0.2.1 - Patch release

This release of FEFlow brings some non-breaking changes that will help supporting modern infrastructure of our dependencies. Namely, full support for pydantic v2, and support for recent versions of the openfe and gufe infrastructure (versions 1.10.* or higher).

What's Changed

• Migrate to native pydantic v2 API by @dotsdl in #138
• Use gufe charge utils. gufe/openfe 1.10+ support by @ijpulidos in #139
• Added setup_minimize setting for NonEquilibriumCyclingProtocol by @dotsdl in #140 . Optional setting to avoid minimizing during setup, convenient for some downstream use cases.

Full Changelog: 0.2.0...0.2.1

0.2.0 - Protein mutation support

This release brings support for protein mutation in the Nonequilibrium cycling protocol. Implemented in its SetupUnit, which could be used as a reference and base for generalizations for other hybrid topology based protocols, therefore potentially making the protein mutation support feature readily available in other protocols.

What's Changed

• Hybrid topology creation speed up by @jthorton in #128
• using GufeQuantity instead of deprecated OpenFF models by @ijpulidos in #130
• Basic functionality for supporting protein mutations in the Nonequlibrium Cycling protocol by @ijpulidos in #132
• Organize tyk2 test data by @ijpulidos in #135

Full Changelog: 0.1.4...0.2.0

0.1.4 - Minor updates and fixes

Dropping use of openff-models. Using vendored models in gufe instead.

What's Changed

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #117
• Importing FloatQuantity from vendored model in gufe by @ijpulidos in #123
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #124
• Updated changelog for 0.1.4 release by @ijpulidos in #125

Full Changelog: 0.1.3...0.1.4

0.1.3 - gufe compatibility update

This release adds support for gufe >= 1.3.0

• Support for gufe >=1.3.0. Defining Settings class in NonEquilibriumCyclingProtocol (#115).

Autogenerated Changelog

• Fix espaloma_charge by @mikemhenry in #111
• ci: update to the new start and stop actions by @ethanholz in #112
• bump disk space for gpu runner by @mikemhenry in #116
• Support for gufe 1.3. Adding settng class attribute to protocol by @ijpulidos in #115
• Update changelog for v0.1.3 release by @IAlibay in #118

New Contributors

• @ethanholz made their first contribution in #112

Full Changelog: 0.1.2...0.1.3

0.1.2

Release supporting recent versions of upstream dependencies, especifically openfe and pymbar packages.

What's Changed

• Support recent openfe and pymbar versions by @ijpulidos in #109

Full Changelog: 0.1.1...0.1.2

0.1.1

What's Changed

• Initial quick support for pydantic 2 (>=1.10.17) by @ijpulidos in #58
• Remove perses references in docs by @ijpulidos in #59
• Add ability to defer minimization from SetupUnit to CycleUnit(s) by @dotsdl in #60
• Add protein-ligand complex testing by @ijpulidos in #61
• add gpu ci by @mikemhenry in #62
• Weekly gpu ci by @ijpulidos in #64
• Fix GPU CI by @IAlibay in #86
• Fix the type hint for the force field settings by @jthorton in #88
• Allow multiple mappings by @jthorton in #90
• Missing changes for rebranding/migration to OpenFE by @ijpulidos in #97

New Contributors

• @jthorton made their first contribution in #88

Full Changelog: 0.1.0...0.1.1

0.1.0

What's Changed

• NEq cycling rebase by @ijpulidos in #4. Rebase what we had in perses into this code base.
• Splitting out SetupUnit from SimulationUnit in NonEquilibriumCyclingProtocol by @dotsdl in #3. Useful for alchemicale-fah integration.
• Cleaning imports and adding dependencies by @ijpulidos in #10
• Migrating HTF object from openfe and writing tests by @ijpulidos in #24
• Adding pre-commit-ci by @ijpulidos in #35
• added .git-blame-ignore-revs to make git blame better by @mikemhenry in #37
• Support version 1.0 for openfe and gufe by @ijpulidos in #38
• state needs to include positions, forces, velocities, and energy to be usable by the Folding@Home openmm-core of alchemiscale-fah by @dotsdl in #45
• Support for different partial charge assignation methods and charge-changing transformations by @ijpulidos in #49
• Protocol as inputs instead of settings by @IAlibay in #53. This makes easier to maintain future changes in the underlying settings models.
• Removing unnecessary file left from cookiecutter. by @ijpulidos in #56
• Release 0.1.0 by @ijpulidos in #57

New Contributors

• @ijpulidos made their first contribution in #4
• @dotsdl made their first contribution in #3
• @mikemhenry made their first contribution in #37
• @pre-commit-ci made their first contribution in #43

Full Changelog: https://github.com/choderalab/feflow/commits/0.1.0