Frequently asked questions
Does passing a context file call an LLM?
No. LLM review runs only when llm_assess=True. Context supplied while review is disabled produces a warning and is ignored.
Can I pass a pandas DataFrame to llm_context_files?
No. Pass local file paths. Use llm_context_text for inline text. Parsed pandas, XML, or document objects are rejected early.
What does sources=["smn"] mean?
It is a strict allowlist. Initial search and retry search may use only SMN. Omitting sources uses role-aware defaults instead.
Are semantic suggestions written into the dictionary automatically?
The package workflow may prefill them, and it marks everything it prefills with REVIEW:. Variable, property, entity and unit IRIs are prefilled whenever a compatible candidate is found. Constraint and statistical modifier are held back unless the column’s own name, label or description carries the evidence for them — a mean_wild_spawner_count column earns both, a bare count column earns neither — and under LLM review (llm_assess=True) they are never prefilled at all. Strict validation fails until review is complete.
(sdp-0.3.0 removed the dictionary method slot, so there is nothing to prefill there. This answer said “method and constraint fields are never automatically applied” until 2026-08-24; it was true of this package and false of metasalmon, and hub Q16 ruled that metasalmon was right.)
Will overwrite=True delete any directory?
No. metasalmonpy replaces only directories it recognizes as metasalmonpy or SDP package directories. It refuses to delete an unrelated non-empty directory.
You do not need overwrite=True for an existing directory that is empty — there is nothing there to destroy. “Empty” is literal: a dot-file, a stale ownership sentinel, or an empty data/ subdirectory all count as content and still require overwrite=True, and emptiness is never recursive.
Does term-gap detection submit GitHub issues?
No. Detection and rendering are local. Live submission requires dry_run=False, confirm=True, credentials, and confirmation for every issue.
Is metasalmonpy published on PyPI?
Not currently. Install the released version from its GitHub tag. GitHub release artifacts include the source distribution and wheel.
Do routine tests spend provider credits?
No. Unit tests and CI blank provider credentials and use injected deterministic responses. Live-provider evaluation is an explicit maintainer activity.