Apply suggestions from code review

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>

pyproject.toml

@@ -90,8 +90,8 @@ Whoosh = "*"
 zipstream-new = "*"
 
 [tool.poetry.dev-dependencies]
-cwltest = "2.2.20210901154959"
 black = "^22.1.0"
+cwltest = "2.2.20210901154959"
 darker = "*"
 fluent-logger = "*"
 httpx = "*"
@@ -127,8 +127,9 @@ line-length = 120
 target-version = ['py37']
 include = '\.pyi?$'
 extend-exclude = '''
-/(
+^/(
   | packages
   | tools
 )/
 '''
+force-exclude = 'lib/galaxy/util/jstree.py'

setup.cfg

@@ -5,12 +5,12 @@ universal = 1
 # These are exceptions allowed by Galaxy style guidelines:
 # B008 Do not perform function calls in argument defaults (for FastAPI Depends and Body)
 # E128 continuation line under-indented for visual indent
+# E203 is whitespace before ':'; we follow black's formatting here. See https://black.readthedocs.io/en/stable/faq.html#why-are-flake8-s-e203-and-w503-violated
 # E402 module level import not at top of file # TODO, we would like to improve this.
 # E501 is line length
-# E203 is whitespace before ':'; we follow black's formatting here.  See https://github.com/psf/black/issues/315
 # W503 is line breaks before binary operators, which has been reversed in PEP 8.
 # D** are docstring linting - which we mostly ignore except D302. (Hopefully we will solve more over time).
-ignore = B008,E128,E203,E501,E402,W503,D100,D101,D102,D103,D104,D105,D106,D107,D200,D201,D202,D204,D205,D206,D207,D208,D209,D210,D211,D300,D301,D400,D401,D402,D403,D412,D413
+ignore = B008,E128,E203,E402,E501,W503,D100,D101,D102,D103,D104,D105,D106,D107,D200,D201,D202,D204,D205,D206,D207,D208,D209,D210,D211,D300,D301,D400,D401,D402,D403,D412,D413
 exclude = lib/galaxy/util/jstree.py
 # For flake8-import-order
 # https://github.com/PyCQA/flake8-import-order/blob/master/tests/test_cases/complete_smarkets.py