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

v0.7.2 - docs and alchemiscale hotfix

What's Changed

• Don't exclude py3.10 macos runners by @IAlibay in #319
• Start adding API docs by @dwhswenson in #325
• fix issue where we would get a key error if OFE_SLOW_TESTS was unset by @mikemhenry in #339
• Issue 292 rfe context usage by @richardjgowers in #345
• Add image building by @mikemhenry in #321
• Fix single file installer by @mikemhenry in #308
• Add Docs for Containers and Single File Installer by @mikemhenry in #347
• DOCS: Core models and CLI usage by @dwhswenson in #340

Full Changelog: v0.7.1...v0.7.2

v0.7.1 easy_campaign hotfix 1

Fixes a small issue in Protocol round tripping against json files. See #336

What's Changed

• pull AlchemicalNetwork into top namespace by @richardjgowers in #327
• Explanation docs (initial work and structure) by @dwhswenson in #317
• Delete cache from closed PRs by @mikemhenry in #330
• autodoc_pydantic is on cf as autodoc-pydantic by @mikemhenry in #331
• fixes #324 by @richardjgowers in #328
• fix packaging by @IAlibay in #323
• Add pytest slow test filter by @IAlibay in #333
• Update package-tests.yaml by @mikemhenry in #337
• Use JSON_HANDLER classes in ResultClient storage by @dwhswenson in #334
• Fix protocol roundtrip by @richardjgowers in #336

Full Changelog: v0.7.0...v0.7.1

v0.7.0 - easy_campaign release

What's Changed

• Silence root logging (on perses imports) by @dwhswenson in #265
• Storage migration: Add to openfe by @dwhswenson in #266
• Openfecli dummyprotocol tests by @richardjgowers in #269
• Add function to visualization_3D.py - show_ComponentCoords by @RiesBen in #262
• Gufe update by @richardjgowers in #270
• Fix serialization of protocol by @dwhswenson in #219
• Get plugcli from conda-forge by @dwhswenson in #271
• Pin libnetcdf to avoid current failures by @dwhswenson in #273
• Maximal network planner by @dwhswenson in #245
• Gufe fixup by @richardjgowers in #286
• Let's try to not import with eyes open by @IAlibay in #287
• Temporarily fix docs building by @IAlibay in #288
• Easy alchemical network planners by @RiesBen in #254
• fix execute_DAG usage following gufe update by @richardjgowers in #304
• Fix Version Info + Switch to pyproject.toml by @mikemhenry in #282
• add fetch-depth to CI version check by @IAlibay in #307
• Quickrun updates by @richardjgowers in #293
• using gufe Settings in RBFE Protocol by @richardjgowers in #267
• Fix typo in CI file - don't allow codecov to run on schedule by @IAlibay in #309
• Add periodicity setting tests by @IAlibay in #281
• Remove tolerance checks by @IAlibay in #274
• Add platform warning for non CUDA selection by @IAlibay in #311
• rbfe -> rfe rename by @IAlibay in #310
• Switch to pydata theme + add readme docs badge by @IAlibay in #316
• Speed up doc building by @mikemhenry in #326
• simple duration printout by @RiesBen in #294

Full Changelog: v0.6.1...v0.7.0

v0.6.1

What's Changed

• convert output of get_estimate and get_uncertainty to openff-units.Qu… by @richardjgowers in #264

Full Changelog: v0.6.0...v0.6.1

v0.6.0

What's Changed

• temporarily pin numpy because of numba issues by @IAlibay in #238
• update mapping visualization of bond changes by @richardjgowers in #241
• Remove LigandAtomMapping by @richardjgowers in #252
• fixup following gufe API change by @richardjgowers in #256
• Api cleanout by @richardjgowers in #255
• Update environment.yml by @richardjgowers in #257
• adding 3D structure Mapping Vis to LigandMapping by @RiesBen in #248
• Sort nodes/edges on creation of NetworkX graph by @dwhswenson in #247
• Remove unused RTD config by @dwhswenson in #258

Full Changelog: v0.5...v0.6.0

v0.5

Mainly bug fixes concerning constraint mapping in the RBFE Protocol

What's Changed

• TST: fix stray directories being made during testing by @richardjgowers in #220
• Dry run now returns sampler via debug dictionary entry by @IAlibay in #217
• MAINT: Fixed up implicit none errors from mypy by @richardjgowers in #226
• Bug hunt fixes by @IAlibay in #225
• Add --log option to CLI by @dwhswenson in #218
• Xml regression tests by @richardjgowers in #231
• MAINT: remove old offtk from test matrix by @richardjgowers in #236
• bump pin on gufe by @richardjgowers in #235

Full Changelog: v0.4...v0.5

v0.4

What's Changed

• Fix the number of production steps being used by @IAlibay in #141
• change Lomap atom mapper to default to threed=True by @richardjgowers in #143
• Mapping distance by @richardjgowers in #145
• added check for element changes in openmm rbfe protocol by @richardjgowers in #146
• Visualization align mapped mols to eachother by @RiesBen in #148
• WIP: Perses atom mappers by @RiesBen in #147
• Add lower pin for lomap2 in environment yaml file by @IAlibay in #157
• Fixes the openmm rbfe protocol by @IAlibay in #159
• Fix rms tolerance check by @IAlibay in #161
• 154 add test for persesmapper not finding a mapping by @RiesBen in #158
• Add vacuum support for relative ligand transform by @IAlibay in #160
• Fix tests by @richardjgowers in #163
• remove py 3.8 from CI by @richardjgowers in #162
• Remove universal bdist_wheel in setup.cfg by @IAlibay in #165
• Fix to json by @richardjgowers in #168
• Add sams and independent samplers to equil RBFE protocol by @IAlibay in #125
• Using gufe protocols by @richardjgowers in #142
• Make dry run return true, add basepath by @IAlibay in #186
• Fix results_cls attribute name by @IAlibay in #188
• Fix result_cls again by @IAlibay in #189
• fix gathering of protocol results by @IAlibay in #191
• Make unit close reporter at end of simulation by @IAlibay in #190
• some mock based tests by @richardjgowers in #193
• quickrun CLI command by @dwhswenson in #171
• pin dependencies for release by @richardjgowers in #194
• Optional codecov failures by @IAlibay in #196
• Atom mapping tests by @richardjgowers in #198
• add logo badge by @richardjgowers in #197
• Expose loaders in CLI by @dwhswenson in #200
• [DOCS] Add quickrun command docs by @dwhswenson in #202
• Are we there yet? The py310 edition by @IAlibay in #185
• squashed a bug in mapping repr by @richardjgowers in #207
• [DOCS] Fixing RTD by @dwhswenson in #204
• fix gufe API usage in _create; move setup/methods -> protocols/ by @richardjgowers in #211
• [DOCS] Add dumping_transformation by @dwhswenson in #210
• [Docs] Installation info by @dwhswenson in #212
• [WIP] quickrun should error if a unit errors by @dwhswenson in #209
• Finish quickrun error handling by @dwhswenson in #215
• Pin to 0.4 gufe series for release by @richardjgowers in #216

New Contributors

• @RiesBen made their first contribution in #148

Full Changelog: v0.3...v0.4