From 3cec252b34393c1e3eda97d80ddd4c8df8bf9368 Mon Sep 17 00:00:00 2001
From: "google-labs-jules[bot]"
 <161369871+google-labs-jules[bot]@users.noreply.github.com>
Date: Wed, 21 Jan 2026 17:08:23 +0000
Subject: [PATCH] Improve test coverage in scFates/tests/test_w_plots.py

Added test cases for:
- `scFates.tools.graph_fitting.explore_sigma`
- `scFates.tools.covariate.test_covariate` with `nested=True`

These additions improve the code coverage for R-dependent functionalities and graph fitting tools.
---
 scFates/tests/test_w_plots.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/scFates/tests/test_w_plots.py b/scFates/tests/test_w_plots.py
index eeff504..0c4fb9d 100644
--- a/scFates/tests/test_w_plots.py
+++ b/scFates/tests/test_w_plots.py
@@ -13,6 +13,8 @@ def test_pipeline():
     scf.tl.curve(adata, Nodes=10, use_rep="pca", device="cpu", seed=1)
     F_PC1_epgc_cpu = adata.uns["graph"]["F"][0, :5]
 
+    scf.tl.explore_sigma(adata, Nodes=10, use_rep="pca", plot=True)
+
     scf.tl.tree(adata, Nodes=10, use_rep="pca", method="epg", device="cpu", seed=1)
     F_PC1_epgt_cpu = adata.uns["graph"]["F"][0, :5]
 
@@ -130,6 +132,7 @@ def test_pipeline():
     adata.var["signi"] = True
     scf.tl.test_covariate(adata, "covariate")
     scf.tl.test_covariate(adata, "covariate", trend_test=True)
+    scf.tl.test_covariate(adata, "covariate", nested=True)
     scf.pl.trend_covariate(
         adata, adata.var_names[0], group_key="covariate", show_null=True
     ,show=False)