Merge remote-tracking branch 'upstream/main' into pytest-8

openforcefield · Jun 7, 2024 · fcfc6a9 · fcfc6a9
2 parents 5ad99d8 + fdf3832
commit fcfc6a9
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diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -2,4 +2,4 @@
 - [ ] Add [tests](https://github.com/openforcefield/openff-toolkit/tree/main/openff/toolkit/_tests)
 - [ ] Update docstrings/[documentation](https://github.com/openforcefield/openff-toolkit/tree/main/docs), if applicable
 - [ ] [Lint](https://open-forcefield-toolkit.readthedocs.io/en/latest/developing.html#style-guide) codebase
-- [ ] Update [changelog](https://github.com/openforcefield/openff-toolkit/blob/main/docs/releasehistory.rst)
+- [ ] Update [changelog](https://github.com/openforcefield/openff-toolkit/blob/main/docs/releasehistory.md)
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -19,17 +19,17 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest]
-        python-version: ["3.9", "3.10", "3.11"]
+        os: [ubuntu-latest, macos-12]
+        python-version: ["3.10", "3.11", "3.12"]
         rdkit: [true, false]
         openeye: [true, false]
         exclude:
           - rdkit: false
             openeye: false
-          - openeye: true
-            python-version: "3.10"
           - openeye: true
             python-version: "3.11"
+          - openeye: true
+            python-version: "3.12"
 
     env:
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
@@ -71,17 +71,10 @@ jobs:
           create-args: >-
             python=${{ matrix.python-version }}
 
-      - name: Additional info about the build
-        run: |
-          uname -a
-          df -h
-          ulimit -a
-
       - name: Make oe_license.txt file from GH org secret "OE_LICENSE"
         env:
           OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }}
-        run: |
-          echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE}
+        run: echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE}
 
       - name: Install package
         run: |
@@ -94,14 +87,13 @@ jobs:
           python -m pip install .
 
       - name: Install test plugins
-        run: |
-          python -m pip install utilities/test_plugins
+        run: python -m pip install utilities/test_plugins
 
       - name: Remove undesired toolkits
         run: |
           if [ ! -z "${{ env.PACKAGES_TO_REMOVE }}" ]; then
             for cpkg in ${{ env.PACKAGES_TO_REMOVE }}; do
-              if [[ $(conda list | grep $cpkg) ]]; then micromamba remove --force $cpkg --yes ; fi
+              if [[ $(micromamba list | grep $cpkg) ]]; then micromamba remove --force $cpkg --yes ; fi
             done
           fi
 
@@ -126,15 +118,16 @@ jobs:
 
       - name: Environment Information
         run: |
-          conda info
-          conda list
+          micromamba info
+          micromamba list
 
       - name: Check links
         if: ${{ matrix.rdkit == true && matrix.openeye == true }}
         run: pytest -r fE --tb=short openff/toolkit/_tests/test_links.py
 
       - name: Run mypy
-        if: ${{ matrix.rdkit == true && matrix.openeye == true }}
+        # subtle differences in Python/mypy versions, just keep it passing on one
+        if: ${{ matrix.rdkit == true && matrix.openeye && matrix.python-version == 3.10 }}
         run: mypy -p "openff.toolkit"
 
       - name: Run unit tests
@@ -145,22 +138,24 @@ jobs:
             PYTEST_ARGS+=" -m 'slow or not slow'"
           fi
 
-          python -m pytest $PYTEST_ARGS $COV
+          python -m pytest --durations=20 $PYTEST_ARGS $COV
 
       - name: Run code snippets in docs
         if: ${{ matrix.rdkit == true && matrix.openeye == true }}
-        run: |
-          pytest -v --no-cov --doctest-glob="docs/*.rst" --doctest-glob="docs/*.md" docs/
+        run: pytest -v --no-cov --doctest-glob="docs/*.rst" --doctest-glob="docs/*.md" docs/
 
       - name: Run notebooks in docs
         if: ${{ matrix.rdkit == true && matrix.openeye == true }}
-        run: |
-          pytest -v --no-cov --durations=5 --nbval --ignore docs/_build/ docs/
+        run: pytest -v --no-cov --nbval --ignore docs/_build/ docs/
 
