Merge remote-tracking branch 'upstream/main' into pydantic-2

.github/workflows/CI.yml

@@ -47,7 +47,7 @@ jobs:
       COV: --cov=openff/toolkit --cov-config=setup.cfg --cov-append --cov-report=xml
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 2
 

.github/workflows/beta_rc.yaml

@@ -28,7 +28,7 @@ jobs:
       COV: --cov=openff/toolkit --cov-config=setup.cfg --cov-append --cov-report=xml
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 2
 

.github/workflows/conda.yml

@@ -32,7 +32,7 @@ jobs:
       PACKAGE: openff-toolkit
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Vanilla install from conda
         uses: mamba-org/setup-micromamba@v1

.github/workflows/examples.yml

@@ -41,7 +41,7 @@ jobs:
       NB_ARGS: -v --nbval-lax --ignore=examples/deprecated --durations=20
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 2
 
@@ -87,7 +87,7 @@ jobs:
 
       - name: Remove undesired toolkits
         run: |
-          # If openmmforcefields is included in examples/environment.yaml,
+          # If openmmforcefields is included in either environment file,
           # remove RDKit and AmberTools brought in by it. Currently it's not included,
           # so don't remove it.
           if [ ! -z "${{ env.PACKAGES_TO_REMOVE }}" ]; then
@@ -136,12 +136,13 @@ jobs:
         run: |
           if [[ ${{ matrix.rdkit }} == false ]]; then
             NB_ARGS+=" --ignore=examples/QCArchive_interface"
+            NB_ARGS+=" --ignore=examples/visualization"
             NB_ARGS+=" --ignore=examples/check_dataset_parameter_coverage"
             NB_ARGS+=" --ignore=examples/conformer_energies"
             NB_ARGS+=" --ignore=examples/using_smirnoff_in_amber_or_gromacs"
             NB_ARGS+=" --ignore=examples/toolkit_showcase"
             NB_ARGS+=" --ignore=examples/using_smirnoff_with_amber_protein_forcefield"
-            NB_ARGS+=" --ignore=examples/SMIRNOFF_simulation/run_simulation.ipynb"
+            NB_ARGS+=" --ignore=examples/SMIRNOFF_simulation"
           fi
 
           python -m pytest $PYTEST_ARGS $NB_ARGS examples

.github/workflows/installer.yml

@@ -20,7 +20,7 @@ jobs:
       PYVER: ${{ matrix.python-version }}
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install conda environment
       uses: mamba-org/setup-micromamba@v1

.github/workflows/lint.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: actions/setup-python@v4
         with:

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ repos:
   - id: end-of-file-fixer
     exclude: '\.(json|pdb)$'
 - repo: https://github.com/psf/black
-  rev: 23.3.0
+  rev: 23.9.1
   hooks:
   - id: black
   - id: black-jupyter
@@ -17,7 +17,7 @@ repos:
   hooks:
   - id: isort
 - repo: https://github.com/PyCQA/flake8
-  rev: 6.0.0
+  rev: 6.1.0
   hooks:
   - id: flake8
     files: ^openff

FAQ.md

@@ -70,19 +70,19 @@ As of August 2022, some upstreams (at least AmberTools, possibly more) are not b
 
 (Keywords `osx-arm64`, M1 Mac, M2 Mac)
 
-## My conda installation of the toolkit doesn't appear to work. What should I try next?
+## My mamba/conda installation of the toolkit doesn't appear to work. What should I try next?
 
-We recommend that you install the toolkit in a fresh conda environment, explicitly passing the channels to be used, in-order:
+We recommend that you install the toolkit in a fresh environment, explicitly passing the channels to be used, in-order:
 
 ```shell
-conda create -n <my_new_env> -c conda-forge openff-toolkit
-conda activate <my_new_env>
+mamba create -n <my_new_env> -c conda-forge openff-toolkit
+mamba activate <my_new_env>
 ```
 
-Installing into a new environment avoids forcing conda to satisfy the dependencies of both the toolkit and all existing packages in that environment.
-Taking the approach that conda environments are generally disposable, even ephemeral, minimizes the chances for hard-to-diagnose dependency issues.
+Installing into a new environment avoids forcing mamba to satisfy the dependencies of both the toolkit and all existing packages in that environment.
+Taking the approach that conda/mamba environments are generally disposable, even ephemeral, minimizes the chances for hard-to-diagnose dependency issues.
 
-## My conda installation of the toolkit STILL doesn't appear to work.
+## My mamba/conda installation of the toolkit STILL doesn't appear to work.
 
 Many of our users encounter issues that are ultimately due to their terminal finding a different `conda` at higher priority in their `PATH` than the `conda` deployment where OpenFF is installed. To fix this, find the conda deployment where OpenFF is installed. Then, if that folder is something like `~/miniconda3`, run in the terminal:
 

README.md

@@ -1,6 +1,6 @@
 | **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/0.14.3.svg)](https://github.com/openforcefield/openff-toolkit/releases/tag/0.14.3) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8225831.svg)](https://doi.org/10.5281/zenodo.8225831)
+| **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/0.14.4.svg)](https://github.com/openforcefield/openff-toolkit/releases/tag/0.14.4) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8412072.svg)](https://doi.org/10.5281/zenodo.8412072)
 | **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)        |
 | **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)          |
@@ -27,7 +27,7 @@ Please cite the OpenFF Toolkit using the [Zenodo record](https://zenodo.org/reco
 
 The Open Force Field Toolkit (`openff-toolkit`) is a Python toolkit, and supports Python 3.9 through 3.11.
 
-### Installing via conda
+### Installing via Mamba/Conda
 
 Detailed installation instructions can be found [here](https://open-forcefield-toolkit.readthedocs.io/en/stable/installation.html).
 

devtools/conda-envs/openeye-examples.yaml

@@ -35,6 +35,7 @@ dependencies:
   - msgpack-python
   - qcelemental
   - qcportal ==0.15.8
+  - qcengine
   - mdtraj
   - parmed =3
   - nbval

devtools/conda-envs/openeye.yaml

@@ -33,5 +33,9 @@ dependencies:
   - toml
   - bson
   - msgpack-python
+  - qcelemental
+  - qcportal ==0.15.8
+  - qcengine
   - mdtraj
+  - nglview
   - parmed =3

devtools/conda-envs/rdkit-examples.yaml

@@ -36,7 +36,6 @@ dependencies:
   - bson
   - msgpack-python
   - qcelemental
-  - qcportal ==0.15.8
   - qcengine
   - nbval
   - mdtraj

devtools/conda-envs/rdkit.yaml

@@ -33,3 +33,7 @@ dependencies:
   - toml
   - bson
   - msgpack-python
+  - qcelemental
+  - qcportal ==0.15.8
+  - qcengine
+  - nglview

devtools/conda-envs/test_env.yaml

@@ -35,6 +35,10 @@ dependencies:
   - toml
   - bson
   - msgpack-python
+  - qcelemental
+  - qcportal ==0.15.8
+  - qcengine
+  - nglview
   - mdtraj
   - nbval
   - mypy