From 6f0eb1c0b910c4fbba2df6b0f95c49f672bbf775 Mon Sep 17 00:00:00 2001
From: Leon Hafner <leon.hafner@icloud.com>
Date: Tue, 14 Jul 2026 18:28:43 +0000
Subject: [PATCH 1/2] Add --epsilon CLI flag to `cell-eval run`

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.
---
 src/cell_eval/_cli/_run.py | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/src/cell_eval/_cli/_run.py b/src/cell_eval/_cli/_run.py
index b62a124..db403f1 100644
--- a/src/cell_eval/_cli/_run.py
+++ b/src/cell_eval/_cli/_run.py
@@ -2,6 +2,7 @@
 import importlib.metadata
 import logging
 import os
+from typing import Any
 
 from .. import KNOWN_PROFILES
 from ._const import DEFAULT_CTRL, DEFAULT_OUTDIR, DEFAULT_PERT_COL
@@ -118,6 +119,14 @@ def parse_args_run(parser: ap.ArgumentParser):
         "the reference, removing the below-detection floor. OFF by default (default DE "
         "behavior unchanged); pass e.g. 5 to enable (T is dataset-dependent).",
     )
+    parser.add_argument(
+        "--epsilon",
+        type=float,
+        default=0.0,
+        help="Epsilon (pseudocount) forwarded to pdex for the log fold-change "
+        "denominator [default: %(default)s]. Pass e.g. 1e-9 to match pdex>=0.2.5 "
+        "behavior.",
+    )
     parser.add_argument(
         "--version",
         action="version",
@@ -154,6 +163,12 @@ def run_evaluation(args: ap.Namespace):
 
     skip_metrics = args.skip_metrics.split(",") if args.skip_metrics else None
 
+    # DE knobs forwarded to pdex (cpm_filter off by default; epsilon default 0.0).
+    pdex_kwargs: dict[str, Any] = {
+        "cpm_filter": args.cpm_filter,
+        "epsilon": args.epsilon,
+    }
+
     if args.celltype_col is not None:
         real = ad.read_h5ad(args.adata_real)
         pred = ad.read_h5ad(args.adata_pred)
@@ -181,7 +196,7 @@ def run_evaluation(args: ap.Namespace):
                 allow_discrete=args.allow_discrete,
                 prefix=ct,
                 skip_de=args.profile == "pds",
-                pdex_kwargs={"cpm_filter": args.cpm_filter},
+                pdex_kwargs=pdex_kwargs,
             )
             evaluator.compute(
                 profile=args.profile,
@@ -210,7 +225,7 @@ def run_evaluation(args: ap.Namespace):
             outdir=args.outdir,
             allow_discrete=args.allow_discrete,
             skip_de=args.profile == "pds",
-            pdex_kwargs={"cpm_filter": args.cpm_filter},
+            pdex_kwargs=pdex_kwargs,
         )
         evaluator.compute(
             profile=args.profile,

From faee50136058c21cf76ca4f55756f5c05abaed0c Mon Sep 17 00:00:00 2001
From: Leon Hafner <leon.hafner@icloud.com>
Date: Tue, 14 Jul 2026 18:39:01 +0000
Subject: [PATCH 2/2] Drop unused ty:ignore[invalid-argument-type] suppressions

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).
---
 src/cell_eval/_baseline.py  | 2 +-
 src/cell_eval/_cli/_prep.py | 2 +-
 tutorials/vcc/vcc.ipynb     | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/cell_eval/_baseline.py b/src/cell_eval/_baseline.py
index a2cbf8d..aab4534 100644
--- a/src/cell_eval/_baseline.py
+++ b/src/cell_eval/_baseline.py
@@ -77,7 +77,7 @@ def build_base_mean_adata(
 
     if output_path is not None:
         logger.info(f"Saving baseline data to {output_path}")
-        baseline_adata.write_h5ad(output_path)  # ty: ignore[invalid-argument-type]
+        baseline_adata.write_h5ad(output_path)
 
     if output_de_path is not None:
         logger.info("Calculating differential expression")
diff --git a/src/cell_eval/_cli/_prep.py b/src/cell_eval/_cli/_prep.py
index dce7b1a..686b8a2 100644
--- a/src/cell_eval/_cli/_prep.py
+++ b/src/cell_eval/_cli/_prep.py
@@ -226,7 +226,7 @@ def strip_anndata(
 
         # Write the h5ad file
         logger.info(f"Writing h5ad output to {tmp_h5ad}")
-        minimal.write_h5ad(tmp_h5ad)  # ty: ignore[invalid-argument-type]
+        minimal.write_h5ad(tmp_h5ad)
 
         # Zstd compress the h5ad file (will create pred.h5ad.zst)
         logger.info(f"Zstd compressing {tmp_h5ad}")
diff --git a/tutorials/vcc/vcc.ipynb b/tutorials/vcc/vcc.ipynb
index 7e64de8..32bf2c9 100644
--- a/tutorials/vcc/vcc.ipynb
+++ b/tutorials/vcc/vcc.ipynb
@@ -259,7 +259,7 @@
    "id": "386ee994",
    "metadata": {},
    "outputs": [],
-   "source": "adata.write_h5ad(\"./example.h5ad\")  # ty: ignore[invalid-argument-type]"
+   "source": "adata.write_h5ad(\"./example.h5ad\")"
   },
   {
    "cell_type": "markdown",