From 70406f845dc35e7a9e3baa570dd6a9c4dfaec00e Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Thu, 15 Oct 2026 11:36:43 -0700
Subject: [PATCH 1/9] update qcportal pin to >=0.70 in CI

---
 devtools/conda-envs/examples.yaml            | 2 +-
 devtools/conda-envs/test_env.yaml            | 2 +-
 devtools/conda-envs/test_env_no_openeye.yaml | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/devtools/conda-envs/examples.yaml b/devtools/conda-envs/examples.yaml
index 488353266..089d5ea11 100644
--- a/devtools/conda-envs/examples.yaml
+++ b/devtools/conda-envs/examples.yaml
@@ -32,7 +32,7 @@ dependencies:
   - msgpack-python
   - pydantic =2
   - qcelemental
-  - qcportal >=0.50
+  - qcportal >=0.70
   - qcengine
   - nbval
   - mdtraj
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index d7e8f98d3..bbdde817d 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -36,7 +36,7 @@ dependencies:
   - msgpack-python
   - pydantic =2
   - qcelemental
-  - qcportal >=0.50
+  - qcportal >=0.70
   - qcengine
   - nglview
   - mdtraj
diff --git a/devtools/conda-envs/test_env_no_openeye.yaml b/devtools/conda-envs/test_env_no_openeye.yaml
index ccb17fca3..05fb9ab67 100644
--- a/devtools/conda-envs/test_env_no_openeye.yaml
+++ b/devtools/conda-envs/test_env_no_openeye.yaml
@@ -34,7 +34,7 @@ dependencies:
   - msgpack-python
   - pydantic =2
   - qcelemental
-  - qcportal >=0.50
+  - qcportal >=0.70
   - qcengine
   - nglview
   - pip:

From 48073adc58ea703846a03139e53fa18fcc145a86 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 15 Oct 2026 18:37:19 +0000
Subject: [PATCH 2/9] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 openff/toolkit/topology/molecule.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/openff/toolkit/topology/molecule.py b/openff/toolkit/topology/molecule.py
index d50301b83..862fbf30f 100644
--- a/openff/toolkit/topology/molecule.py
+++ b/openff/toolkit/topology/molecule.py
@@ -1170,7 +1170,14 @@ def to_dict(self) -> dict:
         # https://mypy.readthedocs.io/en/latest/typed_dict.html#typeddict
         molecule_dict: dict[
             str,
-            str | bytes | dict[str, Any] | list[str] | list[bytes] | list[HierarchyElement] | list[dict[str, Any]] | None,
+            str
+            | bytes
+            | dict[str, Any]
+            | list[str]
+            | list[bytes]
+            | list[HierarchyElement]
+            | list[dict[str, Any]]
+            | None,
         ] = dict()
         molecule_dict["name"] = self._name
 

From 53bc256a8280265af232d07c9513956907596064 Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Thu, 15 Oct 2026 11:53:16 -0700
Subject: [PATCH 3/9] define mypy and typing deps in conda section so their
 deps aren't removed when nagl is uninstalled

---
 devtools/conda-envs/test_env.yaml            | 14 +++++++-------
 devtools/conda-envs/test_env_no_openeye.yaml | 14 +++++++-------
 2 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index bbdde817d..7b951359a 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -41,12 +41,12 @@ dependencies:
   - nglview
   - mdtraj
   - nbval
+  - mypy =2
+  - types-setuptools
+  - types-toml
+  - types-PyYAML
+  - types-networkx
+  - types-xmltodict
+  - types-cachetools
   - pip:
-    - mypy ==2
-    - types-setuptools
-    - types-toml
-    - types-PyYAML
-    - types-networkx
-    - types-xmltodict
-    - types-cachetools
     - mongo-types
diff --git a/devtools/conda-envs/test_env_no_openeye.yaml b/devtools/conda-envs/test_env_no_openeye.yaml
index 05fb9ab67..d9b0d068c 100644
--- a/devtools/conda-envs/test_env_no_openeye.yaml
+++ b/devtools/conda-envs/test_env_no_openeye.yaml
@@ -37,12 +37,12 @@ dependencies:
   - qcportal >=0.70
   - qcengine
   - nglview
+  - mypy =2
+  - types-setuptools
+  - types-toml
+  - types-PyYAML
+  - types-networkx
+  - types-xmltodict
+  - types-cachetools
   - pip:
-    - mypy ==2
-    - types-setuptools
-    - types-toml
-    - types-PyYAML
-    - types-networkx
-    - types-xmltodict
-    - types-cachetools
     - mongo-types

