pyproject fixes - all rules, proper table format

Author: sneakers-the-rat

pyproject.toml

@@ -87,37 +87,37 @@ force-exclude = '''
 )/
 '''
 
-
 [tool.ruff]
 line-length = 120
 target-version = "py39"
+force-exclude = true
+
+# -- Exclude files --
+extend-exclude = [
+    "linkml_runtime/linkml_model/**/*.py",
+    "notebooks/**"
+]
 
+[tool.ruff.lint]
 # -- Rule selection --
 select = [
   "E",  # pycodestyle errors
   "F",  # Pyflakes
   "I",  # isort
   "UP", # pyupgrade
+  "T100", # no debugger imports/usages
 ]
-force-exclude = true
 extend-ignore = [
     "E203",
-    "UP007", # until we drop 3.9
-]
-
-# -- Exclude files --
-extend-exclude = [
-    "tests/**/output",
-    "tests/**/input",
-    "tests/**/__snapshots__",
-    "notebooks/"
 ]
+pyupgrade.keep-runtime-typing = true # until we drop 3.9
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "tests/**/**.py" = ["F841", "E501", "F842", "E741"] # I ain't fixing all that
 
+
 [tool.codespell]
-skip = '.git,*.pdf,*.svg,./tests,pyproject.toml,*.dill,poetry.lock'
+skip = '.git,*.pdf,*.svg,./tests,pyproject.toml,*.dill,poetry.lock,*.ipynb'
 # Ignore table where words could be split across rows
 # Ignore shortcut specifications like [Ff]alse
 ignore-regex = '(\|.*\|.*\|.*\||\[[A-Z][a-z]\][a-z][a-z])'