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* update manifest to include all .gz files * add min openmmforcefields pin
* fix psutils import * swap import order
updates: - [github.com/tox-dev/pyproject-fmt: v2.8.0 → v2.11.1](tox-dev/pyproject-fmt@v2.8.0...v2.11.1) - [github.com/astral-sh/ruff-pre-commit: v0.13.3 → v0.14.10](astral-sh/ruff-pre-commit@v0.13.3...v0.14.10) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…but not chosen as the registry backend. (#1762) * NAGL can no longer be used with oechem installed if you are using the rdkit backend. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
* all the profiling * make progress bar pretty * revert typing thing * news * all the profiling * make progress bar pretty * revert typing thing * news * update expected outputs * update expected outputs
* Update method name in CLI YAML documentation * Fix command option case in CLI YAML guide
* manually add absolute settings news item to changelog * add link
* Fixes docstring to clarify argument does not have a default * Modernize typing
* fix ligand network cropping bug * move to upstream func * whitespace
* add openeye w/ python 3.13 test to CI * only run openeye on unbuntu w/ python 3.13 * add explicit openeye no
* remove mypy rdkit pin * try more explicit import * Revert "try more explicit import" This reverts commit 00cc2a3. * disallow attr-defined error code * try globally disabling attr-defined * try specific override * per-line ignores
…pologyFactory (#1768) * make hybrid samplers not rely on htf but instead on the system & positions.
…1740) * Migrate & add validation to Protocol._validate for hybrid topology Protocol --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com> Co-authored-by: Josh Horton <Josh.Horton@newcastle.ac.uk>
Move RFE protocol files around
* Break down the Hybrid Top protocol unit into various methods. --------- Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
#1772) Make it so that the states A and B are generated using two different SystemGenerator objects, allowing for partial charge transformations.
* change structural analysis from using CLI to using API
* making some language clearer on github-facing things * : * add pre-commit link * clean up
* move the protocols results to a single file and deduplicate * rename base units file * move units out of method files * move a few things in init
* Turn Hybrid Topology protocol into 3 units. --------- Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
* Update docstring for classes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Updated class docstring to clarify the use of Hybrid Topology scheme.
* turn off zenodo retry * remove retry_if_failed arg
* Split the AFE protocol units into setup, simulation, and analysis.
* Move openfe project layout to `src`.
* build with pooch@main to see if hotfix works * add link
* make CLI starting guide easier to find from the landing page * Python API -> API Docs * bump ci * bump example notebooks pin to 2026.01.26 * change a word * clarifying language
* Update pyproject.toml * update classifiers
* import pooch_cache from conftest * remove unused files from pooch cache * move zenodo cache to conftest * remove duplicate code
* fix ligand network cropping bug * move to upstream func * whitespace
* fix scope mismatch with zenodo data * fix session scope
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🚨 API breaking changes detected! 🚨 |
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newsentry, or the changes are not user-facing.pre-commit.ci autofix.Manual Tests: these are slow so don't need to be run every commit, only before merging and when relevant changes are made (generally at reviewer-discretion).
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