arycal 0.2.2

Across Run dYnamic Chromatogram ALignment - A Rust-based tool for aligning extracted ion chromatograms (EICs) across multiple runs

ARYCAL Python Package

This crate contains the Python packaging for arycal, allowing you to install and use the arycal CLI from Python.

Installation

From PyPI (when published)

pip install arycal

From source

# Clone the repository
git clone https://github.com/singjc/arycal.git
cd arycal/crates/arycal_pyo3

# Install maturin (build tool)
pip install maturin

# Build and install the package
maturin develop --bindings bin

Usage

Command Line

Once installed, you can use arycal from the command line:

arycal config.json

Python API

You can also call arycal programmatically from Python:

import arycal

# Run arycal with arguments
exit_code = arycal.run_arycal(["config.json"])

# Or let it use sys.argv
arycal.main()

Building Wheels

To build distributable wheels for different platforms:

# From the arycal_pyo3 directory
cd crates/arycal_pyo3

# Build for the current platform
maturin build --release --bindings bin

# Build with specific features (e.g., MPI support)
maturin build --release --bindings bin --features mpi

The built wheels will be in the ../../dist/ directory and can be installed with:

pip install ../../dist/arycal-*.whl

Requirements

• Python 3.8 or higher
• Rust toolchain 1.84 or higher (for building from source)

Package Structure

• python/arycal/ - Python wrapper module
• pyproject.toml - Python package configuration
• examples/ - Example Python usage scripts
• ../arycal-cli/ - Rust CLI implementation

How It Works

This package uses maturin to build Python packages from Rust code. The bindings = "bin" configuration in pyproject.toml tells maturin to include the arycal binary in the Python wheel. The Python module provides a convenient wrapper to find and execute the binary.