pirl-unc / tsarina / 27109978656
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Consolidate CLI: shared args, unified flags, deprecation aliases (#102)

Audit of the CLI surface found duplication and confusing features; this
fixes them with back-compat deprecation aliases (no hard breaks).

- Add tsarina/cli_common.py: single source of truth for split_csv,
  parse_lengths, SUPPORTED_PREDICTORS, and add_iedb_cedar_args /
  add_predictor_arg / warn_ignored_flags. hits/personalize/panel were
  each re-declaring these, which let them drift.

- Unify IEDB/CEDAR path overrides: every scoring subcommand now accepts
  both --iedb/--cedar and --iedb-path/--cedar-path (panel previously only
  took --iedb-path; hits/personalize only --iedb).

- hits: --healthy-tissue and --skip-ms-evidence are documented as mode
  switches and now WARN (stderr) listing the filtering/aggregation flags
  they ignore, instead of silently dropping them.

- panel: collapse the 3-way progress flags into one --progress
  {auto,on,off}; keep --no-progress / --progress-bars / --no-progress-bars
  as hidden back-compat aliases. Hide the deprecated --max-percentile from
  --help and emit a deprecation warning when used. Note in --show-empty-ctas
  that --ctas forces it on.

- personalize: add --mtec-matrix-path (primary) aliasing --mtec-matrix
  (the dest is mtec_matrix_path).

- data: 'data sources download' -> 'data sources fetch' (verb unified with
  'data fetch'; 'download' kept as deprecated alias). 'data list --all'
  shows the full catalog (soft-deprecating 'data available'), and 'data
  list' now cross-points to 'data sources list'.

New tests for cli_common helpers, panel deprecated-flag back-compat +
hidden-from-help, and the --iedb alias. 415 tests pass.

2653 of 3646 relevant lines covered (72.76%)

0.73 hits per line

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Lines Coverage ∆ File
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Jobs
ID Job ID Ran Files Coverage
1 27109978656.1 37
72.76
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Source Files on build 27109978656