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faba mcp on legume-mcp 0.3.1: producers in the background; README for any client (0.18.1) - #36

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legume-mcp-0.3
Oct 20, 2026
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YPARK merged 2 commits into
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legume-mcp-0.3

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@YPARK YPARK commented Oct 20, 2026 •

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What

You asked that long runs go to the background and that every tool's MCP server move to legume-mcp 0.3.

  • legume-mcp 0.3.1 (from 0.1). 0.3.1 quotes a failed child's error rather than its backtrace, even with RUST_BACKTRACE set, which turned main's CI red. The agent now also gets the built-in job_status, job_wait and job_cancel.
  • background on the producers: count, depth, atoi, dartseq, apa, snp, run, qc and cluster take background: true. The call then returns {job, written, note} at once, and the agent follows the job. It is recorded (runall.sh, INDEX.tsv) when it succeeds, and a person following the server sees it as its own call and can stop it. faba's instructions mention it in one line.
  • The README's agent section covers:
    • connecting any MCP client: generic mcpServers (Claude Desktop, Cursor, Gemini CLI), Claude Code, VS Code and Codex CLI, and why to set LEGUME_MCP_PROJECT;
    • the server's own instructions for clients that don't pass them on, kept identical to the server's text by a test;
    • a tool table, background runs, and records and watching. Noble 2009 is cited.
  • Version 0.18.1: a patch. background is a tool argument only an agent uses; no library API, CLI flag or subcommand changed.

Tests

  • tests/mcp_server.rs checks:
    • the producers advertise background, and the job_* tools are listed;
    • a count with background: true returns a job at once, and job_wait reports it failed, naming the missing BAM;
    • the README carries faba's own instructions.
  • The full suite passes.

YPARK added 2 commits October 20, 2026 14:37
…or any MCP client

The user asked that long runs go to the background and that every tool's
MCP server move to legume-mcp 0.3. count, depth, atoi, dartseq, apa, snp,
run, qc and cluster take `background`: the call returns a job id at once,
followed with job_status / job_wait / job_cancel, and the step is recorded
when it succeeds. The README's agent section now covers any MCP client
(generic mcpServers, Claude Code, VS Code, Codex; LEGUME_MCP_PROJECT), the
server's own instructions for clients that do not pass them on (kept in
step by a test), background runs, records and watching. Version 0.19.0.
@YPARK YPARK changed the title faba mcp on legume-mcp 0.3: producers in the background; README for any client (0.19.0) faba mcp on legume-mcp 0.3.1: producers in the background; README for any client (0.18.1) Oct 20, 2026
@YPARK
YPARK merged commit ba85648 into main Oct 20, 2026
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@YPARK
YPARK deleted the legume-mcp-0.3 branch October 20, 2026 22:22
YPARK added a commit that referenced this pull request Oct 20, 2026
YPARK added a commit that referenced this pull request Oct 20, 2026
faba mcp on legume-mcp 0.3.1: producers in the background; README for any client (0.18.1)
YPARK added a commit that referenced this pull request Oct 20, 2026
YPARK added a commit that referenced this pull request Oct 20, 2026
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