pirl-unc / hitlist / 25031877455

Build # 25031877455

Build Type

push

github

Committed by web-flow

Commit Message

v1.27.0: Export-subcommand cleanup (CLI refactor PR 3) (#169)

Renames and merges three export subcommands so the names match what they
actually emit, and steers users at the new ``hitlist qc`` family for the
allele-validator commands that always-green now.

| canonical | legacy (still works, deprecated) |
|---|---|
| hitlist export bulk-proteomics              | hitlist export bulk |
| hitlist export peptide-counts --by class    | hitlist export summary |
| hitlist export peptide-counts --by study    | hitlist export counts |
| hitlist qc normalization                    | hitlist export alleles |
| hitlist qc resolution                       | hitlist export data-alleles |

Renamed ``bulk`` → ``bulk-proteomics`` because the old name read like part
of the MHC-ligand family it lives next to.  Merged ``summary`` + ``counts``
into one ``peptide-counts`` differentiated by ``--by class|study``; both
counted peptides at different aggregation levels and deserved one verb.

Old commands still parse, dispatch to the same handlers, and emit a
stderr deprecation notice on every invocation.  Removal in v2.0.

Argparse setup factored into ``_add_export_bulk_proteomics_args`` and
``_add_peptide_counts_args`` helpers so the new and legacy entry points
can never drift in flag set.

Tests: tests/test_cli_export_cleanup.py — 5 tests covering canonical
``peptide-counts`` flag routing for both ``--by`` modes, the
``bulk-proteomics`` argparse, and that all five legacy subcommands emit
the expected deprecation notice with the correct replacement hint.

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2790 of 4454 relevant lines covered (62.64%)

0.63 hits per line

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