Merge remote-tracking branch 'upstream/main' into from-openmm-virtual…

…-sites

.github/workflows/beta.yaml

@@ -16,7 +16,7 @@ jobs:
       fail-fast: false
       matrix:
         os:
-          - macos-12
+          - macos-latest
           - ubuntu-latest
         python-version:
           - "3.10"
@@ -33,6 +33,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
 
     - name: Install conda environment
       uses: mamba-org/setup-micromamba@v1

.github/workflows/ci.yaml

@@ -24,7 +24,7 @@ jobs:
     strategy:
       matrix:
         os:
-          - macos-12
+          - macos-latest
           - ubuntu-latest
         python-version:
           - "3.10"
@@ -44,6 +44,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
 
     - name: Install conda environment
       uses: mamba-org/setup-micromamba@v1
@@ -124,7 +126,7 @@ jobs:
         python devtools/scripts/molecule-regressions.py
 
     - name: Run mypy
-      if: ${{ matrix.python-version == '3.10' }}
+      if: ${{ matrix.python-version == '3.11' }}
       run: |
         # As of 01/23, JAX with mypy is too slow to use without a pre-built cache
         # https://github.com/openforcefield/openff-interchange/pull/578#issuecomment-1369979875

.github/workflows/examples.yaml

@@ -25,7 +25,7 @@ jobs:
       matrix:
         os:
           - ubuntu-latest
-          - macos-12
+          - macos-latest
         python-version:
           - "3.10"
 
@@ -35,6 +35,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
 
     - name: Install conda environment
       uses: mamba-org/setup-micromamba@v1
@@ -46,9 +48,6 @@ jobs:
 
     - name: Install package
       run: |
-        # These packages are brought in by conda (via the toolkit) and must be removed manually
-        # since pip doesn't know about the -base split and does not uninstall the -base package
-        micromamba remove --force openff-interchange openff-interchange-base
         python -m pip install .
 
     - name: Environment Information
@@ -65,7 +64,7 @@ jobs:
 
     - name: Run docexamples
       run: |
-        pytest --doctest-modules openff/interchange/ --ignore=openff/interchange/_tests
+        python -m pytest --doctest-modules openff/interchange/ --ignore=openff/interchange/_tests
 
     - name: Run example notebooks
       if: always()

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.6.0
+  rev: v5.0.0
   hooks:
   - id: check-yaml
   - id: end-of-file-fixer
@@ -12,7 +12,7 @@ repos:
   hooks:
   - id: add-trailing-comma
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.6.2
+  rev: v0.7.3
   hooks:
     - id: ruff
     - id: ruff-format
@@ -23,18 +23,18 @@ repos:
       args: ["openff/interchange/", "-e", "openff/interchange/_tests/"]
       pass_filenames: false
 - repo: https://github.com/adamchainz/blacken-docs
-  rev: 1.18.0
+  rev: 1.19.1
   hooks:
   - id: blacken-docs
     files: ^docs/
 - repo: https://github.com/igorshubovych/markdownlint-cli
-  rev: v0.41.0
+  rev: v0.42.0
   hooks:
   - id: markdownlint
     exclude: .github
     args: ["--disable", "MD013", "MD033", "MD024", "MD046", "--ignore", "docs/using/experimental.md", "--ignore", "docs/using/status.md", "--"]
 - repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.8.7
+  rev: 1.9.1
   hooks:
     - id: nbqa-pyupgrade
       files: ^examples
@@ -45,12 +45,12 @@ repos:
       args:
         - --fix
 - repo: https://github.com/kynan/nbstripout
-  rev: 0.7.1
+  rev: 0.8.0
   hooks:
     - id: nbstripout
       files: ^examples
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.17.0
+  rev: v3.19.0
   hooks:
   - id: pyupgrade
     args:

.readthedocs.yml

@@ -1,16 +1,23 @@
-# .readthedocs.yml
-
 version: 2
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    # https://docs.readthedocs.io/en/stable/config-file/v2.html#build-tools-python
-    python: "mambaforge-4.10"
+    python: "mambaforge-latest"
+  jobs:
+    pre_build:
+      - mamba list
 
 sphinx:
   configuration: docs/conf.py
+  # Interchange's docs should not produce warnings; if they start,
+  # something is broken (most likely automatic API doc generation)
   fail_on_warning: true
 
 conda:
   environment: devtools/conda-envs/docs_env.yaml
+
+python:
+  install:
+    - method: pip
+      path: .

