Chore/manuscript update webserver#9
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preRenderEvent rebuilt the visible sets from filters on every change while the dangling-node set was a stale, separately-computed layer. A still-passing dangling node ended up in both idsToShow and idsToHide, and updateElementVisibility's show-then-hide diff resurfaced it; newly-dangling nodes were never re-detected. - Extract the fixpoint detection loop into a pure computeDanglingElements() helper. - Recompute the dangling set against the fresh filtered view in preRenderEvent (when the flag is on) and exclude it from idsToShow, so the layer can no longer go stale on filter changes. - Add tests/hide-disconnected-filter.test.js covering hide+exclude, no show/hide overlap across repeated passes, re-detection of newly-dangling nodes, and full restore when the toggle is cleared.
Numeric properties whose only value is min === max have no range to narrow, so the range slider and its exact-value inputs are inert. Render a read-only checkmark + value badge in their place; the row's activation checkbox stays functional (it still includes/excludes nodes that have the property via the OR-combined query).
# Conflicts: # src/managers/ui_components.js
…b venue names - Rename resource_article/ -> journal/ (driver, numbered.bst, numcompress.sty) - Remove venue-specific names from driver comments and README - Keep bioRxiv preprint and journal flavors sharing shared/content.tex
- Reorder shared body to IMRaD (Materials and Methods before Results); split a Funding section out of Acknowledgements; rename end-matter sections - Split shared body into abstract.tex/keywords.tex/body.tex with content.tex as a wrapper, so the preprint and journal drivers share one prose source - Replace the journal driver with the OUP oup-authoring-template class (numbered citations); drop the now-unused numbered.bst and numcompress.sty - Use itemize for the Supplementary Data list (description env is undefined in the OUP class); both flavors build with plain latexmk - Leave journaltitle/appnotes as neutral placeholders, set at submission
- Drop the OUP `numbered' class option (it forces natbib into author-year
mode, rendering empty brackets with the numbered oup-plain bst)
- Use \bibliographystyle{unsrt} for order-of-appearance numbering
- Add \setcitestyle{numbers,round,comma} for round parenthetical numbers
- Switch the comparison table from full-width (table*) to single-column - Shrink check columns to 0.55cm with tabcolsep 3pt and footnotesize so all eight boolean columns fit \columnwidth; abbreviate Reactome Pathway Browser to keep every tool name on one line - Saves a page; biorxiv inherits it via \columnwidth (renders full-width)
Remove the bioRxiv driver and the shared/ + venue-subdir split; collapse the OUP journal source into a flat manuscript/ (main.tex, body/abstract/ keywords, reference.bib, oup-plain.bst, Fig/). Localize main.tex paths. Drop the now-obsolete add_reference and package_latex_submission helpers and the one-time truncate step; reference-nar.bib becomes reference.bib.
biorxiv.tex reuses body/abstract/keywords under a plain article class, so 'latexmk -pdf biorxiv' produces a preprint PDF with no OUP template. Two-column layout keeps figures beside their captions. main.tex (NAR flow) is untouched.
Fix disconnected nodes resurfacing on filter changes; add checkmark badge for single-value numeric filters. Also includes manuscript revisions.
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Summary
Manuscript rework plus two app fixes bundled in. Bumps to 1.16.1.
App changes
Manuscript
Docs only, no app impact — restructure to IMRaD + OUP template, revised content, figures, and references.
Testing
New tests:
tests/hide-disconnected-filter.test.js,tests/filter-single-value.test.js.