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26 set exp post agg to true by default #27

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Merged
noamteyssier merged 2 commits into from
Jun 11, 2025
Merged

26 set exp post agg to true by default #27

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a970082
fix: perform exponentiation post aggregation
noamteyssier Jun 11, 2025
80bbc23
chore: bump semver
noamteyssier Jun 11, 2025
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3 changes: 1 addition & 2 deletions pyproject.toml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
[project]
name = "pdex"
version = "0.1.13"
version = "0.1.14"
description = "Parallel differential expression for single-cell perturbation sequencing"
readme = "README.md"
authors = [{ name = "noam teyssier", email = "noam.teyssier@arcinstitute.org" }]
Expand All @@ -25,7 +25,6 @@ build-backend = "hatchling.build"
[dependency-groups]
dev = ["pytest>=8.3.5", "ruff>=0.11.8"]


[tool.pyright]
venvPath = "."
venv = ".venv"
6 changes: 3 additions & 3 deletions src/pdex/_single_cell.py
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Expand Up @@ -88,7 +88,7 @@ def _process_target_batch_shm(
metric: str,
tie_correct: bool = False,
is_log1p: bool = False,
exp_post_agg: bool = False,
exp_post_agg: bool = True,
**kwargs,
) -> list[dict[str, float]]:
"""Process a batch of target gene and feature combinations.
Expand Down Expand Up @@ -240,7 +240,7 @@ def parallel_differential_expression(
metric: str = "wilcoxon",
tie_correct: bool = True,
is_log1p: bool | None = None,
exp_post_agg: bool = False,
exp_post_agg: bool = True,
as_polars: bool = False,
**kwargs,
) -> pd.DataFrame | pl.DataFrame:
Expand Down Expand Up @@ -269,7 +269,7 @@ def parallel_differential_expression(
(see `pdex._utils.guess_is_log`).
exp_post_agg: bool
Whether to perform exponential post-aggregation for calculating fold change
(default: perform exponential pre-aggregation)
(default: perform exponential post-aggregation)
as_polars: bool
return the output dataframe as a polars dataframe
**kwargs:
Expand Down