MANIFEST.in

@@ -1,6 +1,5 @@
 include LICENSE
 include MANIFEST.in
-include versioneer.py
 
 graft openff
 global-exclude *.py[cod] __pycache__ *.so

devtools/conda-envs/beta_env.yaml

@@ -8,7 +8,7 @@ dependencies:
   - python
   - numpy >=1.21
   - pydantic >=1.10.17,<3
-  - openmm >=7.6
+  - openmm
   # OpenFF stack
   - openff-toolkit ~=0.16.4
   - openff-nagl ~=0.3.7

devtools/conda-envs/dev_env.yaml

@@ -6,7 +6,7 @@ dependencies:
   # Core
   - python =3.10
   - pip
-  - versioneer-518
+  - versioningit
   - pip
   - numpy
   - pydantic =2
@@ -15,7 +15,7 @@ dependencies:
   - openff-units
   - ambertools =23
   # Optional features
-  - openmm
+  - openmm =8.1.2
   # smirnoff-plugins =2024
   # de-forcefields  # add back after smirnoff-plugins update
   - openff-nagl

devtools/conda-envs/docs_env.yaml

@@ -5,11 +5,12 @@ dependencies:
   # Base depends
   # https://docs.readthedocs.io/en/stable/config-file/v2.html#build-tools-python
   - python =3.10
+  - versioningit
   - pip
   - numpy =1
   - pydantic =2
   - openff-toolkit-base ~=0.16.4
-  - openmm =8
+  - openmm =8.1.2
   - mbuild
   - foyer =1
   - nglview
@@ -20,8 +21,8 @@ dependencies:
   - myst-parser
   - numpydoc
   - autodoc-pydantic =2
-  - sphinx ~=4.4
+  - sphinx ==6.1.3
   - sphinxcontrib-mermaid
   - sphinx-notfound-page
   - pip:
-    - git+https://github.com/openforcefield/openff-sphinx-theme.git@main
+      - git+https://github.com/openforcefield/openff-sphinx-theme.git@main

devtools/conda-envs/examples_env.yaml

@@ -5,7 +5,7 @@ channels:
 dependencies:
   # Core
   - python
-  - versioneer-518
+  - versioningit
   - numpy
   - pydantic =2
   # OpenFF stack

devtools/conda-envs/test_env.yaml

@@ -4,7 +4,7 @@ channels:
 dependencies:
   # Core
   - python
-  - versioneer-518
+  - versioningit
   - numpy
   - pydantic =2
   # OpenFF stack
@@ -14,7 +14,7 @@ dependencies:
   # Needs to be explicitly listed to not be dropped when AmberTools is removed
   - rdkit
   # Optional features
-  - openmm
+  - openmm =8.1.2
   # smirnoff-plugins =2024
   # de-forcefields  # add back after smirnoff-plugins update
   - openff-nagl

docs/conf.py

@@ -14,10 +14,8 @@
 # Incase the project was not installed
 import importlib
 import os
-import sys
-
-sys.path.insert(0, os.path.abspath(".."))
 
+from openff.interchange import __version__
 
 # -- Project information -----------------------------------------------------
 
@@ -27,18 +25,12 @@
     "Computational Molecular Science Python Cookiecutter version 1.2"
 )
 author = "Open Force Field Initiative"
-
-# The short X.Y version
-version = ""
-# The full version, including alpha/beta/rc tags
-release = ""
+version = __version__
 
 
 # -- General configuration ---------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-#
-# needs_sphinx = '1.0'
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
@@ -89,7 +81,6 @@
 autosummary_context = {
     # Modules to exclude from API docs
     "exclude_modules": [
-        "openff.interchange.conftest",
         "openff.interchange._tests",  # Maybe this is excluded by default?
     ],
 }
@@ -102,7 +93,7 @@
 autodoc_default_options = {
     "member-order": "bysource",
     "undoc-members": True,
-    "inherited-members": [],
+    "inherited-members": "",
     "show-inheritance": True,
 }
 autodoc_preserve_defaults = True
@@ -169,7 +160,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -258,7 +249,7 @@
     (
         master_doc,
         "interchange.tex",
-        "openff-interchange Documentation",
+        "Interchange Documentation",
         "interchange",
         "manual",
     ),
@@ -270,7 +261,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, "interchange", "openff-interchange Documentation", [author], 1),
+    (master_doc, "interchange", "Interchange Documentation", [author], 1),
 ]
 
 
@@ -283,7 +274,7 @@
     (
         master_doc,
         "interchange",
-        "openff-interchange Documentation",
+        "Interchange Documentation",
         author,
         "interchange",
         "A molecular interchange object from the Open Force Field Initiative",
@@ -292,4 +283,13 @@
 ]
 
 
-# -- Extension configuration -------------------------------------------------
+# -- ReadTheDocs configuration -------------------------------------------------
+
+if os.environ.get("READTHEDOCS", "") == "True":
+    # Define the canonical URL if you are using a custom domain on Read the Docs
+    html_baseurl = os.environ.get("READTHEDOCS_CANONICAL_URL", "")
+
+    # Tell Jinja2 templates the build is running on Read the Docs
+    if "html_context" not in globals():
+        html_context = {}
+    html_context["READTHEDOCS"] = True

docs/docutils.conf

@@ -0,0 +1,2 @@
+[html writers]
+table-style: colwidths-grid

docs/index.md

@@ -31,6 +31,7 @@ using/plugins.md
 using/status.md
 using/edges.md
 using/experimental.md
+using/advanced.md
 
 ```
 

docs/installation.md

@@ -1,6 +1,6 @@
 # Installation
 
-These instructions assume that the `mamba` package manager is installed. If you do not have Conda/Mamba or a drop-in replacement installed, see the [OpenFF installation documentation](openff.docs:install).
+These instructions assume that the `mamba` package manager is installed. If you do not have Conda/Mamba or a drop-in replacement installed, see the [OpenFF installation documentation](inv:openff.docs#install).
 
 ## Quick Installation