genomoncology/biomcp

0.8.25 — 2026-07-07

New features

• Added Homebrew formula and tap release automation so macOS/Linuxbrew users can
  install BioMCP from the project tap after release publication. (478)
• Added a biomcp mcp-config generator and unified MCP-client setup docs so
  users can copy local stdio config snippets for supported clients. (477)
• Added Docker image publication with CI build and smoke coverage so releases can
  publish ghcr.io/genomoncology/biomcp images. (476)
• Published official MCP Registry metadata for biomcp-cli, including the PyPI
  package distinction from the unrelated biomcp package. (473)
• Annotated MCP tools with read-only hints and human-readable titles for safer
  client presentation. (474)
• Added opt-in variant structure annotation for residue, domain, PDB, AlphaFold,
  and hotspot context without ddG prediction claims. (452)

Fixes

• Emitted JSON usage errors for clap parse failures under --json, keeping CLI
  error output machine-readable on parse errors. (466)
• Fixed variant normalize JSON output so failures no longer look like silent
  successes.
• Normalized protein and phenotype JSON search next commands. (460)
• Added broadening hints for zero-result filtered trial searches and clarified
  --mutation versus --biomarker usage.
• Surfaced the CIViC actionability pointer and currency caveat on default variant
  cards without adding a new network call.
• Accepted advertised drug adverse-events --count and clarified FAERS Summary
  output as sample rows rather than an aggregate.
• Bounded CLI exit latency after disease-survival and CTGov helper output, and
  sped up CTGov alias fan-out tests. (467, 470)
• Stabilized MCP/spec routing with dynamic reserved ports and live-lane routing
  fixes. (468)

Docs

• Added the unified "Add BioMCP to your MCP client" guide and refreshed MCP
  deployment docs while keeping leaked internal spec text out of public docs.
• Documented environment configuration parity with runtime behavior and added
  ratchet coverage. (465)
• Added shell-safe HGVS command examples and separated typed next-command
  ownership from markdown shell quoting. (469)
• Added the variant-structure blog walkthrough from linear sequence to 3D protein
  context. (453)
• Added the skill-authoring guide and normalize-to-codes worked example. (450)
• Refreshed release-prep metadata and public release notes for v0.8.25. (479)

Internal

• Added whole-surface CLI contract ratchets for help, list, docs, specs, and JSON
  metadata. (459)
• Completed helper and parent help discovery for helpers and skills. (463)
• Restored deterministic routine disease-survival bounded-exit coverage with a
  SEER fixture. (472)
• Moved contract and release smokes to tag/release time, removed stale daily
  release cron behavior, and repaired stale WikiPathways probe coverage.
• Removed leaked internal working docs, retired validation profiles, and public
  root clutter from the repo.

Full Changelog: https://github.com/genomoncology/biomcp/compare/v0.8.24...v0.8.25