Exception rework part 1

docs/releasehistory.md

@@ -37,6 +37,19 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
 
 ## 0.10.0 Improvements for force field fitting
 
+### Behaviors changed
+
+- [PR #1021](https://github.com/openforcefield/openforcefield/pull/1021): Renames
+  [`openff.toolkit.utils.exceptions.ParseError`](openff.toolkit.utils.exceptions.ParseError) to
+  [`openff.toolkit.utils.exceptions.SMILESParseError`](openff.toolkit.utils.exceptions.SMILESParseError) to
+  avoid a conflict with an identically-named exception in the SMIRNOFF XML parsing code.
+- [PR #1021](https://github.com/openforcefield/openforcefield/pull/1021): Renames and moves
+  [`openff.toolkit.typing.engines.smirnoff.forcefield.ParseError`](openff.toolkit.typing.engines.smirnoff.forcefield.ParseError) to
+  [`openff.toolkit.utils.exceptions.SMIRNOFFParseError`](openff.toolkit.utils.exceptions.SMIRNOFFParseError).
+  This `ParseError` is deprecated and will be removed in a future release.
+
+## Current Development
+
 ### New features and behaviors changed
 
 - [PR #1027](https://github.com/openforcefield/openforcefield/pull/1027): Corrects interconversion of Molecule objects 

openff/toolkit/tests/conftest.py

@@ -12,11 +12,6 @@
 
 """
 
-
-# =============================================================================================
-# GLOBAL IMPORTS
-# =============================================================================================
-
 import logging
 
 import pytest

openff/toolkit/tests/create_molecules.py

@@ -11,11 +11,6 @@
 
 """
 
-# =============================================================================================
-# GLOBAL IMPORTS
-# =============================================================================================
-
-
 import numpy as np
 from simtk import unit
 

openff/toolkit/tests/test_examples.py

@@ -8,10 +8,6 @@
 Test that the examples in the repo run without errors.
 """
 
-# ======================================================================
-# GLOBAL IMPORTS
-# ======================================================================
-
 import os
 import pathlib
 import re

openff/toolkit/tests/test_forcefield.py

@@ -10,10 +10,6 @@
 """
 
 
-# =============================================================================================
-# GLOBAL IMPORTS
-# =============================================================================================
-
 import copy
 import itertools
 import os
@@ -49,21 +45,25 @@
 from openff.toolkit.typing.engines.smirnoff import (
     ElectrostaticsHandler,
     ForceField,
-    FractionalBondOrderInterpolationMethodUnsupportedError,
-    IncompatibleParameterError,
     LibraryChargeHandler,
     ParameterHandler,
-    ParameterLookupError,
-    PartialChargeVirtualSitesError,
-    SMIRNOFFAromaticityError,
-    SMIRNOFFSpecError,
-    SMIRNOFFSpecUnimplementedError,
     ToolkitAM1BCCHandler,
     XMLParameterIOHandler,
     get_available_force_fields,
     vdWHandler,
 )
 from openff.toolkit.utils import get_data_file_path
+from openff.toolkit.utils.exceptions import (
+    FractionalBondOrderInterpolationMethodUnsupportedError,
+    IncompatibleParameterError,
+    NonintegralMoleculeChargeException,
+    ParameterLookupError,
+    PartialChargeVirtualSitesError,
+    SMIRNOFFAromaticityError,
+    SMIRNOFFSpecError,
+    SMIRNOFFSpecUnimplementedError,
+    UnassignedMoleculeChargeException,
+)
 from openff.toolkit.utils.toolkits import (
     AmberToolsToolkitWrapper,
     ChargeMethodUnavailableError,
@@ -2325,10 +2325,6 @@ def test_nonintegral_charge_exception(self, toolkit_registry, registry_descripti
         """Test skipping charge generation and instead getting charges from the original Molecule"""
         from simtk.openmm import app
 
-        from openff.toolkit.typing.engines.smirnoff.parameters import (
-            NonintegralMoleculeChargeException,
-        )
-
         # Create an ethanol molecule without using a toolkit
         ethanol = create_ethanol()
         ethanol.partial_charges[0] = 1.0 * unit.elementary_charge
@@ -3179,10 +3175,6 @@ def test_library_charges_dont_parameterize_molecule_because_of_incomplete_covera
         """Fail to assign charges to a molecule because not all atoms can be assigned"""
         from simtk.openmm import NonbondedForce
 
-        from openff.toolkit.typing.engines.smirnoff.parameters import (
-            UnassignedMoleculeChargeException,
-        )
-
         molecules = [Molecule.from_file(get_data_file_path("molecules/toluene.sdf"))]
         top = Topology.from_molecules(molecules)
 

openff/toolkit/tests/test_io.py

@@ -9,11 +9,6 @@
 
 """
 
