Fix documentation after PEtab refactoring

[dweindl]

• Fixed missing documentation in deprecated modules
• Added deprecation notices in sphinx docs
• Fixes some python int/enum sphinx issues
• Remove methods inherited from builtins from docs

[codecov]

Codecov Report

Attention: 6 lines in your changes are missing coverage. Please review.

Comparison is base (0cc43f9) 76.64% compared to head (367115b) 76.61%.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #2252      +/-   ##
===========================================
- Coverage    76.64%   76.61%   -0.04%     
===========================================
  Files           91       91              
  Lines        15016    15021       +5     
===========================================
- Hits         11509    11508       -1     
- Misses        3507     3513       +6     

Flag	Coverage Δ
cpp	73.09% <ø> (-0.03%)	⬇️
cpp_python	37.08% <ø> (ø)
petab	53.73% <14.28%> (-0.04%)	⬇️
python	77.91% <14.28%> (-0.06%)	⬇️
sbmlsuite	?

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

Files	Coverage Δ
python/sdist/amici/petab/__init__.py	100.00% <ø> (ø)
python/sdist/amici/petab/petab_import.py	66.66% <ø> (ø)
python/sdist/amici/petab/pysb_import.py	52.72% <ø> (ø)
python/sdist/amici/petab/simulations.py	92.78% <100.00%> (+0.07%)	⬆️
python/sdist/amici/parameter_mapping.py	0.00% <0.00%> (ø)
python/sdist/amici/petab_objective.py	0.00% <0.00%> (ø)
python/sdist/amici/petab_simulate.py	0.00% <0.00%> (ø)
python/sdist/amici/petab_util.py	0.00% <0.00%> (ø)
python/sdist/amici/swig.py	13.51% <0.00%> (ø)

... and 3 files with indirect coverage changes

[FFroehlich]

👍 nice