       - name: Run examples in docstrings
         if: ${{ matrix.rdkit == true && matrix.openeye == true }}
         run: |
-          pytest -v --no-cov --doctest-modules --ignore-glob='openff/toolkit/_tests/test_*' --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@v4

diff --git a/.github/workflows/beta_rc.yaml b/.github/workflows/beta_rc.yaml
@@ -1,8 +1,8 @@
-name: Weekly test against upstream beta and RC builds
+name: Tests against beta/RC builds
 
 on:
   schedule:
-    - cron: "0 0 * * 0"
+    - cron: "0 3 * * 0"
   workflow_dispatch:
 
 defaults:
@@ -11,21 +11,20 @@ defaults:
 
 jobs:
   test:
-    name: Test beta and RC builds on on ${{ matrix.python-version }}
+    name: Test beta/RC builds on ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os:
           - ubuntu-latest
-          - macos-latest
+          - macos-12
         python-version:
-          - 3.9
+          - "3.11"
 
     env:
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
       PYTEST_ARGS: -r fE --tb=short -nauto
-      COV: --cov=openff/toolkit --cov-config=setup.cfg --cov-append --cov-report=xml
 
     steps:
       - uses: actions/checkout@v4
@@ -35,16 +34,17 @@ jobs:
       - name: Install environment with ${{ env.JOBNAME }}
         uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: devtools/conda-envs/beta_rc_env.yaml
+          environment-file: devtools/conda-envs/test_env.yaml
+          condarc: |
+            channels:
+              - conda-forge/label/openmm_rc
+              - conda-forge/label/mdtraj_rc
+              - openeye/label/rc
+              - openeye
+              - conda-forge
           create-args: >-
             python=${{ matrix.python-version }}
 
-      - name: Additional info about the build
-        run: |
-          uname -a
-          df -h
-          ulimit -a
-
       - name: Make oe_license.txt file from GH org secret "OE_LICENSE"
         env:
           OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }}
@@ -57,36 +57,24 @@ jobs:
           python -m pip install .
 
       - name: Install test plugins
-        run: |
-          python -m pip install utilities/test_plugins
+        run: python -m pip install utilities/test_plugins
 
       - name: Environment Information
-        run: |
-          conda info
-          conda list
+        run: micromamba info && micromamba list
 
       - name: Check links
-        run: |
-          pytest -r fE --tb=short openff/toolkit/_tests/test_links.py
+        run: pytest -r fE --tb=short openff/toolkit/_tests/test_links.py
 
       - name: Run mypy
-        run: |
-          mypy --namespace-packages -p "openff.toolkit"
+        run: mypy -p "openff.toolkit"
 
       - name: Run unit tests
         run: |
           PYTEST_ARGS+=" --ignore=openff/toolkit/_tests/test_examples.py"
           PYTEST_ARGS+=" --ignore=openff/toolkit/_tests/test_links.py"
           PYTEST_ARGS+=" -m 'slow or not slow'"
-          pytest $PYTEST_ARGS $COV
+          pytest $PYTEST_ARGS
 
       - name: Run code snippets in docs
         run: |
           pytest -v --doctest-glob="docs/*.rst" --doctest-glob="docs/*.md" docs/
-
-      - name: Codecov
-        uses: codecov/codecov-action@v4
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          file: ./coverage.xml
-          fail_ci_if_error: true
diff --git a/.github/workflows/conda.yml b/.github/workflows/conda.yml
@@ -21,8 +21,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest]
-        python-version: ["3.11"]
+        os: [ubuntu-latest, macos-12]
+        python-version: ["3.10"]
         openeye: ["true", "false"]
 
     env:

diff --git a/.github/workflows/examples.yml b/.github/workflows/examples.yml
@@ -16,8 +16,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest]
-        python-version: ["3.9"]
+        os: [ubuntu-latest, macos-12]
+        python-version: ["3.10"]
         rdkit: [true, false]
         openeye: [true, false]
         exclude:

diff --git a/.github/workflows/installer.yml b/.github/workflows/installer.yml
@@ -12,8 +12,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [macOS-latest, ubuntu-latest]
-        python-version: ["3.9", "3.10"]
+        os: [macOS-12, ubuntu-latest]
+        python-version: ["3.10", "3.11"]
 
