API reference

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Create, inspect, read, and validate Salmon Data Packages.

create_sdp	Create a review-ready Salmon Data Package in one call.
infer_salmon_datapackage_artifacts	Infer the in-memory artifacts needed to write a Salmon Data Package.
read_salmon_datapackage	Read a Salmon Data Package from canonical CSV metadata when available.
validate_salmon_datapackage	Validate package structure, ID alignment, and semantic review state.

Write a package from metadata tables that have already been assembled.

Write the canonical Salmon Data Package layout.

Infer, validate, apply, and inspect SDP data dictionaries.

infer_dictionary	Build a starter dictionary DataFrame aligned with the SDP schema.
validate_dictionary	Validate dictionary structure and value constraints.
apply_salmon_dictionary	Rename columns, coerce types, and apply codes using a validated dictionary.
apply_semantic_suggestions	Apply selected column-level semantic suggestions to a dictionary.
infer_column_role	Infer `column_role` from a column’s name and contents.
infer_value_type	Infer a value_type for a column.

Search vocabularies, rank candidates, and review semantic decompositions.

suggest_semantics	Suggest semantic annotations for SDP metadata targets.
chat_decomposition	Start or resume an explicit measurement-variable decomposition review.
find_terms	Find ontology terms across OLS, NVS, and other vocab sources.
sources_for_role	Return the ordered default retrieval sources for a semantic role.
benchmark_term_ranking_fixtures	Evaluate deterministic term ranking against versioned fixtures.
deduplicate_proposed_terms	Apply I-ADOPT compositional deduplication to a gpt_proposed_terms dataframe.

Fetch ontology sources and report semantic coverage.

fetch_salmon_ontology	Fetch the DFO Salmon Ontology with HTTP caching.
validate_semantics	Validate semantics with graceful gap reporting.
suggest_facet_schemes	Analyze proposed terms and suggest facet schemes instead of proliferating individual terms.

Detect ontology gaps and draft curator-reviewed requests.

detect_semantic_term_gaps	Detect structured ontology gaps from candidate and final LLM evidence.
render_ontology_term_request	Render curator-reviewed ontology term request drafts.
submit_term_request_issues	Preview or explicitly submit rendered ontology request issues.

Crosswalk legacy NuSEDS method labels to canonical method families.

nuseds_enumeration_method_crosswalk	Return the curated NuSEDS enumeration-method crosswalk.
nuseds_estimate_method_crosswalk	Return the curated NuSEDS estimate-method crosswalk.

Suggest and assemble Darwin Core Data Package exports.

suggest_dwc_mappings	Suggest DwC-DP table/field mappings for dictionary columns.
dwc_dp_build_descriptor	Build, optionally write, and optionally validate a DwC-DP descriptor.

Build HNAP-aware EDH metadata exports.

edh_build_hnap_xml	Build the supported DFO EDH HNAP metadata export.
edh_build_iso19139_xml	Build DFO HNAP or generic ISO 19139 XML from dataset metadata.
write_edh_xml_from_sdp	Rebuild HNAP XML from reviewed package metadata.

Read CSV resources from public and private GitHub repositories.

ms_setup_github	Verify GitHub token discovery for private-repository CSV access.
github_raw_url	Build a stable raw.githubusercontent.com URL for a GitHub repository.
read_github_csv	Read a CSV from a GitHub repository.
read_github_csv_dir	Read all CSV files from a GitHub directory.

Browse and search ICES reference codes.

ices_code_types	List ICES controlled vocabulary code types.
ices_codes	List ICES codes for a given code type.
ices_find_code_types	Find ICES code types by simple substring match on key/description.
ices_find_codes	Find ICES codes within a code type by simple substring match on key/description.

Legacy aliases retained for existing callers.

create_salmon_datapackage	Compatibility alias for :func:`write_salmon_datapackage`.
create_salmon_datapackage_from_data	Deprecated one-shot wrapper with its legacy call contract preserved.

Check explicitly for a newer release.

Check the latest GitHub release only when explicitly called.