Fix pytest config, warnings

[mattwthompson]

Closes #2019

• Do not always run slow tests
• Get working with pytest 9
• Consolidate config to pyproject.toml
• Clean up some warnings emitted in tests
• Clean up some repeated warnings
• Tag issue being addressed
• Add tests
• Update docstrings/documentation, if applicable
• Lint codebase
• Update changelog

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 94.17%. Comparing base (b56ac24) to head (08f2d10).

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[Copilot]

Pull request overview

This PR updates the project’s testing and packaging configuration to support newer pytest versions, consolidating legacy setup.cfg pytest settings into pyproject.toml and adjusting tests/envs to reduce warnings and improve compatibility.

Changes:

• Remove legacy pytest settings from setup.cfg and migrate pytest/coverage configuration into pyproject.toml.
• Update several tests to use updated APIs/import styles (notably OpenMM imports and topology/position handling).
• Refresh conda test environments (pytest version pinning adjustments; add pytest-timeout to additional envs).

Reviewed changes

Copilot reviewed 9 out of 9 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
setup.cfg	Removes legacy [tool:pytest] configuration (migration to pyproject.toml).
pyproject.toml	Adds pytest ini options and consolidates coverage settings; updates setuptools config stanza.
openff/toolkit/_tests/test_topology.py	Refactors imports and several tests to new construction patterns; warning cleanup.
openff/toolkit/_tests/test_parameters.py	Switches to from_mapped_smiles for mapped SMILES inputs.
openff/toolkit/_tests/test_forcefield.py	Normalizes expected exception-match metadata in a parameter matrix.
devtools/conda-envs/test_env.yaml	Adjusts dependency constraints and pytest pinning.
devtools/conda-envs/rdkit.yaml	Adds pytest-timeout.
devtools/conda-envs/rdkit-examples.yaml	Adds pytest-timeout.
devtools/conda-envs/openeye.yaml	Adds pytest-timeout.

Comments suppressed due to low confidence (1)

openff/toolkit/_tests/test_forcefield.py:723

• partial_charge_method_resolution_matrix mostly uses exception_match: None when no exception is expected, but this OpenEye/Gasteiger entry still uses an empty string. For consistency (and to avoid confusion about whether the field is meaningful when exception is None), consider switching this to None as well (or omitting the key when exception is None).

        "toolkit": OpenEyeToolkitWrapper,
        "partial_charge_method": "Gasteiger",
        "exception": None,
        "exception_match": "",
    },

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[mattwthompson]

See any recent logs with

 /home/runner/micromamba/envs/openff-toolkit-test/lib/python3.11/site-packages/_pytest/raises.py:624: PytestWarning: matching against an empty string will *always* pass. If you want to check for an empty message you need to pass '^$'. If you don't want to match you should pass `None` or leave out the parameter.

[mattwthompson]

This test takes 100 seconds on my system, confusingly

$ pytest --durations=10 openff/toolkit/_tests/test_topology.py --runslow
===================================================== slowest 10 durations ======================================================
113.81s call     openff/toolkit/_tests/test_topology.py::TestTopologyVisaulization::test_visualize_basic
1.36s call     openff/toolkit/_tests/test_topology.py::TestTopologyVisaulization::test_missing_positions
0.47s call     openff/toolkit/_tests/test_topology.py::TestTopology::test_from_pdb
0.43s call     openff/toolkit/_tests/test_topology.py::TestTopology::test_add_molecules
0.42s call     openff/toolkit/_tests/test_topology.py::TestTopology::test_chemical_environments_matches_OE
0.37s call     openff/toolkit/_tests/test_topology.py::TestTopology::test_from_pdb_input_types
0.36s call     openff/toolkit/_tests/test_topology.py::TestTopology::test_from_to_openmm_hierarchy_metadata
0.29s call     openff/toolkit/_tests/test_topology.py::TestTopology::test_from_openmm
0.25s call     openff/toolkit/_tests/test_topology.py::TestTopology::test_from_openmm_virtual_sites
0.23s setup    openff/toolkit/_tests/test_topology.py::TestTopologyPositions::test_clear_and_re_set_positions
==================================== 173 passed, 2 skipped, 15 warnings in 126.56s (0:02:06) ====================================

Possibly PDB writing is slow ... ?

openff-toolkit/openff/toolkit/utils/_viz.py

Line 102 in b56ac24

self.topology.to_file(f, file_format=self.ext)

Can open a new issue