Merge pull request #715 from openforcefield/v0.3.3-release-notes

Add v0.3.3 release notes

.pre-commit-config.yaml

@@ -63,7 +63,7 @@ repos:
   hooks:
   - id: markdownlint
     exclude: .github
-    args: ["--disable", "MD013", "MD033", "MD024", "MD046", "--"]
+    args: ["--disable", "MD013", "MD033", "MD024", "MD046", "--ignore", "docs/using/experimental.md", "--"]
 - repo: https://github.com/nbQA-dev/nbQA
   rev: 1.7.0
   hooks:

devtools/conda-envs/docs_env.yaml

@@ -13,24 +13,11 @@ dependencies:
   - openff-toolkit-base >=0.13
   - openff-models
   - openmm >=7.6
-  - pint
-  - unyt
   - mbuild
   - foyer >=0.11.3
-  - mdtraj
-  - intermol
-  - jax
-  - nbval
   - nglview
-  - ipywidgets >7,<8  # https://github.com/nglviewer/nglview/issues/1032
-  - mdanalysis
-  - gromacs >=2021=nompi*
-  - lammps
-  # https://github.com/conda-forge/quippy-feedstock/issues/15
   - panedr
-  - mypy =1.2
   - typing-extensions
-  - types-setuptools
   - pandas-stubs >=1.2.0.56
   # readthedocs dependencies
   - myst-parser

devtools/conda-envs/examples_env.yaml

@@ -13,18 +13,15 @@ dependencies:
   # OpenFF stack
   - openff-toolkit >=0.13
   - openff-forcefields >=2023.05
-  - openff-models >=0.0.4
   # Optional features
-  - jax
   - unyt
   - mbuild
   - foyer >=0.11.3
   # Examples
+  - jax
   - mdtraj
   - pdbfixer
-  - intermol
   - nglview
-  - ipywidgets >7,<8  # https://github.com/nglviewer/nglview/issues/1032
   - openeye-toolkits
   - pytest
   - nbval
@@ -33,5 +30,3 @@ dependencies:
   # Drivers
   - gromacs >=2021=nompi*
   - lammps
-  # https://github.com/conda-forge/quippy-feedstock/issues/15
-  - panedr

docs/releasehistory.md

@@ -9,12 +9,28 @@ Releases follow versioning as described in
 
 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.
 
-## Current development
+## 0.3.3 - 2023-05-08
+
+* #703 Clarifies the experimental state of some features, which require opt-in to use.
+
+### Behavior changes
+
+* #706 Updates `pack_box` to return a `Topology`.
+* #716 Removes InterMol and ParmEd conversions, which were untested and not part of the public API.
 
 ### Bugfixes
 
+* #705 Fixes #693 in which 1-4 vdW interactions were not scaled when using `Interchange.to_openmm(combine_nonbonded_forces=False)`
 * #702 Fixes #701 in which `Interchange` was needlessly re-exported in the high-level module.
 
+### Documentation improvements
+
+* #673 Adds a vectorized representation example.
+* #703 Adds a section to the user guide on accessing experimental functionality.
+* #706 Updates the mixed solvent example.
+* #708 Updates the protein-ligand example.
+* #708 Updates the ligand-in-water example.
+
 ## 0.3.2 - 2023-05-02
 
 ### Behavior changes
@@ -96,7 +112,7 @@ Please note that all releases prior to a version 1.0.0 are considered pre-releas
 * #614 Adds support for GBSA parameters in SMIRNOFF force fields.
 * #586 #591 #605 #609 #613 Support custom SMIRNOFF sections with OpenMM.
 
-### Documentation
+### Documentation improvements
 
 * #634 Improves documentation for SMIRNOFF plugins.
 * #610 Adds duplicate documentation on how to covert to OpenMM-styled unit/quantity objects.

docs/using/experimental.md

@@ -30,7 +30,7 @@ $ INTERCHANGE_EXPERIMENTAL=1 jupyter-notbook my_notebook.ipynb
 
 or, with cloud services like Google Colab and Binder, use the [`%env`](https://ipython.readthedocs.io/en/stable/interactive/magics.html#magic-env) magic command:
 
-```jupyter
+```
 %env INTERCHANGE_EXPERIMENTAL=1
 ```
 

openff/interchange/__init__.py

@@ -1,9 +1,14 @@
 """A project (and object) for storing, manipulating, and converting molecular mechanics data."""
 import importlib
 from types import ModuleType
+from typing import TYPE_CHECKING
 
 from openff.interchange._version import get_versions
 
+if TYPE_CHECKING:
+    # Type checkers can't see lazy-imported objects
+    from openff.interchange.components.interchange import Interchange
+
 # Handle versioneer
 versions = get_versions()
 __version__ = versions["version"]

openff/interchange/_tests/interoperability_tests/internal/test_amber.py

@@ -14,7 +14,7 @@
 
 
 class TestAmber(_BaseTest):
-    @pytest.mark.slow()
+    @pytest.mark.skip(reason="Need replacement route to reference positions")
     def test_inpcrd(self, sage):
         mol = Molecule.from_smiles(10 * "C")
         mol.name = "HPER"
@@ -26,6 +26,7 @@ def test_inpcrd(self, sage):
         out.positions = unit.nanometer * np.round(out.positions.m_as(unit.nanometer), 5)
 
         out.to_inpcrd("internal.inpcrd")
+        # This method no longer exists
         out._to_parmed().save("parmed.inpcrd")
 
         coords1 = parmed.load_file("internal.inpcrd").coordinates

openff/interchange/_tests/unit_tests/components/test_mdconfig.py

@@ -63,7 +63,7 @@ def parse_mdp(file: str) -> dict[str, str]:
 
 def parse_sander(file: str) -> dict[str, Union[dict, str]]:
     """Naively parse (sections of) a sander input file into a dict structure."""
-    options = dict()
+    options: dict[str, Union[dict, str]] = dict()
     current_level = options
 
     with open(file) as f:
@@ -79,7 +79,7 @@ def parse_sander(file: str) -> dict[str, Union[dict, str]]:
             if line.startswith("&"):
                 current_section = line[1:]
                 current_level[current_section] = dict()
-                current_level = current_level[current_section]
+                current_level = current_level[current_section]  # type: ignore[assignment]
                 continue
 
             if "=" in line:

openff/interchange/components/interchange.py

@@ -374,11 +374,6 @@ def to_prmtop(self, file_path: Union[Path, str], writer="internal"):
 
             to_prmtop(self, file_path)
 
-        elif writer == "parmed":
-            from openff.interchange.interop._external import ParmEdWrapper
-
-            ParmEdWrapper().to_file(self, file_path)
-
         else:
             raise UnsupportedExportError
 
@@ -414,26 +409,9 @@ def to_inpcrd(self, file_path: Union[Path, str], writer="internal"):
 
             to_inpcrd(self, file_path)
 
-        elif writer == "parmed":
-            from openff.interchange.interop._external import ParmEdWrapper
-
-            ParmEdWrapper().to_file(self, file_path)
-
         else:
             raise UnsupportedExportError
 
-    def _to_parmed(self):
-        """Export this Interchange to a ParmEd Structure."""
-        from openff.interchange.interop._parmed import _to_parmed
-
-        return _to_parmed(self)
-
-    @classmethod
-    def _from_parmed(cls, structure):
-        from openff.interchange.interop._parmed import _from_parmed
-
-        return _from_parmed(cls, structure)
-
     @classmethod
     @requires_package("foyer")
     def from_foyer(