Try using smee-base and no ambertools

.github/workflows/ci.yaml

@@ -20,15 +20,17 @@ jobs:
     - name: Run Tests
       run: |
         apt update && apt install -y git make
-
+        # setuptools-scm calls git to determine the version; git refuses to
+        # run in directories owned by a different user (CVE-2022-24765), which
+        # happens when actions/checkout runs as a different UID than the
+        # container's root. Mark the workspace as safe to unblock the build.
+        git config --global --add safe.directory "$GITHUB_WORKSPACE"
+
         make env
         make lint
         make test
         make docs
 
-        mamba install --name descent --yes "pydantic <2" "openff-toolkit>=0.9.2" "openff-interchange>=0.3.17"
-        make test
-
     - name: CodeCov
       uses: codecov/codecov-action@v4.1.1
       with:

devtools/envs/base.yaml

@@ -9,8 +9,10 @@ dependencies:
   - pip
 
   # Core packages
-  - smee >=0.10.0
-  - pydantic-units  # TODO: Remove this line once smee deps are updated
+  - smee-base >=0.10.0
+  - msgpack-python
+  - pydantic
+  - pydantic-units
   - openff-interchange>=0.3.17
 
   - pytorch
@@ -26,6 +28,7 @@ dependencies:
   - rdkit
   - matplotlib-base
   - panel
+  - openmm
 
   # Examples
   - jupyter
@@ -37,7 +40,6 @@ dependencies:
   - tensorboardX
 
   # Dev / Testing
-  - ambertools
   - rdkit
   - uncertainties