openvax / topiary / 34914989442-1

93%

master: 93%

Build Type

Pull #319

github

Committed by iskandr

Commit Message

Make declared dependencies and exported surface match the code (#314, #315)

Two mechanical issues from today's review. Every claim verified before
changing anything.

Dependencies (#315):

- mhcnames was a hard dependency with no importer anywhere since 2018,
  when lazy_ligandome_dict was deleted. Allele parsing uses mhcgnomes.
  Dropped.
- mhcgnomes and pyensembl are imported directly but were declared by
  nobody, arriving only through mhctools and varcode. pyensembl is
  imported at module scope in topiary/sources.py, so it was never
  optional in the first place. Both declared, with floors matching what
  mhctools already guarantees so resolution is unchanged, and the
  pyensembl <3.0.0 cap matching mhctools and vaxrank - leaving it open
  here could resolve a 3.x that breaks them.
- Confirmed the change reaches built metadata by building a wheel and
  reading Requires-Dist, not just by editing requirements.txt.
- Two ImportError guards deleted as unreachable: gtfparse is imported
  unconditionally in topiary/rna/gtf.py and pyensembl in
  topiary/sources.py, so neither guard's "pip install ..." advice could
  ever print. Genuinely optional integrations keep using
  require_optional_dependency, which names the right extra.

Dead surface (#314):

- _dsl_filter_to_string and CachedPredictor._row_key had no callers.
- A cache_kinds local in predict_peptides_dataframe was computed and
  never read. Removing it orphaned _cache_kinds - so rather than delete
  that too, it is now the one definition of "which kinds does this
  cache hold", since kind_support was recomputing the same set inline.
  The two differed only in a str() coercion that is a no-op on a
  normalized cache, where _normalize has already cast the column.
- The version predicate had three names for one rule. _known_versions,
  documented as a deprecated internal alias, was what internal code
  called, while the public known_versions had no internal users. The
  five sites now call known... (continued)

Pull Request Pull Request #319: Make declared dependencies and exported surface match the code (#314, #315)

Coverage Stats

6 of 7 new or added lines in 5 files covered. (85.71%)

136 existing lines in 3 files now uncovered.

7118 of 7715 relevant lines covered (92.26%)

0.92 hits per line