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v0.4.1: get-sequence expand/region fixes, mcp-ts-core 0.10.14

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@cyanheads cyanheads released this 09 Jul 21:01
v0.4.1
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cyanheads Casey Hand
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cyanheads Casey Hand
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get-sequence expand/region fixes, mcp-ts-core 0.10.14

ensembl_get_sequence stable-ID lookups now forward expansion params,
and region mode accepts a bare chr:start-end id. Framework maintenance
adds a Bun supply-chain guard and Dockerfile hardening.

Added:

  • ensembl_get_sequence accepts id as a bare chr:start-end region when
    species is set, alongside the existing species:chr:start-end form.
    A bare region without species throws the new missing_species
    ValidationError. (#14)

Fixed:

  • ensembl_get_sequence stable-ID genomic lookups now forward
    expand_5prime/expand_3prime to Ensembl, gated to type=genomic. (#13)

Changed:

  • bunfig.toml supply-chain guard: install.minimumReleaseAge (3 days,
    @cyanheads/mcp-ts-core excluded) and
    install.security.scanner = "@socketsecurity/bun-security-scanner"
  • Dockerfile pins oven/bun:1.3.14, adds BuildKit cache mounts to both
    install stages, and runs the build-stage install with
    --ignore-scripts
  • .github/SECURITY.md and .gitattributes added; LICENSE copyright
    year 2025 -> 2026
  • 12 skills re-synced to the framework ^0.10.14 set

Dependency bumps:

  • @cyanheads/mcp-ts-core ^0.10.10 -> ^0.10.14
  • tsc-alias ^1.8.17 -> ^1.9.0
  • vitest ^4.1.9 -> ^4.1.10
  • @socketsecurity/bun-security-scanner ^1.1.2 added

118 tests pass; bun run devcheck clean.

CHANGELOG v0.4.1

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