Merge remote-tracking branch 'upstream/fix-mypy-1-11' into cache-atom…

…-index

README.md

@@ -1,8 +1,8 @@
 | **Status** | [![GH Actions Status](https://github.com/openforcefield/openff-toolkit/workflows/CI/badge.svg)](https://github.com/openforcefield/openff-toolkit/actions?query=branch%3Amain+workflow%3ACI)  [![Codecov coverage](https://img.shields.io/codecov/c/github/openforcefield/openff-toolkit.svg?logo=Codecov&logoColor=white)](https://codecov.io/gh/openforcefield/openff-toolkit) |
 | :------ |:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| **Latest Release** | [![Last release tag](https://img.shields.io/github/release-pre/openforcefield/openff-toolkit.svg)](https://github.com/openforcefield/openff-toolkit/releases)  [![Commits since release](https://img.shields.io/github/commits-since/openforcefield/openff-toolkit/0.16.0.svg)](https://github.com/openforcefield/openff-toolkit/releases/tag/0.16.0)[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10967071.svg)](https://doi.org/10.5281/zenodo.10967071)
+| **Latest Release** | [![Last release tag](https://img.shields.io/github/release-pre/openforcefield/openff-toolkit.svg)](https://github.com/openforcefield/openff-toolkit/releases)  [![Commits since release](https://img.shields.io/github/commits-since/openforcefield/openff-toolkit/0.16.2.svg)](https://github.com/openforcefield/openff-toolkit/releases/tag/0.16.2)[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.12795773.svg)](https://doi.org/10.5281/zenodo.12795773)
 | **Communication** | [![docs stable](https://img.shields.io/badge/docs-stable-5077AB.svg?logo=read%20the%20docs)](https://open-forcefield-toolkit.readthedocs.io/) [![user & dev discussions](https://img.shields.io/badge/user%20%26%20dev%20discussions-GitHub-red?logo=github)](https://github.com/openforcefield/discussions/discussions) |
-| **Foundation** | [![license](https://img.shields.io/github/license/openforcefield/openff-toolkit.svg)](https://opensource.org/licenses/MIT) [![platforms](https://img.shields.io/badge/Platforms-Linux%2C%20MacOS-orange.svg)](https://open-forcefield-toolkit.readthedocs.io/en/stable/installation.html) [![python](https://img.shields.io/badge/python-3.9%2C%203.10%2C%203.11-blue.svg)](https://open-forcefield-toolkit.readthedocs.io/en/stable/installation.html) [![Funding](https://img.shields.io/badge/Funding-Open%20Force%20Field%20Consortium-brightgreen.svg)](http://openforcefield.org)        |
+| **Foundation** | [![license](https://img.shields.io/github/license/openforcefield/openff-toolkit.svg)](https://opensource.org/licenses/MIT) [![platforms](https://img.shields.io/badge/Platforms-Linux%2C%20MacOS-orange.svg)](https://open-forcefield-toolkit.readthedocs.io/en/stable/installation.html) [![python](https://img.shields.io/badge/python-3.10%2C%203.11%2C%203.12-blue.svg)](https://open-forcefield-toolkit.readthedocs.io/en/stable/installation.html) [![Funding](https://img.shields.io/badge/Funding-Open%20Force%20Field%20Consortium-brightgreen.svg)](http://openforcefield.org)        |
 | **Installation** | [![Releases](https://img.shields.io/badge/obtain-latest-green.svg)](https://github.com/openforcefield/openff-toolkit/releases) [![Conda](https://img.shields.io/conda/v/conda-forge/openff-toolkit.svg)](https://anaconda.org/conda-forge/openff-toolkit) [![Last updated](https://anaconda.org/conda-forge/openff-toolkit/badges/latest_release_relative_date.svg)](https://anaconda.org/conda-forge/openff-toolkit) [![Anaconda Cloud downloads](https://anaconda.org/conda-forge/openff-toolkit/badges/downloads.svg)](https://anaconda.org/conda-forge/openff-toolkit)          |
 
