pirl-unc / tsarina / 27141978315

Build # 27141978315

Build Type

push

github

Committed by web-flow

Commit Message

Reorganize CLI: split data/reference, drop legacy flags (no compat) (#103)

Per 'forget cli compat, make it more logically organized'. Clean break.

Command tree — the old 'data' crammed two unrelated domains together
(hitlist MS-evidence verbs plus a nested 'data sources' for HPA/NCBI).
Split into two sibling top-level groups with parallel verbs:

  tsarina data       MS evidence (IEDB/CEDAR/viral + observations index)
    list [--all] | fetch | path | register | remove | build
  tsarina reference  HPA/NCBI curation reference data (RNA, IHC, gene_info)
    list | fetch | path
  tsarina {hits,panel,personalize}   analysis (unchanged shape)

Removed (no aliases):
- 'data sources ...'        -> 'tsarina reference ...'
- 'data available'          -> 'data list --all'
- 'data sources download'   -> 'reference fetch'
- panel --max-percentile    (deprecated shortcut; use per-tier flags)
- panel --no-progress / --progress-bars / --no-progress-bars
                            -> single --progress {auto,on,off}
- --iedb-path / --cedar-path (every command now uses --iedb / --cedar)
- personalize --mtec-matrix -> --mtec-matrix-path

Shared cli_common helpers retained (split_csv, parse_lengths, predictor,
iedb/cedar adder, mode-switch warnings). Tests updated to assert the
removed flags are rejected; docs/scripts point at the new commands.
414 tests pass; lint/format clean.

Coverage Stats

2647 of 3637 relevant lines covered (72.78%)

0.73 hits per line

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