Resolve pre commit after dependency updates

noxfile.py

@@ -1,4 +1,5 @@
 """Nox sessions."""
+
 import os
 import shlex
 import shutil

spapros/evaluation/metrics.py

@@ -858,6 +858,7 @@ def summary_knn_AUC(means_df: pd.DataFrame) -> float:
 # SHARED computations
 # None
 
+
 # PER PROBESET computations
 def xgboost_forest_classification(
     adata: sc.AnnData,
@@ -1160,6 +1161,7 @@ def summary_metric_diagonal_confusion_percentage(
 # marker_corr metric functions #
 ################################
 
+
 # SHARED computations
 def marker_correlation_matrix(
     adata: sc.AnnData,
@@ -1350,6 +1352,7 @@ def summary_marker_corr(cor_df: pd.DataFrame) -> Dict:
 # gene_corr metric functions #
 ##############################
 
+
 # SHARED computations
 def correlation_matrix(
     adata: sc.AnnData,

spapros/plotting/plot.py

@@ -1,4 +1,5 @@
 """Plotting Module."""
+
 import itertools
 from typing import Callable, Dict, List, Literal, Optional, Tuple, Union
 
@@ -1620,7 +1621,7 @@ def masked_dotplot(
     for ct in cts:
         for gene in selector.probeset[selector.probeset["selection"]].index:
             if ct in selector.probeset.loc[gene, "celltypes_marker"].split(",") and (gene in adata.var_names):
-                marker_genes[ct].append(gene)
+                marker_genes[ct].append(gene)  # noqa: B909
         marker_genes[ct] = [g for g in marker_genes[ct] if g in selected_genes]
 
     # Optionally subset genes:

spapros/selection/selection_procedure.py

@@ -2064,7 +2064,6 @@ def select_reference_probesets(
     for method in methods:
         if method not in selection_fcts:
             print(f"Method {method} is not available. Supported methods are {[key for key in selection_fcts]}.")
-            del methods[method]
     methods = {m: methods[m] for m in methods if m in selection_fcts}
 
     # Create list of planed selections

spapros/util/mp_util.py

@@ -1,4 +1,5 @@
 """FRom squidpy's general utility functions."""
+
 from __future__ import annotations
 
 from enum import Enum

tests/conftest.py

@@ -1,4 +1,5 @@
 """Global fixtures for testing."""
+
 import random
 
 import pandas as pd

tests/evaluation/test_evaluation_frame.py

@@ -1,4 +1,5 @@
 """Test cases for the ProbesetEvaluator."""
+
 import anndata
 
 

tests/evaluation/test_metrics.py

@@ -1,4 +1,5 @@
 """Test cases for the metric calculations."""
+
 import numpy as np
 import pandas as pd
 import pytest

tests/test_main.py

@@ -1,4 +1,5 @@
 """Test cases for the __main__ module."""
+
 import pytest
 from click.testing import CliRunner