## genomoncology/biomcp — v0.8.22…v0.8.23

_189+ commits._

### Features
- **Merge Add high-risk request-plan and update-option ratchets** (b776144)
- **code: add high-risk request-plan and update-option ratchets** (b6faac9)
- **design: land failing contract for 400-add-high-risk-request-plan-and-update-option-ratchets** (75efbf5)
- **Merge Add non-PMC Figshare article asset retrieval** (43ddb0f)
- **code: add Figshare article asset fallback** (12eb387)
- **design: land failing contract for 398-add-non-pmc-figshare-article-asset-retrieval** (62864b2)
- **Add BioC miss fixture exploit results** (51b0037)
- **Merge Add article fulltext provenance and quality flags** (ac51a9b)
- **Add article fulltext provenance and quality flags** (51fe701)
- **design: land failing assertions for add-article-fulltext-provenance-and-quality-flags** (41dfc35)
- **Add source coverage exploit artifacts** (27a910c)
- **Add article source coverage spike probe results** (58a2233)
- **Merge Add renderer envelope fixture contracts for request reset** (493cff2)
- **code: add renderer envelope fixture contracts for request reset** (04acf8e)
- **design: land failing assertions for 377-add-renderer-envelope-fixture-contracts-for-request-reset** (c290975)
- **code: add article and variant source request plans** (5ddcfc7)
- **Merge Add request-command seams for disease discover and article** (f89d629)
- **Add request-command seams for disease discover and article** (c54e838)
- **design: land failing assertions for add-request-command-seams-for-disease-discover-and-article** (ce0f5aa)

### Fixes
- **review: relax trivia and fix syntactic red for 410-cancerhotspots-grade-recurrence-counts-for-somatic-oncogenicity-grading-os3-om3-op3** (e1dba3c)
- **code: fix mechanical bug in landed assertion (spec routing)** (71739ec)
- **review: relax trivia and fix syntactic red for 405-refresh-migrated-architecture-and-operator-contracts** (e05ad62)
- **review: relax trivia and fix syntactic red for 406-clarify-remaining-consumer-correctness-contracts** (2605f08)
- **review: relax trivia and fix syntactic red for 401-harden-post-migration-spec-runner-and-cli-surface-ratchets** (2d64b37)
- **code: fix mechanical bug in landed assertion (spec/surface/request-plan-ratchets.md)** (7cd55c3)
- **review: relax trivia and fix syntactic red for 403-bound-remote-waits-and-stabilize-residual-reliability-flakes** (af9a96f)
- **review: relax trivia and fix syntactic red for 409-retrieve-all-figshare-supplementary-records-for-a-paper** (3294513)
- **Merge Fix figshare URL parser version-segment article-id bug** (1d8a85a)
- **Fix figshare URL parser version-segment article-id bug** (fc44b99)
- **review: relax trivia and fix syntactic red for 400-add-high-risk-request-plan-and-update-option-ratchets** (6a4185f)
- **review: relax trivia and fix syntactic red for 398-add-non-pmc-figshare-article-asset-retrieval** (4c43eed)
- **review: relax trivia and fix syntactic red for 396-adopt-mustmatch-ellipsis-and-run-expect-capabilities-across-biomcp-specs-for-robust-assertions** (6a72de1)
- **review: relax trivia and fix syntactic red for 393-migrate-biomcp-spec-runner-to-the-mustmatch-binary-and-the-spec-verify-lane-model** (81f8ed2)
- **review: relax trivia and fix syntactic red for 392-bring-biomcp-to-the-engineering-standard-agents-md-make-test-drop-make-check-skills-gitignore** (1962981)
- **review: relax trivia and fix syntactic red for 386-article-assets-manifest-and-canonical-oa-package-fetch-bytes-not-parsing** (4996e2e)
- **review: relax trivia and fix syntactic red for 385-cover-figures-supplements-and-complex-tables-in-jats-to-markdown-converter** (bb85741)
- **Merge Restore deterministic validation routing (c06d1b51 regression) and fix stale discover spec** (b8ac041)
- **Restore deterministic validation routing (c06d1b51 regression) and fix stale discover spec** (7981eb9)
- **review: relax trivia and fix syntactic red for 383-add-article-fulltext-provenance-and-quality-flags** (b473a59)
- **Reuse coverage rows for regression comparison** (e41b814)
- **review: relax trivia and fix syntactic red for 379-prune-brittle-live-assertions-after-request-contracts-land** (847b52b)
- **review: relax trivia and fix syntactic red for 378-split-routine-validation-from-release-live-smoke** (3994127)
- **review: relax trivia and fix syntactic red for 377-add-renderer-envelope-fixture-contracts-for-request-reset** (8acf6db)
- **review: relax trivia and fix syntactic red for 376-convert-article-and-variant-source-specs-to-fixture-contracts** (4ff640c)
- **review: relax trivia and fix syntactic red for 375-add-request-command-seams-for-disease-discover-and-article** (d2b9b0f)

