Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / OpenFreeEnergy/gufe issues and pull requests
#327 - Allow for storing & retreiving PDBResidueInfo for SMCs
Issue -
State: open - Opened by IAlibay 20 days ago
#326 - Improve partial charge check
Pull Request -
State: closed - Opened by jthorton 22 days ago
- 2 comments
#325 - Improve gufe partial charge checks
Issue -
State: closed - Opened by IAlibay 24 days ago
#324 - [CI] CONDA CRON FAILURE ubuntu-latest python 3.10
Issue -
State: closed - Opened by github-actions[bot] 26 days ago
#323 - Define `AlchemicalArchive` object for use as archival artifact
Issue -
State: open - Opened by dotsdl 28 days ago
Labels: enhancement
#322 - RDKit `Mol` doesn't preserve atom properties when pickled; impacts `ExplicitMoleculeComponent` and subclasses
Issue -
State: open - Opened by dotsdl about 1 month ago
- 2 comments
Labels: bug
#321 - Add compression approach to Numpy arrays when passed through JSON encoder
Issue -
State: open - Opened by dotsdl about 1 month ago
#320 - adds LigandNetwork.remove_edges
Pull Request -
State: open - Opened by richardjgowers about 2 months ago
- 2 comments
#319 - [CI] CONDA CRON FAILURE macos-12 python 3.10
Issue -
State: open - Opened by github-actions[bot] about 2 months ago
#318 - [CI] CONDA CRON FAILURE macos-12 python 3.9
Issue -
State: open - Opened by github-actions[bot] about 2 months ago
#317 - [CI] CONDA CRON FAILURE macos-12 python 3.11
Issue -
State: open - Opened by github-actions[bot] about 2 months ago
#316 - Add tests for PR #265
Issue -
State: open - Opened by IAlibay 2 months ago
#315 - Proposed fix to dag ordering
Pull Request -
State: open - Opened by LilDojd 2 months ago
- 1 comment
#314 - ProtocolDAG._iterate_dag_order is unstable
Issue -
State: open - Opened by LilDojd 2 months ago
#313 - Unpin macos runner
Issue -
State: open - Opened by IAlibay 2 months ago
#312 - Pin CI to macos-12
Pull Request -
State: closed - Opened by IAlibay 2 months ago
- 1 comment
#311 - Make `Transformation` and `NonTransformation` subclass `TransformationBase`
Pull Request -
State: open - Opened by dotsdl 2 months ago
- 3 comments
#310 - [CI] CONDA CRON FAILURE macos python 3.9
Issue -
State: open - Opened by github-actions[bot] 2 months ago
#309 - [CI] CONDA CRON FAILURE macos python 3.10
Issue -
State: open - Opened by github-actions[bot] 2 months ago
#308 - [CI] CONDA CRON FAILURE macos python 3.11
Issue -
State: open - Opened by github-actions[bot] 2 months ago
- 2 comments
#307 - [WIP] Adding ligand network planner
Pull Request -
State: open - Opened by RiesBen 2 months ago
- 2 comments
#306 - Adding a generic atom mapping scorer
Pull Request -
State: open - Opened by RiesBen 2 months ago
- 2 comments
#305 - Docs are a bit hard to read on dark mode
Issue -
State: open - Opened by mikemhenry 2 months ago
- 1 comment
#304 - Update default off version to 2.1.1
Pull Request -
State: closed - Opened by IAlibay 3 months ago
- 2 comments
#303 - Bump up default openforcefield version to 2.1
Issue -
State: closed - Opened by IAlibay 3 months ago
#302 - rdkit MolFromMol2File function assigns "wrong" tautomer, tough this seems to get corrected in the SmallMoleculeComponent
Issue -
State: open - Opened by hannahbaumann 11 months ago
- 1 comment
#301 - [CI] CONDA CRON FAILURE macos python 3.9
Issue -
State: closed - Opened by github-actions[bot] 3 months ago
- 1 comment
#300 - [CI] CONDA CRON FAILURE ubuntu python 3.9
Issue -
State: closed - Opened by github-actions[bot] 3 months ago
#299 - ExplicitSolvationComponent
Issue -
State: open - Opened by IAlibay 3 months ago
#298 - Inccorect connectivity with modified amino acids
Issue -
State: closed - Opened by jthorton 3 months ago
- 4 comments
#297 - SmallMoleculeComponent.to_openff() does not preserve the molecule protonation state
Issue -
State: open - Opened by LilDojd 4 months ago
- 1 comment
#296 - Dep warnings for dict mapping
Pull Request -
State: closed - Opened by richardjgowers 4 months ago
- 3 comments
#295 - [docs] have gufe docs sit in the openfe namespace
Issue -
State: open - Opened by IAlibay 4 months ago
#294 - Add UUID JSON codec
Pull Request -
State: closed - Opened by hmacdope 4 months ago
- 1 comment
#293 - UUID JSON codec?
