Release v1.3.0

What's Changed

• Fix unauthenticated RCE in python_code_executor and harden server exposure by @gasvn in #251
• Discovery batch: PheWAS + MSA/phylogeny + clinical calculators + 10 keyless resource tools + product-safety skill by @gasvn in #248
• Add peptide target deorphanization skill + ProteomicsDB meltome & ClusPro tools by @gasvn in #254
• Add 18 keyless peptide-resource database tools (AMP / therapeutic / venom / immunopeptidomics) by @gasvn in #255
• Fix coding-API stub generator: nullable types and injected-param collisions by @gasvn in #256
• Add Codex plugin packaging for ToolUniverse by @gasvn in #249
• Release tooluniverse 1.3.0 (PyPI) by @gasvn in #257

Full Changelog: v1.2.6...v1.3.0

Release v1.2.6

What's Changed

• Discovery batch: 5 resource tools + 8 analysis skills by @gasvn in #242
• Add PGS Catalog tools (published polygenic scores, EMBL-EBI) by @gasvn in #243
• Fix Round 009: openFDA adverse-event tools silently empty on unknown param by @gasvn in #244
• Fix Rounds 010-018: tool/skill robustness, GraphQL drift, ProtVar/Dfam APIs, +3 new tools by @gasvn in #245

Full Changelog: v1.2.5...v1.2.6

Release v1.2.4

What's Changed

• Sync MCPB bundle version to 1.2.3 + guard against drift by @gasvn in #212
• ci: weekly tool health-check (live-API canary) by @gasvn in #214
• fix: retire OxO tools (EBI deprecated the Ontology Xref Service) by @gasvn in #215
• Fix and expand literature-search skills: adaptive multi-source coverage by @gasvn in #216
• fix: cap honoured Retry-After in request_with_retry (prevent retry-hang) by @gasvn in #217
• ci: weekly health-check highlights NEW failures vs a known-failing baseline by @gasvn in #218
• fix: tool issues surfaced by the weekly sweep (schemas + ImmPort + DynaMut2) by @gasvn in #219
• Add Mendelian randomization skill + harden EpiGraphDB MR/genetic-cor tools by @gasvn in #213
• Round 007: proteins_api_search auto-widens to non-human organisms by @gasvn in #222
• Round 008: PubChem xref_types validation + revive MetaCyc via BioCyc auth by @gasvn in #223
• Fix release-plugin.sh: drift-resilient versioning + tolerate absent manifests by @gasvn in #224
• statistical-modeling skill: report spline peak in fitted x-variable units by @gasvn in #221
• Release v1.2.4 (unified: pip + MCP registry + plugin) by @gasvn in #220

Full Changelog: v1.2.3...v1.2.4

Release v1.2.3

What's Changed

• Round 002: wire NCBI_API_KEY + retry-with-backoff for GEO/E-utilities by @gasvn in #202
• Round 003: fix chembl_search_activities target_chembl_id nullability by @gasvn in #203
• fix: build filter.advanced clause for filter_study_type by @mvanhorn in #195
• Round 004: null-safe PyPI project_urls + fix skopt/pyrosetta package names by @gasvn in #205
• fix(plugin): correct install skill — skill count, .mcp.json args, version pin by @gasvn in #206
• Fix #201: MCPB manifest server.type + bundle import crash by @gasvn in #207
• Round 005: markitdown response shape + swissadme 'n/d' widening by @gasvn in #208
• docs: redirect /tutorials/ → /guide/ for paper-cited URLs by @gasvn in #209
• docs: expand redirect map (15 more paper-cited legacy paths) by @gasvn in #211
• Round 006: tu run shows the real error instead of "unknown error" by @gasvn in #210

New Contributors

• @mvanhorn made their first contribution in #195

Full Changelog: v1.2.2...v1.2.3

Release v1.2.2

What's Changed

• feat: ESM-C SAE variant interpretation + DMS analysis suite by @gasvn in #192
• fix: 16 skills with broken/stale tool references by @gasvn in #193
• Fix: sync SAE/DMS skills to source /skills/ directory by @gasvn in #200
• Add /tooluniverse:setup-keys command for API key configuration by @gasvn in #194
• Fix Round 001: ~250 tool fixes — validator, 8 upstream-API rescues, 200+ schema regenerations by @gasvn in #198

Full Changelog: v1.2.1...v1.2.2

Release v1.2.1

What's Changed

• docs: refresh contributing guide by @SufianTA in #169
• fix: avoid unicode logging errors on non-UTF streams by @SufianTA in #170
• fix: add CTD non-JSON response diagnostics by @SufianTA in #171
• fix: add compact UniProt entry output by @SufianTA in #172
• docs: expand Codex CLI MCP setup by @SufianTA in #173
• fix: add BioModels non-JSON diagnostics by @SufianTA in #180
• fix: add DisGeNET empty-result diagnostics by @SufianTA in #179
• docs: clarify MCPB client scope by @SufianTA in #178
• docs: add OpenCode manual MCP setup by @SufianTA in #177
• fix: stabilize task manager listing by @SufianTA in #176
• Fix triaged ToolUniverse regressions by @SufianTA in #181
• Claude Code plugin: self-contained layout, skill-based routing, ML demo readiness by @gasvn in #161
• Fix: drop deprecated google-generativeai, loosen setuptools cap by @gasvn in #190
• Release 1.2.1 + fix self-healing PyPI publish workflow gate by @gasvn in #191

Full Changelog: v1.1.11...v1.2.1

Release v1.1.11

What's Changed

• Fix/round 155 gaps by @gasvn in #153

Full Changelog: v1.1.10...v1.1.11

Release v1.1.10

What's Changed

• feat: 8 new tools, 4 new skills, 100-skill audit, reasoning frameworks by @gasvn in #151

Full Changelog: v1.1.9...v1.1.10

Release v1.1.9

What's Changed

• fix: skill usefulness audit — reasoning frameworks, computational procedures, 166 tool ref fixes by @gasvn in #150

Full Changelog: v1.1.8...v1.1.9

Release v1.1.8

What's Changed

• fix: Round 134 tool and skill fixes by @gasvn in #149

Full Changelog: v1.1.7...v1.1.8