### Backend
- **Prepare BioMCP 0.8.23 hardening release** (b88dd3f)
- **Merge Cancerhotspots-grade recurrence counts for somatic oncogenicity grading (OS3/OM3/OP3)** (beeaeee)
- **Cancerhotspots-grade recurrence counts for somatic oncogenicity grading (OS3/OM3/OP3)** (5d21fcf)
- **code-review: collateral-damage — isolate cancerhotspots mock tests from cache** (5f4c1f6)
- **code-review: validation-gap — require exact cancerhotspots amino-acid match** (60ff070)
- **code: implement cancerhotspots recurrence enrichment** (a27137d)
- **design: land spec tests for cancerhotspots recurrence counts** (86fb8d7)
- **Merge Refresh migrated architecture and operator contracts** (3d2f1fa)
- **verify: tighten architecture gate wording ratchet** (9fea820)
- **code: refresh architecture and operator contracts** (0b4dcbe)
- **design: land spec tests for 405-refresh-migrated-architecture-and-operator-contracts** (0a64cc0)
- **Merge Clarify remaining consumer correctness contracts** (57b6c95)
- **Clarify remaining consumer correctness contracts** (3b2af0b)
- **code-review: stale-doc — label gene search coordinates with GRCh38 context** (3093ebc)
- **code: implement remaining consumer correctness contracts** (619e24b)
- **design: land spec tests for 406-clarify-remaining-consumer-correctness-contracts** (703b087)
- **Merge Harden post-migration spec runner and CLI surface ratchets** (d976480)
- **verify: pin non-tty retry diagnostics without ansi** (607f2bd)
- **code-review: stale-doc — align missing-mustmatch diagnostic** (b91fa9a)
- **code: implement ticket 401 surface ratchets** (cdeab2d)
- **design: land spec tests for 401-harden-post-migration-spec-runner-and-cli-surface-ratchets** (c43d0d1)
- **Merge Bound remote waits and stabilize residual reliability flakes** (3544014)
- **code-review: weak-assertion — prove retry_send consumes bounded sleep budget** (0b8da0d)
- **code-review: collateral-damage — align semantic scholar docs contract** (ac17ca3)
- **code-review: error-classification — keep malformed retry-after on normal backoff** (c40dc60)
- **code: bound shared retry-after waits** (c2be72b)
- **design: land spec tests for 403-bound-remote-waits-and-stabilize-residual-reliability-flakes** (f04afd7)
- **Merge Complete article supplement retrieval and asset/fulltext contract** (e0023ea)
- **verify: repair live Figshare sibling matching** (6eb39a6)
- **code-review: stale-doc — update asset help and sanitize Figshare errors** (596b58f)
- **design: land spec tests for 409-retrieve-all-figshare-supplementary-records-for-a-paper** (43306b4)
- **Merge Make MCP skill allowlist positive and future-proof** (25a9023)
- **Make MCP skill allowlist positive and future-proof** (fe02279)
- **code-review: weak-assertion — pin update stanza and test command exits** (183d1ad)
- **code-review: validation-gap — harden Figshare file-id handling** (347658a)
- **Merge Raise the OLS4 discover client timeout (the one spike-021 transient fatal)** (1ac7186)
- **Raise the OLS4 discover client timeout (the one spike-021 transient fatal)** (7aa2ef5)
- **Merge Adopt mustmatch ellipsis and run-expect capabilities across biomcp specs for robust assertions** (2de5b02)
- **Adopt mustmatch ellipsis and run-expect capabilities across biomcp specs for robust assertions** (c4f91ed)
- **code-review: silently-relaxed — restore robust spec guarantees** (10d56ef)
- **code: adopt robust mustmatch spec assertions** (cba1ffd)
- **design: land failing contract for 396-adopt-mustmatch-ellipsis-and-run-expect-capabilities-across-biomcp-specs-for-robust-assertions** (65dab41)
- **Merge Migrate biomcp spec runner to the mustmatch binary and the spec/verify lane model** (e8c7f0f)
- **verify: repair mustmatch runner gate regressions** (01c32d8)
- **code-review: validation-gap — sync dev dependencies before markdown specs** (43bbc6c)
- **code: migrate biomcp specs to mustmatch binary runner** (44ffdd3)
- **design: land failing contract for 393-migrate-biomcp-spec-runner-to-the-mustmatch-binary-and-the-spec-verify-lane-model** (2ca8eac)
- **Merge Bring biomcp to the engineering standard (AGENTS.md, make test, drop make check, skills, gitignore)** (d97a0d9)
- **code-review: over-edit — remove duplicate test lane and unused demo constant** (cfb05bc)
- **code: bring biomcp to engineering standard** (cfbdc8a)
