Fail OpenEye checks if installed but not licensed

devtools/conda-envs/test_env.yaml

@@ -1,4 +1,4 @@
-name: test
+name: openff-fragmenter-test
 
 channels:
   - conda-forge
@@ -10,6 +10,7 @@ dependencies:
   - python
 
   - openff-toolkit-base >=0.11.0
+  - openff-utilities >=0.1.9
   - ambertools
   - rdkit
   - pydantic

openff/fragmenter/chemi.py

@@ -8,6 +8,7 @@
 from openff.fragmenter.utils import get_atom_index, get_map_index
 from openff.toolkit.topology import Molecule
 from openff.toolkit.utils import LicenseError, ToolkitUnavailableException
+from openff.utilities import MissingOptionalDependencyError, requires_oe_module
 
 logger = logging.getLogger(__name__)
 
@@ -164,6 +165,7 @@ def find_ring_systems(molecule: Molecule) -> Dict[int, int]:
     return ring_systems
 
 
+@requires_oe_module("oechem")
 def _find_oe_stereocenters(
     molecule: Molecule,
 ) -> Tuple[List[int], List[Tuple[int, int]]]:
@@ -277,7 +279,12 @@ def find_stereocenters(molecule: Molecule) -> Tuple[List[int], List[Tuple[int, i
 
     try:
         stereogenic_atoms, stereogenic_bonds = _find_oe_stereocenters(molecule)
-    except (ModuleNotFoundError, ToolkitUnavailableException, LicenseError):
+    except (
+        ModuleNotFoundError,
+        ToolkitUnavailableException,
+        LicenseError,
+        MissingOptionalDependencyError,
+    ):
         stereogenic_atoms, stereogenic_bonds = _find_rd_stereocenters(molecule)
 
     return stereogenic_atoms, stereogenic_bonds
@@ -379,6 +386,7 @@ def _extract_rd_fragment(
     return fragment
 
 
+@requires_oe_module("oechem")
 def _extract_oe_fragment(
     molecule: Molecule, atom_indices: Set[int], bond_indices: Set[Tuple[int, int]]
 ) -> Molecule:
@@ -471,7 +479,12 @@ def extract_fragment(
 
     try:
         fragment = _extract_oe_fragment(molecule, atom_indices, bond_indices)
-    except (ModuleNotFoundError, ToolkitUnavailableException, LicenseError):
+    except (
+        ModuleNotFoundError,
+        ToolkitUnavailableException,
+        LicenseError,
+        MissingOptionalDependencyError,
+    ):
         fragment = _extract_rd_fragment(molecule, atom_indices, bond_indices)
 
     # Sanity check that all atoms are still bonded

openff/fragmenter/depiction.py

@@ -6,9 +6,11 @@
 from openff.fragmenter.fragment import BondTuple, FragmentationResult
 from openff.fragmenter.utils import get_map_index
 from openff.toolkit.topology import Molecule
+from openff.utilities import MissingOptionalDependencyError, requires_oe_module
 from pkg_resources import resource_filename
 
 
+@requires_oe_module("oechem")
 def _oe_fragment_predicates(map_indices: Collection[int]):
     """Returns an atom and bond predicate which matches atoms whose map index
     appears in the specified ``map_indices`` collection"""
@@ -43,6 +45,7 @@ def CreateCopy(self):
     return PredicateAtoms(map_indices), PredicateBonds(map_indices)
 
 
+@requires_oe_module("oedepict")
 def _oe_wbo_label_display(bond_tuples: Collection[BondTuple]):
     """Returns a ``OEDisplayBondPropBase`` subclass which will label bonds with the
     specified map indices with their WBO values if present.
@@ -75,6 +78,7 @@ def CreateCopy(self):
     return LabelWibergBondOrder(bond_tuples)
 
 
+@requires_oe_module("oedepict")
 def _oe_render_parent(
     parent: Molecule,
     rotor_bonds: Optional[Collection[BondTuple]] = None,
@@ -113,6 +117,8 @@ def _oe_render_parent(
     return svg_contents.decode()
 
 
+@requires_oe_module("oedepict")
+@requires_oe_module("oechem")
 def _oe_render_fragment(
     parent: Molecule,
     fragment: Molecule,
@@ -328,7 +334,7 @@ def depict_fragments(
             for bond_tuple, fragment in fragments.items()
         ]
 
-    except ModuleNotFoundError:
+    except (ModuleNotFoundError, MissingOptionalDependencyError):
         header_svg = _rd_render_parent(parent)
         fragment_svg = [
             _rd_render_fragment(parent, fragment, bond_tuple)

openff/fragmenter/tests/test_chemi.py

@@ -22,6 +22,7 @@
     ToolkitRegistry,
 )
 from openff.units import unit
+from openff.utilities import MissingOptionalDependencyError
 
 
 def test_assign_elf10_am1_bond_orders():
@@ -151,7 +152,7 @@ def test_find_stereocenters(smiles, expected_atoms, expected_bonds, find_method)
 
     try:
         stereogenic_atoms, stereogenic_bonds = find_method(molecule)
-    except ModuleNotFoundError as e:
+    except (ModuleNotFoundError, MissingOptionalDependencyError) as e:
         pytest.skip(str(e))
 
     assert stereogenic_atoms == expected_atoms
@@ -202,7 +203,7 @@ def test_extract_fragment(smiles, atoms, bonds, expected, extract_method):
 
     try:
         fragment = extract_method(molecule, atoms, bonds)
-    except ModuleNotFoundError as e:
+    except (ModuleNotFoundError, MissingOptionalDependencyError) as e:
         pytest.skip(str(e))
 
     expected_fragment = Molecule.from_smiles(expected)

openff/fragmenter/tests/test_depiction.py

@@ -11,6 +11,7 @@
 )
 from openff.fragmenter.fragment import Fragment, FragmentationResult
 from openff.toolkit.topology import Molecule
+from openff.utilities import MissingOptionalDependencyError
 
 
 @pytest.mark.parametrize("draw_function", [_oe_render_parent, _rd_render_parent])
@@ -21,7 +22,7 @@ def test_xx_render_parent(draw_function):
                 "[C:1]([H:5])([H:6])([H:7])[C:2]([H:8])([H:9])[C:3]([H:10])([H:11])[C:4]([H:12])([H:13])([H:14])"
             )
         )
-    except ModuleNotFoundError as e:
+    except (ModuleNotFoundError, MissingOptionalDependencyError) as e:
         pytest.skip(str(e))
 
     assert isinstance(svg_contents, str)
@@ -41,7 +42,7 @@ def test_xx_render_fragment(draw_function):
             (1, 2),
         )
 
-    except ModuleNotFoundError as e:
+    except (ModuleNotFoundError, MissingOptionalDependencyError) as e:
         pytest.skip(str(e))
 
     assert isinstance(svg_contents, str)