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

v0.2.1

Install Instructions

Online Installer

To play with the latest notebook, use this command to install the latest version of our packages:

conda env create openfe/openfe-notebooks
Then run:

conda activate openfe-notebooks
git clone https://github.com/OpenFreeEnergy/ExampleNotebooks.git openfe-example-notebooks
cd openfe-example-notebooks
git checkout april-2022
jupyter notebook openmm-rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb

Offline Installer

Download the relevant installer for your operating system and preferred python version.
We have attached the version of the example notebook that works with the latest release of openfe.

If you used our single file installer from the last release, download new-deps.tar.gz. Then activate the old environment before extracting and installing the packages with pip:

# Be sure the old environment is activated! 
mkdir new-deps && tar xzvf new-deps.tar.gz -C new-deps
pip install new-deps/*

Bug Fixes

Hotfix of results

v0.2

Initial release of relative free energy protocols

Alpha Release

What's Changed

• Initial skeleton by @dwhswenson in #21
• Add some changes requested in PR #21 by @IAlibay in #22
• Fix setup.cfg to include packages by @dwhswenson in #25
• Add base Scorer by @dwhswenson in #26
• atommapping implementation by @richardjgowers in #28
• Prevent CodeCov from running on forks, cron jobs by @dwhswenson in #27
• Convert to normal package; add utils; move errors to utils/errors by @dwhswenson in #32
• AtomMapper base classes by @dwhswenson in #30
• Remove Scorers by @dwhswenson in #33
• Molecule class by @dwhswenson in #39
• [WIP] Network container class by @dwhswenson in #40
• Add a simple coveragerc to ignore tests in reporting by @IAlibay in #44
• Tests for Network object by @dwhswenson in #43
• Add Versioneer by @mikemhenry in #45
• WIP: Lomap atommapper by @richardjgowers in #31
• suggested Network & Molecule changes by @richardjgowers in #46
• update AtomMapping type annotations by @richardjgowers in #48
• Set up basic mypy CI by @IAlibay in #50
• omit _version.py from coverage by @IAlibay in #53
• Proposed API change on AtomMapper by @dwhswenson in #56
• CLI Skeleton by @dwhswenson in #49
• network planning functions started by @richardjgowers in #41
• CLI for AtomMapping by @dwhswenson in #57
• added stubs for Molecule conversions by @richardjgowers in #58
• Molecule serialization/deserialization by @dwhswenson in #63
• Network Serialization by @dwhswenson in #64
• Docsdocsdocs by @richardjgowers in #66
• Skip running OE license check on PR by @mikemhenry in #71
• Add serialization test data script by @dwhswenson in #69
• Add support to get molecule name from _Name prop by @dwhswenson in #68
• Add support for CLI --mol to load SDF by @dwhswenson in #67
• Add visualization to AtomMapping by @mikemhenry in #60
• [WIP] Combine visualization with CLI by @dwhswenson in #72

Full Changelog: https://github.com/OpenFreeEnergy/openfe/commits/v0.1