Added web server subcommand#7
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…ion to export the tree figure with custom sizing and dpi
…ke advantage of short-circuiting
Converted regex to compiled form and fullmatch instead of match
… layer - Remove phylotree.js/D3 SVG renderer; add paper.js CDN - Add Flask static file route for web/js/ ES modules - Implement 8 JS modules: newick, treemodel, layout, renderer, annotations, export, panel, app - Add Visual Options drawer (PearTree-inspired annotation panel) - Add NEXUS export with FigTree-compatible [&!color=] metacomments - Add session save/load (JSON sidecar) - Add interactive parameter sweep bar with diversity sparkline - Fix parseMetadataCsv TSV separator support - Fix ResizeObserver leak in mountRenderer
- Scale canvas height to leaf count (16px/leaf) so all tip labels are visible without zooming; tree-card scrolls vertically - Sync Paper.js viewSize to canvas pixel dimensions to prevent whitespace above tree and clipped exports - Remove Radial layout toggle and Annotate button from toolbar - Move legend to top-right of tree; color legend text to match cluster - Export height always equals actual canvas height to prevent clipping - Re-render with correct dark/light theme colors before PNG/JPG/EPS export so branch colors match the chosen export theme
…ation - Move legend band from bottom to top of tree canvas - Restructure sidebar into tabbed layout: Parameters tab always visible, Results tab revealed after running analysis (auto-activates on run) - Move results panel from viz-area into sidebar Results tab; removes horizontal overflow from side panel - Add collapse button («) in sidebar tab bar with smooth opacity + grid width animation; external toolbar Sidebar button still reopens - Remove plan.md (superseded by .claude/plans/)
- Add collapse toggle to Sampling section (all six sidebar sections now collapsible with consistent chevron pattern) - Animate .collapsible via max-height/opacity instead of display:none for smooth open/close transitions - Debounce ResizeObserver callbacks (140ms) to prevent per-frame full re-render during sidebar grid animation - GPU-composite tree canvas with will-change:transform during slide - Add debounce() utility helper to app.js
…om via CSS scale - Remove #sidebar-collapse in-panel button, .sb-collapse CSS, toggleSidebarCollapse() - Remove #sweep-bar markup (CSS/JS left dormant for later re-add) - Remove #maximize-btn, resizeAfterMaximize(), maximize/Escape handlers, #tree-card.maximized CSS - Fix zoom lag: accumulate CSS scale() during gesture (GPU-composited, no vector repaint), commit to paper.js view.scale() once after 120ms settle; applies to both zoom buttons and ctrl+wheel
…ooltip fix, scroll fix, remove zoom buttons - Task 1: Re-add sweep controls as a sidebar tab (shown only in sample mode) - Task 2: Draw diversity coverage caption beside legend in evaluate mode trees - Task 3: Enable image export in evaluate mode — composites both trees side-by-side as PNG - Task 4: Override Pico CSS tooltip max-width/white-space so tooltips wrap inside the sidebar - Task 5: Add min-height:0 to .sb-panel so vertical scroll engages when submenus expand - Task 6: Remove #zoom-controls toolbar buttons (ctrl+scroll zoom remains) - annotations.js: add setLegendCaption() immutable helper - renderer.js: render ann.legendCaption right-aligned in legend top band
…delay On a cold server, the first call to find_n_medoids_with_diversity blocks ~13s for numba to JIT-compile the solver kernels. Every subsequent call is <5ms. Spawn a daemon thread at run_server() startup that drives a tiny 5-node solve, triggering compilation while the user loads the page and configures a run. Thread is best-effort (exceptions silently swallowed); server port opens immediately as before.
…tion - Move sweep panel into Results tab as collapsible submenu between diversity pill and rep-list; remove separate Sweep tab - Fix sidebar scroll: add grid-template-rows: minmax(0,1fr) to .app-body (implicit auto row was preventing overflow-y from engaging) - Fix sweep chart y-label clipping: dynamic canvas DPR sizing + PAD.l=34 - Fix rep-list not updating on sweep +/-: extract renderSampleReps() helper called from both showResults and _applySweepResult - Fix legend cap: raise MAX_LEGEND_ROWS 4→8 so n≥9 shows all entries - Add Prior Representatives section in eval mode from data.prior_centers - Fix sweep chart draw-before-show: set display:block before draw() so getBoundingClientRect() returns real width
Dead code removed: - Delete panel.js (440 lines, AnnotationPanel never imported/wired) - Remove all .vopt-* CSS rules + #vopt-panel markup (~80 lines) - annotations.js: drop 13 dead exports (setBranchColor, setBranchWidth, setNodeColor, setLabelOverride, upsert/remove Metadata/CladeGroup/Shape, addShape, removeShape, updateShape, parseMetadataCsv, serialise) - treemodel.js: drop mrca, subtreeLeafNames, indexById, parentMap, indexByName - export.js: drop svgToRasterBlob (canvas export uses exportPngWithTheme) - newick.js: drop toNewick (only toNexus used by export) - renderer.js: drop resetView, zoom, fitLabels, exportPng, onNodeClick/ onBranchClick callbacks + _handleClick + _findNodeById - sweep.js: drop setCurrentN (never called) - app.js: remove unused indexByName + svgToRasterBlob imports, drop duplicate theme-toggle listener (merged re-render into restoreTheme handler) - index.html: remove #sweep-bar, standalone .sweep-n/.sweep-div, .toggle-group, #tree-card svg CSS; stray </button>; #vopt-panel div; #exp-render-stage div Optimizations implemented: - renderer.js: rAF-throttle pan mousemove (flush _applyTransform once/frame) - app.js: Run button shares sweepCache with sweep +/- (instant re-run for cached params); LRU cap 20 via _sweepCacheSet() - sweep.js: cache getBoundingClientRect(); invalidate on reset/resize - treemodel.js: maxDepth reuses depthMap result (single traversal) - index.html: rel="preconnect" for 3 CDN origins; defer Paper.js script Add OPTIMIZATION.md: full audit with file:line, impact, and server-side wins (gzip, server LRU cache, threaded Flask, self-host CDN) documented for future.