-
-# =============================================================================================
-# GLOBAL IMPORTS
-# =============================================================================================
-
 import pytest
 
 from openff.toolkit.typing.engines.smirnoff.io import XMLParameterIOHandler

openff/toolkit/tests/test_molecule.py

@@ -19,10 +19,6 @@
 
 """
 
-# =============================================================================================
-# GLOBAL IMPORTS
-# =============================================================================================
-
 import copy
 import os
 import pickle

openff/toolkit/tests/test_parameters.py

@@ -9,42 +9,40 @@
 
 """
 
-
-# ======================================================================
-# GLOBAL IMPORTS
-# ======================================================================
-
 import numpy
 import pytest
 from numpy.testing import assert_almost_equal
 from simtk import unit
 
 from openff.toolkit.topology import Molecule
-from openff.toolkit.typing.engines.smirnoff import SMIRNOFFVersionError
 from openff.toolkit.typing.engines.smirnoff.parameters import (
     BondHandler,
     ChargeIncrementModelHandler,
-    DuplicateParameterError,
     GBSAHandler,
     ImproperTorsionHandler,
-    IncompatibleParameterError,
     IndexedParameterAttribute,
     LibraryChargeHandler,
-    NotEnoughPointsForInterpolationError,
     ParameterAttribute,
     ParameterHandler,
     ParameterList,
-    ParameterLookupError,
     ParameterType,
     ProperTorsionHandler,
-    SMIRNOFFSpecError,
     VirtualSiteHandler,
     _linear_inter_or_extrapolate,
     _ParameterAttributeHandler,
     vdWHandler,
 )
-from openff.toolkit.utils import IncompatibleUnitError, detach_units
+from openff.toolkit.utils import detach_units
 from openff.toolkit.utils.collections import ValidatedList
+from openff.toolkit.utils.exceptions import (
+    DuplicateParameterError,
+    IncompatibleParameterError,
+    IncompatibleUnitError,
+    NotEnoughPointsForInterpolationError,
+    ParameterLookupError,
+    SMIRNOFFSpecError,
+    SMIRNOFFVersionError,
+)
 
 # ======================================================================
 # Test ParameterAttribute descriptor

openff/toolkit/tests/test_toolkit_io.py

@@ -8,10 +8,6 @@
 
 """
 
-# =============================================================================================
-# GLOBAL IMPORTS
-# =============================================================================================
-
 import os
 import pathlib
 import sys
@@ -26,7 +22,11 @@
 from openff.toolkit.tests import create_molecules
 from openff.toolkit.tests.utils import requires_openeye, requires_rdkit
 from openff.toolkit.topology.molecule import Molecule
-from openff.toolkit.utils import OpenEyeToolkitWrapper, RDKitToolkitWrapper, exceptions
+from openff.toolkit.utils import OpenEyeToolkitWrapper, RDKitToolkitWrapper
+from openff.toolkit.utils.exceptions import (
+    SMILESParseError,
+    UndefinedStereochemistryError,
+)
 
 # ================================================================
 # Data records used for testing.
@@ -918,14 +918,14 @@ def _test_3D_sdf_keeps_hydrogens(self, mol):
 
     def test_from_file_with_undefined_stereo(self):
         with pytest.raises(
-            exceptions.UndefinedStereochemistryError,
+            UndefinedStereochemistryError,
             match=f"Unable to make OFFMol from {self.tk_mol_name}: {self.tk_mol_name} has unspecified stereochemistry",
         ):
             self.toolkit_wrapper.from_file(file_manager.chebi_1148_sdf, "sdf")
 
     def test_from_file_obj_with_undefined_stereo(self):
         with pytest.raises(
-            exceptions.UndefinedStereochemistryError,
+            UndefinedStereochemistryError,
             match=f"Unable to make OFFMol from {self.tk_mol_name}: {self.tk_mol_name} has unspecified stereochemistry",
         ):
             self.toolkit_wrapper.from_file_obj(file_obj_manager.chebi_1148_sdf, "sdf")
@@ -1155,9 +1155,7 @@ def test_parse_methane_with_explicit_Hs_and_say_they_are_explicit(self):
         assert mol.n_bonds == 4
 
     def test_parse_bad_smiles(self):
-        with pytest.raises(
-            exceptions.SMILESParseError, match="Unable to parse the SMILES string"
-        ):
+        with pytest.raises(SMILESParseError, match="Unable to parse the SMILES string"):
             mol = self.toolkit_wrapper.from_smiles("QWERT")
 
