Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / OpenFreeEnergy/openfe issues and pull requests

#526 - fixes implementation of transmuting_methyl_into_ring_score

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

#524 - Check the ability to pass user charges

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

#523 - update network layout to use graphviz

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

#521 - Remove softcore electrostatics entry

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

#520 - Cookbook flowchart

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

#519 - Add optional path to sys probe

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

#518 - RelativeHybridTopologyProtocolSettings can not round trip to JSON

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

#517 - pin pydantic and autodoc_pydantic

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

#516 - Protocol to run plain MD simulations

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

#515 - failed when generating RBFE network

Issue - State: open - Opened by wenchangzhou-qtx over 1 year ago

#514 - network_from_indices raises warning on disconnected network

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

#513 - Log system probe info

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

#512 - Migrate common settings to omm_utils

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

#511 - Read network from external files

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

#509 - [WIP] Add flaky markers to flaky tests on macOS GitHub actions runners

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

#508 - see if py311 works okay

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

#507 - Tests in test_openmm_equil_rfe_protocols.py fail with pytest=7.4.0

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

#506 - NES and FEP+ network ingestion

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

#505 - Add system probe

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 18 comments

#504 - Logging improvements in quickrun

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

#503 - remove version name and upload files

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

#502 - Split gather

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

#501 - add ps to the docker image (interline needed this)

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

#500 - Unpin libnetcdf

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

#499 - rfe protocol: Adds bfactor labels to output topology

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

#498 - fix issue with new notebook version

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

#497 - Tell users to install the latest version of openfe

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

#496 - Update `openfecli/tests/data/rbfe_results.tar.gz`

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

#495 - Adds MLE estimates on gather command

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

#494 - cli: Protein Parameter swallows error messages

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

#493 - API docs updates

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

#492 - [WIP] quickrun result error inspection command

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

#491 - [WIP] quickrun result error inspection

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

#490 - cli: version doesn't work on editable installs

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

#489 - Allow Openeye for charge generation

Issue - State: open - Opened by jthorton over 1 year ago - 9 comments

#488 - Plan rbfe network radial

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

#487 - CLI: fetch results should untar

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

#486 - CLI: Allow globs for paths

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

#485 - Use common core option when using the Lomap Atom Mapper

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

#484 - Make super slow tests integration tests

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

#483 - label atoms in output pdb using bfactor column

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

#482 - Network planner functions from indices/names

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

#481 - fixup manifest for new test files

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

#480 - Make toolkit registry choice optional

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

#479 - Force no oechem

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

#478 - use Lomap package's bindings

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

#477 - allow gathering of legacy results

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

#476 - end to end integration tests for tyk2 tutorial

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

#475 - Added DCO

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

#474 - Code of Conduct

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

#473 - Test pin ambertools for runslow

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

#472 - Sort while running gather

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

#471 - Fix minor typo

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

#470 - [WIP: don't review] New storage in network planner CLI

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

#469 - CodeCov only on PR

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

#468 - Reconfigure stdout to be line-buffered in quickrun

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

#467 - Actually actually fix silence_root_logging

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

#466 - Pin units - same thing as in gufe

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

#465 - Update installer and container images to python 310

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

#464 - Create copy of release assets (installers) without version name

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

#463 - Encourage properly setting residue names when building form SDF

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

#462 - Remove micromamba stuff from HPC docs

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

#461 - openff-units 0.2.1 giving typing errors

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

#460 - Run slow tests on push & release

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

#459 - need to update slow tests following execute_DAG update

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

#458 - Allow multithreading in cli test invocation

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

#457 - add Exclusive mode error to docs

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

#456 - cofactors from CLI

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

#455 - explain how to use nvidia-smi to figure out cudatoolkit version

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

#454 - allow single AtomMapper to be passed to network planners

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

#453 - Fix silence_root_logging

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

#452 - Install GUFE after we restore cache to alwasys get a fresh version

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

#451 - test newest version of openmmtools

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

#450 - Add PDB serialization in RFE protocol

Pull Request - State: closed - Opened by IAlibay over 1 year ago - 8 comments

#449 - gather tests need updating

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

#448 - CI caches gufe install

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

#447 - add n_retries=2 to quickrun command

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

#446 - Add to_openff() intermediary for to_openeye() calls

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

#444 - Pin PyMBAR to sub v4

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

#443 - PyMBAR 4 convergence issues

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

#442 - moist test with EG5

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

#441 - rename water molecules so addSolvent doesn't replace with ion

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

#440 - [RFE protocol] system generation can lead to PDB specified waters being replaced by ions

Issue - State: closed - Opened by IAlibay over 1 year ago - 1 comment
Labels: priority:high, openmm_rbfe

#439 - [DNM] see if this speeds up tests

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

#438 - Cautiously allow core element changes

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

#437 - add fetchables for showcase notebook inputs

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

#436 - Test if CI passes with Python 3.11

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

#435 - Don't build docker image on tags

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

#433 - remove rate_of_convergence

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

#432 - Old installation docs need updating

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

#431 - all to not water for writing

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

#430 - Switch rbfe tutorial fetch to point to main; not master

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

#429 - CLI Updates

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

#428 - update readme install instructions

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

#427 - Remove top level settings class entry

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

#426 - Update custom.css

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