Big NEW UI release

[khoroshevskyi]

Changes:

• UI changes almost on each page

TODO:

• Version of pepdbagent updated in __version__.py file - NO API release
• Changelog updated

[cloudflare-workers-and-pages]

Deploying bedhost-ui with    Cloudflare Pages

Latest commit:	3a8885f
Status:	✅  Deploy successful!
Preview URL:	https://75d6371e.bedhost.pages.dev
Branch Preview URL:	https://dev.bedhost.pages.dev

View logs

[Copilot]

Pull request overview

This PR delivers a broad UI refresh across the BEDbase frontend, including a reworked search experience (Text-to-BED, BED-to-BED, Text-to-BEDset), new/updated UMAP embedding UI components, and refreshed styling/layout for several pages.

Changes:

• Refactors the Search page to centrally manage query params/state and adds a dedicated Text-to-BEDset flow.
• Introduces new embedding (UMAP) UI components/styles and integrates embedding interactions into search workflows.
• Updates multiple pages/components for the new UI look-and-feel and adds/adjusts metrics-related UI components.

Reviewed changes

Copilot reviewed 89 out of 97 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
ui/vite.config.ts	Adds a dev-server proxy configuration.
ui/src/utils.ts	Adds date formatting helpers and misc utilities.
ui/src/queries/useUmapEmbeddings.ts	Minor formatting/cleanup of UMAP fetch logic.
ui/src/queries/useText2BedSearch.ts	Adjusts React Query refetch behavior + formatting.
ui/src/queries/useStats.ts	Formatting/cleanup.
ui/src/queries/useDetailedUsage.ts	Formatting/cleanup.
ui/src/queries/useDetailedStats.ts	Formatting/cleanup.
ui/src/queries/useBed2BedSearchPaginate.ts	New paginated BED-to-BED search hook (multipart upload).
ui/src/pages/visualization.tsx	Removes old visualization page implementation.
ui/src/pages/search.tsx	Major refactor: centralized state/URL params, integrated SearchBar + view routing.
ui/src/pages/bedset-splash.tsx	Replaces react-bootstrap grid usage with raw bootstrap classes + layout tweaks.
ui/src/pages/bed-cart.tsx	Redesigns cart UI to card layout + uses navigate().
ui/src/pages/bed-analytics.tsx	Minor header/layout changes around analytics panels.
ui/src/motions/landing-animations.tsx	Quote/style formatting changes.
ui/src/main.tsx	Adds alt home routes, bootstrap bundle import, and embedding styles; Toaster z-index tweak.
ui/src/custom.scss	Adds small-button variants, card hover/transition helpers, fade-in animations.
ui/src/contexts/search-view-context.tsx	Simplifies provider rendering.
ui/src/contexts/mosaic-coordinator-context.tsx	Formatting-only change.
ui/src/contexts/bedcart-context.tsx	Adds toast on multi-add; formatting/cleanup.
ui/src/const.ts	Formatting-only change.
ui/src/components/umap/embedding-table.tsx	New table for selected embedding points.
ui/src/components/umap/embedding-styles.scss	New styles for embedding layouts/expandable card behavior.
ui/src/components/umap/embedding-selections.tsx	New “saved selections” UI for embeddings.
ui/src/components/umap/embedding-legend.tsx	New legend/filter UI for embeddings.
ui/src/components/skeletons/card-skeleton.tsx	Quote/style formatting change.
ui/src/components/seo.tsx	Quote/style formatting change.
ui/src/components/search/text2bedset/text2bedset.tsx	New Text-to-BEDset search component (cards/table + pagination).
ui/src/components/search/text2bedset/t2bs-search-results-table.tsx	New BEDset results table view.
ui/src/components/search/text2bedset/t2bs-search-results-cards.tsx	New BEDset results cards view.
ui/src/components/search/text2bedset.tsx	Removes old Text-to-BEDset component implementation.
ui/src/components/search/text2bed/text2bed.tsx	Refactors Text-to-BED to be controlled via props + supports cards/table layout.
ui/src/components/search/text2bed/t2b-search-results-table.tsx	Updates table styling and switches to navigate().
ui/src/components/search/text2bed/t2b-search-results-cards.tsx	New cards view for Text-to-BED results.
ui/src/components/search/table-toolbar.tsx	Quote/style formatting change.
ui/src/components/search/searching-jumper.tsx	Quote/style formatting change.
ui/src/components/search/search-selector.tsx	Replaces react-bootstrap Nav with raw bootstrap pills.
ui/src/components/search/search-error.tsx	Quote/style formatting change.
ui/src/components/search/search-bedset-table.tsx	Removes old BEDset results table component.
ui/src/components/search/search-bar.tsx	Major refactor: supports file upload (b2b), layout switch, filters, and embedding integration.
