Remove openff.toolkit.typing.chemistry, attempt 2 (#1664)

* Revert "Revert "Remove `openff.toolkit.typing.chemistry` (#1509)" (#1663)" This reverts commit 1456fe0. * update releasehistory
openforcefield · Jul 31, 2023 · 794b699 · 794b699
1 parent b7f33e0
commit 794b699
Show file tree

Hide file tree

Showing 8 changed files with 3 additions and 519 deletions.
diff --git a/docs/releasehistory.md b/docs/releasehistory.md
@@ -10,6 +10,7 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
 ## Current development
 
 ### API-breaking changes
+- [PR #1664](https://github.com/openforcefield/openff-toolkit/pull/1664): Removes `ChemicalEnvironment` and the entire `openff.toolkit.typing.chemistry` submodule, which was deprecated in 0.12.0.
 
 ### Behavior changes
 - [PR #1675](https://github.com/openforcefield/openff-toolkit/pull/1675): Makes InChI parsing failures more informative and gives them their own exception type, `InChIParseError`.

diff --git a/docs/typing.rst b/docs/typing.rst
@@ -3,19 +3,6 @@
 Force field typing tools
 ========================
 
-Chemical environments
----------------------
-
-Tools for representing and operating on chemical environments
-
-.. currentmodule:: openff.toolkit.typing.chemistry
-.. autosummary::
-    :nosignatures:
-    :toctree: api/generated/
-
-    ChemicalEnvironment
-
-
 Force field typing engines
 --------------------------
 

diff --git a/openff/toolkit/_tests/test_chemicalenvironment.py b/openff/toolkit/_tests/test_chemicalenvironment.py
diff --git a/openff/toolkit/_tests/test_molecule.py b/openff/toolkit/_tests/test_molecule.py
@@ -3207,13 +3207,6 @@ def test_add_atoms_and_bonds(self, molecule):
 
         assert molecule == molecule_copy
 
-    def test_chemical_environment_old_arg(self):
-        from openff.toolkit.typing.chemistry import ChemicalEnvironment
-
-        molecule = create_ethanol()
-        with pytest.raises(ValueError, match="'query' must be a SMARTS"):
-            molecule.chemical_environment_matches(ChemicalEnvironment("[*:1]"))
-
     @requires_openeye
     def test_chemical_environment_matches_OE(self):
         """Test chemical environment matches"""

diff --git a/openff/toolkit/_tests/test_parameters.py b/openff/toolkit/_tests/test_parameters.py
@@ -820,25 +820,6 @@ def test_create(self):
         p2 = ParameterType(smirks="[#1:1]")
         ParameterList([p1, p2])
 
-    @pytest.mark.wip(
-        reason="Until ChemicalEnvironment won't be refactored to use the ToolkitRegistry "
-        "API, the smirks assignment will fail with RDKit."
-    )
-    def test_getitem(self):
-        """Test ParameterList __getitem__ overloading."""
-        p1 = ParameterType(smirks="[*:1]")
-        p2 = ParameterType(smirks="[#1:1]")
-        parameters = ParameterList([p1, p2])
-        assert parameters[0] == p1
-        assert parameters[1] == p2
-        assert parameters[p1.smirks] == p1
-        assert parameters[p2.smirks] == p2
-
-        # Note that this call access __getitem__, not __setitem__.
-        parameters["[*:1]"].smirks = "[*X4:1]"
-        assert parameters[0].smirks == "[*X4:1]"
-        assert p1.smirks == "[*X4:1]"
-
     def test_index(self):
         """
         Tests the ParameterList.index() function by attempting lookups by SMIRKS and by ParameterType equivalence.

diff --git a/openff/toolkit/topology/molecule.py b/openff/toolkit/topology/molecule.py
@@ -3531,26 +3531,21 @@ def chemical_environment_matches(
              ``chemical_environment_matches``
 
         """
-        if isinstance(query, str):
-            smirks = query
-        else:
-            raise ValueError("'query' must be a SMARTS/SMIRKS string")
-
         # Use specified cheminformatics toolkit to determine matches with specified aromaticity model
         # TODO: Simplify this by requiring a toolkit registry for the molecule?
         # TODO: Do we have to pass along an aromaticity model?
         if isinstance(toolkit_registry, ToolkitRegistry):
             matches = toolkit_registry.call(
                 "find_smarts_matches",
                 self,
-                smirks,
+                query,
                 unique=unique,
                 raise_exception_types=[],
             )
         elif isinstance(toolkit_registry, ToolkitWrapper):
             matches = toolkit_registry.find_smarts_matches(  # type: ignore[attr-defined]
                 self,
-                smirks,
+                query,
                 unique=unique,
             )
         else:

diff --git a/openff/toolkit/typing/chemistry/__init__.py b/openff/toolkit/typing/chemistry/__init__.py