Add --no-default-groups to uv sync in test CI jobs

Add rule to keep imports to the top of file.

Add ruff check to keep imports at the top of file

Use SPDX license identifier and drop redundant classifier

Set setuptools_scm local_scheme to no-local-version

Adopt tskit-dev repo administration principles

Add an assert to clarify only one of regions or regions_file is set

Support -R/--regions-file and -T/--targets-file

Make samples file optional.

Move samples file parsing out of CLI code

Move from pyranges to ruranges for Python>=3.12

Introduce GenomicRanges abstraction

Fixup the dependency in pyproject

Update CHANGELOG for 0.1.1 release

Support -S/--samples-file in query