/gradient_check.py	93.38% <100.00%> (+0.05%)	⬆️

... and 4 files with indirect coverage changes

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