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- Status: Open.#701 In neurobagel/bagel-cli;
Consider accepting
wwwURLs for URL fields indataset_description.json_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 againusabilityIssue affecting user or developer experience.Issue affecting user or developer experience.Status: Open.#684 In neurobagel/bagel-cli;Switch to using
pytest-covfor code coverage reports_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 againquick 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.#677 In neurobagel/bagel-cli;Remove warning logic for BIDS-supported but not Neurobagel-supported data suffixes
_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 againrefactorSimplifying or restructuring existing code or documentation.Simplifying or restructuring existing code or documentation.Status: Open.#672 In neurobagel/bagel-cli;Test with empty BIDS table fails on pandas>=3
_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 againdependenciesDependency updates and their version upgrades.Dependency updates and their version upgrades.Status: Open.Original TSV column order may not be respected for >1 columns mapped to a single-column variable
_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 againflag: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.Switch to using
bids-standard/python-validatorfor BIDS validation_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 againdependenciesDependency 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.#655 In neurobagel/bagel-cli;Ensure imaging session paths stored by
bagel bidsreflect filesystem BIDS paths_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 againflag: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.Support merging multiple pheno tsv/json pairs into one jsondb file for improved BIDS workflow
_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 againflag: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.#650 In neurobagel/bagel-cli;Match subject IDs between the BIDS table and phenotypic data with
sub-prefix strippedsomedayNot 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.#649 In neurobagel/bagel-cli;issue with pip install bagel
_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 againdependenciesDependency updates and their version upgrades.Dependency updates and their version upgrades.Status: Open.#645 In neurobagel/bagel-cli;Combine subcommands into one command
_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 againflag: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.#638 In neurobagel/bagel-cli;