Treat observableParameter overrides as placeholders in noise formulae

[dilpath]

Currently, linting will fail if an observableParameter (e.g. a scaling or offset) appears in the noise formulae. Having the full observable formulae in the noise formulae is currently the only way to get observable-dependent noise -- this means noise formulae should support observableParameter placeholders.

This fixes the issue for this case: Benchmarking-Initiative/Benchmark-Models-PEtab#197

If I compare the AMICI model from these cases:

• observable-dependent noise via observable ID in noise formulae (invalid PEtab, but compiles fine with AMICI)
• this fix + observable-dependent noise via observable formulae in the noise formulae
  I get the same C++ files.

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (c0158ba) 76.28% compared to head (f907b2e) 76.28%.

Additional details and impacted files

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##           develop     #231   +/-   ##
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  Coverage    76.28%   76.28%           
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  Files           34       34           
  Lines         3188     3188           
  Branches       774      774           
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  Hits          2432     2432           
+ Misses         555      554    -1     
- Partials       201      202    +1     

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[dweindl]

Thanks. Makes sense. Could you please add/extend a test?

We should probably also clarify that in https://github.com/PEtab-dev/PEtab/blob/main/doc/documentation_data_format.rst

[dilpath]

Thanks. Makes sense. Could you please add/extend a test?

Done! I did not see a pre-existing test, so I created a new one in a test script that already provided a PEtab problem to work with. I changed this PEtab problem, because observable_1 is a parameter in the test problem model, and obs1 is the observable ID used in the measurements table.

We should probably also clarify that in https://github.com/PEtab-dev/PEtab/blob/main/doc/documentation_data_format.rst

Sounds good, done here: PEtab-dev/PEtab#574