Release v1.4.1

What's Changed

• Fix: post-1.4.0 bug-hunt + onboarding-experience gaps (consolidates #391 + #392) by @gasvn in #393
• Upgrade to FastMCP 3 and restore CI by @gasvn in #405
• Fix: consolidated post-1.4.0 bug-hunt fixes (consolidates #395–#398) by @gasvn in #399
• Fix 11 tools returning confidently wrong answers instead of failing (bug-hunt round 6) by @gasvn in #400
• Fix deterministic AgenticTool temperature defaults by @gasvn in #403
• fix(profile): copy schema defaults so configs do not share mutable state by @eeshsaxena in #381
• Route mcp_client_tool diagnostics to the logger instead of stdout (stdio safety) by @boldakov in #401
• Add gene liability evaluation skill by @gasvn in #404
• Add a safe opt-in Parallel web search backend by @gasvn in #408
• Update Gemini default to 3.6 Flash by @gasvn in #407
• fix: honor return_json in Gemini client instead of hard-raising by @mvanhorn in #273
• Keep MCP auto-loader output off stdio stdout by @gasvn in #406
• Support return_json environment override by @gasvn in #410
• Validate LLM temperature environment values by @gasvn in #415
• Migrate NCBI Datasets tools to active endpoints by @gasvn in #414
• Add hardened OpenAI-compatible agentic provider by @gasvn in #411
• Add OpenAI-compatible provider for agentic tools by @SufianTA in #184
• Consolidated fixes: return_schema envelope bug (~485 tools), 5 code-level bugs, 4 independently-discovered tool bugs by @gasvn in #463
• Fix self-review intent routing and opt-in scoring by @gasvn in #446
• Fix Python executor sandbox regressions by @gasvn in #439
• Consolidated Rounds 3-4: GDC/ClinicalTrials/cBioPortal/PharmGKB + GWAS/IntAct/OmniPath fixes by @gasvn in #472
• Tool and skill fixes found by running ToolUniverse against biomedical benchmarks by @gasvn in #473
• GWAS sort-default test fix + Round 5: RENCI Automat migration, NHANES/LipidMaps/MetabolomicsWorkbench fixes by @gasvn in #476
• Fix Round 6: CellMarker/Enrichr/HPA/ENCODE/openFDA/DrugBank data-quality issues by @gasvn in #477
• Consolidate test-harness fixes: rounds 7-19 (13 PRs, 16 commits) by @gasvn in #492
• More benchmark-driven fixes: RegulomeDB, SCREEN, STRING, ClinVar, ReMap, FAERS + skill guidance by @gasvn in #478
• Consolidate test-harness fixes: rounds 20-25 (6 PRs, 12 commits) by @gasvn in #499
• Consolidate test-harness fixes: rounds 26-32 (7 PRs, 38 commits) by @gasvn in #507
• Fix FAISS and PyTorch import-order crash by @gasvn in #511
• Fix Round 33: tools that answered without the data they were asked for by @gasvn in #508
• Fix the fitz dependency: CI is blocked repo-wide, and the declared package was never PyMuPDF by @gasvn in #516

New Contributors

• @eeshsaxena made their first contribution in #381
• @boldakov made their first contribution in #401

Full Changelog: v1.4.0...v1.4.1