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

.github/workflows/CI.yml

@@ -150,7 +150,7 @@ jobs:
 
       - name: Run mypy
         if: ${{ matrix.rdkit == true && matrix.openeye == true }}
-        run: mypy -p "openff.toolkit" --exclude "openff/toolkit/data"
+        run: mypy -p "openff.toolkit"
 
       - name: Run unit tests
         run: |
@@ -170,15 +170,19 @@ jobs:
       - name: Run notebooks in docs
         if: ${{ matrix.rdkit == true && matrix.openeye == true && matrix.pydantic-version == 1 }}
         run: |
-          pytest -v --no-cov --nbval --ignore docs/_build/ docs/
+          pytest -v --no-cov --durations=5 --nbval --ignore docs/_build/ docs/
 
       - name: Run examples in docstrings
         if: ${{ matrix.rdkit == true && matrix.openeye == true && matrix.pydantic-version == 1 }}
         run: |
-          pytest -v --no-cov --doctest-modules --ignore=openff/toolkit/_tests/ --ignore=openff/toolkit/data/ --ignore=openff/toolkit/utils/utils.py openff/
+          pytest openff \
+            -v -x -n logical --no-cov --doctest-modules \
+            --ignore-glob='openff/toolkit/_tests*' \
+            --ignore=openff/toolkit/data/ \
+            --ignore=openff/toolkit/utils/utils.py
 
       - name: Codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml

.github/workflows/beta_rc.yaml

@@ -85,7 +85,7 @@ jobs:
           pytest -v --doctest-glob="docs/*.rst" --doctest-glob="docs/*.md" docs/
 
       - name: Codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml

.github/workflows/examples.yml

@@ -37,8 +37,8 @@ jobs:
     env:
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
       PACKAGE: openff
-      PYTEST_ARGS: -r fE --tb=short
-      NB_ARGS: -v --nbval-lax --ignore=examples/deprecated --durations=20
+      PYTEST_ARGS: -r fE -v -x --tb=short -nauto
+      NB_ARGS: --nbval-lax --dist loadscope --ignore=examples/deprecated
 
     steps:
       - uses: actions/checkout@v4
@@ -140,9 +140,14 @@ jobs:
             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"
+            NB_ARGS+=" --ignore=examples/toolkit_showcase"
+          fi
+
+          # GROMACS builds are not stable on macOS + GHA
+          if [[ ${{ matrix.os }} == macos-latest ]]; then
+            NB_ARGS+=" --ignore=examples/using_smirnoff_in_amber_or_gromacs/"
           fi
 
           python -m pytest $PYTEST_ARGS $NB_ARGS examples

.github/workflows/installer.yml

@@ -68,7 +68,7 @@ jobs:
         ls build
 
     - name: Upload installer as artifact
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: ${{ matrix.os }}_py${{ matrix.python-version }}.sh
         path: toolkit-installer-constructor/build/openff-toolkit*/openff-toolkit*.sh

.github/workflows/lint.yml

@@ -12,7 +12,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.10'
 

.pre-commit-config.yaml

@@ -1,23 +1,23 @@
 ci:
   autoupdate_schedule: "quarterly"
-files: ^openff|(^examples/((?!deprecated).)*$)
+files: ^openff|(^examples/((?!deprecated).)*$)|^docs
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.4.0
   hooks:
   - id: end-of-file-fixer
     exclude: '\.(json|pdb)$'
 - repo: https://github.com/psf/black
-  rev: 23.9.1
+  rev: 24.1.1
   hooks:
   - id: black
   - id: black-jupyter
 - repo: https://github.com/PyCQA/isort
-  rev: 5.12.0
+  rev: 5.13.2
   hooks:
   - id: isort
 - repo: https://github.com/PyCQA/flake8
-  rev: 6.1.0
+  rev: 7.0.0
   hooks:
   - id: flake8
     files: ^openff
@@ -27,11 +27,11 @@ repos:
         'flake8-bugbear',
     ]
 - repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.7.0
+  rev: 1.7.1
   hooks:
     - id: nbqa-pyupgrade
       args:
-        - --py37-plus
+        - --py39-plus
     - id: nbqa-isort
     - id: nbqa-flake8
       args:

