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GitHub / openfreeenergy/feflow issues and pull requests

#122 - data.py clean-up

Issue - State: open - Opened by atravitz about 1 month ago

#121 - Improve exception handling for protein mutations

Issue - State: open - Opened by ijpulidos about 1 month ago - 1 comment

#119 - Community: Protein Mutations

Issue - State: open - Opened by jameseastwood 2 months ago
Labels: openfe

#118 - Update changelog for v0.1.3 release

Pull Request - State: closed - Opened by IAlibay 4 months ago - 1 comment

#117 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 4 months ago - 1 comment

#116 - bump disk space for gpu runner

Pull Request - State: closed - Opened by mikemhenry 4 months ago - 3 comments

#115 - Support for gufe 1.3. Adding settng class attribute to protocol

Pull Request - State: closed - Opened by ijpulidos 4 months ago - 1 comment

#114 - Support for latest gufe 1.3 version

Issue - State: closed - Opened by ijpulidos 4 months ago - 3 comments

#113 - Self-hosted GPU CI runner failing with no space left on device

Issue - State: closed - Opened by ijpulidos 4 months ago - 1 comment

#112 - ci: update to the new start and stop actions

Pull Request - State: closed - Opened by ethanholz 5 months ago - 1 comment

#111 - Fix espaloma_charge

Pull Request - State: closed - Opened by mikemhenry 5 months ago - 2 comments

#110 - Changelog notes for release 0.1.2

Pull Request - State: closed - Opened by ijpulidos 5 months ago - 1 comment

#109 - Support recent openfe and pymbar versions

Pull Request - State: closed - Opened by ijpulidos 5 months ago - 1 comment

#108 - Detect when the transformation is the same and output zero as the FE estimate

Issue - State: open - Opened by ijpulidos 6 months ago
Labels: enhancement

#107 - Add API docs and a userguide

Issue - State: open - Opened by IAlibay 6 months ago

#106 - Protein mutation support in Neq Cycling Setup Unit

Pull Request - State: open - Opened by ijpulidos 6 months ago

#105 - Speeding up the HTF

Issue - State: open - Opened by IAlibay 7 months ago - 4 comments

#104 - Added verbose `info` logs to `NonEquilibriumCyclingProtocol` `SetupUnit`

Pull Request - State: open - Opened by dotsdl 7 months ago - 2 comments

#103 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 7 months ago - 1 comment

#100 - Utility functions to acquire components in a system

Issue - State: open - Opened by ijpulidos 8 months ago - 1 comment

#99 - Checking states compatibility

Issue - State: open - Opened by ijpulidos 8 months ago

#98 - Release v0.1.1

Pull Request - State: closed - Opened by ijpulidos 8 months ago - 2 comments

#97 - Missing changes for rebranding/migration to OpenFE

Pull Request - State: closed - Opened by ijpulidos 8 months ago - 1 comment

#96 - Test expected failing or unhandled cases

Pull Request - State: closed - Opened by ijpulidos 9 months ago - 3 comments

#95 - Convergence tests for protein mutation protocol

Pull Request - State: closed - Opened by ijpulidos 9 months ago - 2 comments

#94 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 10 months ago

#93 - [DNM] Test if openmm 8.2 beta works

Pull Request - State: closed - Opened by mikemhenry 10 months ago - 1 comment

#92 - Tests for capped AAs

Pull Request - State: closed - Opened by ijpulidos 10 months ago - 3 comments

#90 - Allow multiple mappings

Pull Request - State: closed - Opened by jthorton 10 months ago - 4 comments

#89 - `NonEquilibriumCyclingProtocol` does not expect multiple atom mappings

Issue - State: closed - Opened by jthorton 10 months ago - 1 comment

#88 - Fix the type hint for the force field settings

Pull Request - State: closed - Opened by jthorton 11 months ago - 2 comments

#86 - Fix GPU CI

Pull Request - State: closed - Opened by IAlibay 11 months ago - 2 comments

#85 - [WIP] Fixing CI

Pull Request - State: closed - Opened by IAlibay 11 months ago - 1 comment

#84 - Update OEChem license decrypting

Issue - State: closed - Opened by IAlibay 11 months ago

#83 - Fail when multiple alchemical components are detected

Issue - State: open - Opened by ijpulidos 11 months ago

#82 - Atom shifting mapping for protein mutations

Issue - State: open - Opened by ijpulidos 11 months ago

#81 - Test insertion codes

Issue - State: open - Opened by ijpulidos 11 months ago - 3 comments

#80 - Write some negative control tests (expected failures)

Issue - State: closed - Opened by ijpulidos 11 months ago

#79 - Test convergence for capped AAs mutation

Issue - State: closed - Opened by ijpulidos 11 months ago - 2 comments

#78 - Test capped AAs for protein mutation protocol

Issue - State: closed - Opened by ijpulidos 11 months ago

#77 - Refactor setup unit to work with protein mutation protocol

Issue - State: open - Opened by IAlibay 11 months ago - 2 comments

#75 - Test cases for protein mutation protocol

Issue - State: open - Opened by ijpulidos 11 months ago

#74 - Create a ProteinMapping subclass

Issue - State: open - Opened by IAlibay 11 months ago

#73 - Allow for ProteinComponent as alchemical component

Issue - State: open - Opened by IAlibay 11 months ago

#72 - Update SetupUnit phase detection

Issue - State: open - Opened by IAlibay 11 months ago - 1 comment

#71 - Add duecredit

Issue - State: open - Opened by IAlibay 11 months ago

#70 - NonEquilibrium switching protocol implementation

Pull Request - State: open - Opened by ijpulidos 11 months ago - 1 comment

#69 - Support for different protein conformations in the protocol

Issue - State: open - Opened by ijpulidos 11 months ago - 1 comment

#66 - `NonEquilibriumCyclingProtocol` : Add ability to have multiple iterations/laps within a single `CycleUnit`?

