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

fix: default import PhyloTreeViewer in alignment, report, and PipelineResults

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

fix: accurate phylogenetic tree visualization — proportional branch lengths, scale bar, bootstrap labels, circular layout mode

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

chore: move @types /three from dependencies to devDependencies

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: convert AlignmentView.tsx light-theme classes to dark void theme tokens

fix: use embed.rcsb.org instead of www.rcsb.org for clean 3D viewer iframe

feat: add PNG/TSV/JSON/CSV/FASTA export to all 8 tool components

fix: use STRING-DB image API for accurate PPI diagram, add PNG/TSV/copy export buttons

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

fix: forward backend error detail in 4 components

fix: handle non-200 responses in domains, interactions, ramachandran, SS components

feat: domains, interactions, primers, structure analysis, wizard, phylo tree, conservation

Fix invisible fonts in Reactome DiagramJs: isolate widget from dark-theme CSS overrides

Fix KEGG search: use find/hsa with symbol matching + parse get/PATHWAY section

Add Reactome diagrams, KEGG search, pathway enrichment (pipeline + standalone)

Security, crash fixes, demo prep, dead code removal

Fix Reactome pathway search: correct param name and response parsing

Add Render Blueprint, GitHub Actions auto-deploy, revert to CORS fix, local startup scripts

Fix structure viewer iframe: embed.rcsb.org is dead → use www.rcsb.org/3d-view/{pdbId}

Fix structure viewer: correct PDB API URL (+/entry/), fix RCSB UniProt search attribute + payload format

Fix MSA: use correct EBI result type 'fa' instead of 'aln-fasta' — confirmed via live API test

Fix MSA: dynamically discover EBI result types instead of hardcoding 'aln-fasta'

Fix MSA alignment: add Accept headers, result retry with delay, better error detail

Fix: alignment sample sequences, reverse complement tool, BLAST program filtering, sample buttons on structure/pathway pages

Fix Phase 1 endpoints: resolve UniProt→PDB in structure viewer, use proper Reactome search, surface real backend errors in frontend