.readthedocs.yaml

@@ -2,6 +2,7 @@
 version: 2
 sphinx:
   configuration: docs/conf.py
+  fail_on_warning: true
 build:
   os: ubuntu-20.04
   tools:

FAQ.md

@@ -66,10 +66,13 @@ This behavior is in line with OpenFF's general attitude of requiring users to ex
 
 ## I'm having troubles installing the OpenFF Toolkit on my Apple Silicon Mac.
 
-As of August 2022, some upstreams (at least AmberTools, possibly more) are not built on `osx-arm64`, so installing the OpenFF stack is only possible with [Rosetta](https://support.apple.com/en-au/HT211861). See the [platform support](installation/m1) section of the installation documentation for more.
+As of August 2022, some upstreams (at least AmberTools, possibly more) are not built on `osx-arm64`, so installing the OpenFF stack is only possible with [Rosetta]. See the [platform support] section of the installation documentation for more.
 
 (Keywords `osx-arm64`, M1 Mac, M2 Mac)
 
+[Rosetta]: https://support.apple.com/en-au/HT211861
+[platform support]: inv:#install_arm
+
 ## 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 environment, explicitly passing the channels to be used, in-order:

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/0.14.4.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)
+| **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/0.15.2.svg)](https://github.com/openforcefield/openff-toolkit/releases/tag/0.15.2)[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10613658.svg)](https://doi.org/10.5281/zenodo.10613658)
 | **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)          |
@@ -21,7 +21,7 @@ The toolkit currently covers two main areas we have committed to stably maintain
 
 ## How to cite
 
-Please cite the OpenFF Toolkit using the [Zenodo record](https://zenodo.org/record/7506404) of the [latest release](https://zenodo.org/record/7506404) or the version that was used. The BibTeX reference of the latest release can be found [here](https://zenodo.org/record/7506404/export/hx#.Y7cYbOzMKrM).
+Please cite the OpenFF Toolkit using the [Zenodo record](https://zenodo.org/record/10103216) of the [latest release](https://zenodo.org/record/10103216) or the version that was used. The BibTeX reference of the latest release can be found [here](https://zenodo.org/record/10103216/export/hx#.Y7cYbOzMKrM).
 
 ## Installation
 

devtools/conda-envs/beta_rc_env.yaml

@@ -1,4 +1,4 @@
-name: test
+name: openff-toolkit-beta-rc-test
 channels:
   - conda-forge/label/openmm_rc
   - openeye/label/rc
@@ -18,8 +18,9 @@ dependencies:
   - openff-forcefields >=2023.05.1
   - smirnoff99Frosst
   - openff-units =0.2.0
+  - openff-amber-ff-ports
   - openff-utilities >=0.1.5
-  - openff-interchange-base >=0.3.10
+  - openff-interchange-base >=0.3.17
   - openff-nagl-base ==0.3.0
   - openff-nagl-models ==0.1.0
     # Toolkit-specific
@@ -35,6 +36,10 @@ dependencies:
   - toml
   - bson
   - msgpack-python
+  - qcelemental
+  - qcportal >=0.50
+  - qcengine
+  - nglview
   - mdtraj
   - nbval
   - mypy

devtools/conda-envs/conda.yaml

@@ -5,5 +5,5 @@ dependencies:
     # Base depends
   - openff-toolkit-examples
     # Tests
-  - pytest
+  - pytest=7.4
   - pytest-rerunfailures

devtools/conda-envs/conda_oe.yaml

@@ -7,5 +7,5 @@ dependencies:
   - openff-toolkit-examples
     # Tests
   - openeye-toolkits
-  - pytest
+  - pytest=7.4
   - pytest-rerunfailures

devtools/conda-envs/openeye-examples.yaml

@@ -13,32 +13,32 @@ dependencies:
   - xmltodict
   - python-constraint
   - openmm >=7.6
-  - openff-forcefields >=2023.05.1
+  - openff-forcefields >=2023.11
   - smirnoff99Frosst
   - openff-amber-ff-ports >=0.0.3
   - openff-units =0.2.0
   - openff-utilities >=0.1.5
-  - openff-interchange-base >=0.3.10
+  - openff-interchange-base >=0.3.17
   - openff-nagl-base ==0.3.0
   - openff-nagl-models ==0.1.0
   - typing_extensions
+  - nglview
     # Toolkit-specific
   - openeye-toolkits
     # Test-only/optional/dev/typing/examples
   - pytest
-  - pytest-cov
   - pytest-xdist
   - pytest-rerunfailures
   - pyyaml
   - toml
   - bson
   - msgpack-python
   - qcelemental
-  - qcportal ==0.15.8
+  - qcportal >=0.50
   - qcengine
   - mdtraj
   - parmed =3
   - nbval
   - pdbfixer
   - openmmforcefields >=0.11.2
-  - gromacs >=2021=nompi*
+  - gromacs =2023.3=nompi_*_101

