Tuple to dataclass

[XLIU-hub]

Pull Request Details

Refactor the crossmapper position API from tuple-based values to typed dataclasses, adding validation for dataclass values and class initialization inputs.

• Add Coord, Locus.Point, MultiLocus.Point, GenomicPoint, NonCodingPoint, CodingPoint, and ProteinPoint dataclasses.
• Update locus, multi-locus, genomic, non-coding, coding, and protein conversions to accept and return the new data models.
• Add validation for position values, offsets, regions, loci, CDS ranges, and reference-length bounds.
• Expand and update tests for validation errors.
• Add typings for all functions.

Breaking Changes:

• Callers must replace tuple position inputs and outputs with the relevant dataclass instances.
• Public dataclass inputs and internal conversion models now raise errors for invalid values.

Validation

• Updated tests for dataclass inputs and outputs for locus, multi_locus, and crossmapper.
• Added coverage for validation errors and error messages.
• Added CI checks for typing compatibility.

[XLIU-hub]

if position in upstream and downstream has been checked at the crossmapper level, maybe the downstream position assigning can be simplified as position = self._exons[1]? the same as the upstream.