Merge remote-tracking branch 'upstream/develop' into to-amber

.github/workflows/beta.yaml

@@ -64,7 +64,7 @@ jobs:
 
     - name: Run all tests
       if: always()
-      run: python -m pytest -v $COV openff/interchange/ -m "slow or not slow"
+      run: python -m pytest -v $COV openff/interchange/
 
     - name: Codecov
       uses: codecov/codecov-action@v4

.github/workflows/ci.yaml

@@ -94,10 +94,7 @@ jobs:
     - name: Run tests
       if: always()
       run: |
-        python -m pytest $COV openff/interchange/ \
-          -r fExs -n logical --durations=10 \
-          -m "slow or not slow" \
-          --ignore=openff/interchange/_tests/energy_tests/test_energies.py
+        python -m pytest $COV openff/interchange/ -r fExs -n logical --durations=10
 
     - name: Run small molecule regression tests
       if: ${{ matrix.python-version == '3.10' && matrix.openeye == true && matrix.openmm == true }}
@@ -127,14 +124,13 @@ jobs:
         python devtools/scripts/molecule-regressions.py
 
     - name: Run mypy
-      continue-on-error: true
-      if: ${{ matrix.python-version == '3.11' }}
+      if: ${{ matrix.python-version == '3.10' }}
       run: |
         # As of 01/23, JAX with mypy is too slow to use without a pre-built cache
         # https://github.com/openforcefield/openff-interchange/pull/578#issuecomment-1369979875
         micromamba remove jax
-        mypy -p "openff.interchange" --exclude "openff/interchange/_tests/"
-        mypy --show-error-codes plugins/nonbonded_plugins/
+        python -m mypy -p "openff.interchange" --exclude "openff/interchange/_tests/"
+        python -m mypy plugins/nonbonded_plugins/
 
     - name: Codecov
       uses: codecov/codecov-action@v4

.github/workflows/examples.yaml

@@ -64,16 +64,11 @@ jobs:
 
     - name: Run docexamples
       run: |
-        # TODO: Add back /interchange.py when `TypedMolecule` is implemented
-        pytest --doctest-modules openff/interchange/ --ignore=openff/interchange/_tests --ignore=openff/interchange/components/interchange.py
+        pytest --doctest-modules openff/interchange/ --ignore=openff/interchange/_tests
 
     - name: Run example notebooks
       if: always()
       run: |
-        python -m pytest --nbval-lax --dist loadscope -n logical --durations=20 \
-          examples/ \
+        python -m pytest --nbval-lax --dist loadscope -n logical --durations=20 examples/ \
           --ignore=examples/deprecated/ \
-          --ignore=examples/experimental/openmmforcefields/ \
-          --ignore=examples/lammps/ \
-          --ignore=examples/protein_ligand/ \
-          --ignore=examples/conformer_energies/conformer_energies.ipynb
+          --ignore=examples/experimental

.pre-commit-config.yaml

@@ -12,9 +12,10 @@ repos:
   hooks:
   - id: add-trailing-comma
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.5.7
+  rev: v0.6.2
   hooks:
     - id: ruff
+    - id: ruff-format
 - repo: https://github.com/econchick/interrogate
   rev: 1.7.0
   hooks:
@@ -46,3 +47,9 @@ repos:
   hooks:
     - id: nbstripout
       files: ^examples
+- repo: https://github.com/asottile/pyupgrade
+  rev: v3.17.0
+  hooks:
+  - id: pyupgrade
+    args:
+      - --py310-plus

devtools/conda-envs/beta_env.yaml

@@ -10,7 +10,7 @@ dependencies:
   - pydantic >=1.10.17,<3
   - openmm >=7.6
   # OpenFF stack
-  - openff-toolkit >=0.15.2
+  - openff-toolkit ~=0.16.4
   - openff-nagl ~=0.3.7
   - openff-nagl-models =0.1
   # Optional features

