More Ruff fixes

Author: marcelm

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ repos:
     rev: 26.5.1
     hooks:
     -   id: black
-- repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: "v0.0.261"
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: "v0.16.7"
   hooks:
-    - id: ruff
+    - id: ruff-check

pyproject.toml

@@ -72,27 +72,16 @@ line-length = 120
 
 [tool.ruff.lint]
 ignore = [
-    # Leave enabled
-    "BLE001",  # Do not catch blind exception: `Exception`
     "C408",    # Unnecessary `dict()` call (rewrite as a literal)
     "S102",    # Use of `exec` detected
     "SIM905",  # Consider using a list literal instead of `str.split`
+    "RUF012",  # Mutable default value for class attribute
 
-    # Possibly disable the following ones:
+    # Possibly fix the following lints:
     "I001",    # Import block is un-sorted or un-formatted
     "PLC0414", # Import alias does not rename original package
-    "ISC004",  # Unparenthesized implicit string concatenation in collection
-    "RUF059",  # Unpacked variable `matches` is never used
-    "SIM102",  # Use a single `if` statement instead of nested `if` statements
     "FA100",   # Add `from __future__ import annotations` to simplify `typing.Optional`
     "D419",    # Docstring is empty
-    "TRY004",  # Prefer `TypeError` exception for invalid type
-    "RUF012",  # Mutable default value for class attribute
-    "FURB188", # Prefer `str.removesuffix()` over conditionally replacing with slice.
-    "PYI029",  # Defining `__repr__` in a stub is almost always redundant
-    "PLR1704", # Redefining argument with the local name `s`
-    "B020",    # Loop control variable `s` overrides iterable it iterates
     "RUF022",  # `__all__` is not sorted
-    "B006",    # Do not use mutable data structures for argument defaults
     "RUF023",  # `SingleMatch.__slots__` is not sorted
 ]

src/cutadapt/_align.pyi

@@ -5,7 +5,6 @@ class DPMatrix:
     n: int
     def __init__(self, reference: str, query: str): ...
     def set_entry(self, i: int, j: int, cost: int) -> None: ...
-    def __str__(self) -> str: ...
 
 class Aligner:
     def __init__(
@@ -18,7 +17,6 @@ class Aligner:
         indel_cost: int = 1,
         min_overlap: int = 1,
     ): ...
-    def __repr__(self) -> str: ...
     def _set_reference(self, reference: str) -> None: ...
     @property
     def dpmatrix(self) -> DPMatrix: ...
@@ -37,7 +35,6 @@ class PrefixComparer:
         wildcard_query: bool = False,
         min_overlap: int = 1,
     ): ...
-    def __repr__(self) -> str: ...
     def locate(self, query: str) -> tuple[int, int, int, int, int, int] | None: ...
 
 class SuffixComparer(PrefixComparer): ...

src/cutadapt/adapters.py

@@ -92,7 +92,7 @@ def __repr__(self):
 
     def __iadd__(self, other: Any):
         if not isinstance(other, self.__class__):
-            raise ValueError("Cannot compare")
+            raise TypeError("Cannot compare")
         if (
             self.max_error_rate != other.max_error_rate
             or self.sequence != other.sequence
@@ -172,7 +172,7 @@ def __repr__(self):
 
     def __iadd__(self, other: "SingleAdapterStatistics"):
         if not isinstance(other, self.__class__):
-            raise ValueError("Cannot iadd")
+            raise TypeError("Cannot iadd")
         self.end += other.end
         self.reverse_complemented += other.reverse_complemented
         return self
@@ -221,7 +221,7 @@ def __repr__(self):
 
     def __iadd__(self, other: "LinkedAdapterStatistics"):
         if not isinstance(other, self.__class__):
-            raise ValueError("Cannot iadd")
+            raise TypeError("Cannot iadd")
         self.front += other.front
         self.back += other.back
         self.reverse_complemented += other.reverse_complemented
@@ -264,7 +264,7 @@ def __repr__(self):
 
     def __iadd__(self, other: "AnywhereAdapterStatistics"):
         if not isinstance(other, AnywhereAdapterStatistics):
-            raise ValueError("Cannot add")
+            raise TypeError("Cannot add")
         self.front += other.front
         self.back += other.back
         self.reverse_complemented += other.reverse_complemented
@@ -490,7 +490,7 @@ def removed_sequence_length(self) -> int:
         return len(self.sequence) - self.rstart
 
