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Fix pytest config, warnings #2170

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Fix pytest config, warnings #2170

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2475c47
Fix some pytest warnings
mattwthompson Apr 7, 2026
756b825
Sync test dependencies across environments
mattwthompson Apr 7, 2026
36dc556
Sync test dependencies across environments
mattwthompson Apr 7, 2026
331351c
Apply suggestions from code review
mattwthompson Apr 7, 2026
3bcf7dd
Run "slow" tests only on cron jobs
mattwthompson Apr 9, 2026
9364328
Merge remote-tracking branch 'upstream/fix-pytest-config' into fix-py…
mattwthompson Apr 9, 2026
cfd65a8
Avoid another warning
mattwthompson Apr 9, 2026
08f2d10
Have RDKit when required
mattwthompson Apr 9, 2026
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5 changes: 3 additions & 2 deletions .github/workflows/CI.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -142,8 +142,9 @@ jobs:
PYTEST_ARGS+=" --ignore=openff/toolkit/_tests/test_examples.py"
PYTEST_ARGS+=" --ignore=openff/toolkit/_tests/test_links.py"

# TODO: Flip back to schedule condition before merge
PYTEST_ARGS+=" --runslow"
if [[ "$GITHUB_EVENT_NAME" == "schedule" ]]; then
PYTEST_ARGS+=" --runslow"
fi

python -m pytest -x --durations=20 $PYTEST_ARGS $COV openff/toolkit/_tests

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1 change: 1 addition & 0 deletions devtools/conda-envs/openeye.yaml
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Expand Up @@ -29,6 +29,7 @@ dependencies:
- pytest-cov
- pytest-xdist
- pytest-rerunfailures
- pytest-timeout
- pyyaml
- toml
- bson
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1 change: 1 addition & 0 deletions devtools/conda-envs/rdkit-examples.yaml
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Expand Up @@ -32,6 +32,7 @@ dependencies:
- pytest =8
- pytest-xdist
- pytest-rerunfailures
- pytest-timeout
- pyyaml
- toml
- bson
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1 change: 1 addition & 0 deletions devtools/conda-envs/rdkit.yaml
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Expand Up @@ -30,6 +30,7 @@ dependencies:
- pytest-cov
- pytest-xdist
- pytest-rerunfailures
- pytest-timeout
- pyyaml
- toml
- bson
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4 changes: 2 additions & 2 deletions devtools/conda-envs/test_env.yaml
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Expand Up @@ -14,7 +14,7 @@ dependencies:
- xmltodict <=1.0.2
- python-constraint
- openmm >=7.6
- openff-forcefields >=2023.05.1
- openff-forcefields >=2025
- openff-units
- openff-amber-ff-ports
- openff-utilities >=0.1.5
Expand All @@ -30,7 +30,7 @@ dependencies:

- openeye-toolkits
# Test-only/optional/dev/typing
- pytest =8
- pytest
- pytest-cov
- pytest-xdist
- pytest-rerunfailures
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18 changes: 9 additions & 9 deletions openff/toolkit/_tests/test_forcefield.py
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Expand Up @@ -695,25 +695,25 @@ def generate_monatomic_ions():
"toolkit": AmberToolsToolkitWrapper,
"partial_charge_method": "AM1-Mulliken",
"exception": None,
"exception_match": "",
"exception_match": None,
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@mattwthompson mattwthompson Apr 9, 2026

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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.

},
{
"toolkit": AmberToolsToolkitWrapper,
"partial_charge_method": "Gasteiger",
"exception": None,
"exception_match": "",
"exception_match": None,
},
{
"toolkit": AmberToolsToolkitWrapper,
"partial_charge_method": "Madeup-ChargeMethod",
"exception": ChargeMethodUnavailableError,
"exception_match": "",
"exception_match": None,
},
{
"toolkit": OpenEyeToolkitWrapper,
"partial_charge_method": "AM1-Mulliken",
"exception": None,
"exception_match": "",
"exception_match": None,
},
{
"toolkit": OpenEyeToolkitWrapper,
Expand All @@ -725,31 +725,31 @@ def generate_monatomic_ions():
"toolkit": OpenEyeToolkitWrapper,
"partial_charge_method": "MMFF94",
"exception": None,
"exception_match": "",
"exception_match": None,
},
{
"toolkit": OpenEyeToolkitWrapper,
"partial_charge_method": "am1bcc",
"exception": None,
"exception_match": "",
"exception_match": None,
},
{
"toolkit": OpenEyeToolkitWrapper,
"partial_charge_method": "am1bccnosymspt",
"exception": None,
"exception_match": "",
"exception_match": None,
},
{
"toolkit": OpenEyeToolkitWrapper,
"partial_charge_method": "am1bccelf10",
"exception": None,
"exception_match": "",
"exception_match": None,
},
{
"toolkit": OpenEyeToolkitWrapper,
"partial_charge_method": "Madeup-ChargeMethod",
"exception": ChargeMethodUnavailableError,
"exception_match": "",
"exception_match": None,
},
]

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4 changes: 2 additions & 2 deletions openff/toolkit/_tests/test_nagl.py
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Original file line number Diff line number Diff line change
Expand Up @@ -95,8 +95,8 @@ def test_atom_order_dependence(self):
)

numpy.testing.assert_allclose(
forward.partial_charges,
reverse.partial_charges[::-1],
forward.partial_charges.m,
reverse.partial_charges.m[::-1],
atol=1e-7,
)

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2 changes: 1 addition & 1 deletion openff/toolkit/_tests/test_parameters.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2202,7 +2202,7 @@ def test_validate_found_match(
):
if unsafe_vsites:
monkeypatch.setenv("OPENFF_UNSAFE_VSITES", "1")
molecule = Molecule.from_smiles(smiles, allow_undefined_stereo=True)
molecule = Molecule.from_mapped_smiles(smiles, allow_undefined_stereo=True)
topology: Topology = molecule.to_topology()

atoms = {i: atom for i, atom in enumerate(topology.atoms)}
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