devtools/conda-envs/openeye.yaml

@@ -18,7 +18,7 @@ dependencies:
   - openff-units =0.2.0
   - openff-amber-ff-ports
   - openff-utilities >=0.1.5
-  - openff-interchange-base >=0.3.10
+  - openff-interchange-base >=0.3.17
   - openff-nagl-base ==0.3.0
   - openff-nagl-models ==0.1.0
   - typing_extensions
@@ -34,7 +34,7 @@ dependencies:
   - bson
   - msgpack-python
   - qcelemental
-  - qcportal ==0.15.8
+  - qcportal >=0.50
   - qcengine
   - mdtraj
   - nglview

devtools/conda-envs/rdkit-examples.yaml

@@ -12,33 +12,34 @@ dependencies:
   - xmltodict
   - python-constraint
   - openmm >=7.6
-  - openff-forcefields >=2023.05.1
+  - openff-forcefields >=2023.11
   - smirnoff99Frosst
   - openff-amber-ff-ports >=0.0.3
   - openff-units =0.2.0
   - openff-utilities >=0.1.5
-  - openff-interchange-base >=0.3.10
+  - openff-interchange-base >=0.3.17
   - openff-nagl-base ==0.3.0
   - openff-nagl-models ==0.1.0
   - typing_extensions
+  - nglview
     # Toolkit-specific
   # AmberTools 23 brings in ParmEd 4, which doesn't yet work with examples
   # https://github.com/openforcefield/openff-toolkit/issues/1532
   - ambertools =22.4
   - rdkit
     # Test-only/optional/dev/typing/examples
   - pytest
-  - pytest-cov
   - pytest-xdist
   - pytest-rerunfailures
   - pyyaml
   - toml
   - bson
   - msgpack-python
   - qcelemental
+  - qcportal >=0.50
   - qcengine
   - nbval
   - mdtraj
   - pdbfixer
   - openmmforcefields >=0.11.2
-  - gromacs >=2021=nompi*
+  - gromacs =2023.3=nompi_*_101

devtools/conda-envs/rdkit.yaml

@@ -17,7 +17,7 @@ dependencies:
   - openff-units =0.2.0
   - openff-amber-ff-ports
   - openff-utilities >=0.1.5
-  - openff-interchange-base >=0.3.10
+  - openff-interchange-base >=0.3.17
   - openff-nagl-base ==0.3.0
   - openff-nagl-models ==0.1.0
   - typing_extensions
@@ -34,6 +34,6 @@ dependencies:
   - bson
   - msgpack-python
   - qcelemental
-  - qcportal ==0.15.8
+  - qcportal >=0.50
   - qcengine
   - nglview

devtools/conda-envs/test_env.yaml

@@ -19,7 +19,7 @@ dependencies:
   - openff-units =0.2.0
   - openff-amber-ff-ports
   - openff-utilities >=0.1.5
-  - openff-interchange-base >=0.3.10
+  - openff-interchange-base >=0.3.17
   - openff-nagl-base ==0.3.0
   - openff-nagl-models ==0.1.0
     # Toolkit-specific
@@ -36,11 +36,13 @@ dependencies:
   - bson
   - msgpack-python
   - qcelemental
-  - qcportal ==0.15.8
+  - qcportal >=0.50
   - qcengine
   - nglview
   - mdtraj
   - nbval
+  # No idea why this is necessary, see https://github.com/openforcefield/openff-toolkit/pull/1821
+  - nomkl
   - mypy
   - typing_extensions
   - pip:

docs/_templates/autosummary/base.rst

@@ -17,4 +17,4 @@ but free functions do not.
 
 .. currentmodule:: {{ module }}
 
-.. auto{{ objtype }}:: {{ objname }}
+.. auto{{ objtype }}:: {{ objname }}