v1.0.2 release

[alexsweeten]

[1.0.2] - 2026-10-11

Changed

• Replaced Export ModDotPlot command with Export ModDotPlot config. It now
  saves one moddotplot_config.json file and no longer builds BEDPE or ZIP output.
• Simplified one-base exact mode to its useful base-colored view and removed the
  identity/base view selector.
• Added always-on coordinate-linked highlighting for computed and imported X and Y
  feature tracks.
• Reduced the palette menu to the requested sequential, qualitative, and diverging
  ColorBrewer choices while retaining the featured Spectral and Viridis palettes.
• Compressed the palette color editor to its content height so it no longer fills the
  plot vertically.
• Restored git history

[Copilot]

🟡 Changes recommended

Ruler state can reuse stale coordinates, exact hover text can misreport missing evidence, and release documentation contains incorrect commands and links.

5 open findings

• Clear cached hover when the comparison changes · New
• Distinguish missing identity from exact k-mer matches · New
• Reset stale hover state when clearing the session · New
• Fix changelog release baseline and comparison references · New
• Include the missing FASTA option in the grid example · New

What changed in this PR

Prepares the v1.0.2 release with streamlined configuration export, remote FASTA loading, revised exact rendering, track highlighting, and release documentation.

Changes:

• Adds remote FASTA streaming, ruler measurements, and coordinate-linked track highlighting.
• Simplifies exact mode, palettes, and ModDotPlot configuration export.
• Updates release metadata, documentation, tests, and bundled-example handling.

File	Description
web/​tests/​track-parser-scale.test.ts	Adds CHM13 annotation fixture coverage.
web/​tests/​ruler.test.ts	Tests ruler calculations.
web/​tests/​renderer.test.ts	Updates exact-rendering expectations.
web/​tests/​remote-fasta.test.ts	Tests remote URL validation.
web/​tests/​palettes.test.ts	Tests curated palettes and defaults.
web/​tests/​moddotplot-config.test.ts	Tests config-only export.
web/​tests/​imported-track.test.ts	Updates feature-limit terminology.
web/​tests/​http-range-blob.test.ts	Tests CORS range requests.
web/​tests/​grid-renderer.test.ts	Updates default palette expectations.
web/​tests/​feature-track.test.ts	Tests hover-highlight geometry.
web/​tests/​example-loader.test.ts	Removes bundled-example tests.
web/​tests/​exact-mode.test.ts	Updates simplified exact-mode tests.
web/​src/​worker.ts	Implements remote FASTA ingestion.
web/​src/​track-parser-worker.ts	Counts retained annotation features.
web/​src/​styles.css	Styles new and revised controls.
web/​src/​ruler.ts	Implements ruler calculations.
web/​src/​renderer.ts	Makes base-colored exact rendering permanent.
web/​src/​remote-fasta.ts	Validates remote FASTA URLs.
web/​src/​protocol.ts	Adds remote-load worker messages.
web/​src/​palettes.ts	Curates palettes and changes defaults.
web/​src/​moddotplot-config.ts	Produces standalone CLI configs.
web/​src/​main.ts	Integrates remote loading, rulers, and UI changes.
web/​src/​imported-track.ts	Highlights overlapping imported features.
web/​src/​imported-track-types.ts	Revises annotation admission terminology.
web/​src/​http-range-blob.ts	Supports credential-free CORS ranges.
web/​src/​feature-track.ts	Highlights computed track bins.
web/​src/​export-controller.ts	Replaces ZIP export with JSON config.
web/​src/​example-loader.ts	Removes bundled-example loader.
web/​src/​exact-mode.ts	Removes exact visualization selection.
web/​src/​bgzf.ts	Exposes BGZF header detection.
web/​public/​examples/​Col-CEN_v1.2.fasta.fai	Removes bundled FASTA index.
web/​package.json	Bumps version and removes example preparation.
web/​package-lock.json	Updates package version metadata.
web/​index.html	Revises landing and workspace controls.
web/​e2e/​exact-periodic-rendering.spec.ts	Updates exact visual regression coverage.
scripts/​prepare-example-assets.mjs	Removes example preparation script.
scripts/​generate-current-parameters.mjs	Updates generated limit terminology.
scripts/​generate-arabidopsis-overview.mjs	Removes overview generator.
scripts/​check-docs.mjs	Expands documentation checks.
SBOM.cdx.json	Bumps application version.
README.md	Revises project note.
docs/​USER_GUIDE.md	Documents new workflows and export.
docs/​RELEASE_CHECKLIST.md	Updates the v1.0.2 checklist.
docs/​PRIVACY.md	Documents remote URL privacy.
docs/​METHODS.md	Updates exact-mode description.
docs/​DEPLOYMENT.md	Updates deployment instructions.
docs/​CITATIONS.md	Revises project note.
CONTRIBUTING.md	Adds contribution guidance.
CITATION.cff	Updates release metadata.
CHANGELOG.md	Restores release history.
Cargo.toml	Bumps workspace version.
Cargo.lock	Updates crate versions.
.gitignore	Removes obsolete example exclusion.

Files not reviewed (1)

• web/package-lock.json: Generated file

🧠 Review effort: Balanced

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