switch user-set partial charges warning to log.info

gufe/components/explicitmoleculecomponent.py

@@ -1,4 +1,5 @@
 import json
+import logging
 import warnings
 from typing import Optional
 
@@ -34,7 +35,7 @@ def _ensure_ofe_name(mol: RDKitMol, name: str) -> str:
     return name
 
 
-def _check_partial_charges(mol: RDKitMol) -> None:
+def _check_partial_charges(mol: RDKitMol, logger=None) -> None:
     """
     Checks for the presence of partial charges.
 
@@ -82,15 +83,18 @@ def _check_partial_charges(mol: RDKitMol) -> None:
                 raise ValueError(errmsg)
 
     if np.all(np.isclose(p_chgs, 0.0)):
-        wmsg = f"Partial charges provided all equal to " "zero. These may be ignored by some Protocols."
+        wmsg = "Partial charges provided all equal to zero. These may be ignored by some Protocols."
         warnings.warn(wmsg)
     else:
-        wmsg = (
-            "Partial charges have been provided, these will "
-            "preferentially be used instead of generating new "
-            "partial charges"
-        )
-        warnings.warn(wmsg)
+        msg = "Partial charges have been provided"
+        if name := mol.GetProp("ofe-name"):
+            msg += f" for {name}"
+        msg += ", these will preferentially be used instead of generating new partial charges."
+
+        if logger is None:
+            logger = logging.getLogger(__name__)
+
+        logger.info(msg)
 
 
 class ExplicitMoleculeComponent(Component):
@@ -106,7 +110,7 @@ class ExplicitMoleculeComponent(Component):
 
     def __init__(self, rdkit: RDKitMol, name: str = ""):
         name = _ensure_ofe_name(rdkit, name)
-        _check_partial_charges(rdkit)
+        _check_partial_charges(rdkit, logger=self.logger)
         conformers = list(rdkit.GetConformers())
         if not conformers:
             raise ValueError("Molecule was provided with no conformers.")

gufe/tests/test_smallmoleculecomponent.py

@@ -12,6 +12,7 @@
 else:
     HAS_OFFTK = True
 import json
+import logging
 import os
 from unittest import mock
 
@@ -21,7 +22,7 @@
 
 import gufe
 from gufe import SmallMoleculeComponent
-from gufe.components.explicitmoleculecomponent import _ensure_ofe_name
+from gufe.components.explicitmoleculecomponent import _check_partial_charges, _ensure_ofe_name
 from gufe.tokenization import TOKENIZABLE_REGISTRY
 
 from .test_explicitmoleculecomponent import ExplicitMoleculeComponentMixin
@@ -242,15 +243,22 @@ def test_to_off_name(self, named_ethane):
 @pytest.mark.skipif(not HAS_OFFTK, reason="no openff tookit available")
 class TestSmallMoleculeComponentPartialCharges:
     @pytest.fixture(scope="function")
-    def charged_off_ethane(self, ethane):
-        off_ethane = ethane.to_openff()
+    def charged_off_ethane(self, named_ethane):
+        off_ethane = named_ethane.to_openff()
         off_ethane.assign_partial_charges(partial_charge_method="am1bcc")
         return off_ethane
 
-    def test_partial_charges_warning(self, charged_off_ethane):
-        matchmsg = "Partial charges have been provided"
-        with pytest.warns(UserWarning, match=matchmsg):
-            SmallMoleculeComponent.from_openff(charged_off_ethane)
+    def test_check_partial_charges_without_gufe_logger(self, charged_off_ethane, caplog):
+        rd_mol = charged_off_ethane.to_rdkit()
+        caplog.set_level(logging.INFO)
+        _check_partial_charges(rd_mol, logger=None)
+        assert "Partial charges have been provided for ethane, these" in caplog.text
+
+    def test_partial_charges_logging(self, charged_off_ethane, caplog):
+        caplog.set_level(logging.INFO)
+        SmallMoleculeComponent.from_openff(charged_off_ethane)
+
+        assert "Partial charges have been provided" in caplog.text
 
     def test_partial_charges_zero_warning(self, charged_off_ethane):
         charged_off_ethane.partial_charges[:] = 0 * unit.elementary_charge
@@ -271,7 +279,7 @@ def test_partial_charges_too_few_atoms(self):
         with pytest.raises(ValueError, match="Incorrect number of"):
             SmallMoleculeComponent.from_rdkit(mol)
 
-    def test_partial_charges_applied_to_atoms(self):
+    def test_partial_charges_applied_to_atoms(self, caplog):
         """
         Make sure that charges set at the molecule level
         are transferred to atoms and picked up by openFF.
@@ -280,9 +288,11 @@ def test_partial_charges_applied_to_atoms(self):
         Chem.AllChem.Compute2DCoords(mol)
         # add some fake charges at the molecule level
         mol.SetProp("atom.dprop.PartialCharge", "-1 0.25 0.25 0.25 0.25")
-        matchmsg = "Partial charges have been provided"
-        with pytest.warns(UserWarning, match=matchmsg):
-            ofe = SmallMoleculeComponent.from_rdkit(mol)
+        caplog.set_level(logging.INFO)
+
+        ofe = SmallMoleculeComponent.from_rdkit(mol)
+        assert "Partial charges have been provided" in caplog.text
+
         # convert to openff and make sure the charges are set
         off_mol = ofe.to_openff()
         assert off_mol.partial_charges is not None