From a7d1d4cd4391f8ff8189a294d0833338d0a953ab Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Thu, 15 Oct 2026 12:15:26 -0700
Subject: [PATCH 4/9] switch deps from python-constraint to python-constraint2
 per https://github.com/conda-forge/openff-toolkit-feedstock/pull/135

---
 devtools/conda-envs/examples.yaml            | 2 +-
 devtools/conda-envs/test_env.yaml            | 2 +-
 devtools/conda-envs/test_env_no_openeye.yaml | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/devtools/conda-envs/examples.yaml b/devtools/conda-envs/examples.yaml
index 089d5ea11..e58fa7f53 100644
--- a/devtools/conda-envs/examples.yaml
+++ b/devtools/conda-envs/examples.yaml
@@ -9,7 +9,7 @@ dependencies:
   - networkx
   - cachetools
   - xmltodict
-  - python-constraint
+  - python-constraint2
   - openmm >=7.6
   - openff-forcefields >=2025
   - openff-amber-ff-ports >=0.0.3
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index 7b951359a..b9a27db40 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -9,7 +9,7 @@ dependencies:
   - networkx
   - cachetools
   - xmltodict
-  - python-constraint
+  - python-constraint2
   - openmm >=7.6
   - openff-forcefields >=2023.05.1
   - openff-units
diff --git a/devtools/conda-envs/test_env_no_openeye.yaml b/devtools/conda-envs/test_env_no_openeye.yaml
index d9b0d068c..6a87ec25f 100644
--- a/devtools/conda-envs/test_env_no_openeye.yaml
+++ b/devtools/conda-envs/test_env_no_openeye.yaml
@@ -9,7 +9,7 @@ dependencies:
   - networkx
   - cachetools
   - xmltodict
-  - python-constraint
+  - python-constraint2
   - openmm >=7.6
   - openff-forcefields >=2023.05.1
   - openff-units

From 7912a5b1dc3c75ea289d0fc9da558410c8cc89d1 Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Thu, 15 Oct 2026 12:37:14 -0700
Subject: [PATCH 5/9] revert to normal python-constraint

---
 devtools/conda-envs/examples.yaml            | 2 +-
 devtools/conda-envs/test_env.yaml            | 2 +-
 devtools/conda-envs/test_env_no_openeye.yaml | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/devtools/conda-envs/examples.yaml b/devtools/conda-envs/examples.yaml
index e58fa7f53..089d5ea11 100644
--- a/devtools/conda-envs/examples.yaml
+++ b/devtools/conda-envs/examples.yaml
@@ -9,7 +9,7 @@ dependencies:
   - networkx
   - cachetools
   - xmltodict
-  - python-constraint2
+  - python-constraint
   - openmm >=7.6
   - openff-forcefields >=2025
   - openff-amber-ff-ports >=0.0.3
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index b9a27db40..7b951359a 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -9,7 +9,7 @@ dependencies:
   - networkx
   - cachetools
   - xmltodict
-  - python-constraint2
+  - python-constraint
   - openmm >=7.6
   - openff-forcefields >=2023.05.1
   - openff-units
diff --git a/devtools/conda-envs/test_env_no_openeye.yaml b/devtools/conda-envs/test_env_no_openeye.yaml
index 6a87ec25f..d9b0d068c 100644
--- a/devtools/conda-envs/test_env_no_openeye.yaml
+++ b/devtools/conda-envs/test_env_no_openeye.yaml
@@ -9,7 +9,7 @@ dependencies:
   - networkx
   - cachetools
   - xmltodict
-  - python-constraint2
+  - python-constraint
   - openmm >=7.6
   - openff-forcefields >=2023.05.1
   - openff-units

