openvax / topiary / 25875561027

90%

master: 90%

Build Type

Pull #167

github

Committed by iskandr

Commit Message

DSL: review polish — drop dead code, simplify repr, harden tests

Five tactical cleanups from the latest review of PR #167:

- `IsIn.__init__` had `isinstance(values, float) and math.isnan(values)`
  as a fallback scalar-detection arm.  `float` is already in the
  preceding `isinstance` tuple, so any NaN short-circuits there.  Drop
  the unreachable arm; add a one-line comment noting NaN's float
  membership.
- `IsIn.__repr__` was a three-level nested ternary.  Rewrite as a
  straight `if len(values) == 1` / else split — three lines shorter
  and reads in one pass.
- `_derive_mhc_class = derive_mhc_class` was a "backwards-compatible
  alias" with exactly one internal caller and no external exposure.
  Update the caller to the public name and drop the alias.
- `test_invert_negates` only asserted "I" is absent from the result;
  strengthen to assert positive retention (DDD + EEE survive) and the
  NaN-survives-`~eq` pandas-vs-SQL semantic.
- `test_parser_string_lhs_raises` was triggering the unrelated
  "Unexpected token" path in `_atom`, not the parser's explicit
  "column reference on the LHS" guard.  Add a separate test using
  `affinity.value == "I"` that does parse the LHS and gets rejected
  at the IsIn-construction site.

Docs: `ranking.md` Equality / membership subsection gains a NaN
semantics footnote — pandas-style (NaN → False for `.eq` / `.isin`,
True for `.ne` / `~.eq`), not SQL `IS NOT NULL`.

144 dsl + pvacseq tests pass; 702 across pvacseq / io / io_lens / dsl
/ ranking / wide.

Pull Request Pull Request #167: Add pVACseq report loader (closes #94)

Coverage Stats

267 of 300 new or added lines in 5 files covered. (89.0%)

4 existing lines in 1 file now uncovered.

4552 of 5065 relevant lines covered (89.87%)

2.7 hits per line