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

#293 - UUID JSON codec?

Issue - State: closed - Opened by hmacdope 12 months ago - 1 comment

#292 - testing

Issue - State: closed - Opened by RiesBen about 1 year ago

#291 - Add linting

Pull Request - State: closed - Opened by mikemhenry about 1 year ago - 3 comments
Labels: ecosystem-standards

#290 - Add rever for changelog

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

#289 - Doc push

Pull Request - State: closed - Opened by richardjgowers about 1 year ago - 2 comments

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

Issue - State: closed - Opened by github-actions[bot] about 1 year ago

#287 - Issue 170 lam validators

Pull Request - State: closed - Opened by richardjgowers about 1 year ago - 2 comments

#286 - Add KeyedChain GufeTokenizable representation

Pull Request - State: closed - Opened by ianmkenney about 1 year ago - 7 comments

#285 - Bump CodeCov action

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

#284 - Test against models Vec3/list patch

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

#283 - fixes issue #263

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

#282 - fixes issue #274

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

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

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

#280 - Conda-Forge package pins too aggressive

Issue - State: closed - Opened by mikemhenry about 1 year ago - 7 comments

#279 - [WIP] Fix for migration of settings

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

#278 - improve 2d vis of mappings

Pull Request - State: closed - Opened by richardjgowers about 1 year ago - 2 comments

#277 - Api docs

Pull Request - State: closed - Opened by richardjgowers about 1 year ago - 2 comments

#276 - Move settings from SystemSettings to ForcefieldSettings

Pull Request - State: closed - Opened by hannahbaumann about 1 year ago - 2 comments

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

Pull Request - State: closed - Opened by dwhswenson about 1 year ago - 2 comments

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

Issue - State: closed - Opened by github-actions[bot] about 1 year ago

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

Issue - State: closed - Opened by github-actions[bot] about 1 year ago

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

Issue - State: closed - Opened by github-actions[bot] about 1 year ago

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

Issue - State: closed - Opened by github-actions[bot] about 1 year ago

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

Issue - State: closed - Opened by github-actions[bot] about 1 year ago

#266 - makes AtomMappers subclass from GufeTokenizable

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

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

Pull Request - State: closed - Opened by RiesBen about 1 year ago - 2 comments

#263 - Improve readability of the settings when printed out

Issue - State: closed - Opened by IAlibay about 1 year ago - 3 comments

#262 - Update solventcomponent to encompass all composition properties

Pull Request - State: open - Opened by IAlibay about 1 year ago - 3 comments

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

Pull Request - State: closed - Opened by richardjgowers about 1 year ago - 7 comments

#259 - [WIP] Serialization of StagingPaths

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

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

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

#257 - External resource updates

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

#256 - Don't run conda_cron on PRs

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

#255 - Settings setting shortcut thing

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

#254 - setting settings shortcuts

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

#253 - Settings could take string inputs for unit Quantities

Issue - State: closed - Opened by richardjgowers over 1 year ago - 1 comment
Labels: enhancement, question

#252 - InfraStructure: build Gufe Ligand Network Planner class

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

#251 - Convenient way extract components from `ChemicalSystem`

Issue - State: open - Opened by ijpulidos over 1 year ago - 3 comments

#250 - add ok() method to ProtocolResult

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

#249 - Create python-publish.yml

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

#248 - unpin numpy in conda-forge feedstock?

Issue - State: closed - Opened by IAlibay over 1 year ago - 5 comments

#247 - Automate the PyPi release of gufe?