     env:
       CI_OS: ${{ matrix.os }}

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,7 +3,7 @@ ci:
 files: ^openff|(^examples/((?!deprecated).)*$)|^docs
 repos:
 - repo: https://github.com/psf/black
-  rev: 24.1.1
+  rev: 24.3.0
   hooks:
   - id: black
   - id: black-jupyter
@@ -22,7 +22,7 @@ repos:
         'flake8-bugbear',
     ]
 - repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.7.1
+  rev: 1.8.5
   hooks:
     - id: nbqa-pyupgrade
       args:
@@ -31,3 +31,8 @@ repos:
     - id: nbqa-flake8
       args:
         - '--select=F'
+- repo: https://github.com/adamchainz/blacken-docs
+  rev: 1.16.0
+  hooks:
+    - id: blacken-docs
+      files: ^docs/.*\.(rst|md)$
diff --git a/FAQ.md b/FAQ.md
@@ -22,7 +22,6 @@ Parameter files used by typical molecular dynamics simulation packages do not cu
 For example, one could take a structure file and infer bond orders based on bond lengths, or attempt to infer bond orders from force constants in a parameter file.
 Such inference work is outside the scope of SMIRNOFF.
 
-
 ## What about starting from a PDB file?
 
 PDB files do not in general provide the chemical identity of small molecules contained therein, and thus do not provide suitable starting points for applying SMIRNOFF to small molecules.
@@ -95,6 +94,18 @@ source ~/miniconda3/etc/profile.d/conda.sh
 
 and then try rerunning and/or reinstalling the Toolkit. 
 
+## How are partial charges assigned in a SMIRNOFF force field?
+
+There are [many charge methods](https://openforcefield.github.io/standards/standards/smirnoff/#partial-charge-and-electrostatics-models) supported by the SMIRNOFF specification. With the exception of water, mainline OpenFF force fields only use AM1-BCC (through `ToolkitAM1BCC`) to assign partial charges. (A future biopolymer force field will likely use library charges for standard residues.)
+
+If OpenEye Toolkits are installed and licensed, the ELF10 variant of AM1-BCC is used. OpenEye's Quacpac (`oequacpac.OEAM1BCCELF10Charges`) is used to generate partial charges.
+
+Otherwise, RDKit is used to generate a conformer which is passed to AmberTool's `sqm` (with `-c bcc`).
+
+Note that, because of differences with the ELF10 variant and other subtle differences between OpenEye Toolkits and RDKit/AmberTools, **assigned partial charges can be expected to differ** based on the available toolkit(s). These numerical differences are often minor but in some molecules or use cases can be significant.
+
+A future charge method may use [NAGL](https://github.com/openforcefield/openff-nagl) to assign partial charges from a graph-convolutional neural network instead of an underlying semi-empirical method. This approach is anticipated to be faster, more scalable, and more consistent than current approaches. As of March 2024, this is under development and not released for general use.
+
 ## The partial charges generated by the toolkit don't seem to depend on the molecule's conformation! Is this a bug?
 
 No! This is the intended behavior. The force field parameters of a molecule should be independent of both their chemical environment and conformation so that they can be used and compared across different contexts. When applying AM1BCC partial charges, the toolkit achieves a deterministic output by ignoring the input conformation and producing several new conformations for the same molecule. Partial charges are then computed based on these conformations. This behavior can be controlled with the `use_conformers` argument to [Molecule.assign_partial_charges()](openff.toolkit.topology.Molecule.assign_partial_charges).

diff --git a/README.md b/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/0.15.2.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)
+| **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)
 | **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)          |

diff --git a/codecov.yml b/codecov.yml
@@ -1,5 +1,3 @@
-
-# Codecov configuration to make it a bit less noisy
 coverage:
   status:
     patch: false
@@ -12,4 +10,6 @@ comment:
   branches: null
   behavior: default
   flags: null
-  paths: null
+  paths: null
+ignore:
+  - "examples/"
diff --git a/devtools/conda-envs/beta_rc_env.yaml b/devtools/conda-envs/beta_rc_env.yaml
diff --git a/devtools/conda-envs/conda.yaml b/devtools/conda-envs/conda.yaml
@@ -0,0 +1,11 @@
+name: latest-deployment
+channels:
+  - conda-forge
+dependencies:
+    # Base depends
+  - openff-toolkit-examples
+    # Tests
+  - pytest=7.4
+  - pytest-rerunfailures
+  - nbval
+  - parmed=3