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Format pyproject.toml (#2111)
* Support PEP 639 * Automatically format config file * Fix * update releasehistory --------- Co-authored-by: Jeff Wagner <[email protected]>
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‎.pre-commit-config.yaml‎

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ci:
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autoupdate_schedule: "quarterly"
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files: ^openff|(^examples/((?!deprecated).)*$)|^docs|(^utilities/((?!deprecated).)*$)
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files: ^pyproject.toml|openff|(^examples/((?!deprecated).)*$)|^docs|(^utilities/((?!deprecated).)*$)
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repos:
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.12.11
@@ -13,3 +13,7 @@ repos:
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hooks:
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- id: blacken-docs
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files: ^docs/.*\.(rst|md)$
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- repo: https://github.com/tox-dev/pyproject-fmt
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rev: v2.7.0
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hooks:
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- id: pyproject-fmt

‎docs/releasehistory.md‎

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@@ -6,21 +6,14 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
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* `minor` increments add features but do not break API compatibility
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* `micro` increments represent bugfix releases or improvements in documentation
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## Current development
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### API-breaking changes
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### Behavior changes
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## 0.17.1
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### Bugfixes
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- [PR #2107](https://github.com/openforcefield/openff-toolkit/pull/2107): Fixes [Issue #2093](https://github.com/openforcefield/openff-toolkit/issues/2093), where in rare cases `Topology.from_pdb` would mangle the order/coordinates of loaded atoms, by making it raise a `PDBMoleculeHasNoncontiguousAtomIndicesError` instead.
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- [PR #2109](https://github.com/openforcefield/openff-toolkit/pull/2109): Fixes [Issue #2108](https://github.com/openforcefield/openff-toolkit/issues/2108) by updating tests to reflect that smirnoff99Frosst is no longer installed as a dependency of the OpenFF Toolkit.
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### New features
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### Improved documentation and warnings
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- [PR #2111](https://github.com/openforcefield/openff-toolkit/pull/2111): Formats and cleans up pyproject.toml.
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## 0.17.0
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‎pyproject.toml‎

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[build-system]
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requires = ["setuptools", "versioningit"]
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build-backend = "setuptools.build_meta"
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requires = [ "setuptools>=77.0.3", "versioningit" ]
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[project]
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name="openff-toolkit"
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name = "openff-toolkit"
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description = "openff-toolkit"
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license = {text = "MIT"}
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urls = {Homepage = "https://github.com/openforcefield/openff-toolkit"}
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authors = [{name = "Open Force Field Consortium", email = "[email protected]"}]
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keywords=["molecular mechanics", "force field", "parameterization",]
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classifiers=[
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"Development Status :: 3 - Alpha",
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"Topic :: Utilities",
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"License :: OSI Approved :: MIT",
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'Programming Language :: Python :: 3',
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]
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readme = "README.md"
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keywords = [ "force field", "molecular mechanics", "parameterization" ]
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license = "MIT"
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license-files = [ "LICENSE" ]
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authors = [ { name = "Open Force Field Consortium", email = "[email protected]" } ]
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requires-python = ">=3.11"
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dynamic = ["version"]
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classifiers = [
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"Development Status :: 3 - Alpha",
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"Programming Language :: Python :: 3 :: Only",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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"Programming Language :: Python :: 3.13",
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"Topic :: Utilities",
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]
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dynamic = [ "version" ]
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urls = { Homepage = "https://github.com/openforcefield/openff-toolkit" }
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[tool.setuptools.packages]
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find = {}
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[tool.versioningit]
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[tool.ruff]
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line-length = 119
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exclude = ["examples/deprecated/", "utilities/deprecated"]
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exclude = [ "examples/deprecated/", "utilities/deprecated" ]
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[tool.ruff.lint]
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ignore = ["E721","D105","D107","D200","D203","D212", "RUF012"]
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select = ["I", "E", "F", "W", "NPY", "UP", "RUF"]
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[tool.ruff.lint.per-file-ignores]
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"openff/toolkit/**/__init__.py" = ["F401"]
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"openff/toolkit/_tests/**/*.py" = ["E501"]
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"openff/toolkit/typing/engines/smirnoff.parameters.py" = ["RUF012"]
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"openff/toolkit/_tests/_stale_tests.py" = ["F821"]
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"docs/users/molecule_cookbook.ipynb" = ["F821", "E402"]
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"examples/visualization/visualization.ipynb" = ["F821"]
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[tool.ruff.lint.isort]
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lint.select = [ "E", "F", "I", "NPY", "RUF", "UP", "W" ]
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lint.ignore = [ "D105", "D107", "D200", "D203", "D212", "E721", "RUF012" ]
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lint.per-file-ignores."docs/users/molecule_cookbook.ipynb" = [ "E402", "F821" ]
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lint.per-file-ignores."examples/visualization/visualization.ipynb" = [ "F821" ]
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lint.per-file-ignores."openff/toolkit/**/__init__.py" = [ "F401" ]
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lint.per-file-ignores."openff/toolkit/_tests/**/*.py" = [ "E501" ]
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lint.per-file-ignores."openff/toolkit/_tests/_stale_tests.py" = [ "F821" ]
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lint.per-file-ignores."openff/toolkit/typing/engines/smirnoff.parameters.py" = [ "RUF012" ]
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lint.isort.known-first-party = [ "openff.toolkit" ]
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# can't find a clean way to get Rust's globset to handle this via regex ...
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# https://docs.astral.sh/ruff/settings/#lint_isort_known-third-party
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known-third-party = ["openff.interchange", "openff.utilities", "openff.units"]
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known-first-party = ["openff.toolkit"]
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lint.isort.known-third-party = [ "openff.interchange", "openff.utilities", "openff.units" ]
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[tool.coverage.run]
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omit = [
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"*/*/_tests/*",
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"*/*/_tests/*",
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]
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[tool.coverage.report]
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exclude_lines = [
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"pragma: no cover",
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"if TYPE_CHECKING:",
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"raise NotImplementedError",
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"@overload",
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"pragma: no cover",
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"if TYPE_CHECKING:",
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"raise NotImplementedError",
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"@overload",
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]
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[tool.mypy]
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[[tool.mypy.overrides]]
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module = [
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"openff.units",
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"openff.units.*",
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"openff.nagl.*",
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"openff.nagl_models.*",
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"mdtraj",
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"openmm",
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"openmm.app",
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"openmm.unit",
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"rdkit",
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"rdkit.Chem",
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"rdkit.Chem.Draw",
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"rdkit.DataStructs.cDataStructs",
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"openeye",
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"openeye.oechem",
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"parmed",
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"msgpack",
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"qcelemental",
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"nglview",
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"nglview.base_adaptor",
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"constraint",
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"openff.units",
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"openff.units.*",
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"openff.nagl.*",
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"openff.nagl_models.*",
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"mdtraj",
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"openmm",
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"openmm.app",
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"openmm.unit",
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"rdkit",
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"rdkit.Chem",
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"rdkit.Chem.Draw",
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"rdkit.DataStructs.cDataStructs",
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"openeye",
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"openeye.oechem",
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"parmed",
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"msgpack",
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"qcelemental",
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"nglview",
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"nglview.base_adaptor",
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"constraint",
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]
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ignore_missing_imports = true
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[tool.versioningit]

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