Ecosyste.ms: Issues

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GitHub / OpenFreeEnergy/gufe issues and pull requests

#348 - [WIP] Fix CI

Pull Request - State: open - Opened by IAlibay 14 days ago - 1 comment

#347 - ChemicalSystem difference method

Issue - State: open - Opened by IAlibay 20 days ago

#346 - [WIP] Fe setup structure remodelling

Pull Request - State: open - Opened by RiesBen 20 days ago - 1 comment
Labels: enhancement

#343 - modify_dependencies does not recursively deserialize gufetokenizables

Issue - State: open - Opened by IAlibay 24 days ago - 2 comments

#342 - Build ComponentMapping, ComponentMappingScorer

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

#341 - Adding atom mapping scorer

Pull Request - State: closed - Opened by RiesBen about 1 month ago - 1 comment

#340 - Bump minimum Python version to 3.10

Pull Request - State: closed - Opened by mattwthompson about 1 month ago - 2 comments

#338 - [CI] CONDA CRON FAILURE ubuntu-latest python 3.9

Issue - State: open - Opened by github-actions[bot] about 1 month ago

#336 - Test new openff-models w/ pydantic v2

Pull Request - State: open - Opened by IAlibay about 1 month ago - 5 comments

#335 - Mention 1.0 Release

Pull Request - State: closed - Opened by mikemhenry about 1 month ago - 1 comment

#333 - mapping affected by charge assignation

Issue - State: open - Opened by ijpulidos 2 months ago

#330 - user-set partial charge warning

Issue - State: open - Opened by JenkeScheen 3 months ago - 1 comment
Labels: priority:low

#329 - Implement settings thermodynamic equality

Issue - State: open - Opened by IAlibay 3 months ago - 1 comment
Labels: enhancement

#328 - Add concept of `samples` to `Protocol.create`?

Issue - State: open - Opened by dotsdl 3 months ago - 2 comments
Labels: enhancement, question

#326 - Improve partial charge check

Pull Request - State: closed - Opened by jthorton 4 months ago - 2 comments

#325 - Improve gufe partial charge checks

Issue - State: closed - Opened by IAlibay 4 months ago

#323 - Define `AlchemicalArchive` object for use as archival artifact

Issue - State: open - Opened by dotsdl 4 months ago
Labels: enhancement

#320 - adds LigandNetwork.remove_edges

Pull Request - State: open - Opened by richardjgowers 5 months ago - 2 comments

#316 - Add tests for PR #265

Issue - State: open - Opened by IAlibay 5 months ago

#315 - Proposed fix to dag ordering

Pull Request - State: open - Opened by LilDojd 5 months ago - 1 comment

#314 - ProtocolDAG._iterate_dag_order is unstable

Issue - State: open - Opened by LilDojd 5 months ago

#313 - Unpin macos runner

Issue - State: open - Opened by IAlibay 5 months ago

#312 - Pin CI to macos-12

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

#311 - Make `Transformation` and `NonTransformation` subclass `TransformationBase`

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

#310 - [CI] CONDA CRON FAILURE macos python 3.9

Issue - State: open - Opened by github-actions[bot] 5 months ago

#309 - [CI] CONDA CRON FAILURE macos python 3.10

Issue - State: open - Opened by github-actions[bot] 5 months ago

#308 - [CI] CONDA CRON FAILURE macos python 3.11

Issue - State: open - Opened by github-actions[bot] 5 months ago - 2 comments

#307 - Adding NetworkPlanner

Pull Request - State: closed - Opened by RiesBen 6 months ago - 3 comments

#306 - Adding a generic atom mapping scorer

Pull Request - State: closed - Opened by RiesBen 6 months ago - 3 comments

#305 - Docs are a bit hard to read on dark mode

Issue - State: open - Opened by mikemhenry 6 months ago - 1 comment

#304 - Update default off version to 2.1.1

Pull Request - State: closed - Opened by IAlibay 6 months ago - 2 comments

#303 - Bump up default openforcefield version to 2.1

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

#301 - [CI] CONDA CRON FAILURE macos python 3.9

Issue - State: closed - Opened by github-actions[bot] 6 months ago - 1 comment

#300 - [CI] CONDA CRON FAILURE ubuntu python 3.9

Issue - State: closed - Opened by github-actions[bot] 6 months ago

#299 - ExplicitSolvationComponent

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

#298 - Inccorect connectivity with modified amino acids

Issue - State: closed - Opened by jthorton 7 months ago - 4 comments

#296 - Dep warnings for dict mapping

Pull Request - State: closed - Opened by richardjgowers 7 months ago - 3 comments

#295 - [docs] have gufe docs sit in the openfe namespace

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

#294 - Add UUID JSON codec

Pull Request - State: closed - Opened by hmacdope 7 months ago - 1 comment

#293 - UUID JSON codec?

