Release v0.8.25 · genomoncology/biomcp

0.8.25 — 2026-07-07

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)

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)

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)

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: v0.8.24...v0.8.25