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Switch to using pytest-cov for code coverage reports

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

testsEnhancing or fixing tests where functioning is not affected.Enhancing or fixing tests where functioning is not affected.

Status: Open.

Maintenance

#677 In neurobagel/bagel-cli;

· alyssadai opened on Apr 11, 2026

Remove warning logic for BIDS-supported but not Neurobagel-supported data suffixes

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

Status: Open.

Enhancement

#672 In neurobagel/bagel-cli;

· alyssadai opened on Mar 28, 2026

Test with empty BIDS table fails on pandas>=3

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

Status: Open.

Bug

#671 In neurobagel/bagel-cli;

· alyssadai opened on Mar 27, 2026

Original TSV column order may not be respected for >1 columns mapped to a single-column variable

flag:detail neededIssue requires additional clarification before a decision can be made or it can be implemented.Issue requires additional clarification before a decision can be made or it can be implemented.

Status: Open.

Bug

#668 In neurobagel/bagel-cli;

· alyssadai opened on Mar 21, 2026

Switch to using bids-standard/python-validator for BIDS validation

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

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

Status: Open.

Exploration

#655 In neurobagel/bagel-cli;

· alyssadai opened on Feb 24, 2026

Ensure imaging session paths stored by bagel bids reflect filesystem BIDS paths

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.

Status: Open.

Bug

#652 In neurobagel/bagel-cli;

· alyssadai opened on Feb 17, 2026

Support merging multiple pheno tsv/json pairs into one jsondb file for improved BIDS workflow

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.

Enhancement

#650 In neurobagel/bagel-cli;

· dominikwelke opened on Feb 16, 2026

Match subject IDs between the BIDS table and phenotypic data with sub- prefix stripped

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.

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

Status: Open.

Enhancement

#649 In neurobagel/bagel-cli;

· alyssadai opened on Feb 12, 2026

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

Combine subcommands into one command

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.

Enhancement

#638 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: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.

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

Consider validating that age values aren't negative numbers

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

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.

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