Code Quality Rules¶

CytoScnPy detects common Python code quality issues and maintains alignment with industry-standard linting codes (Flake8, Bugbear, Pylint).

Enable quality analysis with the --quality flag:

cytoscnpy . --quality

Rule ID Prefixes¶

Prefix	Category
`CSP-L`	Best Practices
`CSP-Q`	Complexity & Maintainability Metrics
`CSP-C`	Maintainability Limits (Args/Length)
`CSP-P`	Performance

Individual rule pages are available for Best Practices and Performance. Maintainability rules are summarized in this index.

Best Practices¶

ID	Rule	Description
CSP-L001	`MutableDefaultArgumentRule`	Detects mutable default arguments (lists, dicts, sets).
CSP-L002	`BareExceptRule`	Detects `except:` blocks without a specific exception class.
CSP-L003	`DangerousComparisonRule`	Detects comparisons to `True`, `False`, or `None` using `==` instead of `is`.

Maintainability & Complexity¶

ID	Rule	Description	Config
`CSP-Q301`	`ComplexityRule`	Function cyclomatic complexity (McCabe) exceeds threshold.	`max_complexity`
`CSP-Q302`	`NestingRule`	Code block is nested too deeply.	`max_nesting`
`CSP-Q303`	Maintainability Index Gate	File MI below threshold (only emitted when `min_mi` is set).	`min_mi`
`CSP-Q304`	`CognitiveComplexityRule`	Cognitive complexity exceeds fixed threshold (default 15).	Fixed threshold (not configurable)
`CSP-Q305`	`CohesionRule`	Class lacks cohesion (LCOM4 > 1).	Fixed threshold (not configurable)
`CSP-C303`	`ArgumentCountRule`	Function has too many arguments.	`max_args`
`CSP-C304`	`FunctionLengthRule`	Function is too long (line count).	`max_lines`

Performance¶

ID	Rule	Description
CSP-P001	`MembershipInListRule`	Membership test in list literal or list comprehension (use set).
CSP-P002	`FileReadMemoryRiskRule`	`read()` / `readlines()` loads entire file into RAM.
CSP-P003	`StringConcatInLoopRule`	Accumulated `+` string concatenation inside loops.
CSP-P004	`UselessCastRule`	Unnecessary `list()`/`tuple()` wrapping `range()`/`map()`/`filter()`.
CSP-P005	`RegexLoopRule`	`re.compile()` or `ast.parse()` called inside loops.
CSP-P006	`AttributeChainHoistingRule`	Deep attribute access inside loops (hoist to local).
CSP-P007	`PureCallHoistingRule`	Pure builtin calls in loops with invariant arguments.
CSP-P008	`ExceptionFlowInLoopRule`	`try/except` used as control flow in loops (KeyError/AttributeError).
CSP-P009	`IncorrectDictIteratorRule`	`.items()` used while discarding key/value (use `.keys()`/`.values()`).
CSP-P010	`GlobalUsageInLoopRule`	Global/constant usage inside loops (hoist to local).
CSP-P011	`MemoryviewOverBytesRule`	Slicing bytes in loops (use `memoryview()` for zero-copy).
CSP-P012	`UseTupleOverListRule`	Constant list literal is immutable (prefer tuple).
CSP-P013	`ComprehensionSuggestionRule`	Loop can be replaced by list/set/dict comprehension.
CSP-P015	`PandasChunksizeRiskRule`	`pandas.read_csv()` without `chunksize`/`nrows`/`iterator`.

Configuration¶

You can tune the thresholds for quality rules in your .cytoscnpy.toml:

[cytoscnpy]
max_complexity = 15    # Default: 10
max_nesting = 4        # Default: 3
max_args = 6           # Default: 5
max_lines = 100        # Default: 50
min_mi = 40.0          # Default: unset (no MI gate)

Suppression¶

Use standard suppression comments. You can suppress all findings or target specific rule IDs:

def my_function(arg=[]):  # noqa
    pass

def risky_compare(x):  # noqa: CSP-L003
    return x == None

for x in items:  # noqa: CSP-P003
    out += x