fix: pin python:3.11-slim-bookworm — trixie's gcc14 errors on fpocket's legacy C (incompatible-pointer-types); gcc12 builds clean

fix: fpocket clone tag 4.2.3 — tags carry no v prefix; wrong tag broke HF Space build (503s)

feat: techspec additions — de novo tier-6 branch, structure export, page capture + final synthesis

feat: optimize CASTp SASA with KDTree, add sequence input to CASTp + Structure Prep, ESMFold integration for unknown genes

fix: remove fpocket from Dockerfiles to unblock HF Spaces build

fix: fpocket build — correct tag 4.2.3, add libnetcdf-dev dependency

feat: structure preparation pipeline — broken chains → SWISS-MODEL repair → PyMOL cleanup → fpocket + CASTp

fix: switch runCastp to longApi (660s timeout)

fix: PDBParser.get_pdb -> get_structure in castp.py

feat: add CASTp pockets, SWISS-MODEL, ESMFold + fix Dockerfiles

fix: NGS fallback to Python aligner when native tools missing; add missing re import in sequence_utils

fix: eliminate infinite re-render loop - remove ResizeObserver, fix ref prop conflict, simplify zoom/pan

fix: prevent infinite re-render loop in GenomeViewer (error #290)

feat: replace igv.js with custom SAM/VCF genome viewer

fix: add --no-same-owner to worker Dockerfile tar command

fix: add --no-same-owner to backend Dockerfile tar commands

fix: retry NGS run on 503 (Render cold start)

chore: remove samUrl prop from IgvBrowser (igv.js only supports BAM)

refactor: require native samtools/minimap2, delete hand-rolled BAM/BAI code

fix: igv.js fetch BAM/BAI as Blobs, client-side SAM-to-BAM conversion, proper BGZF

fix: correct BGZF virtual offsets in BAI, fix duplicate-read bug, install minimap2 everywhere

fix: SAM-only igv.js track, indexed:false reference, debug logging

fix(ngs): dynamic locus + SAM-first igv.js for reliable genome browser

fix: repair BAI index generation and BAM record format for igv.js compatibility

fix(ngs): correct BAM record format and BAI index for igv.js

feat(ngs): pure-Python SAM to BAM converter with BGZF + BAI index for igv.js

chore: remove NGS rate limits

chore: increase daily rate limits for testing (50 global, 20 NGS)

fix: load igv.js from CDN instead of ESM import

fix: igv.js white screen — CIGAR ops, qual strings, locus format

feat: add igv.js genome browser + proper 6-step NGS pipeline

fix: NGS pipeline stuck in queued - worker fallback + migration fix

feat: add full 6-step NGS pipeline + fix sequencing WinError 193

feat(landing): 'Stop tab-switching' hero + docking sample, drop stale New badges

feat(pipeline): multi-database UniProt identifier resolution

feat(seo): JSON-LD structured data — Organization/WebSite graph, SoftwareApplication+HowTo homepage, BreadcrumbList across tools

feat(branding): Synteny rebrand — new identity, signal-coded palette, and pipeline icons

fix(pipeline): stop abandoning slow NCBI BLAST jobs + EBI fallback

feat(results): in-app share dialog + self-normalized dotplot scoring

feat(admet): ProTox 3.0 ML toxicity prediction — backend client + endpoint, frontend ProTox tab, restored sidebar chevron

feat(design): bioluminescent green+violet palette and re-tuned landing hero

feat(landing): trust & craft pass — sample result preview with confidence bands, honest service/status copy, unified CTA verbs, grouped database taxonomy, 44px nav touch targets, calmer motion (no chevron loop, glow under nav)

feat(ui): apple-design conformance — springs for micro-interactions, reduced-motion/transparency/contrast support, typography tracking

feat(theme): dual light/dark mode with Apple light theme, toggle, and theme-aware viewers

feat(seq-tools): share colored MSA viewer across BLAST job, alignment tool, report, shared and phylo surfaces

feat(seq-tools): MSA match/mismatch/gap cell highlighting, consensus row and legend

fix(seq-tools): stop auto-scrolling on job completion, fix structure highlight & AlphaFold viewer loading

feat(seq-tools): wire motif scanner into BLAST, structure, alignment and dot-plot workflows

fix(seq-tools): only link motif highlights to structure when a protein UniProt accession is known

feat(seq-tools): motif categories & structure overlay, dot-plot scoring & features, cross-tool links