Fix: sort imports with isort and fix remaining bare except

Author: marcoreverenna

environment.osx-arm64.yaml

@@ -38,6 +38,7 @@ dependencies:
   - pip
   - pip:
       - build
+      - isort
       - twine
       - hatchling
       - wheel

scripts/fdr_analysis.py

@@ -20,18 +20,19 @@
 __status__ = Dev
 """
 
-import matplotlib.pyplot as plt
-import matplotlib.lines as mlines
-import pandas as pd
-import seaborn as sns
+import json
+import logging
 import os
 import sys
-import logging
-import json
 from pathlib import Path
 
+import matplotlib.lines as mlines
+import matplotlib.pyplot as plt
+import pandas as pd
+import seaborn as sns
+
+from instanexus import helpers, preprocessing, visualization
 from instanexus.assembly import Assembler
-from instanexus import visualization, helpers, preprocessing
 
 SCRIPT_DIR = Path(__file__).resolve().parent
 PROJECT_ROOT = SCRIPT_DIR.parent
@@ -116,7 +117,7 @@ def load_custom_palette():
             color = colors_data.get(json_key, {}).get("scaffold", "#333333")
             custom_palette[category_label] = color
         return custom_palette
-    except:
+    except Exception:
         return default_palette
 
 

src/instanexus/assembly.py

@@ -22,9 +22,9 @@
 
 # import libraries
 import argparse
+import ast
 import logging
 import math
-import ast
 from collections import Counter, defaultdict
 from dataclasses import dataclass
 from itertools import combinations
@@ -36,9 +36,8 @@
 import pandas as pd
 from tqdm import tqdm
 
-from . import helpers
+from . import helpers, preprocessing
 from . import visualization as viz
-from . import preprocessing
 
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)