Issue - State: open - Opened by dotsdl 11 months ago - 1 comment
Labels: enhancement, component-protocol

#65 - Implement NEq switching by transforming current NEq Cycling

Issue - State: open - Opened by ijpulidos 11 months ago
Labels: enhancement

#64 - Weekly gpu ci

Pull Request - State: closed - Opened by ijpulidos 11 months ago

#63 - Failing `test_unsampled_endstate_energies_GPU` test

Issue - State: open - Opened by mikemhenry 11 months ago

#62 - add gpu ci

Pull Request - State: closed - Opened by mikemhenry 11 months ago

#61 - Add protein-ligand complex testing

Pull Request - State: closed - Opened by ijpulidos 12 months ago - 1 comment

#60 - Add ability to defer minimization from SetupUnit to CycleUnit(s)

Pull Request - State: closed - Opened by dotsdl 12 months ago - 5 comments

#59 - Remove perses references in docs

Pull Request - State: closed - Opened by ijpulidos 12 months ago

#58 - Initial quick support for pydantic 2 (>=1.10.17)

Pull Request - State: closed - Opened by ijpulidos 12 months ago - 4 comments

#57 - Release 0.1.0

Pull Request - State: closed - Opened by ijpulidos about 1 year ago

#56 - Removing unnecessary file left from cookiecutter.

Pull Request - State: closed - Opened by ijpulidos about 1 year ago

#55 - Validate systems, components and mapping when creating protocol

Pull Request - State: open - Opened by ijpulidos about 1 year ago - 1 comment

#54 - Add systems, components and mapping validation when creating a protocol

Issue - State: open - Opened by ijpulidos about 1 year ago
Labels: enhancement

#53 - Protocol as inputs instead of settings

Pull Request - State: closed - Opened by IAlibay about 1 year ago - 1 comment

#52 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago

#51 - Stabilize settings before release

Issue - State: open - Opened by ijpulidos about 1 year ago

#50 - Allow passing a `json` file for forcefield parameters cache

Issue - State: open - Opened by ijpulidos about 1 year ago - 1 comment
Labels: enhancement

#49 - Charge handling -- Partial charges settings and charge transformation support

Pull Request - State: closed - Opened by ijpulidos about 1 year ago - 6 comments

#48 - Test against lastest OpenFF release instead of GAFF

Issue - State: open - Opened by ijpulidos about 1 year ago

#47 - Allow for partial charge method setting specification

Issue - State: closed - Opened by ijpulidos about 1 year ago - 5 comments
Labels: enhancement

#46 - [DNM] Feature noneq cycling extends

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 2 comments

#45 - Changes needed in support of `alchemiscale-fah`

Pull Request - State: closed - Opened by dotsdl over 1 year ago - 4 comments

#44 - Enable extending NonEquilibriumCyclingProtocols

Pull Request - State: open - Opened by ianmkenney over 1 year ago - 13 comments

#43 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#42 - refactor HTF `softcore_LJ` to understand literals instead of bools

Issue - State: open - Opened by ijpulidos over 1 year ago
Labels: enhancement

#41 - [NEQCycling] User defined LocalEnergyMinimizer steps

Issue - State: open - Opened by IAlibay over 1 year ago

#40 - Protocols inputs to Units instead of using `Settings`

Issue - State: closed - Opened by ijpulidos over 1 year ago - 1 comment

#38 - Support version 1.0 for openfe and gufe

Pull Request - State: closed - Opened by ijpulidos over 1 year ago - 7 comments

#37 - added .git-blame-ignore-revs to make git blame better

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 3 comments

#36 - Setup Unit should work with different integrators

Issue - State: open - Opened by ijpulidos over 1 year ago
Labels: enhancement

#35 - Adding pre-commit-ci

Pull Request - State: closed - Opened by ijpulidos over 1 year ago - 3 comments

#34 - Integrate code formatting pre-commit hooks in CI

Issue - State: open - Opened by ijpulidos over 1 year ago
Labels: enhancement

#33 - [WIP] update for OFE 1.0rc0

Pull Request - State: closed - Opened by IAlibay over 1 year ago - 1 comment

#32 - Migrate tests for "new" HTF features

Pull Request - State: closed - Opened by IAlibay over 1 year ago - 2 comments

#31 - Changes to support `openfe` 1.0, `gufe` 1.0

Issue - State: closed - Opened by dotsdl over 1 year ago - 4 comments

#30 - Not requiring perses for testing hybrid topology implementation

Issue - State: open - Opened by ijpulidos over 1 year ago
Labels: enhancement, testing

#29 - Miscellaneous HTF improvements

Issue - State: open - Opened by ijpulidos over 1 year ago - 1 comment
Labels: enhancement

#28 - port openfe version of LambdaProtocol into feflow

Pull Request - State: closed - Opened by richardjgowers over 1 year ago

#27 - port test for HTF r_cutoff bug

Issue - State: closed - Opened by richardjgowers over 1 year ago - 1 comment

#26 - Htf migration openfe patches

Pull Request - State: closed - Opened by richardjgowers over 1 year ago

#25 - Protocol : Times Square Sampling

Issue - State: open - Opened by dotsdl over 1 year ago
Labels: component-protocol

#24 - HTF migration

Pull Request - State: closed - Opened by ijpulidos over 1 year ago - 2 comments

#23 - Update system creation to allow for setting barostat frequency

Pull Request - State: closed - Opened by IAlibay over 1 year ago

#22 - Migrate openmm specific settings from upstream

Issue - State: open - Opened by ijpulidos over 1 year ago