SciML linting - allow nn outputs not in params table

[BSnelling]

Allow network outputs to be used in observable and noise formulae without having to appear in the parameters table. The PR updates the get_required_parameters_for_parameter_table check to reflect this.

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 75.80%. Comparing base (f1c7679) to head (6727939).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #511      +/-   ##
==========================================
+ Coverage   75.61%   75.80%   +0.18%     
==========================================
  Files          65       65              
  Lines        7354     7357       +3     
  Branches     1323     1323              
==========================================
+ Hits         5561     5577      +16     
+ Misses       1289     1280       -9     
+ Partials      504      500       -4     

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[dweindl]

Thanks, good after gating on SciML-usage and not hiding the import error.

[dweindl]

This pass doesn't feel safe. I think get_nn_entity_petab_ids should only be imported/called if problem required SciML, but then, any import failure should be an error.

[BSnelling]

Makes sense, I've updated accordingly.

[dweindl]

👍

[dilpath]

Looks good but I think the wording is a bit suboptimal. NN outputs should never appear in the parameter table, right? But currently the PR seems to imply that there are cases where it is OK

[BSnelling]

Looks good but I think the wording is a bit suboptimal. NN outputs should never appear in the parameter table, right?

I thought this was the case, but wasn't 100% sure. I have updated the wording now to say they should not appear.