## genomoncology/biomcp — v0.8.24…v0.8.25

_130 commits._

### Features
- **Merge Add Homebrew formula and release automation via a tap** (ba4d160)
- **Add Homebrew formula release automation** (42a655d)
- **design: land spec tests for add-homebrew-formula-and-release-automation-via-a-tap** (5e3ae5b)
- **Merge Add a unified Add-BioMCP-to-your-MCP-client docs page** (23c9d87)
- **Add a unified Add-BioMCP-to-your-MCP-client docs page** (1b5bcbc)
- **Merge Add biomcp mcp-config client config generator command** (ca4eeb2)
- **code: add mcp-config generator** (486b3ce)
- **design: land spec tests for 477-add-biomcp-mcp-config** (5af626d)
- **code: add MCP registry metadata validation** (e46616d)
- **Merge Align BIOMCP env configuration docs with runtime and add parity ratchet** (4b51524)
- **feat: honor BIOMCP_CACHE_MAX_AGE env config** (59c4d7a)
- **Merge Add whole-surface CLI contract ratchet for help list docs specs JSON meta** (fcfee10)
- **code: add CLI surface contract ratchet** (1854ad6)
- **Merge Quickfix: get variant — surface CIViC actionability pointer on default card + currency caveat (no new network call)** (fce0fd7)
- **Quickfix: get variant — surface CIViC actionability pointer on default card + currency caveat (no new network call)** (cbb1208)
- **feat: add variant structure helper** (18c11a6)
- **code: add skill authoring guide and normalize-to-codes playbook** (04f4eba)
- **Add variant structure spike experiments** (e59960d)

### Fixes
- **review: relax trivia and fix syntactic red for 479-release-prep-v0-8-25-version-bump-curated-changelog** (b9655dc)
- **review: relax trivia and fix syntactic red for 478-add-homebrew-formula-and-release-automation-via-a-tap** (f516542)
- **review: relax trivia and fix syntactic red for 477-add-biomcp-mcp-config-client-config-generator-command** (ff70e3d)
- **review: relax trivia and fix syntactic red for 476-publish-a-biomcp-docker-image-with-ci-build-and-smoke** (f25bedd)
- **review: relax trivia and fix syntactic red for 474-annotate-all-mcp-tools-read-only-with-titles-and-a-coverage-contract-test** (8d00c1c)
- **review: relax trivia and fix syntactic red for 473-publish-biomcp-cli-to-the-official-mcp-registry-and-disambiguate-the-biomcp-pypi-name** (0127215)
- **review: relax trivia and fix syntactic red for 472-restore-deterministic-routine-disease-survival-bounded-exit-check-via-seer-fixture** (59c311a)
- **review: relax trivia and fix syntactic red for 470-bound-ctgov-helper-pivot-exit-and-speed-up-ctgov-alias-fan-out-tests** (7a35cda)
- **review: relax trivia and fix syntactic red for 469-separate-typed-next-command-ownership-from-markdown-shell-quoting** (4655344)
- **review: relax trivia and fix syntactic red for 463-complete-list-and-parent-help-discovery-for-helpers-and-skills** (ca26267)
- **review: relax trivia and fix syntactic red for 468-stabilize-verify-routing** (7926c22)
- **fix: emit JSON parse errors under json mode** (6e4bb4b)
- **review: relax trivia and fix syntactic red for 466-emit-json-usage-errors-for-clap-parse-failures-under-json** (24936de)
- **Merge hotfix: route live disease-survival spec out of routine gate (unblock queue)** (73913f0)
- **review: relax trivia and fix syntactic red for 465-align-biomcp-env-configuration-docs-with-runtime-and-add-parity-ratchet** (9ad7f02)
- **review: relax trivia and fix syntactic red for 467-bound-cli-command-exit-after-output-for-disease-survival-and-ctgov-helpers** (79326ee)
- **Merge Fix variant normalize JSON silent success** (262fbad)
- **Fix variant normalize JSON silent success** (9c963ad)
- **review: relax trivia and fix syntactic red for 460-normalize-protein-and-phenotype-json-search-next-commands** (7cbaf0e)
- **review: relax trivia and fix syntactic red for 459-add-whole-surface-cli-contract-ratchet-for-help-list-docs-specs-json-meta** (62df746)
- **review: relax trivia and fix syntactic red for 453-blog-variant-structure-capability-linear-sequence-to-3d-protein-context-in-a-few-commands** (e61cc36)
- **review: relax trivia and fix syntactic red for 452-build-biomcp-variant-structure-variant-residue-domain-pdb-alphafold-hotspot-annotation-opt-in-no-ddg** (11d1d7a)
- **review: relax trivia and fix syntactic red for 450-skills-skill-authoring-template-guide-with-normalize-to-codes-as-the-worked-example** (133a1a4)
- **Merge Run contract+release smokes only at tag/release time (gatekeep release); remove daily cron; fix stale WikiPathways probe** (5a748d9)
- **Run contract+release smokes only at tag/release time (gatekeep release); remove daily cron; fix stale WikiPathways probe** (636d8f0)

