621 Commits

Author SHA1 Message Date
Alyssa Travitz
cb10892e79 Updated CHANGELOG for 1.11.1 (#1973) 2026-05-01 19:32:51 -07:00
Alyssa Travitz
246c082353 docs: add blurb to release notes (#1970)
* add blurb to release notes

* fix formatting
2026-04-30 12:04:11 -07:00
Alyssa Travitz
3c83972143 fix typo in installation docs (#1971) 2026-04-30 10:17:34 -07:00
Alyssa Travitz
d60fb8e5fe update installation restrictions (#1969) 2026-04-29 14:04:21 -07:00
Alyssa Travitz
db379890b2 release prep for v1.11.0 (#1967)
* Updated CHANGELOG for 1.11.0

* add PR links

* update release prep template

* fix code formatting

* Updated CHANGELOG for 1.11.0

* update example notebook tag

* update comment in env
2026-04-28 18:10:16 +00:00
Josh Horton
7bc31e1df5 Fix 1-4 interpolation for core-dummy interactions (#1856)
* Change the 1-4 interpolation to be on by default.
* Add htf tests including tests for 1-4 interpolation.

---------

Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
2026-04-28 15:05:48 +01:00
Alyssa Travitz
8d229cffe3 membrane CLI support (#1896)
* initial cli ideas

* clean up names

* add test

* update docstrings and fix imports

* fix tests

* use gufe gzip branch

* clean up fixtures

* update fixtures

* adding membrane component to tests

* add membrane barostat check

* make output more consistent and add membrane args test

* error messages

* revert some out of scope typing things

* tidying fixtures

* update protein arg parsing

* clearer var naming

* add protein validate

* add validation

* fix handling for membrane solvents

* update docstring

* point to membrane tutorial branch

* linking

* remove redundant validation

* remove unneeded type hints

* Update src/openfecli/commands/plan_rbfe_network.py

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>

* Update src/openfecli/parameters/protein.py

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>

* clean up suggestions

* use click BadParameter

* testing arg errors

* update examplenotebook branch

* add news item

* use BadParameter

* fix test comments

---------

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
2026-04-27 09:05:43 -07:00
Josh Horton
909d29ad25 Plain MD restart support (#1884)
* split md protocol to setup and simulate, add restart support

* allow for resume in any stage

* add a single run dynamics function

* update restart to only look for checkpoints, split out remaining step logic, update tests

---------

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
2026-04-27 16:04:28 +01:00
Hannah Baumann
fc6689eaf1 User guide updates membrane (#1933)
* Membrane support prototype start

* Point to corresponding branch in gufe

* Make plain md protocol membrane ready

* Dry run for membrane system for debugging

* Add box vectors to modeller

* Adapt htf to allow for membrane barostat

* Fix test

* Add test files membrane

* Change test to cpu

* Prints for debugging

* Some more debugginh stuff, remove later

* Small fix

* Temporarily use branches for openmmtools and openmmforcefield

* Small fixes

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* support membrane in gather

* First pass membrane support for SepTop protocol

* Change validation solvent

* Move changes in solvent validation to validate_solvent

* Some small fixes

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Add membrane test septop

* Change box vector units for handling membrane barostat

* Test box vectors SepTop more

* First pass at ABFE membrane prototype

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Remove some prints

* Revert box changes

* Some fixes in SepTop to fix tests

* Apply suggestion from @hannahbaumann

* Add tests for system creation

* FIx test

* Add ABFE membrane tests

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* More tests membrane septop and more dry outputs in septop

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Add validation for box vector in ProteinMembraneComponent

* Adapt gather for membranes

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* small changes

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Modify box vectors plain md

* Address review comments

* Remove unnecessary prints

* Subclass membrane test

* Small fix

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* remove unnecessary import

* Remove prints

* Small fix

* Small fix

* Larger change to checks for BaseSolventComponent, SolvatedPDBComponent, and adding barostat settings

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Some more changes

* Small fix

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* ABFE enforce timestep complex solvent the same

* Update test files

* Update environment.yaml with new openmmtools and openmmforcefield versions

* Remove unnecessary checks for box_vectors which are handled in gufe

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update openfe/protocols/openmm_afe/equil_binding_afe_method.py

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

* Attempt at rewriting validate_solvent

* Move get barostat to self

* Simplify mapping in test

* Add validator for surface_tension and membrane barostat

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Add membrane barostat to adaptive settings rfe protocol

