From f9302eae203f162d5cfd77f65ca0535036ab314d Mon Sep 17 00:00:00 2001
From: Nick Moore <nick@zoic.org>
Date: Tue, 11 Jun 2024 15:22:12 +1000
Subject: [PATCH] fix up pylint & whitespace

---
 countess/plugins/pivot.py | 6 ++----
 countess/utils/variant.py | 8 ++++----
 pyproject.toml            | 3 ++-
 3 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/countess/plugins/pivot.py b/countess/plugins/pivot.py
index de77e15..7e9eb1f 100644
--- a/countess/plugins/pivot.py
+++ b/countess/plugins/pivot.py
@@ -30,14 +30,12 @@ class PivotPlugin(PandasProcessPlugin):
         "columns": PerColumnArrayParam(
             "Columns", ChoiceParam("Role", "Drop", choices=["Index", "Pivot", "Expand", "Drop"])
         ),
-        "aggfunc": ChoiceParam(
-            "Aggregation Function", "sum", choices=["sum", "mean", "min", "max"]
-        )
+        "aggfunc": ChoiceParam("Aggregation Function", "sum", choices=["sum", "mean", "min", "max"]),
     }
 
     input_columns: Dict[str, np.dtype] = {}
 
-    dataframes: List[pd.DataFrame] = None
+    dataframes: Optional[List[pd.DataFrame]] = None
 
     def prepare(self, sources: List[str], row_limit: Optional[int] = None):
         self.input_columns = {}
diff --git a/countess/utils/variant.py b/countess/utils/variant.py
index 8a4b7d6..604844a 100644
--- a/countess/utils/variant.py
+++ b/countess/utils/variant.py
@@ -438,12 +438,12 @@ def _ref(pos):
             # Handle calling synonymous changes
             assert end - start == opcode.dest_end - opcode.dest_start
             start_ofs = None
-            for ofs in range(0, end-start):
-                src_dna = ref_seq[(start+ofs)*3+frame:][:3]
-                dest_dna = var_seq[(opcode.dest_start+ofs)*3+frame:][:3]
+            for ofs in range(0, end - start):
+                src_dna = ref_seq[(start + ofs) * 3 + frame :][:3]
+                dest_dna = var_seq[(opcode.dest_start + ofs) * 3 + frame :][:3]
                 if src_dna == dest_dna:
                     if start_ofs is not None:
-                        if start_ofs == ofs-1:
+                        if start_ofs == ofs - 1:
                             yield f"{_ref(start+start_ofs)}="
                         else:
                             yield f"{_ref(start+start_ofs)}_{_ref(start+ofs-1)}="
diff --git a/pyproject.toml b/pyproject.toml
index fb0f05f..8d1a90c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -37,7 +37,7 @@ dev = [
     'build==0.10.0',
     'coverage==7.3.2',
     'mypy~=1.0.1',
-    'pylint~=2.17',
+    'pylint~=3.2.3',
     'types-psutil~=5.9.5',
     'types-ttkthemes~=3.2',
     'twine==4.0.2',
@@ -102,6 +102,7 @@ disable = [
     "too-many-branches",
     "too-many-instance-attributes",
     "too-many-locals",
+    "too-many-nested-blocks",
     "too-many-statements",
     "too-few-public-methods",
     "too-many-public-methods",