ui/src/components/search/pagination-bar.tsx	Redesigns pagination UI into numbered/arrow controls.
ui/src/components/search/bed2bed/bed2bed.tsx	Refactors BED-to-BED UI: paginated hook + embedding panel integration + cards/table layout.
ui/src/components/search/bed2bed/b2b-search-results-cards.tsx	New cards view for BED-to-BED results.
ui/src/components/nav/nav.tsx	Nav styling tweaks (background/classes).
ui/src/components/nav/nav-mobile.tsx	Updates mobile nav links and adds Visualization entry.
ui/src/components/nav/nav-logo.tsx	Quote/style formatting change.
ui/src/components/nav/nav-desktop.tsx	Reorders/updates desktop nav links and adds Visualization entry.
ui/src/components/modals/metric-modal.tsx	Formatting + minor layout adjustments.
ui/src/components/modals/figure-modal.tsx	Quote/style formatting change.
ui/src/components/modals/endpoints-modal.tsx	Formatting + multiline link rendering.
ui/src/components/modals/download-cart-modal.tsx	Formatting + minor readability adjustments.
ui/src/components/modals/download-bedset-modal.tsx	Quote/style formatting change.
ui/src/components/modals/create-bedset-modal.tsx	Formatting + minor layout adjustments.
ui/src/components/modals/bed-metadata-modal.tsx	Quote/style formatting change.
ui/src/components/metrics/usage-statistics.tsx	New usage statistics panel.
ui/src/components/metrics/metrics-selector.tsx	New selector UI for metrics view switching.
ui/src/components/metrics/metric-plot.tsx	Tweaks plot sizing/spec formatting and embed options formatting.
ui/src/components/metrics/geo-statistics.tsx	New GEO stats panel.
ui/src/components/layout.tsx	Footer styling and markup tweaks.
ui/src/components/graphics/search-graphic.tsx	New search illustration graphic component.
ui/src/components/graphics/bed-analyzer-graphic.tsx	New analyzer illustration graphic component.
ui/src/components/common/error-page.tsx	Quote/style formatting change.
ui/src/components/bedset-splash-components/plots.tsx	Updates plot card layout/styles and grid density.
ui/src/components/bedset-splash-components/header.tsx	Updates header UI and switches to short date formatting.
ui/src/components/bedset-splash-components/charts/genomic-feature-bar.tsx	Adds chart padding + styling updates.
ui/src/components/bedset-splash-components/cards/stat-card-wrapper.tsx	Updates stat card layout and tooltip behavior.
ui/src/components/bedset-splash-components/cards/median-tss-distance.tsx	Updates stat display layout.
ui/src/components/bedset-splash-components/cards/median-region-width.tsx	Updates stat display layout.
ui/src/components/bedset-splash-components/cards/gc-content-card.tsx	Updates stat display layout.
ui/src/components/bedset-splash-components/beds-table.tsx	Styling/layout changes and minor cleanup.
ui/src/components/bed-splash-components/refgenome-modal.tsx	Updates external link destination + formatting/markup adjustments.
ui/src/components/bed-splash-components/plots.tsx	Updates plot card layout/styles and filters out a plot.
ui/src/components/bed-splash-components/header.tsx	Updates header UI and switches to short date formatting; adds keys in mapped dropdown items.
ui/src/components/bed-splash-components/charts/genomic-feature-bar.tsx	Adds chart padding + styling updates.
ui/src/components/bed-splash-components/cards/stat-card-wrapper.tsx	Updates stat card layout and tooltip behavior.
ui/src/components/bed-splash-components/cards/no-regions-card.tsx	Quote/style formatting change.
ui/src/components/bed-splash-components/cards/median-tss-dist-card.tsx	Quote/style formatting change.
ui/src/components/bed-splash-components/cards/mean-region-width-card.tsx	Quote/style formatting change.
ui/src/components/bed-splash-components/cards/gc-content-card.tsx	Quote/style formatting change.
ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx	Replaces old panel markup with a table-first layout + CSV download button retained.
ui/src/components/bed-analytics-components/bed-plots.tsx	Minor styling and labelExpr formatting.
ui/public/visualizer.svg	Minor SVG metadata/style changes.
ui/package.json	Bumps UI version and updates embedding-atlas dependency.
ui/index.html	Adds theme-color meta and normalizes doctype.
ui/.eslintrc.cjs	Formatting/cleanup.
package-lock.json	Adds a root lockfile (currently empty).
.gitignore	Ignores ui/package-lock.json.

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