Fix JSON serialization with pydantic >=2.12

.github/workflows/ci-pydantic-latest.yaml

@@ -0,0 +1,44 @@
+name: ci-pydantic-latest
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+
+defaults:
+  run:
+    shell: pixi run -e py312amber bash -e {0}
+
+jobs:
+  test:
+    name: Test with latest pydantic on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os:
+          - ubuntu-latest
+          - macos-latest
+
+    steps:
+    - uses: actions/checkout@v6
+
+    - name: Set up virtual environment
+      uses: prefix-dev/setup-pixi@v0.9.5
+      with:
+        pixi-version: v0.41.4
+        environments: py312amber
+        frozen: true
+
+    - name: Upgrade pydantic to latest
+      run: pip install "pydantic>=2.12"
+
+    - name: Run mypy
+      run: pixi run -e py312amber run_mypy
+
+    - name: Run tests
+      run: pixi run -e py312amber run_tests

devtools/conda-envs/docs_env.yaml

@@ -8,7 +8,7 @@ dependencies:
   - setuptools !=76.0.0
   - pip
   - numpy =2
-  - pydantic >=2,<2.12
+  - pydantic >=2
   - openff-toolkit-base =0.17
   - openmm
   - mbuild-base =1

openff/interchange/components/potentials.py

@@ -439,7 +439,20 @@ def validate_collections(
         raise ValueError(f"Validation mode {info.mode} not implemented.")
 
 
+def serialize_collections(v: Any, handler: Any, info: Any) -> dict:
+    """Serialize collections using each collection's actual type schema.
+
+    Without this, pydantic uses the declared Collection base class schema and
+    drops subclass-specific fields (e.g. scale_14, cutoff, periodic_potential).
+    """
+    if info.mode == "json":
+        return {name: json.loads(collection.model_dump_json()) for name, collection in v.items()}
+    else:
+        raise NotImplementedError(f"Serialization mode {info.mode} not implemented.")
+
+
 _AnnotatedCollections = Annotated[
     dict[str, Collection],
     WrapValidator(validate_collections),
+    WrapSerializer(serialize_collections),
 ]

openff/interchange/pydantic.py

@@ -17,4 +17,7 @@ def model_dump(self, **kwargs) -> dict[str, Any]:
         return super().model_dump(serialize_as_any=True, **kwargs)
 
     def model_dump_json(self, **kwargs) -> str:
-        return super().model_dump_json(serialize_as_any=True, **kwargs)
+        # serialize_as_any=True breaks pint.Quantity serialization in pydantic >=2.12
+        # (pydantic/pydantic#12348); the Annotated WrapSerializer on _Quantity handles
+        # JSON serialization correctly without it
+        return super().model_dump_json(**kwargs)