Use cmuts.report for the results page; drop the space's own plotting

Profile diff plot, group-name display polish, misc UI fixes

Show bookmarkable result URL with a Copy button; cache-bust static assets

Multi-ref example, per-tile layout, sequence selector, plot UX fixes

Match cmuts --clip-below/--clip-above; mark local cmuts editable

Rewrite as FastAPI + Jinja + HTMX, replacing Gradio

Replace @gr .render groups with static rows; sweep error/results UX

Consolidate three @gr .render input states into one to avoid DuplicateBlockError

Use canonical Gradio @gr .render pattern correctly

Add CIF upload: per-group defattrs and ChimeraX commands

Use canonical Gradio @gr .render pattern: one state, keyed components

Force re-render after Load example data so UI reflects new state

Empty default group name; preserve initial profile for single-ref runs

Show nucleotide sequence on the reactivity profile x-axis

Fix initial render of group inputs by adding demo.load trigger

Render group inputs dynamically to keep page responsive

Multi-group inputs, cross-group normalization, CSV download

Create job directory upfront and fix pairwise coverage plot

Add pairwise MaP-seq support

Refactor result outputs into ResultUpdate dataclass

Hide input section when loading results via URL query parameter

Fix results page: include HDF5 download and result link when loading saved results

Move result link above HDF5 download so it appears first

Show result link immediately when pipeline starts for visual feedback

Hide output file, result link, and stats table until results are ready

Hide plot tiles until results are ready, fix heatmap aspect ratio

Use cmuts Plotly backend and in-process normalize for all plots

Unify results page with Gradio app

Move FastAPI import to top, fix stale Help tab references

Make runtime constants configurable via environment variables

Add minor ticks and full gridlines to reactivity profile plot

Consolidate yield tuple into _progress_yield helper

Show result link immediately when pipeline starts

Auto-discover example data from examples/ directory by convention

Replace example data with twist-2025 from p390 MaP-seq

Replace markdown stats table with native Gradio Dataframe

Remove heatmap xgap/ygap to fix white gaps, add y-axis label padding

Fix heatmap: cell outlines via shapes, constrain axes to domain

Style modification heatmap: black cell outlines, no gridlines, tighter y labels

Fix modification heatmap dimensions for square cells

Shrink modification heatmap container to match plot size

Distinguish match vs mismatch in heatmap hover labels

Improve modification heatmap hover labels for del/ins/term

Use log scale for modification heatmap to match cmuts normalize

Force square cells in modification heatmap

Fix modification heatmap y-axis to match cmuts normalize orientation

Use gr.Error for input validation instead of log-only messages

Add modification heatmap and multi-sequence reactivity heatmap

Refactor pipeline for robustness and maintainability

Fix NoneType errors from empty Gradio textbox inputs