### Backend
- **Merge README: document Homebrew and Docker install paths** (b533782)
- **README: document Homebrew and Docker install paths** (d55e753)
- **Merge Release prep v0.8.25: version bump + curated changelog** (2003724)
- **code: prepare v0.8.25 release metadata** (a220bca)
- **design: land spec tests for 479-release-prep-v0-8-25-version-bump-curated-changelog** (9fb17c7)
- **Strengthen Homebrew formula spec coverage** (7aa7b89)
- **code-review: error-classification — shell-quote codex absolute-path config** (2f2bdc5)
- **Merge Publish a BioMCP Docker image with CI build and smoke** (73ea6d7)
- **verify: guard Docker image release version** (08bc890)
- **code-review: validation-gap — restore Docker publishing gates** (db4d406)
- **code: publish BioMCP Docker image** (aeea8e1)
- **design: land spec tests for publish-biomcp-docker-image** (8b9e37f)
- **Merge Annotate all MCP tools read-only with titles and a coverage contract test** (5f77e77)
- **design: land spec tests for annotate-all-mcp-tools-read-only** (ce9d3d8)
- **Merge Publish biomcp-cli to the official MCP Registry and disambiguate the biomcp PyPI name** (7ae7856)
- **code-review: security — harden registry metadata release stamping** (2732e1b)
- **design: land spec tests for 473-publish-biomcp-cli** (b7c18f6)
- **Merge Restore deterministic routine disease-survival bounded-exit check via SEER fixture** (b23d18b)
- **verify: harden disease survival fixture cleanup** (f778bba)
- **code-review: resource-leak — clean up disease survival fixture** (0109ee2)
- **design: land spec tests for restore deterministic disease survival** (e762b8c)
- **Merge Replace fixed MCP spec port with dynamic reserved port** (6b4d03a)
- **Replace fixed MCP spec port with dynamic reserved port** (5646fa7)
- **Merge Bound CTGov helper pivot exit and speed up CTGov alias fan-out tests** (7578f0e)
- **code-review: validation-gap — scope CTGov no-count helper flag** (370d545)
- **code: bound ctgov helper count work** (84367fd)
- **design: land spec tests for bound ctgov helper pivot exit** (ce4935d)
- **Merge Quote shell-unsafe HGVS command examples and ratchet next commands** (0844b45)
- **Quote shell-unsafe HGVS command examples and ratchet next commands** (856e3bb)
- **Merge Separate typed next-command ownership from markdown shell quoting** (4207030)
- **verify: close next-command ratchet import gap** (8157da1)
- **code-review: validation-gap — catch entity markdown quote imports** (631257d)
- **code: separate typed next-command rendering** (8410afc)
- **design: land spec tests for separate typed next-command ownership** (68396be)
- **Merge Complete list and parent help discovery for helpers and skills** (a16806f)
- **code: complete helper and parent help discovery** (bca698c)
- **design: land spec tests for complete list and parent help discovery** (6cb78a8)
- **Merge Surface drug ema region alias in help and alias-alignment tests** (e7bd48b)
- **Align drug EMA alias list docs** (dae6f69)
- **Surface drug EMA region alias** (830f4d3)
- **Merge Stabilize verify and spec live-lane routing ports and slow CTGov tests** (e37a3a4)
- **code: route live verify source-pending states** (398f3c8)
- **design: land spec tests for 468-stabilize-verify-routing** (be945df)
- **Merge Emit JSON usage errors for clap parse failures under --json** (33b0772)
- **Merge branch 'main' into march/466-emit-json-usage-errors-for-clap-parse-failures-under-json** (1e96950)
- **verify: cover short json parse errors** (97c97fa)
- **design: land spec tests for 466-emit-json-usage-errors** (ebf078f)
