feat: flatten config examples into a single-level shape - #944
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- Shared arg groups (alignment, model, metadata id, output, ...) serialized under a wrapper key that repeated the field name (alignment.alignment, model_args.model, metadata_id.metadata_id_columns), so a config file read worse than the CLI it mirrors and diverged from the "every key has a matching flag" contract - Flattening the leaf wrapper fields on each command's serde-facing raw type makes config keys one-to-one with CLI flags; schemars inlines them into one flat schema with additionalProperties:false, so strict unknown-key rejection is preserved and validated before deserialization
- Rewrite every example to the flat config shape so each file reads like the CLI it mirrors, and drop redundant default keys - Add faithful full builds on the largest datasets (mpox clade IIb 1000, SARS-CoV-2 2844, influenza H3N2 500) alongside the existing Ebola build, with shared clock constants defined once in typed vars - Correct overstated framing: the mpox example now runs the actual optimize/ancestral/timetree chain from the nextstrain/mpox WIP/new_tt workflow rather than a generic two-step stand-in
ivan-aksamentov
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Depends on: refactor: validate required command arguments before running #943
Mark shared leaf arg groups
#[serde(flatten)]on each command's*Rawtype so config keys match CLI flags [src]Write each step's
output_alland read the alignment input path at the top level in the pipeline resolver [src][src]Rewrite every example config and pipeline to the flat shape and drop redundant default keys [src]
Add full builds on the largest datasets (mpox clade IIb, SARS-CoV-2, influenza H3N2) mirroring the Nextstrain TreeTime chain [src]