Neural Updates: Move GENOTLinProblem, Update SolverOutput Class Hierarchy

[selmanozleyen]

Important things to note:

• removed this class from the user.rst file because I think it should be tested more to be exposed in the docs
• In project_to_transport_matrix I removed the forward argument since for that class forward is always true.
• In general I added a method _apply_forward to the base output class so it includes both the neural and non-neural case. This might seem like more code but checking every time for forward=False and throwing an error is probably more problematic and has more code. For the old moscot classes nothing changes. _apply_forward is also simply supported with def _apply_forward(x): return apply(x, forward=True)

[codecov]

Codecov Report

Attention: Patch coverage is 77.61194% with 15 lines in your changes missing coverage. Please review.

Project coverage is 77.46%. Comparing base (8c31536) to head (b55a0e4).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/moscot/backends/ott/output.py	31.25%	10 Missing and 1 partial ⚠️
src/moscot/neural/problems/generic/_generic.py	91.30%	2 Missing ⚠️
src/moscot/base/cost.py	0.00%	1 Missing ⚠️
src/moscot/base/output.py	83.33%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #778      +/-   ##
==========================================
+ Coverage   77.37%   77.46%   +0.09%     
==========================================
  Files          36       37       +1     
  Lines        4363     4363              
  Branches      678      677       -1     
==========================================
+ Hits         3376     3380       +4     
+ Misses        662      657       -5     
- Partials      325      326       +1     

Files with missing lines	Coverage Δ
src/moscot/_types.py	100.00% <100.00%> (+9.09%)	⬆️
src/moscot/backends/ott/_utils.py	69.71% <100.00%> (+0.21%)	⬆️
src/moscot/backends/ott/solver.py	91.69% <100.00%> (ø)
src/moscot/backends/utils.py	77.77% <100.00%> (ø)
src/moscot/base/problems/_utils.py	64.03% <100.00%> (ø)
src/moscot/problems/generic/_generic.py	94.02% <100.00%> (+1.25%)	⬆️
src/moscot/problems/space/_mapping.py	96.05% <ø> (ø)
src/moscot/problems/space/_mixins.py	82.73% <100.00%> (+0.06%)	⬆️
src/moscot/problems/time/_lineage.py	96.29% <100.00%> (ø)
src/moscot/problems/time/_mixins.py	63.84% <ø> (ø)
... and 4 more

[MUCDK]

Thanks!