- **design: land failing contract for 392-bring-biomcp-to-the-engineering-standard** (2dc5e30)
- **Merge Make routine make spec fully offline; move all live-upstream specs to make verify** (2dd8499)
- **Make routine make spec fully offline; move all live-upstream specs to make verify** (5d0a420)
- **Merge Pin mustmatch to the pytest-plugin release before the binary-only cutover** (123a359)
- **Pin mustmatch to the pytest-plugin release before the binary-only cutover** (e9a8eed)
- **Merge Article assets manifest and canonical OA-package fetch (bytes not parsing)** (bf4817a)
- **Article assets manifest and canonical OA-package fetch (bytes not parsing)** (81b6497)
- **code-review: validation-gap — harden article asset validation and archive paths** (f15f412)
- **Article assets manifest and canonical OA-package fetch** (6c314fc)
- **design: land failing contract for article-assets-manifest-and-canonical-oa-package-fetch-bytes-not-parsing** (447fbbb)
- **Merge Cover figures, supplements, and complex tables in JATS-to-Markdown converter** (db7d03c)
- **Cover figures, supplements, and complex tables in JATS-to-Markdown converter** (487d79a)
- **design: land failing contract for 385-cover-figures-supplements-and-complex-tables** (9c04de0)
- **Merge Quarantine live pathway spec out of routine make spec** (ed8944c)
- **Quarantine live pathway spec out of routine make spec** (316fb77)
- **Merge Collect article fulltext miss fixtures for BioC renderer gate** (1797a1d)
- **Collect article fulltext miss fixtures for BioC renderer gate** (ad1aa27)
- **Document BioC miss collector optimization** (3b57801)
- **Increase BioC miss case worker concurrency** (6083091)
- **Fetch BioC miss search families concurrently** (9339d68)
- **Measure BioC miss cases concurrently** (1f2b19f)
- **Optimize BioC miss collector per-case source fetches** (734e21d)
- **spike: collect BioC miss candidate evidence** (e589b8b)
- **code-review: stale-doc — thread PMC OA provenance fields** (54e6cbe)
- **Merge Spike source-first article Markdown coverage** (ff3fe96)
- **Preserve tracked validation profile during article Markdown spike** (1de83bd)
- **Spike source-first article Markdown coverage** (d34539b)
- **Document source coverage optimization** (961781f)
- **Inline source coverage license extraction** (a5f2dbb)
- **Inline source coverage quality extraction** (0ad5c83)
- **Optimize source coverage count extraction** (3d90d04)
- **Document article source coverage spike decision** (ff7f9d8)
- **Merge Prune brittle live assertions after request contracts land** (8d1a4b7)
- **Prune brittle live assertions after request contracts land** (df9bf99)
- **design: land failing assertions for 379-prune-brittle-live-assertions-after-request-contracts-land** (974e8b6)
- **Merge Split routine validation from release live smoke** (293fbd2)
- **verify: align validation target docs** (a77618f)
- **code-review: silently-relaxed — restore release-gate timing assertion** (f75e101)
- **code: split routine validation from release live smoke** (4a580b6)
- **design: land failing assertions for split-routine-validation-from-release-live-smoke** (8e8a0f0)
- **verify: relax disease provenance assertion** (ab865cb)
- **code-review: trivia-assertion — relax article status-note contract** (a824461)
- **Merge Convert article and variant source specs to fixture contracts** (2f1df4c)
- **Convert article and variant source specs to fixture contracts** (5b321a3)
- **code-review: weak-assertion — replace ticket marker tautologies with behavior** (9a3ce77)
- **code-review: error-classification — keep normalization plan paths endpoint-relative** (14a9919)
- **design: land failing assertions for 376-convert-article-and-variant-source-specs-to-fixture-contracts** (2a94142)
- **Merge Quarantine drug research-code bridge spec** (497eaa6)
- **Quarantine drug research-code bridge spec** (6292d84)
- **Merge Quarantine ambiguous drug research-code fallback spec** (04d2bfa)

### Docs
- **docs: record BioC renderer gate decision** (0984796)

### Chore
- **build: complete article supplement asset retrieval** (abef3ae)
- **chore: normalize BioC candidate matrix output** (547ee98)
- **chore: stop tracking march artifacts** (c06d1b5)
- **build: add article fulltext manifest implementation** (466f685)

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