ruff tweaks and pre-commit only changed files

.github/workflows/testing.yml

@@ -28,7 +28,7 @@ jobs:
       - name: Run pre-commit
         run: |
           pip install pre-commit
-          pre-commit run --all-files
+          pre-commit run
 
   test:
     needs: lint

pyproject.toml

@@ -61,10 +61,10 @@ ignore = [
   "D105",    # Missing docstring in magic method
   "D205",    # 1 blank line required between summary line and description
   "D212",    # Multi-line docstring summary should start at the first line
-  "FA100",   # Missing `from __future__ import annotations`, but uses `typing.XXX`
+  "FA100",   # Missing `from __future__ import annotations`, but uses `typing.XXX` TODO
   "PD011",   # pandas-use-of-dot-values
   "PD901",   # pandas-df-variable-name
-  "PT011",   # `pytest.raises(XXXError)` is too broad, set the `match` parameter...
+  "PT011",   # `pytest.raises(XXXError)` is too broad, set the `match` parameter... TODO
   "PERF203", # try-except-in-loop
   "PERF401", # manual-list-comprehension (TODO fix these or wait for autofix)
   "PLR",     # pylint refactor
@@ -81,6 +81,7 @@ isort.split-on-trailing-comma = false
 "tests/*" = ["D"]
 "src/maggma/api/*" = ["B008", "B021", "RET505", "RET506"]
 "tests/api/*" = ["B017", "B018"]
+"src/maggma/cli/*" = ["EXE001"] # triggered by ! at top of file
 
 [tool.pytest.ini_options]
 addopts = "--color=yes -p no:warnings --import-mode=importlib --durations=30"