Fix type hints for get_aligned_pairs

[gshiba]

Explicitly enumerate all 8 cases. This is a follow up to #1342.

Demo

# test_typing.py
import pysam
a = next(iter(pysam.AlignmentFile("a.bam")))
reveal_type(_ := a.get_aligned_pairs(                                    with_cigar=True ))
reveal_type(_ := a.get_aligned_pairs(                    with_seq=False, with_cigar=True ))
reveal_type(_ := a.get_aligned_pairs(matches_only=False,                 with_cigar=True ))
reveal_type(_ := a.get_aligned_pairs(matches_only=False, with_seq=False, with_cigar=True ))

Output: note the difference in inferred type: List[Tuple[Unknown, ...]] vs List[Tuple[int | None, int | None, CIGAR_OPS]] depending on whether the False is explicitly set in the call signature.

# With mypy
$ uv run --python 3.12 --with pyright --with 'pysam==v0.23.3' --with mypy mypy test_typing.py
test_typing.py:3: note: Revealed type is "builtins.list[builtins.tuple[Any, ...]]"
test_typing.py:4: note: Revealed type is "builtins.list[builtins.tuple[Any, ...]]"
test_typing.py:5: note: Revealed type is "builtins.list[builtins.tuple[Any, ...]]"
test_typing.py:6: note: Revealed type is "builtins.list[tuple[builtins.int | None, builtins.int | None, pysam.libcalignedsegment.CIGAR_OPS]]"
Success: no issues found in 1 source file

# With pyright
$ uv run --python 3.12 --with pyright --with 'pysam==v0.23.3' --with mypy pyright test_typing.py
/home/ec2-user/repos/test_typing.py
  /home/ec2-user/repos/test_typing.py:3:13 - information: Type of "_ := a.get_aligned_pairs(with_cigar=True)" is "List[Tuple[Unknown, ...]]"
  /home/ec2-user/repos/test_typing.py:4:13 - information: Type of "_ := a.get_aligned_pairs(with_seq=False, with_cigar=True)" is "List[Tuple[Unknown, ...]]"
  /home/ec2-user/repos/test_typing.py:5:13 - information: Type of "_ := a.get_aligned_pairs(matches_only=False, with_cigar=True)" is "List[Tuple[Unknown, ...]]"
  /home/ec2-user/repos/test_typing.py:6:13 - information: Type of "_ := a.get_aligned_pairs(matches_only=False, with_seq=False, with_cigar=True)" is "List[Tuple[int | None, int | None, CIGAR_OPS]]"
0 errors, 0 warnings, 4 informations

[gshiba]

I'm not sure what the failing CI / FreeBSD is about...

[jmarshall]

If you rebase onto current master, the CI will fix itself.