pdex-0.2.2

Important: fold_change column is deprecated

The fold_change column has held log2(target/ref) since 0.2.0 despite the misleading name. This silently broke downstream consumers that assumed it was a linear ratio (notably cell-eval ≤ 0.7.0, which double-logged the values and zeroed out roughly half of all DE results — see ArcInstitute/cell-eval#232 for the full discussion).

This release adds an explicit log2_fold_change column with the same values, and emits a FutureWarning on every pdex(...) call.

Migration

pdex version	fold_change	log2_fold_change
< 0.2.0	linear ratio	(not present)
0.2.0 – 0.2.1	log2 (misnamed)	(not present)
0.2.2 (this release)	log2, deprecated alias	log2
0.3.0 (next minor)	removed	log2

Downstream code should switch to log2_fold_change now:

# old (still works in 0.2.2, removed in 0.3.0)
df["fold_change"]

# new
df["log2_fold_change"]

What's Changed

• Rename fold_change column to log2_fold_change (deprecate alias) by @LeonHafner in #74

New Contributors

• @LeonHafner made their first contribution in #74

Full Changelog: pdex-0.2.1...pdex-0.2.2