Toil 5.6.0

.flake8

@@ -1,2 +1,4 @@
 [flake8]
-max-line-length = 888
+ignore = E203, E266, E501, W503, E211, E731
+max-line-length = 88
+select = B,C,E,F,W,T4,B9

.github/workflows/codeql-analysis.yml

@@ -2,27 +2,31 @@ name: "Code scanning - action"
 
 on:
   push:
+    branches: [main]
   pull_request:
+    branches: [main]
   schedule:
     - cron: '0 3 * * 6'
 
+concurrency:
+  group: codeql-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   CodeQL-Build:
 
     runs-on: ubuntu-latest
 
+    permissions:
+      security-events: write
+
     steps:
     - name: Checkout repository
       uses: actions/checkout@v2
       with:
         # We must fetch at least the immediate parents so that if this is
         # a pull request then we can checkout the head.
         fetch-depth: 2
-
-    # If this run was triggered by a pull request event, then checkout
-    # the head of the pull request instead of the merge commit.
-    - run: git checkout HEAD^2
-      if: ${{ github.event_name == 'pull_request' }}
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL

.isort.cfg

@@ -0,0 +1,6 @@
+[settings]
+multi_line_output=3
+include_trailing_comma=True
+force_grid_wrap=0
+use_parentheses=True
+line_length=88