Squashing unintended test warnings due to model recombination rate

[gregorgorjanc]

As triggered by #1598 (comment) I looked into the test warnings due to model specific mutation and recombination rate.

One test warning was not intended, so I fixed that.

I am a bit confused what to do with these ones:

> python3 -m pytest tests/test_models.py
========================================================================= test session starts =========================================================================
platform darwin -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0
rootdir: /Users/ggorjanc/Storages/GitBox/popsim/stdpopsim/stdpopsim_fork
configfile: setup.cfg
plugins: xdist-3.6.1
4 workers [275 items]   
............................................................................................................................................................... [ 57%]
....................................................................................................................                                            [100%]
========================================================================== warnings summary ===========================================================================
tests/test_models.py::TestBosTauHolsteinFriesian_1M13::test_simulation_runs
  /Users/ggorjanc/Storages/GitBox/popsim/stdpopsim/stdpopsim_fork/stdpopsim/engines.py:125: UserWarning: The demographic model has recombination rate 1e-08, but this simulation used the contig's recombination rate 0.0. Patterns of linkage may be different than expected for this species. For details see documentation at https://popsim-consortium.github.io/stdpopsim-docs/stable/tutorial.html
    warnings.warn(

tests/test_models.py::TestBosTauAngus_1B16::test_simulation_runs
  /Users/ggorjanc/Storages/GitBox/popsim/stdpopsim/stdpopsim_fork/stdpopsim/engines.py:125: UserWarning: The demographic model has recombination rate 5e-09, but this simulation used the contig's recombination rate 0.0. Patterns of linkage may be different than expected for this species. For details see documentation at https://popsim-consortium.github.io/stdpopsim-docs/stable/tutorial.html
    warnings.warn(

tests/test_models.py::TestBosTauHolsteinFriesian_1B16::test_simulation_runs
  /Users/ggorjanc/Storages/GitBox/popsim/stdpopsim/stdpopsim_fork/stdpopsim/engines.py:125: UserWarning: The demographic model has recombination rate 3.66e-09, but this simulation used the contig's recombination rate 0.0. Patterns of linkage may be different than expected for this species. For details see documentation at https://popsim-consortium.github.io/stdpopsim-docs/stable/tutorial.html
    warnings.warn(

tests/test_models.py::TestBosTauFleckvieh_1B16::test_simulation_runs
  /Users/ggorjanc/Storages/GitBox/popsim/stdpopsim/stdpopsim_fork/stdpopsim/engines.py:125: UserWarning: The demographic model has recombination rate 3.89e-09, but this simulation used the contig's recombination rate 0.0. Patterns of linkage may be different than expected for this species. For details see documentation at https://popsim-consortium.github.io/stdpopsim-docs/stable/tutorial.html
    warnings.warn(

tests/test_models.py::TestBosTauJersey_1B16::test_simulation_runs
  /Users/ggorjanc/Storages/GitBox/popsim/stdpopsim/stdpopsim_fork/stdpopsim/engines.py:125: UserWarning: The demographic model has recombination rate 4.58e-09, but this simulation used the contig's recombination rate 0.0. Patterns of linkage may be different than expected for this species. For details see documentation at https://popsim-consortium.github.io/stdpopsim-docs/stable/tutorial.html
    warnings.warn(

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=================================================================== 275 passed, 5 warnings in 1.06s ===================================================================

As indicated by @nspope these seem to come from mitochondria (that have rec rate of 0), but I am getting lost in the code of how these tests are autogenerated and called. Can anyone suggest what I could do to capture these tests - they are making noise that we probably don't want?

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.84%. Comparing base (ff79d8d) to head (02e63ee).
Report is 4 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #1626   +/-   ##
=======================================
  Coverage   99.84%   99.84%           
=======================================
  Files         130      130           
  Lines        4416     4416           
  Branches      608      608           
=======================================
  Hits         4409     4409           
  Misses          3        3           
  Partials        4        4           

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[nspope]

If the warnings are intended, then they can be filtered with pytest, by adding the annotation

@pytest.mark.filterwarnings("ignore::UserWarning")

above the test function (grep for "filterwarnings" in tests/*py to see examples).

Or maybe it's be better to be more specific, in case a UserWarning comes up in the future that is unintended (that we would want the tests to make obvious). So we could match the starting text,

@pytest.mark.filterwarnings("ignore: The demographic model has recombination rate")

[petrelharp]

Thanks for the cleanup!