v0.29.0

Feat

• flat: dummy padding for flank_tokens and variant-windows in get_variants_flat
• flat: thread unknown_token onto Haps for dummy token fill
• flat: fill_empty_groups fills flank_tokens with unknown_token
• flat: _FlatVariantWindows.fill_empty_groups (all-unknown_token dummy)
• flat: _fill_empty_fixed kernel for flank_tokens empty-row dummy fill
• flat: double_buffered carries flat buffers without awkward re-wrap
• flat: slice_chunk handles flat containers
• flat: shm write/read flat types (kind 1/2/3) without awkward
• flat: instance-axis getitem on flat containers
• flat: with_settings(dummy_variant=...) + export DummyVariant + non-variant guard
• flat: Haps.dummy_variant + apply empty-group fill in get_variants_flat
• flat: DummyVariant + empty-group fill kernels + fill_empty_groups
• flat: export FlatVariantWindows and VarWindowOpt
• flat: VarWindowOpt-driven per-allele variant-windows (window|allele matrix)
• flat: VarWindowOpt + per-allele window/allele computation + optional window fields
• flat: register variant-windows kind end-to-end
• flat: attach flank_tokens / emit windows from get_variants_flat
• flat: ref/alt window assembly + tokenization
• flat: _FlatWindow + _FlatVariantWindows two-level token types
• flat: compute ride-along flank tokens from reference
• flat: thread flank_length + token LUT settings onto Haps
• flat: byte->int token LUT builder for flank tokenization
• flat: A flat variant decode (get_variants_flat) with no awkward
• flat: A0 flat passthrough for seqs/haps/annot/reference outputs
• flat: output_format field + with_output_format + QueryView.flat_output
• flat: export FlatRagged/FlatAnnotatedHaps/FlatVariants/FlatAlleles
• flat: _FlatVariants/_FlatAlleles types with to_ragged()

Fix

• torch: reject variant-windows output over buffered transport up front
• flat: allow dummy_variant with variant-windows output kind
• flat: _fill_empty_seq preserves input dtype for token windows
• flat: reject flat+buffered variants with flank tokens at construction
• flat: harden _FlatVariants slice for flank_tokens; test polish
• flat: with_settings(dummy_variant=False) is a no-op on non-variant datasets
• flat: narrow _seqs to Haps before flank-field replace (pyrefly)
• flat: clear error for variant-windows + active tracks; drop dead alias
• flat: clear error for VarWindowOpt(ref='allele') on REF-less dataset
• flat: clearer splice-unsupported messages for variant-windows
• flat: windows reshape must keep ploidy dim ([1:-1] not [1:-2])
• flat: guard flank-without-LUT, document Haps fields, test validation paths
• flat: shape-driven _FlatAlleles.to_ragged fixes scalar-scalar squeeze byte-identity
• flat: _FlatAlleles.reshape re-appends ragged axis; docstrings + 2D-index test
• flat: add _FlatAlleles.squeeze so _FlatVariants.squeeze works

Refactor

• flat: clarify flat-variant reader names; annotated shm round-trip test
• flat: retire awkward _get_variants; ragged variants decode via flat path
• flat: normalize _FlatVariants.reshape shape arg; drop redundant import