openvax / topiary / 24208686578

87%

master: 90%

Build Type

Pull #100

github

Committed by iskandr

Commit Message

DSL polish: direction docs, log2/log1p, filter_by, parser errors, argcomplete

Direction clarity:
- Fix norm() docstring (claimed 0.977, actual was 0.023)
- Document that norm() is "higher in → higher out" (use for scores)
- Document that logistic() is "lower in → higher out" (use for IC50)

New transforms:
- .log2() — base-2 logarithm
- .log1p() — log(1+x), accurate for small x

filter_by parameter:
- Rename filter → filter_by on TopiaryPredictor (filter kept as
  deprecated alias)
- Accept string expressions: filter_by="affinity <= 500 | el.rank <= 2"

Parser error quality:
- "Did you mean" suggestions for kind typos (afinity → affinity)
- "Did you mean" suggestions for field typos (rnk → rank)
- Clear "must be a number" error for non-numeric thresholds
- Better error for reversed expressions (500 <= affinity)

argcomplete:
- Move from optional to default dependency (zero deps, 43 kB)
- Remove conditional import, remove [completion] extra
- Tab completion works out of the box after activate-global-python-argcomplete

Remove pirlygenes install note from README (it's an optional dep that
auto-errors with install instructions when needed).

25 new tests, 343 total passing.

Pull Request Pull Request #100: DSL polish: direction docs, log2/log1p, filter_by, parser errors

Coverage Stats

30 of 40 new or added lines in 3 files covered. (75.0%)

61 existing lines in 1 file now uncovered.

1394 of 1616 relevant lines covered (86.26%)

2.59 hits per line