Merge pull request #841 from openforcefield/updates

Assorted updates
openforcefield · Nov 14, 2023 · db845ef · db845ef
2 parents d5ecdb7 + cf8cf30
commit db845ef
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Showing 7 changed files with 13 additions and 16 deletions.
diff --git a/.github/workflows/examples.yaml b/.github/workflows/examples.yaml
@@ -70,7 +70,7 @@ jobs:
     - name: Run example notebooks
       if: always()
       run: |
-        python -m pytest --nbval-lax \
+        python -m pytest --nbval-lax --dist loadscope -nauto \
           examples/ \
           --ignore=examples/deprecated/ \
           --ignore=examples/lammps/ \

diff --git a/devtools/conda-envs/beta_env.yaml b/devtools/conda-envs/beta_env.yaml
@@ -8,7 +8,6 @@ channels:
 dependencies:
   # Core
   - python
-  - pip
   - numpy >=1.21
   - pydantic =1
   - openmm >=7.6
@@ -31,7 +30,7 @@ dependencies:
   - pytest-randomly
   - mdanalysis
   # Drivers
-  - gromacs >=2021=nompi*
+  - gromacs =2023.3=nompi_*_101
   - lammps
   # https://github.com/conda-forge/quippy-feedstock/issues/15
   - panedr

diff --git a/devtools/conda-envs/dev_env.yaml b/devtools/conda-envs/dev_env.yaml
@@ -33,7 +33,7 @@ dependencies:
   - nbval
   - mdanalysis
   # Drivers
-  # gromacs >=2021=nompi*  # No osx-arm64 builds
+  # gromacs =2023.3=nompi_*_101  # No osx-arm64 builds
   - lammps
   - panedr
   # Typing

diff --git a/devtools/conda-envs/docs_env.yaml b/devtools/conda-envs/docs_env.yaml
@@ -9,7 +9,7 @@ dependencies:
   - python =3.10
   - pip
   - numpy >=1.21
-  - pydantic >=1.10.8,<2.0.0a0
+  - pydantic =1
   - openff-toolkit-base >=0.14.2
   - openff-models
   - openmm >=7.6
@@ -18,7 +18,7 @@ dependencies:
   - nglview
   - panedr
   - typing-extensions
-  - pandas-stubs >=1.2.0.56
+  - pandas-stubs
   # readthedocs dependencies
   - myst-parser
   - numpydoc

diff --git a/devtools/conda-envs/examples_env.yaml b/devtools/conda-envs/examples_env.yaml
@@ -24,10 +24,10 @@ dependencies:
   - nglview
   - openeye-toolkits
   - pytest
+  - pytest-xdist
   - nbval
   - openmmforcefields >=0.11.2
   - rich
   # Drivers
-  # https://github.com/conda-forge/gromacs-feedstock/pull/27
-  # gromacs >=2021=nompi*
+  - gromacs =2023.3=nompi_*_101
   - lammps
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -5,20 +5,18 @@ channels:
 dependencies:
   # Core
   - python
-  - pip
   - numpy
   - pydantic
   # OpenFF stack
   - openff-toolkit-base >=0.14.3
   - openff-units
   - openff-models
-  # Needs to be explicitly listed to not be dropped with AmberTools is removed
+  # Needs to be explicitly listed to not be dropped when AmberTools is removed
   - rdkit
   # Optional features
-  - unyt
+  # GMSO does not support Pydantic 2; should come in release after 0.12.0
+  # foyer
   # mbuild
-  # GMSO does not support Pydantic 2
-  # foyer >=0.11.3
   # Testing
   - mdtraj
   - intermol
@@ -31,11 +29,11 @@ dependencies:
   - nglview
   - mdanalysis
   # Drivers
-  - gromacs >=2021=nompi*
+  - gromacs =2023.3=nompi_*_101
   - lammps
   - panedr
   # Typing
   - mypy =1.3
   - typing-extensions
   - types-setuptools
-  - pandas-stubs >=1.2.0.56
+  - pandas-stubs
diff --git a/openff/interchange/components/interchange.py b/openff/interchange/components/interchange.py
@@ -416,7 +416,7 @@ def to_openmm_system(
 
         Parameters
         ----------
-        combine_nonbonded_forces : bool, default=False
+        combine_nonbonded_forces : bool, default=True
             If True, an attempt will be made to combine all non-bonded interactions into a single
             openmm.NonbondedForce.
             If False, non-bonded interactions will be split across multiple forces.