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feat: agent CLI contract, JSON errors, and describe/doctor - #4
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Give agents a single, fail-closed way to operate LamellarSAXS2D: `bsaxs` with no subcommand prints a JSON catalog, `bsaxs doctor` matches bsaxs-doctor, inspect/analyze/batch carry schema and operator guidance, and failures emit a JSON envelope on stdout while keeping the human stderr line. Scientific imports are lazy so describe/doctor/help do not need NumPy. PipelineError lives in a stdlib module. Version 0.4.1. Co-authored-by: Alen <dlgong17s@imr.ac.cn>
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LamellarSAXS2D is now safer for an agent (or any non-interactive operator) to drive without guessing CLI shape or treating solver success as science.
What changed
bsaxs describe(also the default for a barebsaxs) prints a machine-readable catalog: commands, exit codes0/1/2, recommended Identify→Evaluate flags, and invariants (success=Trueis not acceptance; pixel-q is not a period; no overwrite without--force).bsaxs doctoris the same asbsaxs-doctor. Doctor JSON now includes the package version.lamellarsaxs2d.cli_error.v1) on stdout for usage/input/config failures; the human错误：line stays on stderr so existing tests and operators still work.schema_version,tool, and anagentobject with next steps. They do not claimlamellarsaxs2d.result.v1(that remains preflight-only).cli.pyso--help,describe, anddoctordo not need NumPy.PipelineErrormoved tobutterfly_saxs.errors.Verification
ruff check src tests scriptsbsaxs describe,bsaxs doctor --json,bsaxs inspectmissing-input JSON errorScientific analysis behavior is unchanged: default ridge method remains
radial_peak; the catalog recommendsbutterfly_curvatureinstead of silently changing the measurement.