devtools/conda-envs/dev_env.yaml

@@ -4,22 +4,31 @@ channels:
   - openeye
 dependencies:
   # Core
-  - python =3.11
-  - pip
+  - python =3.10
+  - versioneer-518
   - numpy
   - pydantic =2
-  - openmm
   # OpenFF stack
-  - openff-toolkit ~=0.16
-  - openff-interchange-base
+  - openff-toolkit-base ~=0.16.4
+  - openff-units
+  - ambertools =23
+  # Optional features
+  - openmm
   # smirnoff-plugins =2024
+  # de-forcefields  # add back after smirnoff-plugins update
   - openff-nagl
   - openff-nagl-models
-  - ambertools =23
-  # Optional features
-  - mbuild ~=0.17
-  - foyer ~=0.12
+  - mbuild ~=0.18
+  - foyer =1
   - gmso ~=0.12
+  - nglview
+  # Drivers
+  - gromacs =2024
+  - lammps >=2023.08.02
+  - panedr
+  # shim for a build issue that's probably localized to conda-forge
+  # https://github.com/conda-forge/lammps-feedstock/issues/207
+  - openmpi =4
   # Testing
   - mdtraj
   - intermol
@@ -29,21 +38,13 @@ dependencies:
   - pytest-xdist
   - pytest-randomly
   - nbval
-  # de-forcefields  # add back after smirnoff-plugins update
-  # Drivers
-  - gromacs =2024
-  - lammps >=2023.08.02
-  - panedr
   # Typing
   - mypy
   - typing-extensions
   - types-setuptools
   - pandas-stubs
   # Development tools
-  # https://github.com/mamba-org/mamba/issues/1523#issuecomment-1246591319
-  - micromamba
   - jupyterlab
-  - nglview
   - pdbfixer
   - ipdb
   - pre-commit

devtools/conda-envs/docs_env.yaml

@@ -8,10 +8,10 @@ dependencies:
   - pip
   - numpy =1
   - pydantic =2
-  - openff-toolkit-base
-  - openmm >=7.6
+  - openff-toolkit-base ~=0.16.4
+  - openmm =8
   - mbuild
-  - foyer >=0.12.1
+  - foyer =1
   - nglview
   - panedr
   - typing-extensions

devtools/conda-envs/examples_env.yaml

@@ -5,29 +5,35 @@ channels:
 dependencies:
   # Core
   - python
+  - versioneer-518
   - numpy
   - pydantic =2
-  - openmm
   # OpenFF stack
-  - openff-toolkit
-  - openff-nagl
-  - openff-nagl-models
+  - openff-toolkit-base ~=0.16.4
+  - openff-units
   - ambertools =23
   # Optional features
-  - unyt
-  - mbuild =0.17
-  - foyer >=0.12.1
-  - gmso =0.12
+  - openff-nagl
+  - openff-nagl-models
+  - mbuild ~=0.18
+  - foyer =1
+  - gmso ~=0.12
+  - nglview
+  # Drivers
+  - gromacs
+  - lammps >=2023.08.02
+  # shim for a build issue that's probably localized to conda-forge
+  # https://github.com/conda-forge/lammps-feedstock/issues/207
+  - openmpi =4
+  - panedr
+  # Testing
+  - mdtraj
+  - pytest
+  - pytest-xdist
+  - nbval
   # Examples
+  - openmmforcefields
   - jax
-  - mdtraj
   - pdbfixer
-  - nglview
   - openeye-toolkits =2024.1.0
-  - pytest =8.0
-  - pytest-xdist
-  - nbval
   - rich
-  # Drivers
-  - gromacs
-  - lammps >=2023.08.02

devtools/conda-envs/test_env.yaml

@@ -6,17 +6,30 @@ dependencies:
   - python
   - versioneer-518
   - numpy
-  - pydantic >=1.10.17,<3
+  - pydantic =2
   # OpenFF stack
-  - openff-toolkit-base >=0.16
+  - openff-toolkit-base ~=0.16.4
   - openff-units
   - ambertools =23
   # Needs to be explicitly listed to not be dropped when AmberTools is removed
   - rdkit
   # Optional features
-  - foyer >=0.12.1
-  - mbuild
-  - gmso =0.12
+  - openmm
+  # smirnoff-plugins =2024
+  # de-forcefields  # add back after smirnoff-plugins update
+  - openff-nagl
+  - openff-nagl-models
+  - mbuild ~=0.18
+  - foyer =1
+  - gmso ~=0.12
+  - nglview
+  # Drivers
+  - gromacs
+  - lammps >=2023.08.02
+  # shim for a build issue that's probably localized to conda-forge
+  # https://github.com/conda-forge/lammps-feedstock/issues/207
+  - openmpi =4
+  - panedr
   # Testing
   - mdtraj
   - intermol
@@ -26,11 +39,6 @@ dependencies:
   - pytest-xdist
   - pytest-randomly
   - nbval
-  - nglview
-  # Drivers
-  - gromacs
-  - lammps >=2023.08.02
-  - panedr
   # Typing
   - mypy
   - typing-extensions

docs/releasehistory.md

@@ -11,6 +11,22 @@ Dates are given in YYYY-MM-DD format.
 
 Please note that all releases prior to a version 1.0.0 are considered pre-releases and many API changes will come before a stable release.
 