* Add validation/warning for barostat component mismatch

* Fix tests (except CLI)

* More merge fixes

* Remove unnecessary imports

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Add test files

* Update tests

* Add lipid ff in adaptive settings

* remove commented out lines

* Update test abfe

* Update ABFE results with new settings

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Fix solvent validation

* change env to gufe main

* Apply suggestion from @hannahbaumann

* Remove files from before src layout change

* Update tests

* Small fix

* mark slow tests

* Update env file

* Small fix

* Update src/openfe/protocols/openmm_afe/equil_binding_afe_method.py

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

* Update src/openfe/protocols/openmm_afe/equil_binding_afe_method.py

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

* Update src/openfe/protocols/openmm_rfe/_rfe_utils/relative.py

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

* Update src/openfe/protocols/openmm_utils/system_validation.py

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

* Address review comments 1

* update doc string

* Update src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol.py

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

* Update src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol.py

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

* Update src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol.py

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

* Update src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol.py

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

* Address review comments 2

* Address review comments 3

* fix mypy

* Fix system creation tests

* Roundtrip box vectors to remove vec3 issues

* Roundtrip box vectors to remove vec3 issues

* Remove unnecessary imports

* Apply suggestion from @hannahbaumann

* Test mypy failure

* Test mypy failure 2

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* some fixes

* small fixes

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update test files

* Update SepTop results settings

* add more tests for adaptive settings and others

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Add news entry

* Fix for box vectors hybtop

* Make test slow again

* Make mypy happy

* try to make mypy happy again

* Adapt gather RFE membrane component types

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* use reference platform for the membrane energy test

* Add ChemicalSystem Component validation to Protocols

* Add test for chemicalsystem validation

* Apply suggestions from code review

Co-authored-by: Josh Horton <joshua.horton@openforcefield.org>

* Update with slight variation to @jthorton 's suggestion

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* point gufe back at main

* Drop lipid17 from adaptive settings

* just a tiny nit change

* fix typo

* Add extra class to openfecli check

* Add total particle checks to abfe protocol tests

* remove lipid17 check from adaptive settings

* remove lipid17 check from adaptive settings

* Add some checks for number of particles & residues

* Fix up some tests

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Minimized protein

* Update protein

* Revert back to old protein

* Apply suggestion from @hannahbaumann

* Remove box roundtrip and fix solvent from get_components

* Merge conflicts

* Update src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol.py

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Fix merge conflict

* Forgot another one

* Move box roundtrip to _pre_equilibrate

* First go at modifying the user guide for membranes and ABFE and SepTop

* some small fixes

* Add adaptive_settings to user guide

* Add example code loading protein membrane

* Add box vector explanation

* Some smaller changes

* Make adaptive settings subheading

* Some more changes

* Add warning adaptive settings

* Update docs/guide/setup/defining_protocols.rst

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

* Addressing review comments

* some more updates

* Test out subheadings

* Restructure user guide

* merge conflicts

* Small fix

* some small updates

* addressing review comments

* Small fix

* address review comments

* small fix

* Add news entry

* Update docs/guide/setup/chemical_systems_and_thermodynamic_cycles.rst

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

* Update docs/guide/setup/defining_protocols.rst

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

* Update docs/guide/setup/chemical_systems_and_thermodynamic_cycles.rst

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

* Addres review comment

* Update docs/guide/setup/chemical_systems_and_thermodynamic_cycles.rst

Co-authored-by: Josh Horton <Josh.Horton@newcastle.ac.uk>

* Update docs/guide/setup/chemical_systems_and_thermodynamic_cycles.rst

Co-authored-by: Josh Horton <Josh.Horton@newcastle.ac.uk>

* Address review comment

---------

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: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
Co-authored-by: Josh Horton <Josh.Horton@newcastle.ac.uk>
Co-authored-by: Josh Horton <joshua.horton@openforcefield.org>
2026-04-24 14:03:06 +02:00
Alyssa Travitz
90846148c9 update systems and components docs for completeness (#1954)
* update systems and components docs for completeness

* add SolvatedPDBComponent

---------

Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
2026-04-24 13:17:31 +02:00
Irfan Alibay
c81d27cf0d Add Analysis unit for Septop (#1937)
* Add an Analysis unit to SepTopProtocol.
* Update PDB writing via MDTraj in AFE and SepTop Protocols to account for box dimensions with mdtraj_from_openmm utility.
* Split up some SepTop tests into different files.
* Updated the CLI gathering to account for post openfe v1.11 Analysis units

