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mattwthompsonCopilotj-wags
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Drop support for Python 3.11 (#2174)
* Drop support for Python 3.11 * Constrain Python verion in docs build * Update README badge and add ruff target-version for Python 3.12+ Agent-Logs-Url: https://github.com/openforcefield/openff-toolkit/sessions/3eb020f9-690b-47f8-92b3-3c6415445f92 Co-authored-by: mattwthompson <7935382+mattwthompson@users.noreply.github.com> * Possibly update docstring * Fail faster * Revert "Fail faster" This reverts commit 6c9c2b3. * Update hooks * Enable more timing in logs * Apply suggestion from @j-wags * Apply suggestions from code review Co-authored-by: Matt Thompson <matt.thompson@openforcefield.org> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: mattwthompson <7935382+mattwthompson@users.noreply.github.com> Co-authored-by: Jeff Wagner <jeffrey.wagner+github@openforcefield.org>
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‎.github/workflows/CI.yml‎

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strategy:
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matrix:
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os: [ubuntu-latest, macos-latest]
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python-version: ["3.11", "3.12", "3.13"]
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python-version: ["3.12", "3.13"]
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rdkit: [true, false]
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openeye: [true, false]
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nagl: [true, false]
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exclude:
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- rdkit: false
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openeye: false
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- openeye: true
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python-version: "3.12"
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- openeye: true
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python-version: "3.13"
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- rdkit: false
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- name: Run notebooks in docs
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if: ${{ matrix.rdkit == true && matrix.openeye == true }}
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run: python -m pytest -v --no-cov --nbval-lax docs/
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run: python -m pytest -v --durations=10 --no-cov --nbval-lax docs/
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- name: Run examples in docstrings
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if: ${{ matrix.rdkit == true && matrix.openeye == true && matrix.nagl == true }}

‎.github/workflows/beta_rc.yaml‎

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- ubuntu-latest
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- macos-latest
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python-version:
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- "3.11"
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- "3.12"
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env:
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OE_LICENSE: ${{ github.workspace }}/oe_license.txt

‎.github/workflows/conda.yml‎

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fail-fast: false
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matrix:
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os: [ubuntu-latest, macos-latest]
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python-version: ["3.11"]
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python-version: ["3.12"]
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openeye: ["true", "false"]
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env:

‎.github/workflows/examples.yml‎

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fail-fast: false
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matrix:
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os: [ubuntu-latest, macos-latest]
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python-version: ["3.11", "3.12"]
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python-version: [ "3.12"]
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rdkit: [true, false]
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openeye: [true, false]
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nagl: [true, false]

‎.pre-commit-config.yaml‎

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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: v0.15.9
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rev: v0.15.12
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hooks:
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- id: ruff-format
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- id: ruff-check
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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: v2.21.0
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rev: v2.21.1
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hooks:
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- id: pyproject-fmt

‎README.md‎

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| :------ |:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
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| **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/0.18.0.svg)](https://github.com/openforcefield/openff-toolkit/releases/tag/0.18.0)[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17525527.svg)](https://doi.org/10.5281/zenodo.17525527)
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| **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) |
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| **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-3.11%2C%203.12%2C%203.13-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) |
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| **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-3.12%2C%203.13-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) |
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| **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) |
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# The Open Force Field toolkit

‎docs/environment.yml‎

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- sphinx-notfound-page
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- sphinx=6
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# conda build dependencies
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- python <3.13
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- python =3.12
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- setuptools
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- numpy
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- openmm

‎docs/releasehistory.md‎

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### Behavior changes
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- [PR #2174](https://github.com/openforcefield/openff-toolkit/pull/2174): Drop support for Python 3.11
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### Bugfixes
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### New features

‎docs/users/developing.md‎

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## Supported Python versions
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The OpenFF Toolkit roughly follows [NEP 29](https://numpy.org/neps/nep-0029-deprecation_policy.html).
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As of April 2023 this means Python 3.9-3.10 are officially supported (3.11 is missing some upstream dependencies).
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We develop, test, and distribute on macOS and Linux-based operating systems.
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We do not currently support Windows.
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Some CI builds run using only RDKit as a backend, some run using only OpenEye Toolkits, and some run using both installed at once.
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+-----------------------+------------+-----------+-------------+------------+-----------+-------------+
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| | RDKit | OpenEye | RDKit + OE | RDKit | OpenEye | RDKit + OE |
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+=======================+============+===========+=============+============+===========+=============+
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| Python 3.8 and older | No support after April 2023 |
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| Python 3.11 and older | No support after April 2026 |
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+-----------------------+------------+-----------+-------------+------------+-----------+-------------+
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| Python 3.9 | **Test** | **Test** | **Test** | **Test** | **Test** | **Test** |
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| Python 3.12 | **Test** | **Test** | **Test** | **Test** | **Test** | **Test** |
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+-----------------------+------------+-----------+-------------+------------+-----------+-------------+
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| Python 3.10 | **Test** | Skip | Skip | **Test** | Skip | Skip |
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| Python 3.13 | **Test** | Skip | Skip | **Test** | Skip | Skip |
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+-----------------------+------------+-----------+-------------+------------+-----------+-------------+
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| Python 3.11 | **Test** | Skip | Skip | **Test** | Skip | Skip |
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+-----------------------+------------+-----------+-------------+------------+-----------+-------------+
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| Python 3.12 and newer | Pending official releases and upstream support |
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| Python 3.14 and newer | Pending official releases and upstream support |
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+-----------------------+------------+-----------+-------------+------------+-----------+-------------+
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```

‎openff/toolkit/topology/molecule.py‎

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Any,
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Literal,
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TextIO,
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TypeAlias,
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TypeVar,
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Union,
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overload,
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# TODO: These aliases are duplicated in a few places, might make sense to consolidate them
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# into a single location, but that'd weirdly nudge them towards first-class existence
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TKR: TypeAlias = ToolkitRegistry | ToolkitWrapper
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MoleculeLike: TypeAlias = Union["Molecule", "FrozenMolecule", "_SimpleMolecule"]
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type TKR = ToolkitRegistry | ToolkitWrapper
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type MoleculeLike = "Molecule" | "FrozenMolecule" | "_SimpleMolecule"
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FM = TypeVar("FM", bound="FrozenMolecule")
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P = TypeVar("P", bound="Particle")
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A = TypeVar("A", bound="Atom")

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