Turn AFE protocols into multiple units by IAlibay · Pull Request #1776 · OpenFreeEnergy/openfe

IAlibay · 2026-01-04T21:00:28Z

Blocked by #1775
Fixes #1724

TODO:

Run and fix the slow & integration tests
Get new serialized results for ahfe and abfe protocols

Checklist

All new code is appropriately documented (user-facing code must have complete docstrings).
Added a news entry, or the changes are not user-facing.
Ran pre-commit by making a comment with pre-commit.ci autofix before requesting review.

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).

GPU integration tests
example notebook testing
packaging tests: run this for any large feature PRs or PRs that add test data.

Developers certificate of origin

I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

…o multi-unit-afe

openfe/protocols/openmm_afe/base_afe_units.py

openfe/protocols/openmm_afe/equil_binding_afe_method.py

openfe/tests/protocols/openmm_abfe/test_abfe_protocol_results.py

openfe/tests/protocols/openmm_ahfe/test_ahfe_protocol_results.py

jthorton

A few minor things not related to the move though so feel free to ignore, LGTM!

hannahbaumann

Thanks @IAlibay ! This looks great, just the one comment about the output name to be for phases for that protocol as well. Would also need to be changed in the tests.

openfe/protocols/openmm_afe/equil_solvation_afe_method.py

IAlibay · 2026-01-22T01:35:50Z

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…o multi-unit-afe

IAlibay · 2026-01-22T12:45:13Z

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github-actions · 2026-01-22T12:45:52Z

No API break detected ✅

IAlibay · 2026-01-22T13:38:28Z

Failures are zenodo related - merging.

* Split the AFE protocol units into setup, simulation, and analysis.

* 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](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> * 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 00cc2a3. * 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 --------- 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 (#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>

IAlibay added 30 commits January 1, 2026 09:23

move the protocols results to a single file and deduplicate

49ede96

rename base units file

6b504a8

fix some imports

8abf04f

import fix

a3e228f

fix some more imports

efcee64

update some docstring

d11ab5a

some changes

65bfb04

Store for a second

aa42720

udpate system_generator getter

f72c23d

Some progress

d0c1889

Add a few things

b2e266f

Some sampler stuff

7091102

some more things

696b806

some more progress

9bc47f1

finish analysis unit

312d19e

Migrate some things along

7aa9930

Hook up multi-units to the protocols

889ea7c

some fixes

c745599

fix tokenization tests

fbcef69

fix various tokenization things

ba716b6

fix gather tests

e914d56

some more progress

9198e9e

various fixes

4cf4d66

various more AHFE test fixes

a802eac

some test fixes

1665431

fix everything

58b9fcd

fix energies tests

7c3d5c3

various fixes for the abfe tests

2443250

remove extra run parameter

5fcacaf

fix some ahfe slow tests

a119264

IAlibay added 2 commits January 16, 2026 21:37

fix ignore statement

5716ea4

Merge branch 'multi-unit-afe' of github.com:OpenFreeEnergy/openfe int…

20c991d

…o multi-unit-afe