(fix): ci

.github/workflows/pythonpackage.yml

@@ -2,9 +2,9 @@ name: Python package
 
 on:
   push:
-    branches: [master]
+    branches: [main]
   pull_request:
-    branches: [master]
+    branches: [main]
   schedule:
     - cron: "0 5 1,15 * *"
 
@@ -15,7 +15,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", 3.11, 3.12]
+        python-version: ["3.10", "3.12"]
 
     steps:
     - uses: actions/checkout@v4

muon/_atac/preproc.py

@@ -116,7 +116,7 @@ def tfidf(
     if log_tfidf:
         tf_idf = np.log1p(tf_idf)
 
-    res = np.nan_to_num(tf_idf, 0)
+    res = np.nan_to_num(tf_idf, nan=0.0)
     if not inplace:
         return res
 

pyproject.toml

@@ -16,7 +16,7 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "Intended Audience :: Science/Research"
 ]
-requires-python = ">= 3.8"
+requires-python = ">= 3.10"
 requires = [
     "numpy",
     "pandas",

tests/test_muon_tools.py

@@ -142,9 +142,9 @@ def test_multi_group(self, filepath_hdf5):
 
         assert all(mdata.obs.group.values == mdata.obs.true_group.values)
 
-        for sample, value in (("sample9_groupA", 1.719391), ("sample17_groupB", -2.057848)):
+        for sample, value in (("sample9_groupA", -1.719391), ("sample17_groupB", 2.057848)):
             si = np.where(mdata.obs.index == sample)[0]
-            assert mdata.obsm["X_mofa"][si, 0] == pytest.approx(value)
+            assert mdata.obsm["X_mofa"][si, 0].item() == pytest.approx(value)
 
 
 if __name__ == "__main__":