---------

Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
2026-04-24 10:00:06 +01:00
Mike Henry
dd2ee4bbd2 Simplify how to install correct cuda-version (#1910)
* Simplify how to install correct cuda-version

* fix rst syntax
2026-04-01 10:27:26 -07:00
Alyssa Travitz
adb19162b5 Release v1.10.0 (#1902)
* Updated CHANGELOG for 1.10.10

* clean up links

* consistent formatting

* add link to new docs
2026-03-30 16:07:38 -07:00
Irfan Alibay
8fcd47b4df Update the userguide CLI docs to mention resuming (#1878)
* Modify quickrun to allow resuming

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* store protocol dag using transformation key

* use assert_click_success

* Update the CLI quickrun help info

* Add userguide documentation on how to use quickrun

* this reference instead?

* fix things a little bit

* update the title

* Update environment.yml

* Update docs/guide/cli/quickrun.rst

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

* update for new name for now

* Update docs/guide/cli/quickrun.rst

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

* update for new changes

* Add to the execution guide instead

* some fixes

* Add `>` where it's a CLI command

* formatting fixes

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Alyssa Travitz <alyssa.travitz@omsf.io>
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
2026-03-30 14:47:02 -07:00
Irfan Alibay
461bf6017e Fixing various typos (#1882)
* Playing around with codespell

* revert some things

---------

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
2026-03-19 18:11:03 -07:00
Mike Henry
a64bd4427e Update openfe analysis pin (#1859)
* bump min pin of openfe_analysis to fix https://github.com/OpenFreeEnergy/openfe/issues/1834

* add note in changelog about RMSD analysis fixed
2026-02-25 11:27:02 -08:00
Alyssa Travitz
90764128f6 Updated CHANGELOG for 1.9.1 (#1850) 2026-02-16 08:29:38 -08:00
Alyssa Travitz
ad07917131 Release/v1.9.0 (#1835)
* Updated CHANGELOG for 1.9.0

* add links to changelog

* fix ci path

* Apply suggestions from code review

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

* Updated CHANGELOG for 1.9.0

* update changelog

---------

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
2026-02-11 10:21:55 -08:00
Alyssa Travitz
8577e43bdb changelog updates for 1.8.1 (#1832)
* 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

---------

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>
2026-02-05 08:54:59 -08:00
Alyssa Travitz
1f28ee131b manually add absolute settings news item to changelog (#1821)
* manually add absolute settings news item to changelog

* add link
2026-02-02 09:12:28 -08:00
Alyssa Travitz
79ac79d910 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
2026-01-26 12:27:08 -08:00
Irfan Alibay
27c0d79cd1 Turn AFE protocols into multiple units (#1776)
* Split the AFE protocol units into setup, simulation, and analysis.
2026-01-22 13:38:57 +00:00
Irfan Alibay
548f060cfa Fix issue 1795 (#1796)
* Update method name in CLI YAML documentation

* Fix command option case in CLI YAML guide
2026-01-16 20:08:36 +00:00
Alyssa Travitz
cb569010a0 update docs for multiple protocol units (#1793) 2026-01-16 16:00:27 +00:00
Alyssa Travitz
a4531b00f1 add dill mock to fix openfe docs build (#1792) 2026-01-16 07:49:56 -08:00
Alyssa Travitz
ea1ae647db expose KartografAtomMapper alongside other AtomMappers (#1751) 2025-12-16 15:38:45 -08:00
Alyssa Travitz
f331d0abb4 update install instructions (#1744) 2025-12-08 13:51:46 -08:00
Alyssa Travitz
e64964daab release/1.8.0 (#1734)
* Updated CHANGELOG for 1.8.0

* format changelog

* Update docs/CHANGELOG.rst

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>

---------

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
2025-12-08 11:17:28 -08:00
Alyssa Travitz
a3e1108ad8 add docs for gathering septop and abfe (#1737)
* add autodocs for gathering septop and abfe