 
-def _generate_adapter_name(_start=[1]) -> str:
+def _generate_adapter_name(_start=[1]) -> str:  # noqa: B006
     name = str(_start[0])
     _start[0] += 1
     return name
@@ -1415,7 +1415,7 @@ def _make_index(self) -> tuple[list[int], "AdapterIndexDict", int]:
             if adapter.indels:
                 for s, errors, matches in edit_environment(sequence, k):
                     if s in index:
-                        other_adapter, other_errors, other_matches = index[s]
+                        other_adapter, _other_errors, other_matches = index[s]
                         if matches < other_matches:
                             continue
                         if other_matches == matches and s not in ambiguous:
@@ -1428,7 +1428,7 @@ def _make_index(self) -> tuple[list[int], "AdapterIndexDict", int]:
                     matches = n - errors
                     for s in hamming_sphere(sequence, errors):
                         if s in index:
-                            other_adapter, other_errors, other_matches = index[s]
+                            other_adapter, _other_errors, other_matches = index[s]
                             if matches < other_matches:
                                 continue
                             if other_matches == matches and s not in ambiguous:

src/cutadapt/align.py

@@ -83,17 +83,17 @@ def naive_edit_environment(s: str, k: int) -> Iterator[str]:
     yield s
     if k == 0:
         return
-    for s in naive_edit_environment(s, k - 1):
-        n = len(s)
+    for t in naive_edit_environment(s, k - 1):
+        n = len(t)
         for ch in "ACGT":
             for i in range(n):
-                prefix = s[:i] + ch
-                yield prefix + s[i:]  # insertion
-                yield prefix + s[i + 1 :]  # substitution
-            yield s + ch  # insertion into final position
+                prefix = t[:i] + ch
+                yield prefix + t[i:]  # insertion
+                yield prefix + t[i + 1 :]  # substitution
+            yield t + ch  # insertion into final position
         # all deletions
         for i in range(n):
-            yield s[:i] + s[i + 1 :]
+            yield t[:i] + t[i + 1 :]
 
 
 def py_edit_environment(s: str, k: int) -> Iterator[tuple[str, int, int]]:

src/cutadapt/info.pyi

@@ -8,4 +8,3 @@ class ModificationInfo:
     cut_suffix: str
     is_rc: bool | None
     def __init__(self, read: SequenceRecord) -> None: ...
-    def __repr__(self) -> str: ...

src/cutadapt/json.py

@@ -69,4 +69,4 @@ def dumps(obj, indent: int = 2, _level: int = 0) -> str:
             + "}"
         )
     else:
-        raise ValueError(f"cannot serialize type {obj.__class__.__name__}")
+        raise TypeError(f"cannot serialize type {obj.__class__.__name__}")

src/cutadapt/modifiers.py

@@ -562,8 +562,7 @@ def __repr__(self):
 
     def __call__(self, read, info: ModificationInfo):
         read = read[:]
-        if read.name.endswith(self.suffix):
-            read.name = read.name[: -len(self.suffix)]
+        read.name = read.name.removesuffix(self.suffix)
         return read
 
 

src/cutadapt/parser.py

@@ -228,7 +228,7 @@ def parse(cls, spec: str, adapter_type: str) -> "AdapterSpecification":
         if adapter_type not in ("front", "back", "anywhere"):
             raise ValueError("adapter_type must be front, back or anywhere")
 
-        spec, middle, parameters_spec = spec.partition(";")
+        spec, _middle, parameters_spec = spec.partition(";")
         name, spec = cls._extract_name(spec)
         spec = spec.strip()
         parameters = parse_search_parameters(parameters_spec)

src/cutadapt/report.py

@@ -82,7 +82,7 @@ def __init__(self) -> None:
 
     def __iadd__(self, other: Any):
         if not isinstance(other, Statistics):
-            raise ValueError(f"Cannot add {other.__type__.__name__}")
+            raise TypeError(f"Cannot add {other.__type__.__name__}")
         self.n += other.n
         self.read_length_statistics += other.read_length_statistics
 
@@ -869,12 +869,14 @@ def minimal_report(stats: Statistics, time: float, gc_content: float) -> str:
     warning = False
     for which_in_pair in (0, 1):
         for adapter_statistics in stats.adapter_stats[which_in_pair]:
-            if isinstance(adapter_statistics, BackAdapterStatistics):
-                if AdjacentBaseStatistics(
+            if (
+                isinstance(adapter_statistics, BackAdapterStatistics)
+                and AdjacentBaseStatistics(
                     adapter_statistics.end.adjacent_bases
-                ).should_warn:
-                    warning = True
-                    break
+                ).should_warn
+            ):
+                warning = True
+                break
     if warning:
         fields[0] = "WARN"
     header = [