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
#216 - Prevent `_GufeTozenizableMeta.__call__` from overwriting signature of `__init__`
Pull Request -
State: closed - Opened by Yoshanuikabundi 11 months ago
- 1 comment
#215 - Always raise, don't swallow exception, if exception is `KeyboardInterrupt` in `ProtocolUnit.execute`
Pull Request -
State: closed - Opened by dotsdl 11 months ago
- 3 comments
#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
#154 - `SmallMoleculeComponent._rdkit` not equal upon roundtrip with `to_json`, `from_json`
Issue -
State: closed - Opened by dotsdl 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
#143 - Force field assignment as a separate object on `Transformation` outside of `Settings`, similar to `Mapping`
Issue -
State: open - Opened by dotsdl over 1 year ago
Labels: question
#142 - `GufeTokenizableTestsMixin`: remove `.clear()` from teardown
Issue -
State: open - Opened by dwhswenson over 1 year ago
#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