User option to fail if model needs to be compiled

[dilpath]

e.g. in model selection, often a single superset model is compiled in advance, then many pyPESTO problems/AMICI models are loaded during model selection, by loading and customizing the superset model. If the model is not compiled in advance, this can lead to many models being compiled simultaneously into the same output directory.

The job usually fails immediately, and is easy to fix. Recently, a user reported that they forgot to compile in advance, but the jobs didn't fail immediately. Instead, the job failed after the first iteration of model selection, which took some hours. Somehow, each of their 8 parallel model selection jobs all compiled the AMICI model separately into the same directory, and were able to complete model selection, but then the next set of jobs failed, due to model import/compilation issues.

This PR allows users to set compile_=False, in the case that the user knows there must be an error if the model needs to be compiled.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (fa7c0bd) 77.78% compared to head (7ff5adf) 77.75%.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #2289      +/-   ##
===========================================
- Coverage    77.78%   77.75%   -0.03%     
===========================================
  Files          318      318              
  Lines        20511    20511              
  Branches      1436     1436              
===========================================
- Hits         15954    15948       -6     
- Misses        4554     4560       +6     
  Partials         3        3              

Flag	Coverage Δ
cpp	73.53% <ø> (-0.03%)	⬇️
cpp_python	33.99% <ø> (ø)
petab	36.40% <ø> (ø)
python	72.30% <ø> (-0.03%)	⬇️
sbmlsuite	?

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

Files	Coverage Δ
python/sdist/amici/petab/petab_import.py	66.66% <ø> (ø)

... and 2 files with indirect coverage changes

[dilpath]

I think the errors are unrelated, e.g. the 4 failing C++/Python tests are all due to

FAILED python/tests/test_bngl.py::test_compare_to_pysb_simulation[Motivating_example_cBNGL] - ValueError: ComplexPatterns that span multiple volume compartments must have these volume compartments separated by a single surface compartment.

[FFroehlich]

I think the errors are unrelated, e.g. the 4 failing C++/Python tests are all due to

FAILED python/tests/test_bngl.py::test_compare_to_pysb_simulation[Motivating_example_cBNGL] - ValueError: ComplexPatterns that span multiple volume compartments must have these volume compartments separated by a single surface compartment.

Yes, those are unrelated, will have a closer look at what's going on.

[FFroehlich]

👍

[FFroehlich]

I think the errors are unrelated, e.g. the 4 failing C++/Python tests are all due to

FAILED python/tests/test_bngl.py::test_compare_to_pysb_simulation[Motivating_example_cBNGL] - ValueError: ComplexPatterns that span multiple volume compartments must have these volume compartments separated by a single surface compartment.

Yes, those are unrelated, will have a closer look at what's going on.

hopefully fixed in pysb/pysb@52570c3

[dilpath]

hopefully fixed in pysb/pysb@52570c3

Oh nice, thanks for the quick fix there! Fine with me to leave this open until the next PySB comes out, although I'm unfamiliar with the dev cycle there.

[sonarcloud]

Quality Gate passed

Issues
0 New issues

Measures
0 Security Hotspots
No data about Coverage
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