NEWS

PERCEPTIONx 0.3.0

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.

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).

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.

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

Initial release.