twobitreader 0.2.0

Fast 2bit file reader
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56

# Changelog

All notable changes to this project are documented here.

The format follows [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), and this
project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). The Rust
crate `twobitreader` and the Python package `twobitreader_rs` share a version number.

## [Unreleased]

## [0.2.0] - 2026-10-01

`twobitreader` is now available from Python as **`twobitreader_rs`**, built with PyO3 and
published as a wheel. The Python API mirrors the Rust one, with speed close to pure Rust.

### Added

- **Python bindings** (`twobitreader_rs`), exposing `TwobitReader` and `reverse_complement`.
  Available for CPython 3.9+ on Linux, macOS and Windows.
- **Free-threaded CPython support.** The extension is marked `gil_used = false` and the
  reader is immutable and shareable. A thread pool over batches scales across cores on a
  free-threaded build.
- **Type stubs** (`py.typed` and `__init__.pyi`), so editors and type checkers see full
  signatures for the compiled module.
- **`prefetch_inclusive`**, the 1-based counterpart of `prefetch`, which was missing.

### Changed

- CI moved from CircleCI to GitHub Actions, now also building and testing the Python wheel.

### Security

Hardened against malformed 2bit files; the issues were unbounded allocations triggered by
a crafted file, not memory-safety defects.

### Known issues

- Reading a 2bit file that another process modifies concurrently yields undefined behaviour.

## [0.1.1] - 2026-09-25

### Changed

- Documentation fixes and updated crate keywords.

## [0.1.0] - 2026-09-24

Initial release of the `twobitreader` crate: sequence extraction with `get`, batched
extraction with `get_batch`, exon concatenation with `concat`, reverse complement, and
`prefetch` for cold files. Sequence records are parsed lazily so that opening a large file
stays cheap. No git tag was made for this version.

[Unreleased]: https://github.com/andrewdelong/twobitreader-rust/compare/v0.2.0...HEAD
[0.2.0]: https://github.com/andrewdelong/twobitreader-rust/compare/v0.1.1...v0.2.0
[0.1.1]: https://github.com/andrewdelong/twobitreader-rust/releases/tag/v0.1.1
[0.1.0]: https://crates.io/crates/twobitreader/0.1.0