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

#227 - Versioning and migration for `GufeTokenizable`s

Pull Request - State: closed - Opened by dwhswenson 10 months ago - 9 comments

#226 - test pydantic v2

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

#225 - support pydantic v1 and v2

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

#224 - docs: fixup docs on enlarge graph

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

#223 - Clarify `ProtocolDAG` docstrings

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

#222 - Add support for capturing instrumentation data in ProtocolUnitResult

Issue - State: open - Opened by jchodera 10 months ago - 1 comment

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

Issue - State: open - Opened by dotsdl 10 months ago

#220 - Improve docstrings as needed for OpenFE

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

#219 - Add checks for partial charges

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

#218 - Issue 217 ligand network no edges

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

#217 - LigandNetwork with no edges raises TypeError

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

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

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

#213 - Pin autodoc_pydantic

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

#212 - Support Protein Mutations

Issue - State: open - Opened by mikemhenry 11 months ago - 4 comments

#211 - Protocol Atom Mapper Assumptions

Issue - State: closed - Opened by mikemhenry 11 months ago - 12 comments

#210 - Transformation docstrings fixes

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

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

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

#208 - Makes start_time, end_time optional args for ProtocolUnitResult

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

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

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

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

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

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

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

#204 - LigandNetwork.to_*_alchemical_network

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

#203 - Issue 192 execute dag restarts

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

#202 - nontetrahedral SmallMoleculeComponent

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

#201 - AttributeError with GUFE 0.8 + RDKit 2022

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

#200 - Docs: Overview of gufe

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

#199 - joblib requirement fixed upstream

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

#198 - Fix packaging issues

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

#197 - Gufetok annotations

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

#196 - remove get_rate_of_convergence

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

#195 - Add ligand network

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

#194 - fixup execute_DAG docs to not raise warnings

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

#193 - Issue 168 basic telemetry

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

#192 - Implement restart in `execute_DAG`.

Issue - State: open - Opened by IAlibay about 1 year ago - 5 comments
Labels: enhancement, priority-high

#191 - updated off models pin to 0.0.5

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

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

Issue - State: closed - Opened by github-actions[bot] about 1 year ago - 3 comments

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

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

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

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

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

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

#186 - PathLike wrapper/cache for ExternalStorage

Pull Request - State: open - Opened by dwhswenson about 1 year ago - 5 comments

#185 - Chemicalsystem docfixup

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

#184 - Packaging force field files along with Protocols

Issue - State: open - Opened by IAlibay about 1 year ago - 5 comments

#183 - Openfe issue 278

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

#182 - Change default hydrogen mass to 3.0 amu

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

#181 - Reconsider default hydrogen_mass setting

Issue - State: closed - Opened by IAlibay about 1 year ago - 2 comments

#180 - Issue 166 167 footguns

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

#179 - Make `dry` an option in protocol execution?

Issue - State: open - Opened by dwhswenson about 1 year ago - 3 comments

#178 - Delete cache from closed PRs

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

#177 - Improved readonly settings

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

#176 - [CI] CONDA CRON FAILURE

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

#175 - [CI] CONDA CRON FAILURE

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

#174 - remove box_vector from ChemicalSystem

Pull Request - State: closed - Opened by richardjgowers about 1 year ago - 3 comments

#173 - Package test on CI

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

#172 - Docs cleanup

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

#171 - Add intersphinx and speed up builds

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

#170 - `LigandAtomMapping` validator for mapping

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

#169 - Readonly settings

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

#168 - basic telemetry

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

#167 - anti footgun: Proteins

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

#166 - anti footgun: Check for H on SmallMoleculeComponent

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

#165 - Just checking version import

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

#164 - Link docs to openfe

Issue - State: open - Opened by mikemhenry about 1 year ago
Labels: documentation

#163 - A hill I'm ready to die upon [nomenclature changes]

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

#162 - Fix Version Info and Switch to pyproject.toml

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

#161 - Clarify / fix some of the settings documentation

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

#160 - bring sdf-dir this to gufe

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

#159 - Default settings depending on the chemical system in the future?

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

#158 - Change ion default to something useful

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

#157 - Clarify docstring for componentA_to_componentB

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

#156 - Issue 154 smc roundtrip

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

#155 - Specifying component B to A in ligand mapping

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

#153 - Optional offtk and remove oechem

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

#152 - Settings revision

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

#151 - Make `shared` into an `ExternalStorage` object

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

#150 - Alchemiscale compute 2

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

#149 - Change deduplication docs

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

#148 - Added scratch_basedir override to `execute_DAG`

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

#147 - True flyweight 2

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

#146 - Make `GufeTokenizable` use a true flyweight pattern

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 5 comments

#145 - RDKit properties are not stored in `SmallMoleculeComponent.to_dict`

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

#144 - Determine ComponentMapping approach to ChemicalSystems from perspective of a Protocol

Issue - State: open - Opened by dotsdl over 1 year ago - 3 comments
Labels: question

#141 - Improved coverage

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

#140 - add support methods to LigandAtomMapping

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

#139 - rename ProteinComponent to PDBComponent?

Issue - State: open - Opened by richardjgowers over 1 year ago - 8 comments

#138 - make settings Readonly once inside Protocol

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

#137 - remove custom eq methods from Transformation

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

#136 - Protein-Protein mapping

Issue - State: open - Opened by richardjgowers over 2 years ago

#135 - [WIP] Use PDBInf

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

#134 - WIP: Protocol.validate API point

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

#133 - redundant label on Protocol create signature?

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

#132 - Add test data to MANIFEST.in

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

#131 - Storage migration: Remove from `gufe`

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

#130 - Update Protocol tests to use Settings object

Pull Request - State: closed - Opened by richardjgowers over 1 year ago - 6 comments

#129 - Fix #128

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

#128 - `Settings` object not hashable

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