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

#193 - Issue 168 basic telemetry

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

#192 - Implement restart in `execute_DAG`.

Issue - State: open - Opened by IAlibay almost 2 years ago - 5 comments
Labels: enhancement, priority-high

#191 - updated off models pin to 0.0.5

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

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

Issue - State: closed - Opened by github-actions[bot] almost 2 years ago - 3 comments

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

Issue - State: closed - Opened by github-actions[bot] almost 2 years ago

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

Issue - State: closed - Opened by github-actions[bot] almost 2 years ago

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

Issue - State: closed - Opened by github-actions[bot] almost 2 years ago

#186 - PathLike wrapper/cache for ExternalStorage

Pull Request - State: open - Opened by dwhswenson almost 2 years ago - 5 comments

#185 - Chemicalsystem docfixup

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

#184 - Packaging force field files along with Protocols

Issue - State: open - Opened by IAlibay almost 2 years ago - 5 comments

#183 - Openfe issue 278

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

#182 - Change default hydrogen mass to 3.0 amu

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

#181 - Reconsider default hydrogen_mass setting

Issue - State: closed - Opened by IAlibay almost 2 years ago - 2 comments

#180 - Issue 166 167 footguns

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

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

Issue - State: open - Opened by dwhswenson almost 2 years ago - 3 comments

#178 - Delete cache from closed PRs

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

#177 - Improved readonly settings

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

#176 - [CI] CONDA CRON FAILURE

Issue - State: closed - Opened by github-actions[bot] almost 2 years ago

#175 - [CI] CONDA CRON FAILURE

Issue - State: closed - Opened by github-actions[bot] almost 2 years ago - 1 comment

#174 - remove box_vector from ChemicalSystem

Pull Request - State: closed - Opened by richardjgowers almost 2 years ago - 3 comments

#173 - Package test on CI

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

#172 - Docs cleanup

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

#171 - Add intersphinx and speed up builds

Pull Request - State: closed - Opened by mikemhenry almost 2 years ago - 3 comments

#170 - `LigandAtomMapping` validator for mapping

Issue - State: closed - Opened by ijpulidos almost 2 years ago - 1 comment

#169 - Readonly settings

Pull Request - State: closed - Opened by richardjgowers almost 2 years ago - 6 comments

#168 - basic telemetry

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

#167 - anti footgun: Proteins

Issue - State: closed - Opened by richardjgowers almost 2 years ago

#166 - anti footgun: Check for H on SmallMoleculeComponent

Issue - State: closed - Opened by richardjgowers almost 2 years ago

#165 - Just checking version import

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

#164 - Link docs to openfe

Issue - State: open - Opened by mikemhenry almost 2 years ago
Labels: documentation, docs-developer

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

Pull Request - State: closed - Opened by IAlibay almost 2 years ago - 7 comments

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

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

#161 - Clarify / fix some of the settings documentation

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

#160 - bring sdf-dir this to gufe

Issue - State: open - Opened by RiesBen almost 2 years ago - 2 comments

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

Issue - State: open - Opened by RiesBen almost 2 years ago - 2 comments

#158 - Change ion default to something useful

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

#157 - Clarify docstring for componentA_to_componentB

Pull Request - State: closed - Opened by dwhswenson almost 2 years ago - 4 comments

#156 - Issue 154 smc roundtrip

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

#155 - Specifying component B to A in ligand mapping

Issue - State: closed - Opened by ijpulidos almost 2 years ago - 3 comments

#154 - `SmallMoleculeComponent._rdkit` not equal upon roundtrip with `to_json`, `from_json`

Issue - State: closed - Opened by dotsdl almost 2 years ago - 3 comments

#153 - Optional offtk and remove oechem

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

#152 - Settings revision

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

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

Pull Request - State: closed - Opened by dwhswenson almost 2 years ago - 3 comments

#150 - Alchemiscale compute 2

Pull Request - State: closed - Opened by richardjgowers almost 2 years ago - 3 comments

#149 - Change deduplication docs

Issue - State: open - Opened by dwhswenson almost 2 years ago

#148 - Added scratch_basedir override to `execute_DAG`

Pull Request - State: closed - Opened by dotsdl almost 2 years ago - 3 comments

#147 - True flyweight 2

Pull Request - State: closed - Opened by richardjgowers almost 2 years ago - 3 comments

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

Pull Request - State: closed - Opened by dwhswenson almost 2 years ago - 5 comments

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

Issue - State: closed - Opened by dwhswenson almost 2 years ago - 1 comment

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

Issue - State: open - Opened by dotsdl almost 2 years ago - 4 comments
Labels: question

#141 - Improved coverage

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

#140 - add support methods to LigandAtomMapping

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

#139 - rename ProteinComponent to PDBComponent?

