Code quality improvement, investigate ignored failures

[stephenworsley]

Repo-review

• "PC170", # PyGrep hooks (Add PyGrep hooks #498)
• "PC180", # Uses prettier
• "PY005", # Test folder location (ruff src #501, fix unit test schemes dunder imports #499)
• "GH104", # Unique names for upload artifact (support unique name for upload/download artifact #507)
• "GH212", # Require GHA update grouping (use groups for dependabot #505)

Numpydoc

• "PR01", # Undocumented parameters
• "PR02", # Unknown parameters
• "PR04", # Untyped parameters
• "PR05", # Improper "." (Ruff/numpydoc fixes #439)
• "PR07", # Undescribed parameter
• "PR09", # Missing "." (Ruff/numpydoc fixes #439)
• "PR10", # Missing space before colon (Ruff/numpydoc fixes #439)
• "RT01", # Missing returns section
• "RT03", # Undescribed return section
• "RT05", # Missing "." (Ruff/numpydoc fixes #439)
• "GL08", # Missing docstring
• "SS02", # Missing capitalisation (Ruff/numpydoc fixes #439)
• "SS05", # Third person grammar (Ruff/numpydoc fixes #439)

Ruff

• "ANN001", "ANN002", "ANN003", "ANN101", "ANN201", "ANN202", "ANN204", # Missing type annotations
• "B904", # Try except handling (Fix try except handling #510)
• "C408", # Unnecessary dict call (Ruff/numpydoc fixes #439)
• "C901", # McCabe complexity (Ruff/numpydoc fixes #439)
• "D104", # Misssing docstring
• "E501", # Line too long
• "EM101", "EM102", # Exceptions using string literals (Ruff/numpydoc fixes #439)
• "ERA001", # Commented out code
• "F401", "F403", # imports not used, consider adding to all
• "FBT002", # Boolean default positional argument in function definition
• "FIX002", # Line contains TODO
• "FLY002", # Replace join with f-string (Ruff/numpydoc fixes #439)
• "INP001", # Missing init (Replace asserts #508)
• "N802", "N806" # Upper case names
• "PERF401", # Use a list comprehension to create a transformed list (Ruff/numpydoc fixes #439)
• "PLR0912", "PLR0913", "PLR0915", # Too many branches, arguments, statements (Ruff/numpydoc fixes #439)
• "PLR2004", # Magic value used in comparison
• "PLW2901", # for loop target overwritten by assignment target (Ruff/numpydoc fixes #439)
• "PYI024", # Use typing.NamedTuple instead of collections.namedtuple (Ruff/numpydoc fixes #439)
• "RET504", # Unnecessary assignment before return
• "S101", # Use of assert (Replace asserts #508)
• "SIM108", # Use ternary operator instead of if-else-block
• "SLF001", # Private member accessed
• "TD002", "TD003", # Incomplete TODOs
• "TID252", # Prefer absolute imports over relative imports from parent modules (Ruff/numpydoc fixes #439)
• "TRY003", # Avoid specifying long messages outside the exception class

per file:

tests

• "B006", # Do not use mutable data structures for argument defaults
• "N999", # Invalid module name
• "PT006", "PT007", # Wrong types passed to @pytest.mark.parametrize (Ruff/numpydoc fixes #439)
• "PT011", # pytest.raises(ValueError) is too broad
• "PTH118", "PTH123", # Replace os with Path
• "S101", # Use of assert

benchmarks

• "ANN205", # Missing type annotations
• "ARG001", "ARG002", # Unused arguments
• "B018", # Found useless expression
• "B028", # No explicit stacklevel keyword argument found
• "D102", "D103", # Missing docstring
• "DTZ005", # datetime.datetime.now() called without a tz argument
• "PLW1510", # subprocess.run without explicit check argument
• "PTH107", "PTH110", # Replace os with Path
• "RET503", # Missing explicit return at the end of function able to return non-None value
• "RUF005", # Consider replacing concatenation
• "RUF012", # Mutable class attributes should be annotated with typing.ClassVar
• "S101", # Use of assert
• "S603", "S607", # Untrusted subprocess call
• "TRY002", # Create your own exception

conf

• "A001", # shadowing python builtin
• "E402", # Module level import not at top of file
• "DTZ005", # datetime.datetime.now() called without a tz argument

noxfile

• "FBT001", # Boolean-typed positional argument in function definition
• "PIE810", # Call startswith/endswith once with a tuple (Ruff/numpydoc fixes #439)
• "S310", # Audit URL open for permitted schemes. Allowing use of file: or custom schemes is often unexpected.
• "S506", # Consider yaml.safe_load
• "SIM105", # Use contextlib.suppress(FileExistsError) instead of try-except-pass
• "T201", # print found

setup

• "EXE001", # Shebang is present but file is not executable