Issue - State: open - Opened by IAlibay over 1 year ago - 2 comments

#246 - Error when trying to read in phosphorylated threonine

Issue - State: closed - Opened by hannahbaumann over 1 year ago - 3 comments

#245 - [Question] ProtocolUnit key stability

Issue - State: closed - Opened by LilDojd over 1 year ago - 3 comments
Labels: question

#244 - Clarify "DAG dependency order" in docstrings

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

#243 - Obtaining ligand names from Transformations in failed Tasks

Issue - State: open - Opened by ijpulidos over 1 year ago - 2 comments

#242 - Switch to OFE theme

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

#241 - adding mol name labels from ofe-name to mapping vis

Pull Request - State: closed - Opened by RiesBen over 1 year ago - 3 comments
Labels: enhancement

#240 - Expand documentation on extends and extends_key for Protocol

Issue - State: closed - Opened by LilDojd over 1 year ago - 2 comments
Labels: question

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

Issue - State: closed - Opened by github-actions[bot] over 1 year ago

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

Issue - State: closed - Opened by github-actions[bot] over 1 year ago

#237 - Adding multiMapping plots

Pull Request - State: open - Opened by RiesBen over 1 year ago - 2 comments
Labels: enhancement

#236 - Fix quantity array codec

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

#235 - need encoder for numpy masked array

Issue - State: open - Opened by richardjgowers over 1 year ago - 2 comments

#234 - [WIP DNM] Per-Unit Execution

Pull Request - State: open - Opened by dwhswenson over 1 year ago - 1 comment

#233 - adding mol name to mapping figure?

Issue - State: closed - Opened by RiesBen over 1 year ago - 3 comments
Labels: enhancement

#232 - Fix conda-cron

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

#231 - ci: update micromamba action

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

#230 - Fixes ProtocolResult.from_dict

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

#228 - Add NPY dtype codec

Pull Request - State: closed - Opened by IAlibay over 1 year ago - 11 comments

#227 - Versioning and migration for `GufeTokenizable`s

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 9 comments

#226 - test pydantic v2

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

#225 - support pydantic v1 and v2

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

#224 - docs: fixup docs on enlarge graph

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

#223 - Clarify `ProtocolDAG` docstrings

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

#222 - Add support for capturing instrumentation data in ProtocolUnitResult

Issue - State: open - Opened by jchodera over 1 year ago - 1 comment

#221 - multi-GPU execution for single `ProtocolDAG`

Issue - State: open - Opened by dotsdl over 1 year ago - 1 comment

#220 - Improve docstrings as needed for OpenFE

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

#219 - Add checks for partial charges

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

#218 - Issue 217 ligand network no edges

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

#217 - LigandNetwork with no edges raises TypeError

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

#216 - Prevent `_GufeTozenizableMeta.__call__` from overwriting signature of `__init__`

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

#214 - FEAT: add LigandNetwork.is_connected() method

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

#213 - Pin autodoc_pydantic

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

#212 - Support Protein Mutations

Issue - State: open - Opened by mikemhenry over 1 year ago - 7 comments

#211 - Protocol Atom Mapper Assumptions

Issue - State: closed - Opened by mikemhenry over 1 year ago - 12 comments

#210 - Transformation docstrings fixes

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

#209 - proteincomponent: tweak conversions to/from openmm/rdkit

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

#208 - Makes start_time, end_time optional args for ProtocolUnitResult

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

#207 - Have a `from_pdb_string` and `to_pdb_string` method in `ProteinComponent`?

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

#206 - Pin openff-units, pint to avoid typing issues

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

#205 - Clear partial charges or allow them only if asked for

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

#204 - LigandNetwork.to_*_alchemical_network

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

#203 - Issue 192 execute dag restarts

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

#202 - nontetrahedral SmallMoleculeComponent

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

#201 - AttributeError with GUFE 0.8 + RDKit 2022

Issue - State: closed - Opened by craabreu over 1 year ago - 5 comments

#200 - Docs: Overview of gufe

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

#199 - joblib requirement fixed upstream

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

#198 - Fix packaging issues

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

#197 - Gufetok annotations

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

#196 - remove get_rate_of_convergence

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

#195 - Add ligand network

Pull Request - State: closed - Opened by richardjgowers almost 2 years ago - 1 comment

#194 - fixup execute_DAG docs to not raise warnings

Pull Request - State: closed - Opened by richardjgowers almost 2 years ago