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

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

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

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

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

feat(md): temperature/KE, Rg and SASA traces; fix OpenMM in deployed image

fix: OpenMM via micromamba/conda-forge + worker phantom job guards

debug: add OpenMM verification steps + startup check so we can see what fails

fix: install OpenMM directly into system Python, remove conda/micromamba

fix: install OpenMM into conda env used by CMD so it's actually importable

fix: OpenMM via micromamba + BioPython structural fallback, real error messages

feat: scientifically accurate MD simulation with OBC2 solvent, Kabsch RMSD, per-residue RMSF

Phase 3a/4/5: ADMET descriptors (RDKit), MD simulation (OpenMM), function prediction (DeepFRI-inspired) — backend + frontend

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

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

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

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

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

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

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

Fix Reactome pathway search: correct param name and response parsing

Deploy prep: Render config + Dockerfile, refactored backend auth flow, dashboard, landing page, error states, guest flow