docs: add documentation comments to JSON schema types#1756
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ivan-aksamentov wants to merge 17 commits intomasterfrom
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docs: add documentation comments to JSON schema types#1756ivan-aksamentov wants to merge 17 commits intomasterfrom
ivan-aksamentov wants to merge 17 commits intomasterfrom
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…esultsJson, NextcladeErrorOutputs - Add field-level doc comments to all ~40 NextcladeOutputs fields, PeptideWarning, PhenotypeValue - Add field-level doc comments to ResultsJson fields - Add struct and field doc comments to NextcladeErrorOutputs - Regenerate JSON/YAML schema files with new description fields
- QcStatus, QcResult, QcResultMissingData, QcResultMixedSites - QcResultPrivateMutations, QcResultSnpClusters, ClusteredSnp - QcResultFrameShifts, QcResultStopCodons
- Fix `//` to `///` on QcRulesConfigMixedSites so description propagates to schema - Add field-level doc comments to all QC config structs: QcRulesConfigMissingData, QcRulesConfigMixedSites, QcRulesConfigPrivateMutations, QcRulesConfigSnpClusters, QcRulesConfigFrameShifts, QcRulesConfigStopCodons, FrameShiftLocation, StopCodonLocation, QcConfig
geneName was renamed to cdsName in the v2-to-v3 migration.
- Add aaMutLabelMap example to mutLabels JSON snippet - Fix pathogenJson -> pathogen.json typo
- Clarify files field is required for datasets, not by schema - Add includeNearestNodeInfo to generalParams - Add deletion weight fields to privateMutations example - Document alignmentPreset field and fix missing closing parenthesis
- Change qry and node from "object" to "array of objects" per schema - Add [] notation to sub-field paths for consistency - Document qry[].name field
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Add comprehensive doc comments to Rust structs used for JSON schema generation, improving documentation quality for pathogen.json configuration, dataset index structures, QC rules, output formats, and Auspice tree extensions. The doc comments propagate to generated JSON/YAML schema files via schemars, making schemas self-documenting for dataset authors and API consumers.