* 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.
---------
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>
* 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.
---------
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.
---------
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
---------
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
* Disable JAX acceleration by default
* ruff fmt
* add logging info
* fix url
* fix list
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* add example of error message
* added note about disabling jax acel by default
---------
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Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* updating install recommendations to prioritize miniconda and conda-lock
* fix formatting
* Update docs/installation.rst
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
* recommend openfe test
* remove miniforge
* update language and clean up install instructions
* add link
* adding news item
* add back miniforge instructions at the end
* make testing its own section
* clearer language and formatting
* why is rst like this
* why is rst like this??
* one sentence per line!
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
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Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
* do we test this at all?
* start of logging improvements
* first pass at logging, worried about performance
* setup a base class + add type hints
* add placeholder url ref
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* update to new logging control
* Fix imports
* remove bit left over from being able to delete these log controlers
* looks like ... is used more than pass
* formatting fix
* Grab new format rule from main
* run ruff check --fix on conflicting files
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Added tests
* see if this fixes the doc build
* add back debugging code
* update openmm doc url
* add note about jax warning
* bump
* Remove debugging code to see if that fixes doc build
* ruff format
* Add url
* switch to using module instead of class w/ static methods
* Update docs/guide/troubleshooting.rst
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
* ruff fixes
* Ruff fix
* Added news entry
* Refactor to move things to private namespace
---------
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Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
* bump example notebooks branch
* add ipykernel to env
* roll back to fixing septop branch
* i dont think we want ipykernel
* bump to tmp_fix_docs branch
* point to branch revert-237-v1.7_cookbooks
* point to latest example notebooks release
* add more checks
* make precommit manual
* apply formatting to pyproject.toml
* add TODO
* remove unneeded, add a few more
* add ruff, but turn everything off
* add openfe known first party
* format highest-level files
* first half of openfe protocols
* second half of openfe protocols
* openfe protocols formatting, with alyssa's fmt skips
* add ruff formatter to precommit
* fmt: off all vendored _rfe_utils code
* addressing review comments
* fix nb link
* bump examplenotebooks version
* add dark mode option back in
* temporary pin to working ofe theme branch
* remove unused code
* bump ci
* bump ofe-sphinx-theme pin
* update partial charge tests now that a production NAGL model is available (#1506)
* update tests now that a production NAGL model is available
* fix mock
* clean up mocking
* add nagl test news item
* debug slow python 3.13 tests (#1468)
* Turn off minimization when we do a dry run
---------
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* update quickrun execution docs and add MPS link (#1483)
* add jq cookbook (#1488)
* add jq code blocks
* use tutorial data
* news
* debug docs build (#1489)
* don't build openmm
* mambaforge->miniconda for rtd
* artifically small build for debugging
* dont build env
* just build python
* add channels
* add sphinx packages to env
* add all non-openfe-ecosystem deps
* remove shim channel
* add openfe package
* add everything except openmm and toolkit
* add openmm
* add openff-toolkit
* only openff-toolkit
* try openff-toolkit-base
* try latest openff
* everybody back in
* build without openmm
* build with openff-toolkit-base
* bump rtd
* add pip build
* remove any openff-toolkit
* build w/o openmm
* add pip install
* build everything without pip install
* try no deps
* try custom build
* only python and pip
* try openfe-toolkit-base
* add temp deps for build with openff-toolkit-base
* add temp deps for build with openff-toolkit-base
* mock imports
* dont mock with toolkit base
* bump toolkit version
* Revert "bump toolkit version"
This reverts commit 6e3108a836.
* add mocks
* try pinnint to toolkit-base 0.13.0, no mocks
* back to >= 0.13.0 toolkit to make sure it wasn't a fluke
* mock imports
* add pipe example for jq (#1505)
* add pipe example for jq
* pin to docutil 0.20
* try to avoid memory error
* debug rtd build memory error (#1510)
* try mambaforge build
* Revert "try mambaforge build"
This reverts commit 683e07f1ea.
* try explicit build
* try removing ambertools
* use the right env
* just add gufe pip install back
* add back openfe eco packages
* mock py3dmol
* add note for pip installs
* fix quote
* temporarily resort to SettingsBaseModel to get build
* specific imports
* dont use base settings placeholder
* temp pin numpy (#1542)
* Removing unnecessary limit on resids (#1539)
* Removing unnecessary limit on resids indices gathering
* Updated CHANGELOG for 1.6.1
* add summary
* update docs theme (#1545)
* adding new branding assets
* remove images
* update theme branch
* CantinaPurple accent
* lowercase convention
* updating text
* remove dark mode for now
* fix sidebars
* fix formatting
* capitalization
* don't break spaces
* bump ci
* favicon!
* whitespace :(
* pin to sphinx release
* pin to gufe 1.6.1
* move env info before test imports
* bump single file installer to 3.12.11 to match colab
---------
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Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com>
* SepTop docs improvements lambda schedule and restraint selection
* Remove set_openmm_threads_1 logic from test_septop_slow
* change femto acknowledgements
* update method docstring limitations
* Make sure we fail when we have virtual sites and reassign_velocities is False
* clean up usage of openmm imports
* clean up equil settings output indices so that it enforces all
* generate smc_off_B on the fly
* Update enforcement of all output indices
* Simulation overview unclear on if the same restraint is used between repeats
* Add test for output indices validation
---------
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
* try mambaforge build
* Revert "try mambaforge build"
This reverts commit 683e07f1ea.
* try explicit build
* try removing ambertools
* use the right env
* just add gufe pip install back
* add back openfe eco packages
* mock py3dmol
* add note for pip installs
* fix quote
* temporarily resort to SettingsBaseModel to get build
* specific imports
* dont use base settings placeholder
