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issue with pip install bagel

dependenciesDependency updates and their version upgrades.Dependency updates and their version upgrades.

Status: Open.

Bug

#645 In neurobagel/bagel-cli;

· romainVala opened on Feb 5, 2026

Consider relaxing “sub-“ prefix requirement in BIDS table file

Status: Open.

#644 In neurobagel/bagel-cli;

· michellewang opened on Feb 5, 2026

Adopt uv for dependency management

dependenciesDependency updates and their version upgrades.Dependency updates and their version upgrades.

processImprovement to internal processesImprovement to internal processes

Status: Open.

Maintenance

#643 In neurobagel/bagel-cli;

· surchs opened on Jan 30, 2026

Combine subcommands into one command

usabilityIssue affecting user or developer experience.Issue affecting user or developer experience.

Status: Open.

Enhancement

#638 In neurobagel/bagel-cli;

· alyssadai opened on Jan 20, 2026

More informative error when <code>AccessEmail</code> in dataset description is an empty string

documentationChanges only affect the documentationChanges only affect the documentation

Status: Open.

Bug

#637 In neurobagel/bagel-cli;

· alyssadai opened on Jan 20, 2026

Having to rerun the CLI for changes in the dataset description to take effect is inconvenient

flag:discussFlag issue that needs to be discussed before it can be implemented.Flag issue that needs to be discussed before it can be implemented.

usabilityIssue affecting user or developer experience.Issue affecting user or developer experience.

Status: Open.

Exploration

#636 In neurobagel/bagel-cli;

· alyssadai opened on Jan 19, 2026

Revisit warning message for unsupported BIDS suffixes in <code>bids2tsv</code>

refactorSimplifying or restructuring existing code or documentation.Simplifying or restructuring existing code or documentation.

usabilityIssue affecting user or developer experience.Issue affecting user or developer experience.

Status: Open.

Maintenance

#613 In neurobagel/bagel-cli;

· alyssadai opened on Nov 26, 2025

Consider validating that age values aren't negative numbers

quick fixMinimal planning and/or implementation work required.Minimal planning and/or implementation work required.

usabilityIssue affecting user or developer experience.Issue affecting user or developer experience.

Status: Open.

Maintenance

#585 In neurobagel/bagel-cli;

· alyssadai opened on Nov 7, 2025

Investigate running tests on CLI as a container

_flag:stale[BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again[BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again

Status: Open.

Exploration

#573 In neurobagel/bagel-cli;

· alyssadai opened on Oct 24, 2025

Consider expanding ISO8601 duration calculation to include days

somedayNot a priority right now, but we want to keep this around to think or discuss more.Not a priority right now, but we want to keep this around to think or discuss more.

Status: Open.

Enhancement

#568 In neurobagel/bagel-cli;

· alyssadai opened on Oct 21, 2025

Restore mutually exclusive treatment of healthy control vs other diagnoses

_flag:stale[BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again[BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again

flag:discussFlag issue that needs to be discussed before it can be implemented.Flag issue that needs to be discussed before it can be implemented.

refactorSimplifying or restructuring existing code or documentation.Simplifying or restructuring existing code or documentation.

Status: Open.

Maintenance

#528 In neurobagel/bagel-cli;

· alyssadai opened on Sep 8, 2025

Investigate speeding up CLI

_flag:stale[BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again[BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again

performancePerformance improvement or fix to performance degradation.Performance improvement or fix to performance degradation.

Status: Open.

#520 In neurobagel/bagel-cli;

· alyssadai opened on Aug 28, 2025