v0.11.1 - Lomap performance patch

What's Changed

• Use common core option when using the Lomap Atom Mapper by @richardjgowers in #485

Full Changelog: v0.11.0...v0.11.1

v0.11.0 - Cofactor CLI support

What's Changed

• Update installer and container images to python 310 by @mikemhenry in #465
• Pin units - same thing as in gufe by @IAlibay in #466
• Actually actually fix silence_root_logging by @dwhswenson in #467
• CodeCov only on PR by @dwhswenson in #469
• cofactors from CLI by @richardjgowers in #456
• Fix minor typo by @slochower in #471
• Sort while running gather by @dwhswenson in #472
• Reconfigure stdout to be line-buffered in quickrun by @dwhswenson in #468
• Add PDB serialization in RFE protocol by @IAlibay in #450
• Code of Conduct by @mikemhenry in #474
• end to end integration tests for tyk2 tutorial by @richardjgowers in #476
• allow gathering of legacy results by @richardjgowers in #477
• Force no oechem by @richardjgowers in #479
• fixup manifest for new test files by @richardjgowers in #481

New Contributors

• @slochower made their first contribution in #471

Full Changelog: v0.10.1...v0.11.0

v0.10.1 - Hotfix

Fixes some test failures that weren't actually harmful.

What's Changed

• Install GUFE after we restore cache to alwasys get a fresh version by @mikemhenry in #452
• Update to support the newest version of openmmtools by @mikemhenry in #451
• allow single AtomMapper to be passed to network planners by @richardjgowers in #454
• Fix silence_root_logging by @dwhswenson in #453
• explain how to use nvidia-smi to figure out cudatoolkit version by @mikemhenry in #455
• need to update slow tests following execute_DAG update by @richardjgowers in #459
• Run slow tests on push & release by @IAlibay in #460

Full Changelog: v0.10.0...v0.10.1

v0.10.0

What's Changed

• Cautiously allow core element changes by @IAlibay in #438
• Fix handling of ThreeParticleAverageSite virtual sites by @IAlibay in #395
• Pin PyMBAR to sub v4 by @IAlibay in #444
• Add to_openff() intermediary for to_openeye() calls by @IAlibay in #446
• rename water molecules so addSolvent doesn't replace with ion by @richardjgowers in #441
• quickrun command now retries simulations by @richardjgowers in #447
• add fetchables for showcase notebook inputs by @mikemhenry in #437
• remove rate_of_convergence by @richardjgowers in #433
• Update gather.py - protocol failure robustness by @RiesBen in #381

Full Changelog: v0.9.1...v0.10.0

v0.9.1

By default, now not water is the selection used to write out particle coordinates instead of all.
This setting is controlled by the output_indices setting in SimulationSettings for the RFE Settings object.

What's Changed

• Don't build docker image on tags by @mikemhenry in #435
• all to not water for writing by @IAlibay in #431

Full Changelog: v0.9.0...v0.9.1

v0.9.0

Improvements to the OpenMM RBFE Protocol. see #387

What's Changed

• Switch rbfe tutorial fetch to point to main; not master by @dwhswenson in #430
• [RFE protocol] Allow multiple small molecules + allow running with non-OpenFF force fields by @IAlibay in #387

Full Changelog: v0.8.1...v0.9.0

v0.8.1

Lots of fixes around CLI docs and documentation styling

What's Changed

• Speed up first output from plan-*-network by @dwhswenson in #412
• Fix problem with ligand loading order in test_plan_*_network by @dwhswenson in #416
• Regroup CLI Sections by @dwhswenson in #414
• Add comment to docs that first import is slow by @dwhswenson in #417
• adding style to the docs by @RiesBen in #419
• Fix links in docs by @dwhswenson in #423
• Progress bar for maximal network by @dwhswenson in #411
• Update custom.css by @RiesBen in #426
• Update equil_rfe_settings.py by @richardjgowers in #424
• Update links to docs by @dwhswenson in #425
• update readme install instructions by @IAlibay in #428
• CLI Updates by @dwhswenson in #429

Full Changelog: v0.8.0...v0.8.1

v0.8.0 - OMSF Symposium release

Highlights:

• Big overhaul to documentation.
• Lots of new CLI features

What's Changed

• update package versions by @mikemhenry in #371
• CLI: Remove openfe import required for help by @dwhswenson in #374
• Semi "wet" test by @richardjgowers in #378
• test CLI command by @dwhswenson in #373
• Switching to micromamba for install and add cluster docs by @mikemhenry in #376
• CLI: mol_dir => molecules by @dwhswenson in #383
• CLI: ligand network viewer by @dwhswenson in #384
• CLI: Network Planners: Flatten output directories by @dwhswenson in #382
• update offmodels and offtk pins by @richardjgowers in #377
• Install docs: Use Mambaforge by @dwhswenson in #389
• Don't trigger docker build on non-main branch pushes by @IAlibay in #391
• autodoc pydantic for openmm_rfe settings by @richardjgowers in #385
• CLI fetch command by @dwhswenson in #380
• Improving our landing page by @IAlibay in #396
• Enable online-analysis by default by @IAlibay in #388
• Fix nesting of shared directory for checkpoint by @dwhswenson in #397
• Silence openmmtools.multistate API warnings by @dwhswenson in #398
• Add ligand network output to CLI network planners by @dwhswenson in #399
• Add tutorial fetchables by @dwhswenson in #404
• Pull execute dag by @richardjgowers in #405
• Update gather.py - output file refactor by @RiesBen in #393
• DOCS: Cleanup guide intro by @dwhswenson in #341
• Make docs reasonable to be user facing by @IAlibay in #401
• add missing settings docs by @richardjgowers in #407
• Rbfe fetch assets by @richardjgowers in #409
• receptor => complex by @dwhswenson in #410
• Remove mapper from plan-*-network command by @dwhswenson in #402

Full Changelog: v0.7.4...v0.8.0

v0.7.4

What's Changed

• Fix analyzer cleaning up scope issues by @IAlibay in #361
• Remove test skipping by @mikemhenry in #359
• lomap mapper updates for 2.3.0 by @richardjgowers in #364
• Push Apptainer Image to GHCR + Build Installer & Docker Image using Conda-Forge Package by @mikemhenry in #353
• Update hash for hmass change upstream by @IAlibay in #367
• Swap LangevinSplittingDynamicMove to LangevinDynamicsMove by @IAlibay in #332
• Issue 368 init docs by @richardjgowers in #369
• cookbook docs by @richardjgowers in #318

Full Changelog: v0.7.3...v0.7.4

v0.7.3 - multi-DAG result and memory fixes

What's Changed

• Use pip instead of conda for sphinx-toolbox by @IAlibay in #351
• only build installer on demand by @mikemhenry in #352
• openmm_rfe: make repeat_ids non 0 assuming by @richardjgowers in #356
• Fix test incompatibility by @dwhswenson in #358
• Cleanup contexts upon calculation completion, failure by @dotsdl in #354

New Contributors

• @dotsdl made their first contribution in #354

Full Changelog: v0.7.2...v0.7.3