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

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

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

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)

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

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

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

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

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

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

fix: remove PhyML source build from Docker (fails on HF), add graceful missing-binary error in phylo.py

fix: add libtool + ca-certificates to PhyML build, remove -j for low-mem environments

fix: PhyML build — disable -march=native, split RUN steps, remove -q from wget

feat: dedicated phylo router (NJ/UPGMA/ML), local PhyML binary, standalone phylo page, PhyloTreeViewer redesign

feat: in-memory pipeline v2 with MSA, phylo tree, domains; PipelineResults component; standalone phylo page; report page; wizard step checkboxes

chore: remove unused celery dependency (worker uses threading, not Celery)

fix: add logging to init_redis() so Redis failures are visible in server logs

fix: make primer3-py optional (separate install step, router handles missing import gracefully)

fix: Foldseek alignments are [dict] lists, parse target format

fix: debug alignment structure types

fix: debug Foldseek result structure

fix: Foldseek alignments are dicts, parse with .get() correctly

fix: debug Foldseek alignment format (list vs dict)

fix: add full traceback to Foldseek error

fix: use aiohttp for Foldseek multipart upload

fix: debug Foldseek submit response type

fix: use sync httpx in thread pool for Foldseek submit

fix: restore nested alignments loop, remove debug raw

fix: return raw Foldseek data for debugging

fix: Foldseek returns list directly, no alignments sub-key

fix: move fetch inside httpx async with block

fix: manual multipart for Foldseek, add secrets import

fix: use sync httpx.Client for Foldseek multipart upload

fix: add error detail to Foldseek, use bytes, longer timeout

fix: simplify Foldseek integration, use full PDB, encode as bytes

fix: primer error handling, interactions scores, structure comparison API

fix: handle null name in InterPro domain response