v0.7.3 - Hydrogenmass hotfix

Hotfix for default hydrogen mass to ensure stability.

What's Changed

• Change default hydrogen mass to 3.0 amu by @IAlibay in #182
• Chemicalsystem docfixup by @richardjgowers in #185
• Openfe issue 278 by @richardjgowers in #183

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

v0.7.2 - hotfix doc fixes and some user input checks

What's Changed

• Issue #166 #167 footguns by @richardjgowers in #180

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

v0.7.1easy_campaign hotfix 1

What's Changed

• Package test on CI by @IAlibay in #173
• Delete cache from closed PRs by @mikemhenry in #178
• remove box_vector from ChemicalSystem by @richardjgowers in #174

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

v0.7.0 - easy_campaign

What's Changed

• type annotations for ProtocolResult by @richardjgowers in #127
• Fix #128 by @dotsdl in #129
• Add test data to MANIFEST.in by @dwhswenson in #132
• Storage migration: Remove from gufe by @dwhswenson in #131
• remove custom eq methods from Transformation by @richardjgowers in #137
• Update Protocol tests to use Settings object by @richardjgowers in #130
• Make GufeTokenizable use a true flyweight pattern by @dwhswenson in #146
• Improved coverage by @richardjgowers in #141
• Optional offtk and remove oechem by @richardjgowers in #153
• Issue 154 smc roundtrip by @richardjgowers in #156
• Clarify docstring for componentA_to_componentB by @dwhswenson in #157
• Change ion default to something useful by @IAlibay in #158
• Settings revision by @richardjgowers in #152
• Clarify / fix some of the settings documentation by @IAlibay in #161
• Added scratch_basedir override to execute_DAG by @dotsdl in #148
• Fix Version Info and Switch to pyproject.toml by @mikemhenry in #162
• Just checking version import by @IAlibay in #165
• A hill I'm ready to die upon [nomenclature changes] by @IAlibay in #163
• Add intersphinx and speed up builds by @mikemhenry in #171
• Docs cleanup by @dwhswenson in #172

Full Changelog: v0.6...v0.7.0

v0.6.1

Full Changelog: v0.6...v0.6.1

Contains hotfix for using nonstandard residues

Fixes errors relating to “KeyError: AROMATIC”

v0.6

What's Changed

• MAINT: bump openff-units to v0.2.0 by @richardjgowers in #107
• Add build badge to README by @mikemhenry in #113
• Speed up protein test loading by @dwhswenson in #100
• Move LigandAtomMappers from openfe to gufe by @richardjgowers in #116
• Implementation of topological approach for relationships between ProtocolDAGResults by @dotsdl in #111
• Custom json updates and default settings by @mikemhenry in #110
• Update environment.yml by @richardjgowers in #123
• Update environment.yml by @richardjgowers in #124
• [DOCS] Serialization by @dwhswenson in #81
• Load/Store of transformations/networks by @dwhswenson in #42
• Add PerFileJSONMetadataStore by @dwhswenson in #33

Full Changelog: v0.5...v0.6

v0.5

What's Changed

• Add Settings by @mikemhenry in #37
• Remove old-offtk from CI env by @dotsdl in #78
• Fix ProtocolUnit deserialization by @dwhswenson in #62
• mypy: Fixing implicit None errors by @richardjgowers in #94
• [DOCS] Now build without warnings, and fail on warning on RTD by @richardjgowers in #91
• Add class-level loggers to GufeTokenizables by @dwhswenson in #89
• Added raise_error kwarg for protocoldag.execute, ProtocolUnit.execute by @dotsdl in #95
• change default of execute_DAG shared to cwd by @richardjgowers in #99
• succesful results -- Adding Property to ProtocolDag by @RiesBen in #97
• Some cleanup of GufeTokenizable by @dwhswenson in #90
• Protocoldagresult multiple results by @richardjgowers in #103
• [WIP] Various result handling improvements from working on fah-alchemy by @dotsdl in #102
• Follows #102; meant to push doc fixes. by @dotsdl in #104
• Made ProtocolDAGResult.terminal_protocol_unit_results a property by @dotsdl in #106

New Contributors

• @mikemhenry made their first contribution in #37
• @RiesBen made their first contribution in #97

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

0.4 release

What's Changed

• Update README.md by @richardjgowers in #83
• Transformation dump by @dwhswenson in #82
• Fix the way exception class names are made strings by @dwhswenson in #87

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

v0.3

Project Fedex release.

What's Changed

• Add initial implementations of Transformation, AlchemicalNetwork, Protocol; stubs for Executor components by @dotsdl in #13
• Fix coveragerc ellipsis exclusion by @dwhswenson in #28
• to_dict on unitted quantities should use to_tuple by @dwhswenson in #31
• Change ion defaults by @dwhswenson in #32
• Raw data storage by @dwhswenson in #21
• added Failure result by @richardjgowers in #25
• Reorganized component modules within a submodule of their own by @dotsdl in #41
• Solvent: make concentration always a unit, even if 0.0M by @richardjgowers in #40
• to_dict serialization of SmallMoleculeComponent by @richardjgowers in #43
• remove python 3.8 CI by @richardjgowers in #44
• Serialization and tokenization via GufeTokenizable by @dotsdl in #39
• rename base to tokenize_base by @richardjgowers in #47
• DAGs now constructed using ProtocolUnit inputs; inputs can be mapped into keyword arguments of ProtocolUnit._execute by @dotsdl in #36
• update for offtk 0.11 by @richardjgowers in #53
• Added tokenization, serialization methods for AlchemicalNetwork, Transformation by @dotsdl in #55
• Raise NotImplementedError in abstract classmethods by @dwhswenson in #58
• Old offtk by @richardjgowers in #59
• Use the gufe key for DAG name, not hash by @dwhswenson in #61
• Protein serialization by @dwhswenson in #45
• Use clear names openff-toolkit versions in CI by @dwhswenson in #65
• Small fix to typing of TOKENIZABLE_REGISTRY by @dotsdl in #67
• Add init.py to vendor/ by @dwhswenson in #75
• Add test for roundtrip with cleared registry by @dwhswenson in #69
• Add GufeTokenizableTestsMixin to TestTransformation by @dwhswenson in #74
• Protein rework by @richardjgowers in #77
• Performance improvements to tokenization, deterministic sorting by @dotsdl in #76
• added ABCs for AtomMapping behaviour by @richardjgowers in #35
• Add custom_json from OpenPathSampling / SimStore by @dwhswenson in #68
• Add tokenization to top namespace by @richardjgowers in #80

Full Changelog: v0.2...v0.3

v0.2

April release