Issue - State: closed - Opened by hmacdope 7 months ago - 1 comment

#292 - testing

Issue - State: closed - Opened by RiesBen 7 months ago

#291 - Add linting

Pull Request - State: open - Opened by mikemhenry 8 months ago - 1 comment

#290 - Add rever for changelog

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

#289 - Doc push

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

#288 - [CI] CONDA CRON FAILURE macos python 3.10

Issue - State: closed - Opened by github-actions[bot] 8 months ago

#287 - Issue 170 lam validators

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

#286 - Add KeyedChain GufeTokenizable representation

Pull Request - State: open - Opened by ianmkenney 8 months ago - 7 comments

#285 - Bump CodeCov action

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

#284 - Test against models Vec3/list patch

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

#283 - fixes issue #263

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

#282 - fixes issue #274

Pull Request - State: open - Opened by richardjgowers 8 months ago - 1 comment

#281 - Test latest openff-toolkit with gufe `main`

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

#280 - Conda-Forge package pins too aggressive

Issue - State: closed - Opened by mikemhenry 8 months ago - 7 comments

#279 - [WIP] Fix for migration of settings

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

#278 - improve 2d vis of mappings

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

#277 - Api docs

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

#276 - Move settings from SystemSettings to ForcefieldSettings

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

#273 - Support `name` in `SmallMoleculeComponent.copy_with_replacements`

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

#271 - [CI] CONDA CRON FAILURE macos python 3.10

Issue - State: closed - Opened by github-actions[bot] 9 months ago

#270 - [CI] CONDA CRON FAILURE macos python 3.9

Issue - State: closed - Opened by github-actions[bot] 9 months ago

#269 - [CI] CONDA CRON FAILURE ubuntu python 3.10

Issue - State: closed - Opened by github-actions[bot] 9 months ago

#268 - [CI] CONDA CRON FAILURE ubuntu python 3.11

Issue - State: closed - Opened by github-actions[bot] 9 months ago

#267 - [CI] CONDA CRON FAILURE ubuntu python 3.9

Issue - State: closed - Opened by github-actions[bot] 9 months ago

#266 - makes AtomMappers subclass from GufeTokenizable

Pull Request - State: closed - Opened by richardjgowers 9 months ago - 1 comment

#265 - Adding CA ions to parsing list - proteincomponent.py

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

#263 - Improve readability of the settings when printed out

Issue - State: closed - Opened by IAlibay 9 months ago - 3 comments

#262 - Update solventcomponent to encompass all composition properties

Pull Request - State: open - Opened by IAlibay 9 months ago - 3 comments

#260 - change signature of Protocol.create to have a list of ComponentMappings

Pull Request - State: closed - Opened by richardjgowers 10 months ago - 7 comments

#259 - [WIP] Serialization of StagingPaths

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

#258 - [WIP] Use `StorageManager` in `execute_DAG`

Pull Request - State: open - Opened by dwhswenson 10 months ago - 1 comment

#257 - External resource updates

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

#256 - Don't run conda_cron on PRs

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

#255 - Settings setting shortcut thing

Pull Request - State: closed - Opened by richardjgowers 11 months ago - 4 comments

#254 - setting settings shortcuts

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

#253 - Settings could take string inputs for unit Quantities

Issue - State: closed - Opened by richardjgowers 11 months ago - 1 comment
Labels: enhancement, question

#252 - InfraStructure: build Gufe Ligand Network Planner class

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

#251 - Convenient way extract components from `ChemicalSystem`

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

#250 - add ok() method to ProtocolResult

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

#249 - Create python-publish.yml

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