Add PEtab SciML example notebook

[BSnelling]

The notebook uses the Dandekar petab sciml benchmark. It demonstrates loading the problem, running simulations and implementing a basic training loop.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 77.83%. Comparing base (65a652a) to head (feb4740).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3208      +/-   ##
==========================================
- Coverage   78.46%   77.83%   -0.63%     
==========================================
  Files         317      317              
  Lines       20974    20974              
  Branches     1482     1482              
==========================================
- Hits        16458    16326     -132     
- Misses       4508     4640     +132     
  Partials        8        8              

Flag	Coverage Δ
cpp	72.09% <ø> (ø)
cpp_python	36.67% <ø> (ø)
petab	47.15% <ø> (ø)
petab_sciml	16.21% <ø> (ø)
petab_sciml_benchmarks	14.76% <ø> (ø)
python	70.31% <ø> (ø)
sbmlsuite-jax	?

Flags with carried forward coverage won't be shown. Click here to find out more.
see 4 files with indirect coverage changes

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[FFroehlich]

👍 @dweindl does this look good to you?

[dweindl]

@dweindl does this look good to you?

The example itself looks good to me, thanks.
Is it meant to be executed on GitHub actions / Read The Docs?
If so, generally preferred, please clear the output. However, I assume that urlretrieve will often fail due to rate-limiting, and we'd have to obtain those files from some place other than raw.githubusercontent.com.
If not, please rerun with a fresh kernel for clean output (first code cell starting at [1], all cells executed in order).

[dweindl]

and we'd have to obtain those files from some place other than raw.githubusercontent.com.

See PEtab-dev/libpetab-python#503 for an alternative

[socket-security]

Review the following changes in direct dependencies. Learn more about Socket for GitHub.

Diff	Package	Supply Chain Security	Vulnerability	Quality	Maintenance	License
	pypi/​petab-sciml@​0.0.1

View full report

[BSnelling]

Thanks @dweindl! I cleared the notebook outputs so it executes like the others do and updated the file fetch to use the CDN you recommended.

[dweindl]

Great, thanks. Looks good now.