feat!: Rust COITrees backend for gvl.Table; promote to public API

[d-laub]

Summary

Replaces gvl.Table's polars-bio overlap backend with a self-contained Rust COITrees module (src/tables.rs, RustTable PyO3 class), and promotes Table from genvarloader.experimental to the public API.

This:

• Fixes the max_mem blow-up during gvl.write()/update() for Table/annot tracks — the Rust streaming writer bounds the working set to one region's overlaps + one contig's lazily-built trees, and raises if a single region exceeds the budget.
• Removes the non-deterministic polars-bio segfault source (#395) for the Table path. (polars-bio remains a transitive dep via genoray's var_ranges, so it is not fully removed from the tree.)
• Promotes Table to the public API (from genvarloader import Table); deletes the experimental subpackage and the [table] extra.

Architecture

• src/tables.rs — immutable interval store grouped by (chrom_code, sample_code), a COITrees overlap engine (count + materialize), and a streaming writer. Trees are built lazily one contig at a time and dropped on contig change.
• python/genvarloader/_table.py — thin polars constructor/validator that factor-encodes the frame (sorted by (chrom, sample_id, start)) and delegates all overlap to RustTable.
• On-disk format is byte-identical to the existing reader (INTERVAL_DTYPE, 12 bytes/row LE; i64 LE offsets), so datasets read back unchanged via np.memmap.

Breaking change

genvarloader.experimental.Table is removed; use genvarloader.Table. The [table] extra is gone.

Testing

• Rust: cargo tests for store grouping, COITrees count (vs brute force), ordered interval materialization, and the streaming writer (byte-identical to a count→offsets→intervals oracle + max_mem error).
• Python: brute-force numpy oracle unit tests + hypothesis property tests (100 examples each) for count_intervals, _intervals_from_offsets, and annot_overlap; a max_mem regression test; the end-to-end annot-DataFrame integration test is now un-skipped and runs in CI.
• Full tree green: 800 passed, 20 skipped, 4 xfailed; cargo test --release 12 passed; ruff + pyrefly clean.

Notes / follow-up

• annot_overlap now returns an all-empty RaggedIntervals for an empty annotation BED (previously crashed).
• Equal-start tie ordering follows the Table's stored (post-sort) order — see the parity test docstring.

🤖 Generated with Claude Code