Changes in version 0.3.0                        

New features

  - Help tab gained a "Supported Drugs" catalogue: the full
    ~1,450-compound DepMap screen with the 44 pre-trained models marked,
    filterable by Pre-trained / Demo / All compounds with debounced
    search.
  - New guided walkthroughs on the Help tab (Demo and Advanced tours)
    with retaken, correctly-sized screenshots.
  - Reworked the Advanced tour steps: three input files, Seurat
    clustering, pre-trained vs. trained models, training output,
    prediction and visualisation reading order.

Improvements

  - README, vignettes and tutorial sections rearranged and synced with
    the app.

                        Changes in version 0.2.0                        

New features

  - Redesigned the visualization tab as a "plot gallery": all 7 plot
    types visible as clickable cards, a data-readiness bar showing what
    is loaded, and click-to-draw (no Generate button). Parameter changes
    (drug / gene / ROC pair) redraw the plot automatically; hovering a
    card previews its description before you commit; generated-at
    timestamps are shown in UTC.
  - Seurat clustering now reports live stage progress (normalizing /
    variable features / PCA / clustering / UMAP / ...) in the Load Demo
    overlay.
  - Demo data is more realistic and reproducible: tumor-heterogeneity
    mixing (responder/non-responder cells mixed 65/35 per patient)
    brings the ROC AUC from a perfect 1.0 to ~0.86, tighter noise-gene
    range sharpens the UMAP clone layout, and a fixed seed makes every
    Load Demo identical.
  - Layout widths unified across Train / Predict / Visualize (sidebar
    ratio 4:8); Data readiness order now groups the three user-uploaded
    inputs first.
  - annotate_clones() / prepare_data() gained an optional progress_cb
    and a variable_selection option (vst default; dispersion/mvp for
    speed).

Bug fixes

  - Background workers could not start in container deployments ("Failed
    to start the background worker ... invalid connection"). Spawning
    now tries a ladder of progressively simpler callr configs (supervise
    + stderr file -> /dev/null -> inherited stdio) and reports rich
    diagnostics on final failure.
  - stdout = FALSE was rejected with EACCES in the rocker/shiny-verse
    container; stdout now redirects to /dev/null instead.
  - Removed closeAllConnections() from the Shiny session-end callback;
    it corrupted the process connection table and killed later spawns.
  - DepMap load no longer disconnects the session; demo load failures
    fixed.
  - Clearing demo data now also drops stale predictions; invalid
    expression files are rejected up front.
  - ROC curve corners (0,0) / (1,1) no longer render as a broken line
    (smoothed coords are densified onto a uniform FPR grid).
  - ROC / boxplot defaulted to the first drug on first click instead of
    the selected "Combination" (selectize init race); Gene Expression no
    longer shows "Select a gene first" on first draw.
  - DepMap cache is never auto-expired on disk (removed the TTL cleanup
    that could delete a 567 MB pre-downloaded cache); cache_ttl_hours
    <= 0 no longer deletes the file immediately.
  - Removed a stray inst/shiny/app/FALSE binary file from the
    repository.

Changes

  - Removed the on-disk TTL mechanism for the DepMap cache; memory is
    instead released by the master worker's idle timeout.

                        Changes in version 0.1.0                        

Initial release.