* add boilerplate
* define pooch cache at top level
* try downloading one file
* put pooch cache in utils
* use dict
* add all cli data
* keep registry data all in one place
* move downloader to openfe from openfecli
* add both registries to test
* rename for clarity
* better docstring
* update install instructions (#1744)
* update manifest to include all .gz files (#1746)
* update manifest to include all .gz files
* add min openmmforcefields pin
* bump cuda version to 11.8 (#1749)
* fix deprecation warning on view_components_3d (#1750)
* expose KartografAtomMapper alongside other AtomMappers (#1751)
* fix psutils import (#1779)
* fix psutils import
* swap import order
* [pre-commit.ci] pre-commit autoupdate (#1778)
updates:
- [github.com/tox-dev/pyproject-fmt: v2.8.0 → v2.11.1](https://github.com/tox-dev/pyproject-fmt/compare/v2.8.0...v2.11.1)
- [github.com/astral-sh/ruff-pre-commit: v0.13.3 → v0.14.10](https://github.com/astral-sh/ruff-pre-commit/compare/v0.13.3...v0.14.10)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Disable NAGL as a partial charge backend when OEToolkit is installed but not chosen as the registry backend. (#1762)
* NAGL can no longer be used with oechem installed if you are using the rdkit backend.
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Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
* rename openfecli fixture to avoid duplication with openfe fixture (#1755)
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
* openfe gather: add progress bar for loading JSONs (#1786)
* 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
* add dill mock to fix openfe docs build (#1792)
* Fix issue 1795 (#1796)
* Update method name in CLI YAML documentation
* Fix command option case in CLI YAML guide
* manually add absolute settings news item to changelog (#1821)
* manually add absolute settings news item to changelog
* add link
* Fixes docstring to clarify argument does not have a default (#1819)
* Fixes docstring to clarify argument does not have a default
* Modernize typing
* fix ligand network cropping bug (#1822)
* fix ligand network cropping bug
* move to upstream func
* whitespace
* fix pydantic deprecation of copy method
* fix pydantic deprecation of dict method - septop (#1831)
* Updated CHANGELOG for 1.8.1
* fix changelog links
* add openeye w/ python 3.13 test to CI (#1745)
* add openeye w/ python 3.13 test to CI
* only run openeye on unbuntu w/ python 3.13
* add explicit openeye no
* bump python version for conda cron (#1748)
* remove mypy rdkit pin (#1753)
* remove mypy rdkit pin
* try more explicit import
* Revert "try more explicit import"
This reverts commit 00cc2a3729.
* disallow attr-defined error code
* try globally disabling attr-defined
* try specific override
* per-line ignores
* Make the multistate hybrid topology samplers not require the HybridTopologyFactory (#1768)
* make hybrid samplers not rely on htf but instead on the system & positions.
* Migrate validation to Protocol._validate in HybridTopologyProtocol (#1740)
* Migrate & add validation to Protocol._validate for hybrid topology Protocol
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Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
Co-authored-by: Josh Horton <Josh.Horton@newcastle.ac.uk>
* Move rfe protocol (#1769)
Move RFE protocol files around
* HybridTop Unit methods (#1770)
* Break down the Hybrid Top protocol unit into various methods.
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Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
* Have two separate system generators for state A & B in hybrid protocol (#1772)
Make it so that the states A and B are generated using two different SystemGenerator objects, allowing for partial charge transformations.
* HybridTop structural analysis via API rather than CLI (#1771)
* change structural analysis from using CLI to using API
* making some language clearer on github-facing things (#1758)
* making some language clearer on github-facing things
* :
* add pre-commit link
* clean up
* Moving AFE Protocols around a bit (#1775)
* 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
* Create setup, run, and analysis units for HybridTop Protocol (#1773)
* Turn Hybrid Topology protocol into 3 units.
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Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
* update docs for multiple protocol units (#1793)
* Update docstring for hybridtop classes (#1794)
* 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>
* Small improvement in RelativeHybridTopologyProtocol docstring (#1797)
Updated class docstring to clarify the use of Hybrid Topology scheme.
* turn off zenodo retry (#1802)
* turn off zenodo retry
* remove retry_if_failed arg
* only run CI on macos python 3.12 (#1803)
* Turn AFE protocols into multiple units (#1776)
* Split the AFE protocol units into setup, simulation, and analysis.
* move to src layout (#1805)
* Move openfe project layout to `src`.
* Temporarily build pooch from main w/ hotfix (#1806)
* build with pooch@main to see if hotfix works
* add link
* make CLI starting guide easier to find from the landing page (#1787)
* 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 (#1813)
* Update pyproject.toml
* update classifiers
* refactor: clean up test data handling (#1815)
* import pooch_cache from conftest
* remove unused files from pooch cache
* move zenodo cache to conftest
* remove duplicate code
* min pin pooch to fix data fetching (#1820)
* fix ligand network cropping bug (#1822)
* fix ligand network cropping bug
* move to upstream func
* whitespace
* fix api break check path (#1825)
* fix pydantic deprecation of copy method (#1829)
* fix scope mismatch with zenodo data (#1828)
* fix scope mismatch with zenodo data
* fix session scope
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Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Irfan Alibay <IAlibay@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>
* 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 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>
* 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
* 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>
