MNT: Fix assorted simple pylint errors

src/caosadvancedtools/loadFiles.py

@@ -375,9 +375,7 @@ exclude is given preference over include.
     logger.addHandler(logging.StreamHandler(stream=sys.stdout))
     logger.setLevel(logging.INFO)
 
-    con = db.get_connection()
-    con.timeout = float(args.timeout)
-    con._login()
+    db.configure_connection(timeout=float(args.timeout))
 
     loadpath(
         path=args.path,

src/caosadvancedtools/pandoc_header_tools.py

@@ -107,12 +107,10 @@ it is not at the beginning, it must be preceded by a blank line.
         textlines = f.readlines()
 
     state = 0
-    found_0 = -1
     found_1 = -1
     found_2 = -1
     for i, line in enumerate(textlines):
         if len(line) == 1 and state in {-1, 0}:
-            found_0 = i
             state = 0
             continue
         if line.rstrip() == "---" and state == 0:

src/caosadvancedtools/suppressKnown.py

@@ -28,6 +28,7 @@ class SuppressKnown(logging.Filter):
     """
 
     def __init__(self, db_file=None):
+        super().__init__()
         if db_file:
             self.db_file = db_file
         else:

src/caosadvancedtools/utils.py

@@ -27,7 +27,7 @@ import logging
 import os
 
 import linkahead as db
-from linkahead.exceptions import TransactionError
+from linkahead.exceptions import TransactionError, BadQueryError
 
 logger = logging.getLogger(__name__)
 
@@ -232,7 +232,7 @@ def find_records_that_reference_ids(referenced_ids, rt="", step_size=50):
                             [str(el) for el in subset]))
             exps = db.execute_query(q_string)
             record_ids.update([exp.id for exp in exps])
-        except Exception as e:
+        except (TransactionError, BadQueryError) as e:
             print(e)
 
         index += step_size