Remove outdated ESM1b/ΔΔG coverage warning

Fix mechanism sort: tier by displayed label, not raw mechLabel

Sort mechanism column alphabetically, Unassigned always last

Replace list_repo_files() with per-protein lazy path probe

Fix event-loop blocking: make DB endpoints sync + raise timeouts

Add precomputed ML mechanistic labels as parquet (ml_preds/)

Add Colab notebook for mechanistic label classifier

Fix disk space management in join_rasp_ddg: skip re-extraction, delete early

Replace vaex with h5py for RaSP conversion (no gcc required)

Add RaSP ΔΔG JOIN + proteome-wide download script

Fix esm1b fallback: force eager validation to catch httpfs 404

Bump CACHEBUST=8 + route esm1b/ parquets to separate data dir

Fix upload_large_folder: bake esm1b/ prefix into local dir structure

Switch to upload_large_folder + persistent output dir for resumable upload

Add ESM1b/VESM++ JOIN to backend get_db() + fix hf_index scoping

Fix join_vesm_scores: bulk download + local join + single upload_folder

Add VESM++ join script for proteome-wide ESM enrichment

Add ESM2 LLR pipeline for full proteome (20K proteins)

Add demo walkthrough + rewrite README for v2

Add VEP debug logging + robust position/matching fallbacks

Fix VEP variant matching: parse result.input instead of exact string compare

Fix buildRows not-a-function error + add VEP debug logging

Improve VCF results page: risk filter banner, row coloring, better labels

Add cancer driver structures + updated VCF example + CACHEBUST=7

Remove COPY mutfunc.html from Dockerfile

Remove mutfunc.html links from all nav menus

Remove mutfunc.html — redundant with mutvar

mutfunc: load pathogenic variants (min_am=0.5) so highlights span whole protein

CACHEBUST=6: rebuild with ESM-IF1 DDG + Stability mechanism for 5 proteins

Fix ESM1b/DDG null display: show — instead of +0.00, fix scatter plot & detail panel

Add AlphaFold structures for 5 new proteins + AlphaFold EBI fallback + update demo chips

Update demo chips to ESM-enriched proteins + default to P60709 (β-actin)

Add 3D AlphaFold structure viewer with pLDDT coloring + variant highlighting

CACHEBUST=5 + fix download script to always overwrite parquets

Bump CACHEBUST=4 to pick up all 5 ESM2-enriched proteins

Bump CACHEBUST to re-download updated P60709/P61247 with ESM2 LLR

fix: add huggingface_hub dep + httpfs fallback + cache bust

fix: add huggingface_hub dep + httpfs fallback + cache bust

fix: add huggingface_hub dep + httpfs fallback + cache bust

fix: remove volume mount that was shadowing baked-in parquet data

refactor: serve parquet from local disk — baked in at build time

refactor: serve parquet from local disk — baked in at build time

refactor: serve parquet from local disk — baked in at build time

refactor: serve parquet from local disk — baked in at build time

fix: proxy_read_timeout 30s→120s — HF httpfs reads can be slow

fix: persistent httpfs conn + skip INSTALL on warm requests

fix: hive_partitioning=true on direct-path reads — protein_id column was missing

fix: increase /api/info fetch timeout to 30s for HF cold start

fix: /api/info returns instantly on HF — no glob scan ever

fix: HF file index + direct-path reads — eliminates 429 rate-limit errors