chore(deps): consolidate compatible Dependabot updates by VibhavSetlur · Pull Request #265 · ModelSEED/ModelSEED-UI

VibhavSetlur · 2026-09-16T19:20:30Z

Summary

Consolidates Dependabot PRs chore(deps): bump brace-expansion #258–chore(deps-dev): bump the development-dependencies group with 7 updates #263 into one staging-targeted dependency maintenance PR.
Updates compatible production dependencies (Next, React, React Query, Zustand) and development tooling (Playwright, Testing Library, Vite React plugin, dotenv, eslint-config-next, happy-dom, tsx), plus brace-expansion, @humanfs/node, browserslist, and js-yaml.
Resolves the combined package-lock.json conflict while preserving a valid npm lockfile.

Deliberately excluded

chore(deps-dev): bump eslint from 9.39.4 to 10.10.0 #247 (ESLint 10), chore(deps): bump @mui/material from 7.3.10 to 9.4.0 #249/chore(deps): bump @mui/icons-material from 7.3.10 to 9.4.0 #250 (MUI 9), chore(deps-dev): bump vitest from 4.1.3 to 5.0.0 #254 (Vitest 5), and chore(deps-dev): bump @testing-library/jest-dom from 6.9.1 to 7.0.1 #255 (jest-dom 7): their own CI is failing or they require compatibility/root-cause work, so they are not bundled here.
Merged Remove ontology; read participant aliases via cross-core join #264 had no actionable review comments.

Verification

npm run lint
npx tsc --noEmit
npm run test:run  # 36 files, 423 passed, 4 skipped
npm run build
npm audit --omit=dev --audit-level=high  # 0 vulnerabilities

Closes/replaces #258 #259 #260 #261 #262 #263.

Bumps and [brace-expansion](https://github.com/juliangruber/brace-expansion). These dependencies needed to be updated together. Updates `brace-expansion` from 1.1.13 to 1.1.21 - [Release notes](https://github.com/juliangruber/brace-expansion/releases) - [Commits](juliangruber/brace-expansion@v1.1.13...v1.1.21) Updates `brace-expansion` from 5.0.5 to 5.0.12 - [Release notes](https://github.com/juliangruber/brace-expansion/releases) - [Commits](juliangruber/brace-expansion@v1.1.13...v1.1.21) --- updated-dependencies: - dependency-name: brace-expansion dependency-version: 1.1.21 dependency-type: indirect - dependency-name: brace-expansion dependency-version: 5.0.12 dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com>

Bumps [@humanfs/node](https://github.com/humanwhocodes/humanfs/tree/HEAD/packages/node) from 0.16.7 to 0.16.8. - [Release notes](https://github.com/humanwhocodes/humanfs/releases) - [Changelog](https://github.com/humanwhocodes/humanfs/blob/main/packages/node/CHANGELOG.md) - [Commits](https://github.com/humanwhocodes/humanfs/commits/node-v0.16.8/packages/node) --- updated-dependencies: - dependency-name: "@humanfs/node" dependency-version: 0.16.8 dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com>

Bumps [browserslist](https://github.com/browserslist/browserslist) from 4.28.2 to 4.29.0. - [Release notes](https://github.com/browserslist/browserslist/releases) - [Changelog](https://github.com/browserslist/browserslist/blob/main/CHANGELOG.md) - [Commits](browserslist/browserslist@4.28.2...4.29.0) --- updated-dependencies: - dependency-name: browserslist dependency-version: 4.29.0 dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com>

Bumps [js-yaml](https://github.com/nodeca/js-yaml) from 4.1.1 to 4.3.2. - [Changelog](https://github.com/nodeca/js-yaml/blob/4.3.2/CHANGELOG.md) - [Commits](nodeca/js-yaml@4.1.1...4.3.2) --- updated-dependencies: - dependency-name: js-yaml dependency-version: 4.3.2 dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com>

Bumps the production-dependencies group with 5 updates: | Package | From | To | | --- | --- | --- | | [@tanstack/react-query](https://github.com/TanStack/query/tree/HEAD/packages/react-query) | `5.96.2` | `5.102.8` | | [next](https://github.com/vercel/next.js) | `16.3.4` | `16.3.5` | | [react](https://github.com/react/react/tree/HEAD/packages/react) | `19.2.3` | `19.3.0` | | [react-dom](https://github.com/react/react/tree/HEAD/packages/react-dom) | `19.2.3` | `19.3.0` | | [zustand](https://github.com/pmndrs/zustand) | `5.0.12` | `5.0.15` | Updates `@tanstack/react-query` from 5.96.2 to 5.102.8 - [Release notes](https://github.com/TanStack/query/releases) - [Changelog](https://github.com/TanStack/query/blob/main/packages/react-query/CHANGELOG.md) - [Commits](https://github.com/TanStack/query/commits/@tanstack/react-query@5.102.8/packages/react-query) Updates `next` from 16.3.4 to 16.3.5 - [Release notes](https://github.com/vercel/next.js/releases) - [Commits](vercel/next.js@v16.3.4...v16.3.5) Updates `react` from 19.2.3 to 19.3.0 - [Release notes](https://github.com/react/react/releases) - [Changelog](https://github.com/react/react/blob/main/CHANGELOG.md) - [Commits](https://github.com/react/react/commits/v19.3.0/packages/react) Updates `react-dom` from 19.2.3 to 19.3.0 - [Release notes](https://github.com/react/react/releases) - [Changelog](https://github.com/react/react/blob/main/CHANGELOG.md) - [Commits](https://github.com/react/react/commits/v19.3.0/packages/react-dom) Updates `zustand` from 5.0.12 to 5.0.15 - [Release notes](https://github.com/pmndrs/zustand/releases) - [Commits](pmndrs/zustand@v5.0.12...v5.0.15) --- updated-dependencies: - dependency-name: "@tanstack/react-query" dependency-version: 5.102.8 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: production-dependencies - dependency-name: next dependency-version: 16.3.5 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: production-dependencies - dependency-name: react dependency-version: 19.3.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: production-dependencies - dependency-name: react-dom dependency-version: 19.3.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: production-dependencies - dependency-name: zustand dependency-version: 5.0.15 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: production-dependencies ... Signed-off-by: dependabot[bot] <support@github.com>

