0.21.1

Fix

• rag: handle indexed empty row in Ragged.to_numpy

0.21.0

Feat

• rag: add Ragged.hash / sp.rag.hash (md5/sha256/rapidhash)
• rust: add _ragged_hash kernel (md5/sha256/rapidhash, rayon)

0.20.0

Feat

• rag: to_numpy(validate=False) skips the uniformity scan
• rag: contiguous-slice fast path for record R=2 getitem
• rag: contiguous-slice fast path for record R=1 getitem
• rag: contiguous-slice fast path for opaque-string getitem
• rag: contiguous-slice fast path for R=2 getitem
• rag: contiguous-slice fast path for R=1 getitem

Fix

• rag: preserve middle fixed dim in record R=2 slice shape-tail

Perf

• rust: release the GIL during PyO3 kernel compute
• rag: lean from_offsets — elide ascontiguousarray, gate size-check behind validate

0.19.1

bump: version 0.19.0 → 0.19.1

0.19.0

Feat

• rag: port reverse_complement to seqpro-core Rust; rag layer numba-free
• rag: port to_padded to seqpro-core Rust, drop numba kernel

Refactor

• rag: truthful _ops docstring; guard reverse_complement_inplace empty offsets
• rust: extract pyo3-free seqpro-core crate owning the Ragged layout

0.18.0

Feat

• rag: reshape/squeeze/to_packed preserve Ragged subclass
• rag: getitem preserves subclass on positional indexing
• rag: add _with_layout subclass-preserving constructor

Fix

• rag: non-tuple record indexing matches numpy (A[x] == A[(x,)])

0.17.0

Feat

• rag: concatenate() along ragged axis (Rust kernel)
• rag: to_packed() on record and opaque-string-under-axis Ragged
• wire rag-gate pixi task; record throughput gate outcome
• string-conversion op cells for Ragged throughput gate
• nested R=2 op cells for Ragged throughput gate
• record (SoA) op cells for Ragged throughput gate
• single-level op cells for Ragged throughput gate
• harness core for rust-vs-awkward Ragged throughput gate
• _ingest bridge for R=2 + string-under-axis (oracle interop)
• nested record indexing + record-aware to_packed/to_padded/to_numpy
• nested + string-under-axis record fields sharing full offsets list
• R=2 lengths/squeeze/reshape
• per-axis nested to_padded + rectangular to_numpy (R=2); trailing-dim support in to_padded
• nested to_packed via nested_pack kernel
• nested_pack Rust kernel + binding for two-level pack
• per-group inner mask/int-array indexing via nested_gather
• nested_gather Rust kernel + binding for per-group middle selection
• per-group inner int/slice indexing (rag[:, k], rag[:, a:b])
• R=2 tuple indexing + leaf access via peel chaining
• R=2 outer-row indexing (lazy gather, peel to 1-level)
• string-under-axis leaf + nested to_chars/to_strings
• nested constructors from_offsets(list)/from_lengths(tuple) for R=2
• validate R=2 nested ragged layouts; cap at R<=2
• ingest/emit record layouts via awkward bridge (oracle interop)
• record to_numpy/to_padded dicts; raise view/ufunc on records
• record-aware to_packed (one shared packed offsets across fields)
• per-field squeeze/reshape on record Ragged
• record row-axis indexing (slice/mask -> record, int -> dict)
• record field access (key/attr) and setitem mutation
• record-branch properties (data/dtype/offsets/shape/fields/state)
• add Ragged.from_fields record constructor and rag.zip alias
• add RecordLayout value object and validation arm
• add zero-copy to_chars/to_strings between opaque-string and char Ragged
• disambiguate opaque-string vs char layout by presence of None in shape
• report np.dtype('S') for opaque-string Ragged (string/char duality)
• rust: ragged_validate and ragged_select kernels
• rag: awkward ingestion and to_ak shim
• rag: to_numpy, to_packed, to_padded
• rag: squeeze and reshape on regular dims
• rag: element-wise ufunc interop
• rag: getitem indexing and slicing
• rag: state predicates and view
• rag: Ragged constructors and core properties
• rag: RaggedLayout value object + validation
• translate: self-contained Rust OHE<->AA path with native drop
• translate: route truncate_stop through Rust
• translate: route unknown=drop compaction through Rust
• translate: route ragged bytes pad path through Rust
• translate: route dense pad path through Rust
• rust: add codon-stride translate kernels
• tokenize: route ragged path through Rust, drop Numba gather
• tokenize: route dense path through Rust _tokenize
• rust: add tokenize LUT gather kernel

Fix

• rag: to_ak() on multi-leading-axis record Ragged
• rag: _core.Ragged/tokenize fixes found via genvarformer audit
• rag: add len, np.newaxis support, and element-wise fancy indexing to _core.Ragged
• rag: _ops.to_padded record detection works for both _array and _core backends
• rag: _core.to_numpy returns dict for records (restore designed contract); update _array-era test
• rag: correct _core getitem tuple routing for rag_dim==1 found via SeqPro own-suite audit
• rag: port _ops + _core to_packed/is_rag_dtype/to_numpy to _core object model
• rag: precise _core getitem routing — _core contract + genoray parity both green
• rag: repair _core.Ragged getitem regressions (string leaf, to_strings, r2 int array)
• rag: match _array is_base semantics for non-ndarray base
• rag: _core.Ragged fixes found via genoray audit
• bench: time to_packed on unpacked input so single-level pack compares equal work
• forward --repeats CLI flag into time_callable
• R=2 is_contiguous checks all offset levels; guard string-under-axis to_packed/to_numpy
• panic-safety in nested_pack (checked_mul, elem>0, o0-range guard)
• reject negative inner-slice bounds in rag[:, a:b]
• -O-safe record guards on is_string/to_chars/to_strings; note latent S4 over-acceptance
• raise TypeError on np.asarray of a record Ragged (-O-safe, was a bare assert)
• rag: reject mismatched boolean masks and bounds-check ragged_select
• translate: handle empty dense input in unknown=drop path

Refactor

• rag: delete awkward _array backend; relocate interop to _ak_interop
• resolve clippy findings for -D warnings
• rag: route index/validate hot paths through Rust
• rag: use NDArrayOperatorsMixin for operator dunders
• tokenize: restore np.take/Numba path; Rust port regressed vs baseline

Perf

• validate pack output size up-front; test parallel pack path
• Rust single-level pack kernel for to_packed (parallel gather)
• opt-in Ragged validation (default off) + slice indexing fast-path
• drop redundant per-field copy in record to_packed; align record is_base with single-level one-indirection rule
• translate: optimize LUT gather kernel (validity table + coarse chunking)
• translate: add rayon parallel path for large inputs

0.16.0

Feat

• tokenize: add parallel escape hatch overriding the size heuristic

0.15.2

Fix

• tokenize: accept readonly input on parallel path; guard int32 out=

Perf

• tokenize: parallel Numba LUT gather with small-input np.take fast path
• tokenize: use 256-entry LUT gather instead of linear scan

0.15.1

Fix

• rag: traverse IndexedArray in unbox/_extract_list_offsets