- **specs: route live disease-survival bounded-exit check out of routine gate** (0a5c19d)
- **code-review: weak-assertion — tighten env parity scanner** (d87b910)
- **design: land spec tests for align-biomcp-env-configuration-docs** (88ef8da)
- **Merge Bound CLI command exit after output for disease survival and CTGov helpers** (6e4423a)
- **design: land spec tests for 467-bound-cli-command-exit-after-output-for-disease-survival-and-ctgov-helpers** (b43ee00)
- **Merge Normalize protein and phenotype JSON search next commands** (c496a42)
- **verify: strengthen protein phenotype json spec** (eb966ed)
- **code-review: over-edit — remove empty search-surface placeholder** (6cdba5b)
- **code: normalize protein and phenotype json next commands** (9b6b7f4)
- **design: land spec tests for normalize-protein-and-phenotype-json-search-next-commands** (60baebb)
- **Verify CLI surface shell safety ratchet** (5d5dfae)
- **code-review: weak-assertion — require aliases outside source corpus** (6a1367c)
- **design: land spec tests for cli contract ratchet** (5427103)
- **Merge Quickfix: search trial — broadening hint on 0-result filtered search + clarify --mutation vs --biomarker** (eaff868)
- **Quickfix: search trial — broadening hint on 0-result filtered search + clarify --mutation vs --biomarker** (ec5b045)
- **Merge Quickfix: drug adverse-events — accept advertised --count + honest FAERS Summary (sample vs aggregate)** (a2754cf)
- **Quickfix: drug adverse-events — accept advertised --count + honest FAERS Summary (sample vs aggregate)** (8c59079)
- **Merge Quickfix: discover code-label canary credential-gates UMLS (green make verify without UMLS_API_KEY)** (e063980)
- **Quickfix: discover code-label canary credential-gates UMLS (green make verify without UMLS_API_KEY)** (1cf027d)
- **Merge Blog: variant structure capability — linear sequence to 3D protein context in a few commands** (7c1b746)
- **design: land spec tests for 453-blog-variant-structure** (ce7b2cc)
- **Merge Build: biomcp variant structure <variant> — residue/domain/PDB/AlphaFold/hotspot annotation (opt-in, no ddG)** (e9761f5)
- **code-review: data-completeness — normalize HGVSp aliases and hotspot inputs** (9caabfc)
- **design: land spec tests for variant structure helper** (4e84fe8)
- **Merge Docs hygiene: rewrite mcp-server.md (strip leaked spec test) + MCP-deploy FAQ + docs-leak lint guard** (6693656)
- **Docs hygiene: rewrite mcp-server.md (strip leaked spec test) + MCP-deploy FAQ + docs-leak lint guard** (16a4c04)
- **Merge Skills: skill-authoring template + guide, with normalize-to-codes as the worked example** (2fe3fd2)
- **verify: clarify normalize sidecar docs** (be4172b)
- **design: land spec tests for skill-authoring-template-guide** (498e646)
- **Merge Spike: scope variant to protein-structure annotation (residue/domain/PDB/AlphaFold), no ddG** (b0faf2c)
- **Harden variant structure spike library interface** (e7fb6cc)
- **Document variant structure optimization results** (795b974)
- **Stop tracking generated variant structure results** (ff0d153)
- **Parallelize variant structure source probes** (4242946)
- **Optimize variant structure cancerhotspots probe** (b5bd001)
- **Record variant structure exploit results** (5387c9a)
- **Document variant structure spike decision** (4537f10)

### Tests
- **test: cover MCP registry validation seam** (bd1d508)

### Docs
- **docs: document MCP tool annotation contract** (97c72d8)
- **docs: add variant structure blog walkthrough** (1c92887)

_Recap by [Repo Wrapped](https://repowrapped.com/gh/genomoncology/biomcp?utm_source=github-action)._