* update docstrings

* add blurb to openfe gather docs

* add missing docstrings

* add warning

* add zstandard to docs mocks

* Apply suggestions from code review

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

* add cinnabar to doc mocks

---------

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
2025-12-08 08:41:26 -08:00
Alyssa Travitz
3e2976c61e bump ExampleNotebooks version (#1738) 2025-12-05 07:20:07 -08:00
Alyssa Travitz
bd7c683690 docs: handle common case where ExampleNotebooks already exists and is on a tagged release (#1735) 2025-12-04 12:37:47 -07:00
Mike Henry
f491184b58 Disable JAX acceleration by default (#1694)
* 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

---------

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2025-12-02 21:12:24 +00:00
Alyssa Travitz
44a3f7df3b updating install recommendations to prioritize miniconda and conda-lock (#1692)
* 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>

---------

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
2025-12-01 10:24:55 -08:00
Alyssa Travitz
12815c8ac9 add links to ecosystem on docs landing page (#1619)
* add links to ecosystem on docs landing page

* switch some docs links to github

* formatting

* address comments

* ordering

* fix typo and formatting

* typo

* links syntax

* update datryllic link

* oxford comma
2025-11-24 09:26:48 -08:00
Mike Henry
b0789ff0ae Add logging control (#1585)
* 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

---------

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>
2025-11-21 07:30:53 -08:00
Alyssa Travitz
588f552ca9 add ruff isort linting rule (#1665)
* isort for docs and utils

* isort for top-level openfe, analysis, setup

* isort setup/

* isort storage/

* isort protocols

* isort openn_afe

* isort openmm_rfe

* isort all protocols

* apply isort to openfe/tests

* apply isort to openfecli

* apply isort to devtools/

* add TODO for setup init
2025-11-10 21:58:30 +00:00
Irfan Alibay
d46db57e32 expose the septop and abfe analysis tutorials (#1664)
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
2025-11-07 07:25:27 -08:00
Alyssa Travitz
25933de40b fix docs links for cli and api on landing page (#1620)
* fix links for cli and api

* fix cli link

* clearer language
2025-10-24 12:14:56 -07:00
Alyssa Travitz
59bedc0535 drop scipy intersphinx link (#1621)
* drop scipy as intersphinx link

* clean up comments
2025-10-24 12:08:27 -07:00
Alyssa Travitz
d7d6f9dbb4 remove colab button, point to updated example notebooks, reorg landing page (#1618)
* remove colab button from example notebooks in docs

* point to example notebooks 2025.10.2

* replace 'try' with CLI
2025-10-24 19:06:25 +01:00
Alyssa Travitz
dcc457d825 update example notebooks branch for v1.7.0 docs changes (#1615)
* 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
2025-10-24 07:20:00 -07:00
Alyssa Travitz
3a08b6809f Ci/add ruff format to openfe protocols (#1604)
* 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
2025-10-22 16:04:13 -07:00
Alyssa Travitz
6e2f068952 add notes about dropping 3.10 maintenance (#1605)
* add notes about dropping 3.10 maintenance

* add version

* formatting
2025-10-22 11:35:26 -07:00
Irfan Alibay
84e090bfbe Prepare for release v1.7 (#1601)
* Updated CHANGELOG for 1.7.0

---------

Co-authored-by: Alyssa Travitz <alyssa.travitz@omsf.io>
2025-10-21 17:52:37 +01:00
Irfan Alibay
66d14f61bc ABFE protocol (#1045)
Add an Absolute Binding Free Energy Protocol to openfe.

Key features & limitations:
* Automatic Boresch restraint assignment.
* Does not handle net charge corrections yet.

---------

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
Co-authored-by: hannahbaumann <hbaumann@uci.edu>
Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
2025-10-21 11:45:37 +01:00
Alyssa Travitz
141960944b deprecate openfe utils 3dviz in favor of gufe method (#1592)
* deprecate openfe utils 3dviz in favor of gufe method

* add news item

* update news

* fix deprecation warning capture

* update guide

---------

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
2025-10-20 23:56:23 +00:00
Josh Horton
f681d5160b add a note on the equilibration method (#1581) 2025-10-15 13:16:06 +00:00
Alyssa Travitz
e81f2bcda1 add dark mode to docs (#1565)
* 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
2025-10-14 20:10:13 -07:00
Alyssa Travitz
d87dd8ffc0 fix nb link (#1574)
* fix nb link

* bump examplenotebooks version
2025-10-13 18:56:26 +01:00
Alyssa Travitz
b9f7593b2d migrate to pydantic v2 (#1535) 2025-10-10 23:02:57 +00:00