Issue - State: open - Opened by richardjgowers almost 2 years ago - 9 comments

#138 - make settings Readonly once inside Protocol

Issue - State: closed - Opened by richardjgowers almost 2 years ago - 3 comments

#137 - remove custom eq methods from Transformation

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

#136 - Protein-Protein mapping

Issue - State: open - Opened by richardjgowers almost 3 years ago

#135 - [WIP] Use PDBInf

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

#134 - WIP: Protocol.validate API point

Pull Request - State: open - Opened by richardjgowers almost 2 years ago - 4 comments

#133 - redundant label on Protocol create signature?

Issue - State: open - Opened by richardjgowers almost 2 years ago - 2 comments

#132 - Add test data to MANIFEST.in

Pull Request - State: closed - Opened by dwhswenson almost 2 years ago - 7 comments

#131 - Storage migration: Remove from `gufe`

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

#130 - Update Protocol tests to use Settings object

Pull Request - State: closed - Opened by richardjgowers about 2 years ago - 6 comments

#129 - Fix #128

Pull Request - State: closed - Opened by dotsdl about 2 years ago - 2 comments

#128 - `Settings` object not hashable

Issue - State: closed - Opened by dotsdl about 2 years ago

#127 - type annotations for ProtocolResult

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

#126 - [WIP]: Proposal for a LigandNetwork class in gufe in stead of OpenFE

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

#125 - test_json_round_trip fails without openff-models pin

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

#124 - Update environment.yml

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

#123 - Update environment.yml

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

#122 - Number of replicates in `Settings` object

Issue - State: open - Opened by ijpulidos about 2 years ago - 5 comments

#121 - `OpenMMSystemGeneratorFFSettings` cleanups

Issue - State: open - Opened by dwhswenson about 2 years ago

#120 - Change `shared` from directory to an object

Issue - State: open - Opened by dwhswenson about 2 years ago

#118 - protein request fixture causing failures

Issue - State: closed - Opened by richardjgowers about 2 years ago - 2 comments

#117 - Add docstrings to `LigandAtomMapping` methods

Issue - State: open - Opened by dotsdl about 2 years ago - 3 comments

#116 - Move LigandAtomMappers from openfe to gufe

Pull Request - State: closed - Opened by richardjgowers about 2 years ago - 3 comments

#115 - Move `openfe` `LigandAtomMapping` into `gufe`?

Issue - State: closed - Opened by dotsdl about 2 years ago - 5 comments

#112 - Add black check for PRs?

Issue - State: closed - Opened by dotsdl about 2 years ago - 3 comments
Labels: ecosystem-standards

#111 - Implementation of topological approach for relationships between `ProtocolDAGResult`s

Pull Request - State: closed - Opened by dotsdl about 2 years ago - 5 comments

#110 - Custom json updates and default settings

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

#109 - Default Settings

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

#107 - MAINT: bump openff-units to v0.2.0

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

#106 - Made ProtocolDAGResult.terminal_protocol_unit_results a property

Pull Request - State: closed - Opened by dotsdl about 2 years ago - 1 comment

#105 - Fix issues with custom JSON codecs

Pull Request - State: closed - Opened by dwhswenson about 2 years ago - 6 comments

#104 - Follows #102; meant to push doc fixes.

Pull Request - State: closed - Opened by dotsdl about 2 years ago - 1 comment

#102 - [WIP] Various result handling improvements from working on `fah-alchemy`

Pull Request - State: closed - Opened by dotsdl about 2 years ago - 3 comments

#100 - Speed up protein test loading

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

#88 - Flyweight pattern not working on Transformation

Issue - State: closed - Opened by richardjgowers over 2 years ago - 7 comments

#84 - pypi package

Issue - State: open - Opened by richardjgowers over 2 years ago - 1 comment

#81 - [DOCS] Serialization

Pull Request - State: closed - Opened by dwhswenson over 2 years ago - 6 comments

#76 - Performance improvements to tokenization, deterministic sorting

Pull Request - State: closed - Opened by dotsdl over 2 years ago - 16 comments

#60 - gufe objects not giving informative signatures

Issue - State: closed - Opened by dwhswenson over 2 years ago - 2 comments

#56 - an attempt to simplify ProtocolUnits:

Pull Request - State: closed - Opened by richardjgowers over 2 years ago - 4 comments

#54 - nans in box in ChemicalSystem make round trip tests fail

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

#52 - ProteinComponent.to_openff should give offtk.Topology not Molecule

Issue - State: open - Opened by richardjgowers over 2 years ago - 1 comment

#51 - openff tk made optional dependency

Pull Request - State: closed - Opened by richardjgowers over 2 years ago - 3 comments

#42 - Load/Store of transformations/networks

Pull Request - State: closed - Opened by dwhswenson over 2 years ago - 7 comments