fix: fully sync _worker_sync — replaces asyncio.run with subprocess.run + httpx.Client to avoid Python 3.14 thread crash

chore: add /api/docking/debug diagnostic endpoint

fix: remove pybel bindings (causes segfault on Render), use obabel CLI subprocess only

fix: run docking worker in thread pool to keep event loop responsive + add vina download timeout

fix: move global to first line of function (Python 3.14 SyntaxError)

fix: strip ROOT/BRANCH from receptor PDBQT (rigid-receptor compat)

fix: use low-level OB API with AddOption('r') for rigid receptor PDBQT

fix: move global OBABEL_CMD declaration to function top (Python 3.14 SyntaxError)

fix: reduce OOM by using in-process obabel bindings + lower vina exhaustiveness

fix: simplify build.sh to only pip install (no risky binary downloads) + fix vina download path

fix: obabel self-healing — openbabel-wheel in requirements, runtime pip fallback, Vina download

fix: switch Render to Python buildpack with build.sh (openbabel via wheel, vina/phyml via wget)

fix: revert backend build to pip install (build.sh/apt-get broke the Render build, taking the backend down -> 404 on all routes incl. /api/audit)

fix: install openbabel/vina/phyml via build.sh in Python buildpack (deploy hook cannot switch runtime to docker)

fix: deploy backend via Docker (render.yaml runtime: docker) so openbabel/vina/phyml system binaries are installed; honor Render "

fix: add missing /api prefix to audit fetch URLs so rewrite proxy reaches backend router at /api/audit/event

fix: check obabel availability early with clear error message, use OBABEL_CMD variable

feat: add interaction fingerprinting and 3Dmol.js viewer to molecular docking page

fix: remove orphaned context = { line causing SyntaxError in deploy

feat: add query coverage, organism, and query accession to BLAST results

fix: stabilize useAuditTrail return reference with useMemo, remove setLoading(true) from effect re-fetches

fix: robust Foldseek parsing, add logging, handle missing results key and variant target formats

fix: remove opacity:0 flicker from all pages

fix: prevent opacity flicker on job results page, add pathway_enrichment migration

fix: handle NCBI UNKNOWN status and add pathway_enrichment to frontend status order

feat: add DNA sequence output across BLAST, UniProt, sequencing, primers, and SequenceRetrieval

fix: resolve Vercel build errors (handleFind, SAMPLE_DNA, Set iteration)

feat: add Translate CDS tool to /analyze/tools page

feat: implement 8 tool bridges (F1-F8) + audit child components

fix: prevent page scroll when zooming phylo tree (non-passive wheel listener)

feat: interactive phylo tree — pan/zoom, hover highlight, collapse/expand, node selection

feat: improve phylo tree viz — branch length labels, bigger nodes, hub labels, tooltips, ML recommendation

feat: instrument 7 tool pages with usage audit trail

feat: 4-layer audit/observability system

fix: replace dead lambda reference FTP URL with NCBI E-utilities

fix: resolve 10 bugs in sequencing/docking pipelines

Fix pipeline stuck issue: synthetic FASTQ fallback and demo mode

Move minimap2 download to runtime (avoids build failures on HF cpu-basic)

Fix sequencing dropdown: hardcoded defaults so dropdown works before backend deploys

Phase 3: Sequencing pipeline (FASTQ -> QC -> alignment -> variant calling -> report)

fix: load .env.deploy explicitly in config.py

fix: replace iframe structure viewer with PDBe Molstar web component

fix: replace broken PDBe embed URL with Mol* viewer (molstar.org)

fix: correct AutoDock Vina URL in Dockerfile (ccsb-scripps/AutoDock-Vina v1.2.7)

feat: molecular docking (AutoDock Vina) + docs site + Sentry + cache stats + Phase 2 docs update

fix: replace dead embed.rcsb.org iframe with PDBe Mol* viewer

feat: complete Phase 2 — API keys, share links, export, pipeline steps, guest upgrade

refactor: enhance dashboard with quick tools, jobs with filter tabs, settings with profile identity

feat: download pre-compiled PhyML binary from bioconda instead of source build

fix: use valid EBI email (example.com), remove PhyML build from Docker