Issue -
State: closed - Opened by hmacdope 4 months ago
- 1 comment
#292 - testing
Issue -
State: closed - Opened by RiesBen 4 months ago
#291 - Add linting
Pull Request -
State: open - Opened by mikemhenry 4 months ago
- 1 comment
#290 - Add rever for changelog
Pull Request -
State: closed - Opened by richardjgowers 4 months ago
- 1 comment
#289 - Doc push
Pull Request -
State: closed - Opened by richardjgowers 5 months ago
- 2 comments
#288 - [CI] CONDA CRON FAILURE macos python 3.10
Issue -
State: closed - Opened by github-actions[bot] 5 months ago
#287 - Issue 170 lam validators
Pull Request -
State: closed - Opened by richardjgowers 5 months ago
- 2 comments
#286 - Add KeyedChain GufeTokenizable representation
Pull Request -
State: open - Opened by ianmkenney 5 months ago
- 7 comments
#285 - Bump CodeCov action
Pull Request -
State: closed - Opened by mattwthompson 5 months ago
- 1 comment
#284 - Test against models Vec3/list patch
Pull Request -
State: closed - Opened by mattwthompson 5 months ago
- 2 comments
#283 - fixes issue #263
Pull Request -
State: closed - Opened by richardjgowers 5 months ago
- 1 comment
#282 - fixes issue #274
Pull Request -
State: open - Opened by richardjgowers 5 months ago
- 1 comment
#281 - Test latest openff-toolkit with gufe `main`
Pull Request -
State: closed - Opened by mikemhenry 5 months ago
- 2 comments
#280 - Conda-Forge package pins too aggressive
Issue -
State: closed - Opened by mikemhenry 5 months ago
- 7 comments
#279 - [WIP] Fix for migration of settings
Pull Request -
State: closed - Opened by dwhswenson 5 months ago
- 1 comment
#278 - improve 2d vis of mappings
Pull Request -
State: closed - Opened by richardjgowers 5 months ago
- 2 comments
#277 - Api docs
Pull Request -
State: closed - Opened by richardjgowers 5 months ago
- 2 comments
#276 - Move settings from SystemSettings to ForcefieldSettings
Pull Request -
State: closed - Opened by hannahbaumann 5 months ago
- 2 comments
#275 - Remove settings remove_com from OpenMMSystemGeneratorFFSettings (added to openfe IntegratorSettings)
Pull Request -
State: closed - Opened by hannahbaumann 5 months ago
- 4 comments
#274 - extend `Protocol.default_settings` to take chemistry to generate better default settings
Issue -
State: open - Opened by richardjgowers 5 months ago
#273 - Support `name` in `SmallMoleculeComponent.copy_with_replacements`
Pull Request -
State: closed - Opened by dwhswenson 5 months ago
- 2 comments
#272 - Add `__module_version__` to special items in `GufeTokenizable` dict representation
Issue -
State: closed - Opened by dotsdl 5 months ago
- 1 comment
#271 - [CI] CONDA CRON FAILURE macos python 3.10
Issue -
State: closed - Opened by github-actions[bot] 5 months ago
#270 - [CI] CONDA CRON FAILURE macos python 3.9
Issue -
State: closed - Opened by github-actions[bot] 5 months ago
#269 - [CI] CONDA CRON FAILURE ubuntu python 3.10
Issue -
State: closed - Opened by github-actions[bot] 5 months ago
#268 - [CI] CONDA CRON FAILURE ubuntu python 3.11
Issue -
State: closed - Opened by github-actions[bot] 5 months ago
#267 - [CI] CONDA CRON FAILURE ubuntu python 3.9
Issue -
State: closed - Opened by github-actions[bot] 5 months ago
#266 - makes AtomMappers subclass from GufeTokenizable
Pull Request -
State: closed - Opened by richardjgowers 6 months ago
- 1 comment
#265 - Adding CA ions to parsing list - proteincomponent.py
Pull Request -
State: closed - Opened by RiesBen 6 months ago
- 2 comments
#264 - Not possible to use `SmallMoleculeComponent.copy_with_replacements(name='...')`
Issue -
State: closed - Opened by dotsdl 6 months ago
#263 - Improve readability of the settings when printed out
Issue -
State: closed - Opened by IAlibay 6 months ago
- 3 comments
#262 - Update solventcomponent to encompass all composition properties
Pull Request -
State: open - Opened by IAlibay 6 months ago
- 3 comments
#261 - Update SolventComponent properties to include those that define the composition of the solvent
Issue -
State: open - Opened by IAlibay 6 months ago
- 2 comments
