_pkgdown.yml

url: https://salmon-data-mobilization.github.io/metasalmon/

template:
  bootstrap: 5
  bslib:
    primary: "#0d7377"

home:
  title: "metasalmon: Salmon Data Package Utilities"
  description: |
    Create portable, ontology-aware Salmon Data Packages from your analysis-ready
    tables. Link your data to the DFO Salmon Ontology with semantic fields (IRIs,
    concept schemes) while preserving your original data structure.

  sidebar:
    structure: [license, community, citation, authors, dev]
    components:
      citation:
        title: Citation
        text: |
          If you use metasalmon in your research, please cite it.
      license:
        title: License
        text: |
          MIT + file LICENSE
      community:
        title: Community
        text: |
          - [Report a bug](https://github.com/salmon-data-mobilization/metasalmon/issues)
          - [Request a feature](https://github.com/salmon-data-mobilization/metasalmon/issues)
      dev:
        title: Development
        text: |
          This package is under active development.

reference:
  - title: "Start Here"
    desc: "One-shot package creation from raw tables"
    contents:
      - metasalmon
      - metasalmon_configuration
      - create_sdp
      - infer_salmon_datapackage_artifacts
      - read_salmon_datapackage
      - validate_salmon_datapackage

  - title: "Advanced Package Assembly"
    desc: "Manual writing when you already have the SDP metadata tables assembled"
    contents:
      - write_salmon_datapackage

  - title: "Dictionary Functions"
    desc: "Infer, validate, and apply semantic data dictionaries"
    contents:
      - infer_dictionary
      - validate_dictionary
      - apply_salmon_dictionary
      - apply_semantic_suggestions

  - title: "Review and Edit (in R)"
    desc: "Review the seeded IRIs in the console, decide them in a script, fill in the remaining metadata, and write it all back — no spreadsheet required"
    contents:
      - review_semantics
      - accept_suggestion
      - apply_sdp_semantics
      - review_metadata
      - set_sdp_dataset
      - semantic_suggestions
      - semantic_llm_assessments

  - title: "Harness Review (packet and ingest)"
    desc: "Model judgement runs outside the package: write a review packet, have your harness judge it, and read the assessments back"
    contents:
      - write_semantic_review_packet
      - ingest_semantic_assessments

  - title: "Semantic Helpers"
    desc: "Semantic suggestion, vocabulary search, and ranking benchmark capabilities"
    contents:
      - suggest_semantics
      - chat_decomposition
      - find_terms
      - sources_for_role
      - benchmark_term_ranking_fixtures
      - deduplicate_proposed_terms

  - title: "Ontology + Validation"
    desc: "Fetch the ontology and validate semantic coverage"
    contents:
      - fetch_salmon_ontology
      - validate_semantics
      - suggest_facet_schemes

  - title: "Term Request Workflow"
    desc: "Detect missing terms, route SMN, GCDFO, profile, or uncertain requests, and draft curator-reviewed GitHub issues"
    contents:
      - detect_semantic_term_gaps
      - render_ontology_term_request
      - submit_term_request_issues

  - title: "NuSEDS Helpers"
    desc: "Crosswalk legacy NuSEDS method labels to canonical method families"
    contents:
      - nuseds_enumeration_method_crosswalk
      - nuseds_estimate_method_crosswalk
      - nuseds_estimate_classification_crosswalk

  - title: "Darwin Core (DwC-DP)"
    desc: "Darwin Core Data Package mapping and export helpers"
    contents:
      - suggest_dwc_mappings
      - dwc_dp_build_descriptor

  - title: "Enterprise Data Hub (EDH)"
    desc: "HNAP-aware EDH XML export helpers for Enterprise Data Hub workflows"
    contents:
      - edh_build_hnap_xml
      - edh_build_iso19139_xml
      - write_edh_xml_from_sdp

  - title: "Semantic Review Supplements"
    desc: "Validated SSSOM concept alignments and ordered measurement decompositions"
    contents:
      - read_sssom_mapping_set
      - write_sdp_sssom
      - validate_sdp_sssom
      - read_sdp_measurement_decompositions
      - write_sdp_measurement_decompositions
      - validate_sdp_measurement_decompositions

  - title: "Extended SDP Structure and Reproducibility"
    desc: "SOSA procedures, measure-specific observation structures, and closed reproducibility sidecars"
    contents:
      - migrate_sdp_methods
      - read_sdp_observation_structures
      - write_sdp_observation_structures
      - validate_sdp_observation_structures
      - extract_sdp_observations
      - read_sdp_reproducibility_manifest
      - write_sdp_reproducibility_manifest
      - validate_sdp_reproducibility_manifest

  - title: "EML and KNB"
    desc: "Reviewed EML 2.2.0 export and verified DataONE/KNB publication, starting from the semantic closure both require"
    contents:
      - write_sdp_semantic_closure
      - write_eml_from_sdp
      - publish_sdp_to_knb

  - title: "GitHub Access"
    desc: "Authenticate once and read CSVs from private GitHub repositories"
    contents:
      - ms_setup_github
      - github_raw_url
      - read_github_csv
      - read_github_csv_dir

  - title: "ICES Vocabulary"
    desc: "Access ICES reference codes and vocabulary"
    contents:
      - ices_vocab
      - ices_code_types
      - ices_codes
      - ices_find_code_types
      - ices_find_codes

  - title: "Maintenance"
    desc: "Version and update helpers"
    contents:
      - check_for_updates

articles:
  - title: "Getting Started"
    navbar: ~
    contents:
      - setup
      - metasalmon
      - llm-context-review

  - title: "Guides"
    navbar: ~
    desc: "Step-by-step guides for common workflows"
    contents:
      - tidy-data-for-sdp
      - semantic-review
      - post-review-package-publication
      - data-dictionary-publication
      - reusing-standards-salmon-data-terms
      - github-csv-access

  - title: "Migration"
    navbar: ~
    desc: "Moving an existing package to a newer specification version"
    contents:
      - migrating-to-sdp-0-3-0

  - title: "Reference"
    navbar: ~
    desc: "Glossary definitions and frequently asked questions"
    contents:
      - glossary
      - faq

navbar:
  structure:
    left: [intro, reference, articles, news]
    right: [search, github]

footer:
  structure:
    right: [built_with]
    left: [developed_by]