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Commits on Jul 22, 2026

• Consolidate test-harness rounds 72-80 (8 PRs): error-path, cross-tool-consistency, and schema-conformance findings (#376)

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Commits on Jul 20, 2026

• Land rounds 42-45 + PR #339 review fixes into main

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• Consolidate test-harness rounds 1-41 (13 PRs) into one (#339)

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Commits on Jul 17, 2026

• Fix: correct return_schema envelope mismatch for 9 tools (#246) (#287)

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Commits on Jul 16, 2026

• Fix: document ArXiv_search_papers AND-query and date-filter semantics (#286)

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Commits on Jul 7, 2026

• Fix: give actionable guidance for USPTO auth (401/403) and no-record (404) responses (#281)

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• Extend DNA_virtual_digest to resolve uncommon restriction enzymes (#280)

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Commits on Jul 2, 2026

• Release tooluniverse 1.3.1: OpenTargets migration follow-through + full-registry drift fixes (#268)

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Commits on Jun 30, 2026

• Fix #264: adapt OpenTargets tools to EFO→MONDO migration + harden GraphQL not-found handling (#266)

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• Add Enformer, Borzoi, scVI, LDSC as remote ML tools (#261)

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• Fix DisGeNET tools to use the DisGeNET v1 summary API (#265)

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Commits on Jun 6, 2026

• Fix Rounds 010-018: tool/skill robustness, GraphQL drift, ProtVar/Dfam APIs, +3 new tools (#245)

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Commits on Jun 2, 2026

• Round 006: tu run shows the real error instead of "unknown error" (#210)

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Commits on May 25, 2026

• feat: ESM-C SAE variant interpretation + DMS analysis suite (#192)

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Commits on May 14, 2026

• Fix triaged ToolUniverse regressions

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Commits on May 13, 2026

• Merge pull request #179 from mims-harvard/fix/disgenet-empty-result-diagnostics

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Commits on May 10, 2026

• fix: align BioModels non-JSON diagnostics

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• fix: add BioModels non-JSON diagnostics

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• test: preserve environment in DisGeNET key check

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• fix: add DisGeNET empty-result diagnostics

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Commits on May 3, 2026

• fix: add compact UniProt entry output

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Commits on Mar 29, 2026

• feat: add reasoning frameworks, data wrangling, and 31 new tools (#153)

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Commits on Mar 25, 2026

• fix: resolve round-81 feedback bugs across 6 tools (#140)

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Commits on Mar 17, 2026

• fix: CryoET and ESM tools validated per devtu-fix-tool guidelines

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• Add pytest test suites for CryoET and ESM tools

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Commits on Mar 14, 2026

• fix: resolve formatwarning Python 3.12 signature, MyDisease HPO list … (#132)

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Commits on Mar 9, 2026

• fix: Round 79 tool fixes - ChEMBL lookup, STITCH SSL, HMDB names, MW guidance, PDB metadata (#127)

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Commits on Mar 8, 2026

• fix: researcher simulation bugs across 14 tools + response truncation (#126)

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Commits on Mar 6, 2026

• fix: tool discoverability, ChEMBL/Orphanet/EuropePMC bug fixes (#125)

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• fix: paper search tool improvements (Round 80) (#123)

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Commits on Mar 5, 2026

• Fix/round 79 literature feature improvments (#124)

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• fix: literature tool improvements (Round 79) (#121)

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• feat: suppress API key warnings by default, add --verbose flag, rename BUG- to Feature- across codebase (#119)

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Commits on Mar 4, 2026

• fix: consolidated bug fixes rounds 67-78 (#116)

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Commits on Mar 3, 2026

• Fix Round 54 bugs: AR gene_symbol, expression units, CIViC therapy, GtoPdb multi-word (#95)

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