Add --epsilon flag to cell-eval run - #244
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This pull request introduces a new --epsilon command-line argument to forward a pseudocount to pdex for log fold-change calculations, updating the evaluator setup to pass this parameter. The review feedback recommends adding validation to ensure that the epsilon value is non-negative to prevent potential mathematical errors during computation.
Expose pdex's log fold-change pseudocount as a CLI option. Defaults to 0.0 (no behavior change from the current pinned default); pass e.g. 1e-9 to match pdex>=0.2.5 behavior. Forwarded via pdex_kwargs to both the --celltype-col split path and the single-evaluator path, and thus into the data-ceiling DE, mirroring how --cpm-filter is handled.
LeonHafner
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A newer ty no longer reports invalid-argument-type on AnnData.write_h5ad, so these three suppressions are now flagged unused-ignore-comment and fail the typing CI. Remove them (no functional change).
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What
Adds an
--epsilonflag tocell-eval runthat forwards a pseudocount to pdex for the log fold-change denominator.Why
Epsilon is currently pinned to
0.0internally with no CLI override. Exposing it lets users pass e.g.1e-9(matchingpdex>=0.2.5behavior) to avoid unstable / divide-by-zero log fold-changes when a gene's reference mean is 0.Details
--epsilonargument,type=float,default=0.0— no behavior change for existing invocations.pdex_kwargsto both the--celltype-colsplit path and the single-evaluator path, so it also reaches the data-ceiling DE (mirrors how--cpm-filteris handled).Also (CI fix)
Drops three now-unused
# ty: ignore[invalid-argument-type]suppressions (src/cell_eval/_baseline.py,src/cell_eval/_cli/_prep.py,tutorials/vcc/vcc.ipynb). A newertyno longer reportsinvalid-argument-typeonAnnData.write_h5ad, so these were failing thetypingjob asunused-ignore-comment. Pure comment removals, no functional change.Test plan
cell-eval run --helpshows--epsilonwith[default: 0.0]ruff format --check,ruff check,ty checkall pass locally