From d952de9ed9291cd333dff7ccfef7ba7ca9a4c6e2 Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Thu, 15 Oct 2026 13:29:58 -0700
Subject: [PATCH 6/9] ruff suggested fixes

---
 README.md                           | 8 +++++---
 docs/api/toolkits.md                | 5 +----
 openff/toolkit/topology/molecule.py | 4 ++--
 openff/toolkit/topology/topology.py | 4 ++--
 4 files changed, 10 insertions(+), 11 deletions(-)

diff --git a/README.md b/README.md
index a5c2d3b7b..6c031d884 100644
--- a/README.md
+++ b/README.md
@@ -56,16 +56,19 @@ SMIRNOFF force fields can be parsed by the `ForceField` class, which offers meth
 # Load a molecule into the OpenFF Molecule object
 from openff.toolkit import Molecule
 from openff.toolkit.utils import get_data_file_path
-sdf_file_path = get_data_file_path('molecules/ethanol.sdf')
+
+sdf_file_path = get_data_file_path("molecules/ethanol.sdf")
 molecule = Molecule.from_file(sdf_file_path)
 
 # Create an OpenFF Topology object from the molecule
 from openff.toolkit import Topology
+
 topology = Topology.from_molecules(molecule)
 
 # Load the latest OpenFF force field release: version 2.1.0, codename "Sage"
 from openff.toolkit import ForceField
-forcefield = ForceField('openff-2.3.0.offxml')
+
+forcefield = ForceField("openff-2.3.0.offxml")
 
 
 # Create an Interchange object for representations in other formats
@@ -73,7 +76,6 @@ interchange = forcefield.create_interchange(topology)
 
 # Create an OpenMM system representing the molecule with SMIRNOFF-applied parameters
 openmm_system = interchange.to_openmm(topology)
-
 ```
 
 Detailed examples of using SMIRNOFF with the toolkit can be found [in the documentation](https://open-forcefield-toolkit.readthedocs.io/en/stable/examples.html).
diff --git a/docs/api/toolkits.md b/docs/api/toolkits.md
index e69865304..7e418fe52 100644
--- a/docs/api/toolkits.md
+++ b/docs/api/toolkits.md
@@ -65,11 +65,8 @@ The [`toolkit_registry_manager`] context manager allows `GLOBAL_TOOLKIT_REGISTRY
 >>> from openff.toolkit.utils import toolkit_registry_manager
 >>> print(len(GLOBAL_TOOLKIT_REGISTRY.registered_toolkits))
 5
->>> with toolkit_registry_manager(
-...     ToolkitRegistry([RDKitToolkitWrapper(), AmberToolsToolkitWrapper()])
-... ):
+>>> with toolkit_registry_manager(ToolkitRegistry([RDKitToolkitWrapper(), AmberToolsToolkitWrapper()])):
 ...     print(len(GLOBAL_TOOLKIT_REGISTRY.registered_toolkits))
-...
 2
 
 ```
diff --git a/openff/toolkit/topology/molecule.py b/openff/toolkit/topology/molecule.py
index 862fbf30f..3d1f04851 100644
--- a/openff/toolkit/topology/molecule.py
+++ b/openff/toolkit/topology/molecule.py
@@ -298,7 +298,7 @@ def add_bond(self, bond: "Bond"):
 
         self._bonds.append(bond)
 
-    def to_dict(self) -> dict[str, None | str | int | bool | dict[Any, Any]]:
+    def to_dict(self) -> dict[str, str | int | bool | dict[Any, Any] | None]:
         """Return a dict representation of the :class:`Atom` class instance.
 
         Output dictionary keys and values align with parameters used to initialize
@@ -1960,7 +1960,7 @@ def are_isomorphic(
         bond_stereochemistry_matching: bool = True,
         strip_pyrimidal_n_atom_stereo: bool = True,
         toolkit_registry: TKR = GLOBAL_TOOLKIT_REGISTRY,
-    ) -> tuple[bool, None | dict[int, int]]:
+    ) -> tuple[bool, dict[int, int] | None]:
         """
         Determine if ``mol1`` is isomorphic to ``mol2``.
 