#260 - change signature of Protocol.create to have a list of ComponentMappings
Pull Request -
State: closed - Opened by richardjgowers 6 months ago
- 7 comments
#259 - [WIP] Serialization of StagingPaths
Pull Request -
State: closed - Opened by dwhswenson 7 months ago
- 1 comment
#258 - [WIP] Use `StorageManager` in `execute_DAG`
Pull Request -
State: open - Opened by dwhswenson 7 months ago
- 1 comment
#257 - External resource updates
Pull Request -
State: closed - Opened by dwhswenson 7 months ago
- 1 comment
#256 - Don't run conda_cron on PRs
Pull Request -
State: closed - Opened by dwhswenson 7 months ago
- 1 comment
#255 - Settings setting shortcut thing
Pull Request -
State: closed - Opened by richardjgowers 7 months ago
- 4 comments
#254 - setting settings shortcuts
Issue -
State: closed - Opened by richardjgowers 7 months ago
#253 - Settings could take string inputs for unit Quantities
Issue -
State: closed - Opened by richardjgowers 8 months ago
- 1 comment
Labels: enhancement, question
#252 - InfraStructure: build Gufe Ligand Network Planner class
Issue -
State: open - Opened by RiesBen 7 months ago
Labels: enhancement
#251 - Convenient way extract components from `ChemicalSystem`
Issue -
State: open - Opened by ijpulidos 8 months ago
- 3 comments
#250 - add ok() method to ProtocolResult
Issue -
State: open - Opened by richardjgowers 8 months ago
#249 - Create python-publish.yml
Pull Request -
State: closed - Opened by richardjgowers 8 months ago
- 1 comment
#248 - unpin numpy in conda-forge feedstock?
Issue -
State: closed - Opened by IAlibay 8 months ago
- 5 comments
#247 - Automate the PyPi release of gufe?
Issue -
State: open - Opened by IAlibay 8 months ago
- 1 comment
#246 - Error when trying to read in phosphorylated threonine
Issue -
State: closed - Opened by hannahbaumann 8 months ago
- 3 comments
#245 - [Question] ProtocolUnit key stability
Issue -
State: closed - Opened by LilDojd 8 months ago
- 3 comments
Labels: question
#244 - Clarify "DAG dependency order" in docstrings
Pull Request -
State: closed - Opened by Yoshanuikabundi 9 months ago
- 2 comments
#243 - Obtaining ligand names from Transformations in failed Tasks
Issue -
State: open - Opened by ijpulidos 9 months ago
- 2 comments
#242 - Switch to OFE theme
Pull Request -
State: closed - Opened by Yoshanuikabundi 9 months ago
- 1 comment
#241 - adding mol name labels from ofe-name to mapping vis
Pull Request -
State: closed - Opened by RiesBen 9 months ago
- 3 comments
Labels: enhancement
#240 - Expand documentation on extends and extends_key for Protocol
Issue -
State: closed - Opened by LilDojd 9 months ago
- 2 comments
Labels: question
#239 - [CI] CONDA CRON FAILURE ubuntu python 3.9
Issue -
State: closed - Opened by github-actions[bot] 9 months ago
#238 - [CI] CONDA CRON FAILURE ubuntu python 3.10
Issue -
State: closed - Opened by github-actions[bot] 9 months ago
#237 - [WIP] Adding multiMapping plots
Pull Request -
State: open - Opened by RiesBen 10 months ago
Labels: enhancement
#236 - Fix quantity array codec
Pull Request -
State: closed - Opened by richardjgowers 10 months ago
- 1 comment
#235 - need encoder for numpy masked array
Issue -
State: open - Opened by richardjgowers 10 months ago
- 2 comments
#234 - [WIP DNM] Per-Unit Execution
Pull Request -
State: open - Opened by dwhswenson 10 months ago
- 1 comment
#233 - adding mol name to mapping figure?
Issue -
State: closed - Opened by RiesBen 10 months ago
- 3 comments
Labels: enhancement
#232 - Fix conda-cron
Pull Request -
State: closed - Opened by IAlibay 10 months ago
- 1 comment
#231 - ci: update micromamba action
Pull Request -
State: closed - Opened by richardjgowers 10 months ago
- 1 comment
#230 - Fixes ProtocolResult.from_dict
Pull Request -
State: closed - Opened by richardjgowers 10 months ago
- 2 comments
#229 - RelativeHybridTopologyProtocolResult does not round trip through to_dict/from_dict
Issue -
State: closed - Opened by richardjgowers 10 months ago
#228 - Add NPY dtype codec
Pull Request -
State: closed - Opened by IAlibay 10 months ago
- 11 comments