Switch to using skip_if_missing

[mikemhenry]

This PR unifies how we skip tests.

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• Added a news entry

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• I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

[github-actions]

No API break detected ✅

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 92.89%. Comparing base (e48d641) to head (b25674e).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1640      +/-   ##
==========================================
- Coverage   95.33%   92.89%   -2.45%     
==========================================
  Files         183      183              
  Lines       15762    15779      +17     
==========================================
- Hits        15027    14658     -369     
- Misses        735     1121     +386     

Flag	Coverage Δ
fast-tests	92.89% <100.00%> (?)
slow-tests	?

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[atravitz]

I agree with unification, but I would generally prefer we use a built-in pytest functionality over an openff utils dependency. is there a benefit to openff's implementation here?

[mikemhenry]

It started with me thinking that pytest.importskip was deprecated in 8.3, BUT a closer read is that the behavior of how it handles ImportError differently than ModuleNotFoundError

I like how the openff-utils version only skips on a ModuleNotFoundError and instead would let an ImportError bubble up. I also like how the openff-utils version is a decorator where the pytest version should really be used like this:

np = pytest.importskip("numpy")

def test_cos(rad):
    assert np.cos(0) == 1

so we were not really using it correctly (and often our tests don't really have an import of the optinal package so it looks a bit weird to have pytest.importskip("numpy") inside each test we want to skip).

I am happy to switch to using the built in pytest version, it has some nice things like a minversion arg so if we had a test that needs a newer version of a package but we still supported older versions, this method would just work (assuming we had 2 CI legs testing the new and old version).

I am not really worried about the openff-utilities dep since other packages need it as well:

 openff-interchange-base 0.4.8   pyhd8ed1ab_1   openff-utilities >=0.1.5 conda-forge noarch
 openff-toolkit-base     0.17.1  pyhd8ed1ab_0   openff-utilities         conda-forge noarch
 openff-units            0.3.1   pyhd8ed1ab_2   openff-utilities         conda-forge noarch

[atravitz]

Thanks for articulating this @mikemhenry - I think the benefits (especially decorator) of openff utils is worth it here (and probably why openff added it in the first place 😄) i'm fine with this solution!

[mikemhenry]

As a bonus, b/c we switch to this method, the output looks like this now:

$ pytest -v -k perses                                                                                                                                                       
==================================================================================== test session starts =====================================================================================
platform linux -- Python 3.13.9, pytest-8.4.2, pluggy-1.6.0 -- /home/mmh/micromamba/envs/openfe-1.7.0/bin/python3.13
cachedir: .pytest_cache
rootdir: /home/mmh/Projects/openfe
configfile: pyproject.toml
plugins: datadir-1.8.0, anyio-4.11.0, regressions-2.8.3
collected 1513 items / 1506 deselected / 7 selected                                                                                                                                          

openfe/tests/setup/atom_mapping/test_perses_atommapper.py::test_simple SKIPPED (Package perses is required, but was not found.)                                                        [ 14%]
openfe/tests/setup/atom_mapping/test_perses_atommapper.py::test_generator_length SKIPPED (Package perses is required, but was not found.)                                              [ 28%]
openfe/tests/setup/atom_mapping/test_perses_atommapper.py::test_empty_atommappings SKIPPED (Package perses is required, but was not found.)                                            [ 42%]
openfe/tests/setup/atom_mapping/test_perses_atommapper.py::test_dict_round_trip SKIPPED (Package perses is required, but was not found.)                                               [ 57%]
openfe/tests/setup/atom_mapping/test_perses_scorers.py::test_perses_normalization_not_using_positions SKIPPED (Package perses is required, but was not found.)                         [ 71%]
openfe/tests/setup/atom_mapping/test_perses_scorers.py::test_perses_not_implemented_position_using SKIPPED (Package perses is required, but was not found.)                            [ 85%]
openfe/tests/setup/atom_mapping/test_perses_scorers.py::test_perses_regression SKIPPED (Package perses is required, but was not found.)                                                [100%]

instead of

$ pytest -v -k perses                                                                                                                                                       
==================================================================================== test session starts =====================================================================================
platform linux -- Python 3.13.9, pytest-8.4.2, pluggy-1.6.0 -- /home/mmh/micromamba/envs/openfe-1.7.0/bin/python3.13
cachedir: .pytest_cache
rootdir: /home/mmh/Projects/openfe
configfile: pyproject.toml
plugins: datadir-1.8.0, anyio-4.11.0, regressions-2.8.3
collected 1500 items / 1500 deselected / 3 skipped / 0 selected