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Ran 09 May 2026 12:55PM UTC

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Committed 09 May 2026 12:54PM UTC coverage: 71.268% (-0.2%) from 71.429%

Job # 25601641224.1

Build Type

push

github

Committed by

web-flow

Commit Message

Warn when filter knobs no-op on missing columns (#25)

Audit Gap #5 from the v0.6.0–v0.7.4 review. The donor / method /
timepoint / APC / TIL filter knobs added across #15 + #9 + #20 are
all guarded with `if value > 0 and column in df.columns:` — fully
silent when the column isn't there. A user passing `--min-donors 2`
against a sheet that doesn't carry `patient_id` saw all clones pass
through with no signal that the knob was ignored.

Now emits a logger.warning naming the missing column and the relevant
sample-sheet axis, so the mismatch surfaces as terminal output.

Same pass DRYs the nine repeated knob blocks (min_donors, the four
per-method knobs, min_timepoints + per-donor variant, min_apcs + per-
donor variant, min_til_cells_per_donor) into one loop driven by a
list of (value, column, label) tuples. ~70 lines down to ~25, with
identical filtering semantics — verified by the existing knob tests
all still passing.

Tests:
  - warning fires with both knob name and column name when source
    column is absent
  - no warning when knob is at default (zero)
  - no warning when source column is present (success path)

Bumps version to 0.7.5 — additive log output, no behavior change for
correct usage; warning visibility is the only effect.

Coverage Stats

4321 of 6063 relevant lines covered (71.27%)

0.71 hits per line

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