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rustkmer Development Guidelines

Auto-generated from all feature plans. Last updated: 2025-11-28

Active Technologies

  • Rust 1.80+ stable channel + clap v4.0+ (CLI), serde (serialization), thiserror (error handling), anyhow (error handling), rayon (parallel processing), bio (FASTA/FASTQ parsing), memmap2 (memory-mapped files)
  • Custom binary database format (.rkdb) with indexed k-mer storage
  • Rust 1.80+ stable channel + clap v4.0+ (CLI), serde (serialization), rayon (parallel processing), bio (FASTA parsing), memmap2 (memory-mapped files)
  • Binary RKDB format for database storage
  • Rust 1.80+ stable + Python 3.8+ + PyO3 (Rust-Python bindings), setuptools-rust, serde, thiserror, anyhow, rayon
  • RKDB binary database format + memory-mapped file access
  • Rust 1.80+ stable channel + PyO3 0.23.4 (Python bindings), serde 1.0 (serialization), thiserror 2.0 (error handling), rayon 1.10 (parallel processing), clap 4.5 (CLI), bio 2.0 (genomics), memmap2 0.9 (memory mapping)
  • Hybrid JSON + binary .rkdb format for database persistence, memory-mapped files for large datasets
  • Rust 1.80+ stable + Python 3.8+ via PyO3 0.23.4 + PyO3 (Python bindings), serde (serialization), thiserror (error handling), rayon (parallel processing), clap (CLI), bio (genomics)
  • Single binary .rkdb files (RKDB format) - unified storage for both CLI and Python API
  • Rust 1.80+ stable + PyO3 0.23.4, clap, serde, byteorder, rayon, criterion
  • Binary RKDB files with memory-mapped access
  • Rust 1.80+ stable channel + clap v4.0+, serde, thiserror, anyhow, rayon, criterion, bio, memmap2
  • Rust 1.80+ stable channel + clap v4.5 (CLI), serde 1.0 (serialization), rayon 1.10 (parallel processing), memmap2 0.9 (memory mapping)
  • Binary RKDB format (custom k-mer database format)
  • Rust 1.80+ (stable) + Python 3.10+ + PyO3 0.23.4, serde, thiserror, anyhow, rayon, clap, bio, memmap2
  • RKDB二进制格式文件（自定义k-mer数据库格式）
  • Rust 1.80+ stable with Python 3.10+ via PyO3 0.23 + PyO3, serde, thiserror, rayon, memmap2
  • Rust 1.80+ stable, Python 3.10+ + PyO3 0.27.2 (Python bindings), serde 1.0 (serialization)
  • Binary RKDB files (custom k-mer database format)
  • Rust 1.80+ stable, Python 3.10+ + PyO3 0.27.2 (Python bindings), serde 1.0+ (序列化), thiserror 2.0.17 (错误处理), clap 4.5.53 (CLI)
  • 二进制RKDB文件（自定义k-mer数据库格式）
  • Rust 1.80+ stable, Python 3.10+ + PyO3 0.27.2 (Python bindings), pytest 8.4+ (testing), subprocess (CLI invocation)
  • Python 3.10+ + mkdocs, mkdocstrings[python], mkdocs-material theme
  • Documentation files in docs/ directory
  • Python 3.10+ with PyO3 0.27.2 bindings to Rust 1.80+ + pytest 9.0+, pytest-benchmark, hypothesis, numpy, matplotlib
  • Python 3.10+ (for the API), Rust 1.80+ (existing CLI) + subprocess (Python standard library), pytest for testing
  • Binary .rkdb files (existing format)
  • Rust 1.80+ (stable) + Python 3.10+ via PyO3 0.27.2
  • Rust 1.80+ (stable) + Python 3.10+ via subprocess
  • Rust 1.80+ stable channel (latest stable for performance optimizations) + clap v4.0+ (CLI with derive macros), serde (serialization), thiserror (error handling), anyhow (error handling), rayon (parallel processing), criterion (benchmarks), bio (FASTA/FASTQ parsing), memmap2 (memory-mapped files)

Project Structure

src/
tests/

Commands

cargo test [ONLY COMMANDS FOR ACTIVE TECHNOLOGIES][ONLY COMMANDS FOR ACTIVE TECHNOLOGIES] cargo clippy

Code Style

Rust 1.80+ stable channel (latest stable for performance optimizations): Follow standard conventions

Recent Changes

  • 001-python-fuzzy-query: Added Rust 1.80+ (stable) + Python 3.10+ via subprocess
  • 001-python-fuzzy-query: Added Rust 1.80+ (stable) + Python 3.10+ via PyO3 0.27.2
  • 001-python-binding: Added Python 3.10+ (for the API), Rust 1.80+ (existing CLI) + subprocess (Python standard library), pytest for testing
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