Bumps the development-dependencies group with 7 updates: | Package | From | To | | --- | --- | --- | | [@playwright/test](https://github.com/microsoft/playwright) | `1.59.1` | `1.63.0` | | [@testing-library/react](https://github.com/testing-library/react-testing-library) | `16.3.2` | `16.3.3` | | [@vitejs/plugin-react](https://github.com/vitejs/vite-plugin-react/tree/HEAD/packages/plugin-react) | `6.0.1` | `6.1.1` | | [dotenv](https://github.com/motdotla/dotenv) | `17.4.1` | `17.4.2` | | [eslint-config-next](https://github.com/vercel/next.js/tree/HEAD/packages/eslint-config-next) | `16.3.0` | `16.3.5` | | [happy-dom](https://github.com/capricorn86/happy-dom) | `20.8.9` | `20.14.5` | | [tsx](https://github.com/privatenumber/tsx) | `4.21.0` | `4.23.13` | Updates `@playwright/test` from 1.59.1 to 1.63.0 - [Release notes](https://github.com/microsoft/playwright/releases) - [Commits](microsoft/playwright@v1.59.1...v1.63.0) Updates `@testing-library/react` from 16.3.2 to 16.3.3 - [Release notes](https://github.com/testing-library/react-testing-library/releases) - [Changelog](https://github.com/testing-library/react-testing-library/blob/main/CHANGELOG.md) - [Commits](testing-library/react-testing-library@v16.3.2...v16.3.3) Updates `@vitejs/plugin-react` from 6.0.1 to 6.1.1 - [Release notes](https://github.com/vitejs/vite-plugin-react/releases) - [Changelog](https://github.com/vitejs/vite-plugin-react/blob/main/packages/plugin-react/CHANGELOG.md) - [Commits](https://github.com/vitejs/vite-plugin-react/commits/plugin-react@6.1.1/packages/plugin-react) Updates `dotenv` from 17.4.1 to 17.4.2 - [Changelog](https://github.com/motdotla/dotenv/blob/master/CHANGELOG.md) - [Commits](motdotla/dotenv@v17.4.1...v17.4.2) Updates `eslint-config-next` from 16.3.0 to 16.3.5 - [Release notes](https://github.com/vercel/next.js/releases) - [Commits](https://github.com/vercel/next.js/commits/v16.3.5/packages/eslint-config-next) Updates `happy-dom` from 20.8.9 to 20.14.5 - [Release notes](https://github.com/capricorn86/happy-dom/releases) - [Commits](capricorn86/happy-dom@v20.8.9...v20.14.5) Updates `tsx` from 4.21.0 to 4.23.13 - [Release notes](https://github.com/privatenumber/tsx/releases) - [Changelog](https://github.com/privatenumber/tsx/blob/master/release.config.cjs) - [Commits](privatenumber/tsx@v4.21.0...v4.23.13) --- updated-dependencies: - dependency-name: "@playwright/test" dependency-version: 1.63.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: development-dependencies - dependency-name: "@testing-library/react" dependency-version: 16.3.3 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: development-dependencies - dependency-name: "@vitejs/plugin-react" dependency-version: 6.1.1 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: development-dependencies - dependency-name: dotenv dependency-version: 17.4.2 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: development-dependencies - dependency-name: eslint-config-next dependency-version: 16.3.5 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: development-dependencies - dependency-name: happy-dom dependency-version: 20.14.5 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: development-dependencies - dependency-name: tsx dependency-version: 4.23.13 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: development-dependencies ... Signed-off-by: dependabot[bot] <support@github.com>

VibhavSetlur and others added 9 commits September 14, 2026 09:53

merge: align staging with upstream PR 244

acbb0cf

Merge remote-tracking branch 'upstream/staging' into staging

9eddb3b

fix(deps): resolve consolidated lockfile

224a19b

chore(deps): run Dependabot monthly

5b4da10

samseaver merged commit cc9531b into ModelSEED:staging Sep 17, 2026
2 checks passed

samseaver deleted the chore/consolidate-safe-dependabot branch September 17, 2026 20:12

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chore(deps): consolidate compatible Dependabot updates - #265

chore(deps): consolidate compatible Dependabot updates#265
samseaver merged 10 commits into
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VibhavSetlur:chore/consolidate-safe-dependabot

VibhavSetlur commented Sep 16, 2026

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VibhavSetlur commented Sep 16, 2026

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