Skip to main content

Changelog

All notable changes to zsasa. See GitHub Releases for full details.

v0.2.3 — 2026-03-10​

Fixed​

  • Windows build: fall back to heap allocation where POSIX mmap is unavailable
  • Windows build: replace std.mem.zeroes with undefined for JsonlStreamWriter placeholder
  • Third-party license: add BSD-2-Clause notice for libxdrfile in src/xtc.zig, create THIRD_PARTY_NOTICES.md
  • Correct Lahuta author name (Besian I. Sejdiu)

Changed​

  • Remove legacy docs/ directory (migrated to website)
  • Add acknowledgments section to README and comparison page

v0.2.2 — 2026-03-10​

Added​

  • Bitmask variants for Python MD wrappers: use_bitmask option for MDTraj, MDAnalysis, XTC, and DCD integrations
  • JSONL streaming batch output: --format=jsonl for memory-efficient batch results
  • Documentation site overhaul: comparison page, landing page, Python autodoc, CLI docs split, benchmarks overview, changelog, all benchmark pages rewritten

Performance​

  • mmap file reading, flat buffer NeighborList, trajectory parallel worker alignment, 64KB write buffer for JSONL

Fixed​

  • Corrected Lahuta/RustSASA metadata in benchmark docs
  • Various PDB generation fixes (chain names, serial numbers, CRYST1)

v0.2.1 — 2026-02-25​

Changed​

  • Relaxed bitmask n_points from fixed 64/128/256 to any value 1–1024, with internal storage expanded from [4]u64 to [16]u64

v0.2.0 — 2026-02-25​

Added​

  • Bitmask-optimized Shrake-Rupley (--use-bitmask): precomputed occlusion bitmask LUT with SIMD 4-neighbor batching
  • Batch and trajectory mode bitmask support (shared LUT, built once)
  • Python use_bitmask=True parameter for calculate_sasa() and calculate_sasa_batch()
  • C API bitmask exports (zsasa_calc_sr_bitmask, etc.)

Changed​

  • BREAKING: CLI now requires subcommands: zsasa calc, zsasa batch, zsasa traj
  • BREAKING: Removed --parallelism option
  • Trajectory mode: --include-hydrogens is now the default

Removed​

  • Pipeline parallelism mode

Performance​

  • E. coli batch (f32, 10 threads, 128 points): 4.92s → 2.57s with bitmask SR (1.9x speedup)

v0.1.3 — 2026-02-25​

Added​

  • Directory batch processing C API and Python process_directory()
  • Docusaurus documentation site

Fixed​

  • json_writer performance regression: reverted to in-memory string building (~8x speedup)

Removed​

  • Streaming output (--stream, --stream-format, --stream-output)

v0.1.2 — 2026-02-22​

Added​

  • DCD trajectory reader (native Zig): NAMD/CHARMM DCD support with endianness auto-detection
  • JSON streaming output for batch processing
  • Zig package manager distribution (zig fetch)
  • TOML format support for custom classifier configs
  • Fuzz tests for parsers

v0.1.1 — 2026-02-22​

Added​

  • Pre-built wheels for Linux, macOS, and Windows via cibuildwheel
  • Windows support (Zig build, tests, CLI, Python bindings)
  • PyPI publish workflow with OIDC trusted publishing
  • CODE_OF_CONDUCT.md, CITATION.cff, issue/PR templates