Redesign: Static HTML site with updated ecosystem

[ypriverol]

Summary

Replaces Vue CLI app with static HTML/CSS/JS site (no build step needed).

What changed

• New static HTML pages: index.html, tools.html, publications.html, about.html
• quantmsdiann added as separate DIA workflow (split from quantms)
• ibaqpy -> mokume migration documented — mokume supersedes ibaqpy with full citation
• sdrf-pipelines replaces quantms-utils in ecosystem
• 8 ecosystem tools with consistent brand palette (blue/indigo/violet)
• All citations linked to DOIs (clickable to original papers)
• Stats loaded dynamically from data/portal-stats.json
• GitHub Pages Actions deployment (no Vue build needed)

Data preserved

• AE.json (103 datasets), DE.json (35 datasets), MSNet.json (114 datasets)
• single_cell.json (6 datasets), tissueJson.json.gz, cellJson.json.gz
• Moved from public/data/ to data/

Test plan

• Open each HTML page locally — all sections render correctly
• Check all citation DOI links open the correct paper
• Verify data/portal-stats.json loads (stats counter on home page)
• Check CNAME file contains quantms.org
• Test mobile responsive layout
• Verify GitHub Actions workflow deploys correctly

Generated with Claude Code

Summary by CodeRabbit

• New Features

  • Added static pages for About, Publications, and Tools sections
  • Introduced animated interactions and navigation features
  • Configured custom domain (quantms.org) and GitHub Pages deployment
  • Added dynamic portal statistics display with counter animations

• Chores

  • Migrated from single-page application to static HTML site
  • Removed legacy framework dependencies and build configuration

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📝 Walkthrough

Walkthrough

The pull request transforms the quantms website from a Vue 3 single-page application with dynamic routing into a static HTML-based site. It removes SPA infrastructure (Vue bootstrap, router, Vuex store, components), Vue view pages, and complex SCSS styling systems. New static HTML pages, unified CSS/JavaScript assets, GitHub Pages deployment configuration, and domain setup replace the previous SPA architecture.

Changes

Cohort / File(s)	Summary
SPA Infrastructure & Bootstrap Removal src/main.js, src/router/index.js, src/store/index.js, src/App.vue, public/index.html, vue.config.js	Deleted Vue app entrypoint, router configuration with all route definitions, Vuex store with state/mutations/actions, root App component with transitions, SPA HTML template, and Vue CLI webpack configuration.
Vue Components Removal src/components/AeShow/..., src/components/GitHubContributors/index.vue, src/components/MSNetShow/index.vue, src/components/Table/index.vue, src/components/MetaTags.vue, src/components.d.ts, src/auto-imports.d.ts	Removed interactive chart component with ECharts integration, GitHub contributors fetcher, dataset table with expansion/sorting, Meta tags handler, and all TypeScript auto-import/component declarations.
View Pages & Layouts Removal src/views/home/..., src/views/about/..., src/views/publications/..., src/views/tools/..., src/views/information/..., src/views/overview/..., src/layout/...	Deleted all Vue page components and layout wrappers including home with ECharts visualizations, dataset tables with search/filtering, baseline search UI, publications listings, and navigation menu/footer components.
SCSS Variables & Global Styling Removal src/assets/styles/_variables.scss, src/assets/styles/global.scss, src/assets/styles/main.scss, src/styles/variables.scss, src/styles/element/index.scss	Eliminated Sass design system (color palette, typography scales, spacing tokens, breakpoints, z-index layers), global typography/reset rules, Element Plus theme overrides, and utility class definitions.
API & Utilities Removal src/api/request.js, src/api/getTable.js, src/api/search.js, src/utils/date.js, src/composables/useMetaTags.js, public/site.webmanifest	Deleted Axios HTTP client with interceptors and error handling, dataset/expression/search API wrappers, date formatting utility, meta tags composable, and PWA manifest configuration.
Static HTML Pages index.html, about.html, publications.html, tools.html	Replaced SPA index.html with comprehensive marketing landing page; added complete About Us page with team and contributors; added Publications page with tabbed publication listings and citation guide; added Tools & Libraries showcase page with categorized tool cards.
Shared Frontend Assets assets/style.css, assets/script.js, data/portal-stats.json	Added unified 296-line CSS stylesheet with design system, responsive layouts, animations, and dark footer; added 88-line JavaScript with scroll-triggered navigation state, intersection-based animations, tab switching, stat counter animations with fetch integration; added JSON file with portal statistics for dynamic counter initialization.
Deployment & Configuration .github/workflows/deploy.yml, CNAME, .gitignore	Added GitHub Actions workflow triggering on main push/manual dispatch to deploy repository contents to GitHub Pages; added custom domain configuration file (quantms.org); updated gitignore to replace .idea/ with specific entries (.idea/node_modules, .DS_Store, .idea).

Estimated Code Review Effort

🎯 4 (Complex) | ⏱️ ~60 minutes

Possibly related PRs

• Add MSNet datasets #31: Directly conflicts with MSNet-related files removal (src/api/getTable.js, src/components/MSNetShow, src/views/information/index.vue are deleted in this PR but targeted by that PR).

Poem

🐰 Hop hop, the SPA is retired,
Static pages now inspire!
No Vue routing, no Vuex store,
Pure HTML opens wider door. 🌐✨
CSS flows, JavaScript gleams,
quantms.org now follows our dreams!

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title accurately summarizes the primary change: transitioning from a Vue SPA to a static HTML site with ecosystem updates.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch redesign/static-site

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