- treemodel.js: memoize leaves() with a module-level WeakMap keyed on root node; subtree calls also cached; auto-GC on tree replacement. Eliminates ~15 redundant preorder walks per render/resize/sweep cycle. - app.js: replace hasWeights boolean with weightsFile name+size string in both sweepCache key builders (Run button + sweepTo); prevents stale cache hit when user swaps weights file between runs. - .gitignore: exclude parnas/web/OPTIMIZATION.md (local working notes).
- _effectiveColors: cache result keyed on reference identity of ann, nodeColors, repsSet, repColors; skip full leaf+postorder walk on theme toggle and resize where inputs are unchanged. - _redraw: build cladeMap (Map<nodeId, cladeGroup>) once before drawSubtree; replaces two O(n × groups) cladeGroups.find() calls per node with O(1) map lookups.
Regular leaf dots sharing the same (radius, color) now map to a single SymbolDefinition; SymbolItem is placed at each leaf position instead of creating a unique Path.Circle. For a 1000-leaf tree with 9 cluster colors this reduces unique path items from ~1000 to ~10 for dots. Rep dots (~n total) keep Path.Circle since each has a per-instance stroke. SymbolDefinitions are stored in _dotSymDefs and removed in _clearLayers() to avoid accumulation in the paper.js project across redraws.
Make _dotSymCache persistent on the instance instead of local per-redraw. SymbolItems (scene children) are already cleaned by layer.removeChildren(); SymbolDefinitions (project-level, bounded by color count) need no removal. Removes the invalid sd.remove() call that caused TypeError on second render.
This reverts commit dbddd8b.
This reverts commit 4dd8cac.
- Add n-sweep mode: runs one request at nMax, plots diversity_curve, detects elbow via max-perpendicular-distance, auto-selects elbow n - Add threshold-sweep mode: new server endpoint (sweep=threshold), sweeps similarity threshold, detects elbow, auto-runs cover at elbow - Refactor SweepChart into generalized X/Y renderer with axis labels, titles, elbow markers (x or y axis), and PNG/SVG/EPS export - Relax server n-range validation to skip threshold-sweep requests - Track lastNTaxa from API responses to cap n-sweep range - Fix sweep guard: allow cold-start sweep before treeRoot is set - Fix regex match: use re.match instead of re.fullmatch for taxa filter
- Wider sidebar (360→420px) and taller sweep chart (200→280px) - Larger exported figure fonts (tick, axis title, plot title) - Hide theme selector when CSV export format selected - Fix "undefined" overlay after n-sweep (showOverlay→hideOverlay) - Smoother trackpad/touch pinch zoom (exponential scaling, clamp 0.2–8x) - Touch pinch support for tree viewer - Reset view button on tree toolbar - Sweep plot hover tooltips (canvas hit-test, no d3 dependency) - Fix y-label/y-tick overlap: PAD.l 72→90, textBaseline top→middle - Run button moved outside scrollable params panel (stays visible)
Add bench/benchmark_api.py and bench/plot_bench.py to measure POST /api/run latency and server RSS memory across synthetic birth-death trees of 100–5000 taxa. Results support the W2 performance analysis in the manuscript. - benchmark_api.py: launches live parnas server, generates dendropy trees with fixed seed (reproducible), measures median latency over 5 requests and peak RSS via psutil, writes bench_results.csv - plot_bench.py: reads CSV, emits dual-axis latency+memory figure (manuscript/images/bench-latency.png) and bench_table.tex - Add psutil and requests to pyproject.toml / uv.lock - Ignore outputs/ and manuscript/ in .gitignore - Fix minor server.py issue
- README: add Web UI section documenting `parnas server [--ip] [--port]` - .gitignore: whitelist data/ so application-study datasets are tracked - data/: H10 GISAID alignments, fasta, and tree used in the application study - supplementary/: manuscript supplementary figure and representative lists - web/app.js: evaluate-mode diversity display + themed export refinements
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