 # The Open Force Field toolkit

devtools/conda-envs/openeye-examples.yaml

@@ -20,8 +20,8 @@ dependencies:
   - openff-units =0.2.0
   - openff-utilities >=0.1.5
   - openff-interchange-base >=0.3.19
-  - openff-nagl-base ~=0.3.7
-  - openff-nagl-models ==0.1.0
+  - openff-nagl-base ~=0.4.0
+  - openff-nagl-models ==0.3.0
   - typing_extensions
   - nglview
     # Toolkit-specific

devtools/conda-envs/openeye.yaml

@@ -20,8 +20,8 @@ dependencies:
   - openff-amber-ff-ports
   - openff-utilities >=0.1.5
   - openff-interchange-base >=0.3.19
-  - openff-nagl-base ~=0.3.7
-  - openff-nagl-models ==0.1.0
+  - openff-nagl-base ~=0.4.0
+  - openff-nagl-models ==0.3.0
   - typing_extensions
     # Toolkit-specific
   - openeye-toolkits

devtools/conda-envs/rdkit-examples.yaml

@@ -19,8 +19,8 @@ dependencies:
   - openff-units =0.2.0
   - openff-utilities >=0.1.5
   - openff-interchange-base >=0.3.19
-  - openff-nagl-base ~=0.3.7
-  - openff-nagl-models ==0.1.0
+  - openff-nagl-base ~=0.4.0
+  - openff-nagl-models ==0.3.0
   - typing_extensions
   - nglview
     # Toolkit-specific

devtools/conda-envs/rdkit.yaml

@@ -19,8 +19,8 @@ dependencies:
   - openff-amber-ff-ports
   - openff-utilities >=0.1.5
   - openff-interchange-base >=0.3.19
-  - openff-nagl-base ~=0.3.7
-  - openff-nagl-models ==0.1.0
+  - openff-nagl-base ~=0.4.0
+  - openff-nagl-models ==0.3.0
   - typing_extensions
     # Toolkit-specific
   - ambertools >=22

devtools/conda-envs/test_env.yaml

@@ -20,8 +20,8 @@ dependencies:
   - openff-amber-ff-ports
   - openff-utilities >=0.1.5
   - openff-interchange-base >=0.3.19
-  - openff-nagl-base ~=0.3.7
-  - openff-nagl-models ==0.1.0
+  - openff-nagl-base ~=0.4.0
+  - openff-nagl-models ==0.3.0
     # Toolkit-specific
   - ambertools >=22
     # https://github.com/rdkit/rdkit/issues/7221

docs/releasehistory.md

@@ -6,12 +6,24 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
 * `minor` increments add features but do not break API compatibility
 * `micro` increments represent bugfix releases or improvements in documentation
 
-
 ## Current development
 
+### API-breaking changes
+
+### Behavior changes
+
+### Bugfixes
+
+### New features
+
+### Improved documentation and warnings
+
+
+## 0.16.2
+
 ### Bugfixes
 
-- [PR #1898](https://github.com/openforcefield/openff-toolkit/pull/1898) and [PR #1904](https://github.com/openforcefield/openff-toolkit/pull/1904): Fixes [#1897](https://github.com/openforcefield/openff-toolkit/pull/1897) in which `to_inchi` methods would return an empty string in some rare cases. Now these cases result in an `EmptyInchiError` being raised. 
+- [PR #1898](https://github.com/openforcefield/openff-toolkit/pull/1898) and [PR #1904](https://github.com/openforcefield/openff-toolkit/pull/1904): Fixes [#1897](https://github.com/openforcefield/openff-toolkit/pull/1897) in which `to_inchi` and `to_inchikey` methods would return an empty string in some rare cases. Now these cases result in an `EmptyInchiError` being raised. 
 - [PR #1890](https://github.com/openforcefield/openff-toolkit/pull/1890): Fixes [#1888](https://github.com/openforcefield/openff-toolkit/pull/1888) in which `ParameterAttribute.unit` was sometimes not validated when stringified.
 - [PR #1894](https://github.com/openforcefield/openff-toolkit/pull/1894): Fixes [#1893](https://github.com/openforcefield/openff-toolkit/issues/1893) in which int-based virtual site parameter lookups were mistakenly forbidden in changes in 0.16.0.