+## 0.4.0 - 2024
+
+* Pydantic v2 is now used at runtime. As a consequence, models containing `Interchange`s cannot also use models from the v1 API.
+* `Interchange.to_gromacs` and similar methods now raise an error if no box is defined.
+  * Previously, this was a warning.
+  * GROMACS dropped support for (proper) vacuum simulations in version 2020 and there are no immediate plans to re-introduce it.
+  * Users freqently approximate vacuum simulation with periodic boundary conditions by applying a large box. This has some performance issues and some non-bonded terms likely differ numerically compared to similar implementations in other engines.
+* The wrapped use of external readers and writers is removed, and with it arguments like `writer` in many `Interchange.to_x` calls.
+* Several classes and methods which were deprecated in the 0.3 line of releases are now removed.
+* Previously-deprecated examples are removed.
+* `ProperTorsionKey` no longer accepts an empty tuple as atom indices.
+
+## 0.3.30 - 2024-08
+
+* #1039 Updates support of "cutoff" electrostatics in `.to_openmm` to better reflect what OpenMM supports. Set `"reaction-field"` to force the use of `CutoffPeriodic`, provided the vdW and electrostatic cutoff distances match. The potential/method `"cutoff"` is no longer supported but may be re-added in the future.
+
 ## 0.3.29 - 2024-08-01
 
 * #1023 Fixes a bug in which non-bonded parameter lookup sometimes crashed when virtual sites were present.

docs/using/plugins.md

@@ -217,7 +217,7 @@ At this point, we have created a class that can parse sections of a custom OFFXM
 from openff.toolkit import Topology
 
 from typing import Literal, Type
-from openff.models.types import FloatQuantity
+from openff.interchange._annotations import DistanceQuantity
 from openff.interchange.smirnoff._nonbonded import _SMIRNOFFNonbondedCollection
 from openff.interchange.components.potentials import Potential
 
@@ -231,7 +231,7 @@ class SMIRNOFFBuckinghamCollection(_SMIRNOFFNonbondedCollection):
 
     mixing_rule: str = "Buckingham"
 
-    switch_width: FloatQuantity["angstrom"] = unit.Quantity(1.0, unit.angstrom)
+    switch_width: DistanceQuantity = unit.Quantity(1.0, unit.angstrom)
 
     @classmethod
     def allowed_parameter_handlers(cls):

examples/README.md

@@ -5,18 +5,14 @@
 
 Jupyter notebooks demonstrating use cases.
 
-* `conformer_energies.ipynb`: Given a SMILES string, generate conformers and compute the single-point energy via GROMACS and OpenMM and compare to a result generated by the OpenFF toolkit.
+* `conformer_energies/conformer_energies.ipynb`: Given a SMILES string, generate conformers and compute the single-point energy via GROMACS and OpenMM and compare to a result generated by the OpenFF toolkit.
 * `ligand_in_water/ligand_in_water.ipynb`: Solvate a ligand in water and prepare a simulation.
 * `packed_box/packed_box.ipynb`: Prepare a box of organic species for a simulation and compare the
   results of OpenMM, GROMACS, Amber, and LAMMPS.
 * `protein_ligand/protein_ligand.ipynb`: Prepare a protein-ligand system for simulation using
   OpenFF tools and compare the results of OpenMM, GROMACS, Amber, and LAMMPS.
 * `openmm/openmm.ipynb`: Prepare a box of organic species for a simulation with OpenMM.
 * `lammps/lammps.ipynb`: Prepare a box of organic species for a simulation with LAMMPS.
-* `foyer-showcase/solvated-nanoparticle.ipynb`: Use [`mBuild`](https://mbuild.mosdef.org/) to construct a silica nanoparticle solvated in tetrahydrofuran and then parametrize the nanoparticle with OPLS-AA via [`Foyer`](https://foyer.mosdef.org/) and Sage.
-
-## Deprecated examples
-
-* `optimize-with-jax.ipynb`: Run a minimal parameter optimization using JAX.
-* `parameter_replacement.ipynb`: Partially replace parameters in a parametrized system with values from a second force field.
-* `parameter_splitting.ipynb`: Split one SMIRKS pattern into two after parametrization.
+* `vectorized_representations/vectorized_representations.ipynb`: Export systems to vectorized representations.
+* `host_guest/host_guest.ipynb`: Prepare a host-guest system.
+* `virtual_sites/virtual_sites.ipynb`: Apply several types of SMIRNOFF virtual sites to ligands.

examples/conformer_energies/conformer_energies.ipynb

@@ -65,7 +65,7 @@
    "outputs": [],
    "source": [
     "molecule = Molecule.from_smiles(SMILES)\n",
-    "molecule.generate_conformers(n_conformers=20, rms_cutoff=0.1 * unit.angstrom),\n",
+    "(molecule.generate_conformers(n_conformers=20, rms_cutoff=0.1 * unit.angstrom),)\n",
     "topology = molecule.to_topology()"
    ]
   },