[TheNetherWatcher]

proc_ann_bytes and its helpers decode an annotation file by indexing the Nx2 NumPy byte array one element at a time (filebytes[bpi, 1], np.int64(...), .astype("i1")), and build each aux note with "".join(chr(c) for c in ...). Each of those makes a NumPy scalar, which is slow in a Python loop.

This converts the byte pairs to a list once with .tolist() and does the rest with plain ints. Signed subtype/num bytes are converted with a small helper, and aux notes are decoded with bytes(...).decode("latin-1"), which gives the same characters as chr() for 0-255. Since no NumPy scalars are involved any more, the decoding no longer depends on NumPy's scalar type promotion rules, which caused the OverflowError in #493 and #522 (already worked around on main with np.int64).

The output is unchanged: I compared every field (sample, symbol, subtype, chan, num, aux_note, fs, label_store, custom labels, and dtypes) for all 15 annotation files in sample-data, with and without sampto, against main.

Benchmark (median, Apple Silicon, alternating runs of main and this branch; the machine was busy, so the absolute numbers are noisy):

file	main	this PR	speedup
rdann 100.atr	4.10 ms	2.01 ms	2.0x
rdann 1003.atr	6.24 ms	3.31 ms	1.9x
rdann 12726.wabp (many aux notes)	16.5 ms	6.4 ms	2.6x
rdann 03700181.gqrsl	2.99 ms	1.64 ms	1.8x
rdann, 100,000 beats with some aux notes (written with wrann)	176 ms	76 ms	2.3x
proc_ann_bytes only, 12726.wabp	22.4 ms	7.6 ms	2.9x

Tests: added a round-trip test for subtype, chan and num values (including negative subtypes). uv run pytest -m "not network" passes, tests/test_annotation.py passes with network tests, ruff format/ruff check are clean, and the docs build without warnings. Added a changelog entry.

Open PRs #491 and #498 also touch annotation.py, but only how the file is opened and read into bytes, not the decoding, so they shouldn't conflict beyond nearby lines.

[tompollard]

Thanks, this looks good to me. I checked the decoding against main: rdann converts subtype/chan/num with lists_to_int_arrays and samples to int64 afterwards, so the output dtypes are unchanged, _to_signed_char matches .astype("i1"), and latin-1 gives the same characters as chr() for 0–255. Existing tests already cover SKIP pairs (huge.qrs, 12726.anI) and odd-length aux notes (1003.atr), and the new round-trip test covers signed subtypes.