Formatting fixes from ruff

Author: tomwhite

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

tests/test_vcf_writer.py

@@ -85,7 +85,7 @@ def test_write_vcf__filtering(tmp_path, include, exclude, expected_chrom_pos):
     assert len(variants) == len(expected_chrom_pos)
     assert v.samples == ["NA00001", "NA00002", "NA00003"]
 
-    for variant, chrom_pos in zip(variants, expected_chrom_pos):
+    for variant, chrom_pos in zip(variants, expected_chrom_pos, strict=False):
         chrom, pos = chrom_pos
         assert variant.CHROM == chrom
         assert variant.POS == pos
@@ -141,7 +141,7 @@ def test_write_vcf__regions(tmp_path, regions, targets,
 
     assert v.samples == ["NA00001", "NA00002", "NA00003"]
 
-    for variant, chrom_pos in zip(variants, expected_chrom_pos):
+    for variant, chrom_pos in zip(variants, expected_chrom_pos, strict=False):
         chrom, pos = chrom_pos
         assert variant.CHROM == chrom
         assert variant.POS == pos
@@ -230,7 +230,7 @@ def test_write_vcf__regions_samples_filtering(
     assert len(variants) == len(expected_chrom_pos)
     assert v.samples == ["NA00001"]
 
-    for variant, chrom_pos in zip(variants, expected_chrom_pos):
+    for variant, chrom_pos in zip(variants, expected_chrom_pos, strict=False):
         chrom, pos = chrom_pos
         assert variant.CHROM == chrom
         assert variant.POS == pos

vcztools/filter.py

@@ -1,6 +1,6 @@
 import functools
 import operator
-from typing import Callable
+from collections.abc import Callable
 
 import numpy as np
 import pyparsing as pp

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
@@ -62,10 +62,10 @@ def __call__(self, *args, **kwargs):
 class QueryFormatGenerator:
     def __init__(
         self,
-        query_format: Union[str, pp.ParseResults],
+        query_format: str | pp.ParseResults,
         *,
-        include: Optional[str] = None,
-        exclude: Optional[str] = None,
+        include: str | None = None,
+        exclude: str | None = None,
     ):
         if isinstance(query_format, str):
             parser = QueryFormatParser()
@@ -99,7 +99,7 @@ def generate(root):
                     end = start + v_chunk_size
 
                     for gt_row, phase in zip(
-                        gt_zarray[start:end], phase_zarray[start:end]
+                        gt_zarray[start:end], phase_zarray[start:end], strict=False
                     ):
 
                         def stringify(gt_and_phase: tuple):
@@ -113,7 +113,7 @@ def stringify(gt_and_phase: tuple):
                             return separator.join(gt)
 
                         gt_row = gt_row.tolist()
-                        yield map(stringify, zip(gt_row, phase))
+                        yield map(stringify, zip(gt_row, phase, strict=False))
             else:
                 # TODO: Support datasets without the phasing data
                 raise NotImplementedError
@@ -219,8 +219,8 @@ def _compose_sample_loop_generator(
 
         def generate(root):
             iterables = (generator(root) for generator in generators)
-            zipped = zip(*iterables)
-            zipped_zipped = (zip(*element) for element in zipped)
+            zipped = zip(*iterables, strict=False)
+            zipped_zipped = (zip(*element, strict=False) for element in zipped)
             flattened_zipped_zipped = (
                 (
                     subsubelement
@@ -234,7 +234,7 @@ def generate(root):
         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":
@@ -261,7 +261,7 @@ def generate(root):
             return generate
 
     def _compose_filter_generator(
-        self, *, include: Optional[str] = None, exclude: Optional[str] = None
+        self, *, include: str | None = None, exclude: str | None = None
     ) -> Callable:
         assert not (include and exclude)
 
@@ -294,8 +294,8 @@ def _compose_generator(
         self,
         parse_results: pp.ParseResults,
         *,
-        include: Optional[str] = None,
-        exclude: Optional[str] = None,
+        include: str | None = None,
+        exclude: str | None = None,
     ) -> Callable:
         generators = (
             self._compose_element_generator(element) for element in parse_results
@@ -308,7 +308,9 @@ def generate(root) -> str:
             iterables = (generator(root) for generator in generators)
             filter_iterable = filter_generator(root)
 
-            for results, filter_indicator in zip(zip(*iterables), filter_iterable):
+            for results, filter_indicator in zip(
+                zip(*iterables, strict=False), filter_iterable, strict=False
+            ):
                 if filter_indicator:
                     results = map(str, results)
                     yield "".join(results)
@@ -321,8 +323,8 @@ def write_query(
     output=None,
     *,
     query_format: str,
-    include: Optional[str] = None,
-    exclude: Optional[str] = None,
+    include: str | None = None,
+    exclude: str | None = None,
 ):
     if include and exclude:
         raise ValueError(

vcztools/regions.py

@@ -1,5 +1,5 @@
 import re
-from typing import Any, Optional
+from typing import Any
 
 import numcodecs
 import numpy as np
@@ -52,7 +52,7 @@ def create_index(vcz) -> None:
     )
 
 
-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)
@@ -67,7 +67,7 @@ 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."""
 
@@ -90,7 +90,7 @@ 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
@@ -100,8 +100,8 @@ 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:
@@ -113,8 +113,8 @@ 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,
 ):
@@ -158,8 +158,8 @@ 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/stats.py

@@ -38,7 +38,7 @@ def stats(vcz, output):
         ).astype(np.int64)
 
         for contig, contig_length, nr in zip(
-            contigs, contig_lengths, num_records_per_contig
+            contigs, contig_lengths, num_records_per_contig, strict=False
         ):
             if nr > 0:
                 print(f"{contig}\t{contig_length}\t{nr}", file=output)

vcztools/utils.py

@@ -18,7 +18,7 @@ def open_file_like(file):
     """A context manager for opening a file path or string (and closing on exit),
     or passing a file-like object through."""
     with ExitStack() as stack:
-        if isinstance(file, (str, Path)):
+        if isinstance(file, str | Path):
             file = stack.enter_context(open(file, mode="w"))
         yield file
 

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
@@ -89,8 +88,8 @@ def write_vcf(
     no_update=None,
     samples=None,
     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.