     ### Copied from test_toolkits.py
@@ -1173,7 +1171,7 @@ def test_parse_bad_smiles(self):
     )
     def test_smiles_missing_stereochemistry(self, title, smiles):
         if "unspec" in title:
-            with pytest.raises(exceptions.UndefinedStereochemistryError):
+            with pytest.raises(UndefinedStereochemistryError):
                 self.toolkit_wrapper.from_smiles(smiles)
             mol = self.toolkit_wrapper.from_smiles(smiles, allow_undefined_stereo=True)
         else:

openff/toolkit/tests/test_toolkits.py

@@ -9,9 +9,6 @@
 
 """
 
-# =============================================================================================
-# GLOBAL IMPORTS
-# =============================================================================================
 import logging
 import os
 from tempfile import NamedTemporaryFile
@@ -38,22 +35,24 @@
 )
 from openff.toolkit.topology.molecule import Molecule
 from openff.toolkit.utils import get_data_file_path
-from openff.toolkit.utils.toolkits import (
-    GLOBAL_TOOLKIT_REGISTRY,
-    AmberToolsToolkitWrapper,
-    BuiltInToolkitWrapper,
+from openff.toolkit.utils.exceptions import (
     ChargeMethodUnavailableError,
-    GAFFAtomTypeWarning,
     IncorrectNumConformersError,
     IncorrectNumConformersWarning,
     InvalidIUPACNameError,
     InvalidToolkitError,
+    ToolkitUnavailableException,
+    UndefinedStereochemistryError,
+)
+from openff.toolkit.utils.toolkits import (
+    GLOBAL_TOOLKIT_REGISTRY,
+    AmberToolsToolkitWrapper,
+    BuiltInToolkitWrapper,
+    GAFFAtomTypeWarning,
     OpenEyeToolkitWrapper,
     RDKitToolkitWrapper,
     ToolkitRegistry,
-    ToolkitUnavailableException,
     ToolkitWrapper,
-    UndefinedStereochemistryError,
 )
 
 # =============================================================================================

openff/toolkit/tests/test_topology.py

@@ -9,10 +9,6 @@
 
 """
 
-# =============================================================================================
-# GLOBAL IMPORTS
-# =============================================================================================
-
 from unittest import TestCase
 
 import numpy as np
@@ -32,11 +28,7 @@
     requires_rdkit,
 )
 from openff.toolkit.topology import (
-    DuplicateUniqueMoleculeError,
     ImproperDict,
-    InvalidBoxVectorsError,
-    InvalidPeriodicityError,
-    MissingUniqueMoleculesError,
     Molecule,
     TagSortedDict,
     Topology,
@@ -49,6 +41,12 @@
     OpenEyeToolkitWrapper,
     RDKitToolkitWrapper,
 )
+from openff.toolkit.utils.exceptions import (
+    DuplicateUniqueMoleculeError,
+    InvalidBoxVectorsError,
+    InvalidPeriodicityError,
+    MissingUniqueMoleculesError,
+)
 
 # =============================================================================================
 # UTILITY FUNCTIONS
@@ -1169,7 +1167,6 @@ def test_chemical_environments_matches_RDK(self):
     ],
 )
 def test_nth_degree_neighbors(n_degrees, num_pairs):
-    pass
     smiles = ["c1ccccc1", "N1ONON1"]
     topology = Topology.from_molecules([Molecule.from_smiles(smi) for smi in smiles])
 

openff/toolkit/tests/test_utils.py

@@ -9,10 +9,6 @@
 
 """
 
-# =============================================================================================
-# GLOBAL IMPORTS
-# =============================================================================================
-
 import ast
 import os
 
@@ -133,3 +129,16 @@ def test_sort_smirnoff_dict():
     assert smirnoff_dict == OrderedDict(
         sort_smirnoff_dict(forcefield._to_smirnoff_data())
     )
+
+
+def test_import_message_exception_raises_warning(caplog):
+    # TODO: Remove when removing MessageException
+    msg = "DEPRECATED and will be removed in a future release of the OpenFF Toolkit"
+
+    with pytest.warns(DeprecationWarning, match=msg):
+        from openff.toolkit.utils.exceptions import MessageException
+
+    with pytest.warns(None) as rec:
+        from openff.toolkit.utils.exceptions import SMILESParseError
+
+    assert len(rec) == 0

openff/toolkit/tests/test_utils_callback.py

@@ -9,17 +9,10 @@
 
 """
 
-# =====================================================================
-# GLOBAL IMPORTS
-# =====================================================================
-
 import pytest
 
-from openff.toolkit.utils.callback import (
-    Callbackable,
-    CallbackRegistrationError,
-    callback_method,
-)
+from openff.toolkit.utils.callback import Callbackable, callback_method
+from openff.toolkit.utils.exceptions import CallbackRegistrationError
 
 # =====================================================================
 # UTILITY CLASSES AND FUNCTIONS