diff --git a/openff/toolkit/topology/topology.py b/openff/toolkit/topology/topology.py
index ea8e56bee..8a7eeaa4e 100644
--- a/openff/toolkit/topology/topology.py
+++ b/openff/toolkit/topology/topology.py
@@ -1329,7 +1329,7 @@ def from_openmm(
         cls,
         openmm_topology: "openmm.app.Topology",
         unique_molecules: Iterable[FrozenMolecule] | None = None,
-        positions: Union[None, Quantity, "OMMQuantity"] = None,
+        positions: Union[Quantity, "OMMQuantity", None] = None,
     ) -> "Topology":
         """
         Construct an OpenFF Topology object from an OpenMM Topology object.
@@ -2124,7 +2124,7 @@ def from_mdtraj(
         cls,
         mdtraj_topology: "mdtraj.Topology",
         unique_molecules: Iterable[MoleculeLike] | None = None,
-        positions: Union[None, "OMMQuantity", Quantity] = None,
+        positions: Union["OMMQuantity", Quantity, None] = None,
     ):
         """
         Construct an OpenFF ``Topology`` from an MDTraj ``Topology``

From 928f648c1fba15bee172ae3fa09fecfacd8cba40 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 15 Oct 2026 20:30:12 +0000
Subject: [PATCH 7/9] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 docs/api/toolkits.md | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/docs/api/toolkits.md b/docs/api/toolkits.md
index 7e418fe52..e69865304 100644
--- a/docs/api/toolkits.md
+++ b/docs/api/toolkits.md
@@ -65,8 +65,11 @@ The [`toolkit_registry_manager`] context manager allows `GLOBAL_TOOLKIT_REGISTRY
 >>> from openff.toolkit.utils import toolkit_registry_manager
 >>> print(len(GLOBAL_TOOLKIT_REGISTRY.registered_toolkits))
 5
->>> with toolkit_registry_manager(ToolkitRegistry([RDKitToolkitWrapper(), AmberToolsToolkitWrapper()])):
+>>> with toolkit_registry_manager(
+...     ToolkitRegistry([RDKitToolkitWrapper(), AmberToolsToolkitWrapper()])
+... ):
 ...     print(len(GLOBAL_TOOLKIT_REGISTRY.registered_toolkits))
+...
 2
 
 ```

From 3dab0064aa54a14d02b97103d5f07787997b3109 Mon Sep 17 00:00:00 2001
From: Jeffrey Wagner <jwagnerjpl@gmail.com>
Date: Thu, 15 Oct 2026 14:07:56 -0700
Subject: [PATCH 8/9] remove blacken-docs

---
 .pre-commit-config.yaml | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 65b6163db..a484c63cf 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -8,11 +8,6 @@ repos:
     - id: ruff-format
     - id: ruff-check
       args: [--fix]
-- repo: https://github.com/adamchainz/blacken-docs
-  rev: 1.20.0
-  hooks:
-    - id: blacken-docs
-      files: ^docs/.*\.(rst|md)$
 - repo: https://github.com/tox-dev/pyproject-fmt
   rev: v2.30.1
   hooks:

From 2c9bc2fb71ea5986c6eb24013080814a853f6517 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 15 Oct 2026 21:08:19 +0000
Subject: [PATCH 9/9] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 docs/api/toolkits.md | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/docs/api/toolkits.md b/docs/api/toolkits.md
index e69865304..7e418fe52 100644
--- a/docs/api/toolkits.md
+++ b/docs/api/toolkits.md
@@ -65,11 +65,8 @@ The [`toolkit_registry_manager`] context manager allows `GLOBAL_TOOLKIT_REGISTRY
 >>> from openff.toolkit.utils import toolkit_registry_manager
 >>> print(len(GLOBAL_TOOLKIT_REGISTRY.registered_toolkits))
 5
->>> with toolkit_registry_manager(
-...     ToolkitRegistry([RDKitToolkitWrapper(), AmberToolsToolkitWrapper()])
-... ):
+>>> with toolkit_registry_manager(ToolkitRegistry([RDKitToolkitWrapper(), AmberToolsToolkitWrapper()])):
 ...     print(len(GLOBAL_TOOLKIT_REGISTRY.registered_toolkits))
-...
 2
 
 ```