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cinnabar error handling from cli needs improvements

clicommand-line interfacecommand-line interface

Status: Open.

#998 In OpenFreeEnergy/openfe;

· atravitz opened on Nov 1, 2024

[CLI] inspect command for json output files

clicommand-line interfacecommand-line interface

priority:low

Status: Open.

#872 In OpenFreeEnergy/openfe;

· IAlibay opened on Jun 18, 2024

docs review: cli

clicommand-line interfacecommand-line interface

documentationImprovements or additions to documentationImprovements or additions to documentation

Status: Open.

#1013 In OpenFreeEnergy/openfe;

· atravitz opened on Nov 12, 2024

document all yaml input settings

clicommand-line interfacecommand-line interface

documentationImprovements or additions to documentationImprovements or additions to documentation

priority:medium

Status: Open.

#993 In OpenFreeEnergy/openfe;

· atravitz opened on Oct 29, 2024

Use MBAR error as uncertainty with a single protocol repeat in RBFE

priority:medium

Status: Draft (not ready).

OpenFreeEnergy/openfenumber 883

#883 In OpenFreeEnergy/openfe;

· frannerin opened on Jul 4, 2024

openfe gather --debug option

clicommand-line interfacecommand-line interface

enhancementNew feature or requestNew feature or request

Status: Open.

#978 In OpenFreeEnergy/openfe;

· atravitz opened on Oct 22, 2024

Dry option for quickrun

clicommand-line interfacecommand-line interface

Status: Open.

#284 In OpenFreeEnergy/openfe;

· IAlibay opened on Apr 1, 2023

Network status for local runs

clicommand-line interfacecommand-line interface

Status: Open.

#970 In OpenFreeEnergy/openfe;

· jthorton opened on Oct 21, 2024

Make predictions on broken networks

clicommand-line interfacecommand-line interface

Status: Open.

#972 In OpenFreeEnergy/openfe;

· jthorton opened on Oct 21, 2024

[WIP] quickrun result error inspection command

clicommand-line interfacecommand-line interface

Status: Open (in progress).

OpenFreeEnergy/openfenumber 492

#492 In OpenFreeEnergy/openfe;

· dwhswenson opened on Jul 18, 2023

cli yaml: implement auto documenter

Status: Open.

#653 In OpenFreeEnergy/openfe;

· richardjgowers opened on Nov 21, 2023

Cli protocol settings via yaml input

clicommand-line interfacecommand-line interface

Status: Open (in progress).

OpenFreeEnergy/openfenumber 770

#770 In OpenFreeEnergy/openfe;

· richardjgowers opened on Mar 8, 2024

cli gather: add alchemical_network.json awareness

clicommand-line interfacecommand-line interface

usability

Status: Open.

#1211 In OpenFreeEnergy/openfe;

· atravitz opened on Mar 25, 2025

CLI improvements: openfe v1.y

clicommand-line interfacecommand-line interface

openfe

Status: Open.

#1322 In OpenFreeEnergy/openfe;

· IAlibay opened on Jun 1, 2025

openfe gather: explicitly state when a json file is excluded from the output table.

clicommand-line interfacecommand-line interface

Status: Open.

#1391 In OpenFreeEnergy/openfe;

· atravitz opened on Jun 27, 2025

plan-rbfe-network overwrites existing files by default

clicommand-line interfacecommand-line interface

Status: Open.

#1338 In OpenFreeEnergy/openfe;

· IAlibay opened on Jun 1, 2025

rewrite rbfe/rhfe cli docstrings

clicommand-line interfacecommand-line interface

documentationImprovements or additions to documentationImprovements or additions to documentation

Status: Open.

#1345 In OpenFreeEnergy/openfe;

· atravitz opened on Jun 5, 2025

--output-dir is used to define the alchemical network JSON name but only claims settings the output directory

clicommand-line interfacecommand-line interface

Status: Open.

#1337 In OpenFreeEnergy/openfe;

· IAlibay opened on Jun 1, 2025

CLI does not properly return PDB parsing errors

clicommand-line interfacecommand-line interface

usability

Status: Open.

#1335 In OpenFreeEnergy/openfe;

· IAlibay opened on Jun 1, 2025

improve rich table testing

clicommand-line interfacecommand-line interface

Status: Open.

#1251 In OpenFreeEnergy/openfe;

· atravitz opened on Apr 24, 2025

add error pass-through when validating results jsons

clicommand-line interfacecommand-line interface

Status: Open.

#1200 In OpenFreeEnergy/openfe;

· atravitz opened on Mar 19, 2025

BespokeFit interface

clicommand-line interfacecommand-line interface

Status: Open.

#973 In OpenFreeEnergy/openfe;

· jthorton opened on Oct 21, 2024