Don't add strict=False to zips (B905)

Author: tomwhite

pyproject.toml

@@ -75,7 +75,8 @@ indent-width = 4
 [tool.ruff.lint]
 select = ["E", "F", "B", "W", "I", "N", "UP", "A", "PT"]
 #Allow uppercase names for e.g. call_AD
-ignore = ["N806", "N802", "N803", "A001", "A002"]
+#Don't add strict=False to zips (B905)
+ignore = ["N806", "N802", "N803", "A001", "A002", "B905", "RUF", "UP038"]
 
 fixable = ["ALL"]
 unfixable = []

tests/test_regions.py

@@ -1,5 +1,3 @@
-from typing import Optional
-
 import pytest
 
 from vcztools.regions import parse_region_string
@@ -15,6 +13,6 @@
     ],
 )
 def test_parse_region_string(
-    targets: str, expected: tuple[str, Optional[int], Optional[int]]
+    targets: str, expected: tuple[str, int | None, int | None]
 ):
     assert parse_region_string(targets) == expected

vcztools/query.py

@@ -1,7 +1,7 @@
 import functools
 import itertools
 import math
-from typing import Callable, Optional, Union
+from collections.abc import Callable
 
 import numpy as np
 import pyparsing as pp
@@ -232,7 +232,7 @@ def generate(chunk_data):
         return generate
 
     def _compose_element_generator(
-        self, element: Union[str, pp.ParseResults], *, sample_loop=False
+        self, element: str | pp.ParseResults, *, sample_loop=False
     ) -> Callable:
         if isinstance(element, pp.ParseResults):
             if element.get_name() == "subfield":
@@ -287,8 +287,8 @@ def write_query(
     output,
     *,
     query_format: str,
-    include: Optional[str] = None,
-    exclude: Optional[str] = None,
+    include: str | None = None,
+    exclude: str | None = None,
 ):
     root = zarr.open(vcz, mode="r")
     filter_expr = filter_mod.FilterExpression(

vcztools/regions.py

@@ -1,12 +1,12 @@
 import re
-from typing import Any, Optional
+from typing import Any
 
 import numpy as np
 import pandas as pd
 from pyranges import PyRanges
 
 
-def parse_region_string(region: str) -> tuple[str, Optional[int], Optional[int]]:
+def parse_region_string(region: str) -> tuple[str, int | None, int | None]:
     """Return the contig, start position and end position from a region string."""
     if re.search(r":\d+-\d*$", region):
         contig, start_end = region.rsplit(":", 1)
@@ -21,7 +21,7 @@ def parse_region_string(region: str) -> tuple[str, Optional[int], Optional[int]]
 
 
 def regions_to_pyranges(
-    regions: list[tuple[str, Optional[int], Optional[int]]], all_contigs: list[str]
+    regions: list[tuple[str, int | None, int | None]], all_contigs: list[str]
 ) -> PyRanges:
     """Convert region tuples to a PyRanges object."""
 
@@ -44,7 +44,7 @@ def regions_to_pyranges(
     return PyRanges(chromosomes=chromosomes, starts=starts, ends=ends)
 
 
-def parse_regions(regions: Optional[str], all_contigs: list[str]) -> Optional[PyRanges]:
+def parse_regions(regions: str | None, all_contigs: list[str]) -> PyRanges | None:
     """Return a PyRanges object from a comma-separated set of region strings."""
     if regions is None:
         return None
@@ -54,8 +54,8 @@ def parse_regions(regions: Optional[str], all_contigs: list[str]) -> Optional[Py
 
 
 def parse_targets(
-    targets: Optional[str], all_contigs: list[str]
-) -> tuple[Optional[PyRanges], bool]:
+    targets: str | None, all_contigs: list[str]
+) -> tuple[PyRanges | None, bool]:
     """Return a PyRanges object from a comma-separated set of region strings,
     optionally preceeded by a ^ character to indicate complement."""
     if targets is None:
@@ -68,8 +68,8 @@ def parse_targets(
 
 
 def regions_to_chunk_indexes(
-    regions: Optional[PyRanges],
-    targets: Optional[PyRanges],
+    regions: PyRanges | None,
+    targets: PyRanges | None,
     complement: bool,
     regions_index: Any,
 ):
@@ -113,8 +113,8 @@ def regions_to_chunk_indexes(
 
 
 def regions_to_selection(
-    regions: Optional[PyRanges],
-    targets: Optional[PyRanges],
+    regions: PyRanges | None,
+    targets: PyRanges | None,
     complement: bool,
     variant_contig: Any,
     variant_position: Any,

vcztools/retrieval.py

@@ -1,5 +1,4 @@
 import collections.abc
-from typing import Optional
 
 import numpy as np
 import zarr
@@ -140,8 +139,8 @@ def variant_chunk_index_iter_with_filtering(
     *,
     variant_regions=None,
     variant_targets=None,
-    include: Optional[str] = None,
-    exclude: Optional[str] = None,
+    include: str | None = None,
+    exclude: str | None = None,
 ):
     """Iterate over variant chunk indexes that overlap the given regions or targets
     and which match the include/exclude filter expression.
@@ -179,11 +178,11 @@ def variant_chunk_index_iter_with_filtering(
 def variant_chunk_iter(
     root,
     *,
-    fields: Optional[list[str]] = None,
+    fields: list[str] | None = None,
     variant_regions=None,
     variant_targets=None,
-    include: Optional[str] = None,
-    exclude: Optional[str] = None,
+    include: str | None = None,
+    exclude: str | None = None,
     samples_selection=None,
 ):
     query_fields_reader = VariantChunkReader(root, fields=fields)

vcztools/samples.py

@@ -1,5 +1,4 @@
 import logging
-from typing import Optional
 
 import numpy as np
 
@@ -9,8 +8,8 @@
 
 
 def parse_samples(
-    samples: Optional[str], all_samples: np.ndarray, *, force_samples: bool = True
-) -> tuple[np.ndarray, Optional[np.ndarray]]:
+    samples: str | None, all_samples: np.ndarray, *, force_samples: bool = True
+) -> tuple[np.ndarray, np.ndarray | None]:
     """Parse a bcftools-style samples string.
 
     Returns an array of the sample IDs, and an array indicating the selection

vcztools/vcf_writer.py

@@ -3,7 +3,6 @@
 import re
 import sys
 from datetime import datetime
-from typing import Optional
 
 import numpy as np
 import zarr
@@ -86,8 +85,8 @@ def write_vcf(
     samples=None,
     force_samples: bool = False,
     drop_genotypes: bool = False,
-    include: Optional[str] = None,
-    exclude: Optional[str] = None,
+    include: str | None = None,
+    exclude: str | None = None,
 ) -> None:
     """Convert a dataset to a VCF file.