[MNT] Review and triage open _bot PRs across all neurobagel repos

[Copilot]

Reviewed all 36 open _bot-labelled PRs across 14 neurobagel repositories against merge criteria: opened by dependabot, no major version bump, CI passes, up to date with main, no conflicting sync PR.

Changes proposed in this pull request:

• Ready to merge (dependabot, no major bump, CI green, up to date, no sync conflict):

  • annotation-tool #456 — axios 1.13.5→1.13.6
  • react-bagel #285 — @fontsource/roboto + zustand patch bumps
  • react-bagel #286 — rollup 4.36→4.59
  • react-bagel #287 — webpack 5.95→5.105
  • react-bagel #288 — minimatch 3.1.2→3.1.5

• Needs @dependabot rebase first (CI passes but behind main):

  • annotation-tool #450 — minimatch 3.1.2→3.1.5
  • react-bagel #284 — js-yaml 3.14.1→3.14.2 (security fix)
  • ui #322 — minimatch 3.1.2→3.1.5
  • ui #325 — axios 1.13.5→1.13.6

• Skip — CI failures: annotation-tool Bump rollup from 4.40.0 to 4.59.0 #449, Bump the development-dependencies group across 1 directory with 11 updates #457; api Should a new mapping for single column SVs be allowed to overwrite an existing mapping #486, [CI] Update netlify auth token #531; bagel-cli #648; query-tool #731, #751; react-bagel Make instructions easier to maintain #291; ui (whitespace) limit the maximum vertical height of a column in value annotation #326

• Skip — major version bumps: annotation-tool Bump actions/upload-artifact from 6 to 7 #454/Bump actions/download-artifact from 7 to 8 #455; communities Replace Ramda logic with Immer #66/Implement custom hook for pagination and column updates #67; openneuro-annotations Bump eslint from 8.57.1 to 9.21.0 #57/Discuss how to handle inline CSS styles #58; query-tool #728 (eslint 8→9); react-bagel Split e2e test into specific user flows #289/[ENH] Show full text of options on hover #290

• Skip — sync PR open in same repo: documentation Nothing happens if an invalid JSON file is uploaded #373, [FIX] Keep BIDS data type and descriptions from data dictionary for Collection columns #391, [FIX] fix error when marking categorical values as missing during a debounced description save #392 (blocked by open sync PR Bump react-window from 2.2.3 to 2.2.4 in the production-dependencies group #393)

• Skip — not dependabot: configure-nb Bump lint-staged from 15.2.10 to 15.4.1 #11, documentation Bump react-window from 2.2.3 to 2.2.4 in the production-dependencies group #393, neurobagel_examples Disallow column annotation of >1 participant ID/session ID columns #95

• Skip — stale/conflicts: federation-api Bump form-data from 4.0.1 to 4.0.4 in the npm_and_yarn group #185 (dirty), tools [MNT] Set up devtools for zustand #63 (stale)

Checklist

This section is for the PR reviewer

• PR has an interpretable title with a prefix ([ENH], [FIX], [REF], [TST], [CI], [MNT], [INF], [MODEL], [DOC]) (see our Contributing Guidelines for more info)
• PR has a label for the release changelog or skip-release (to be applied by maintainers only)
• PR links to GitHub issue with mention Closes #XXXX
• Tests pass
• Checks pass
• If the PR changes the default Neurobagel config.json or any of the term files, make sure their respective counterparts in neurobagel/communities have been updated accordingly.

For new features:

• Tests have been added

For bug fixes:

• There is at least one test that would fail under the original bug conditions.

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• https://api.github.com/graphql
  • Triggering command: /usr/bin/gh gh auth status (http block)
• https://api.github.com/repos/neurobagel/annotation-tool
  • Triggering command: /usr/bin/curl curl -s -I -H Authorization: token ****** REDACTED (http block)
  • Triggering command: /usr/bin/curl curl -sk -H Authorization: token ****** REDACTED (http block)
  • Triggering command: /usr/bin/gh gh api /repos/neurobagel/annotation-tool --jq .name (http block)
• https://api.github.com/repos/neurobagel/annotation-tool/pulls/456
  • Triggering command: /usr/bin/curl curl -s -H Authorization: token ****** REDACTED (http block)
  • Triggering command: /usr/bin/curl curl -sv -H Authorization: token ****** REDACTED (http block)
  • Triggering command: /home/REDACTED/work/_temp/ghcca-node/node/bin/node /home/REDACTED/work/_temp/ghcca-node/node/bin/node --enable-source-maps /home/REDACTED/work/_temp/copilot-developer-action-main/dist/index.js (http block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

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