Installation Instructions for DeLeakage

Python bindings for the Contamination C++ implementation, built with pybind11, CMake, and OpenMP.

Overview

This package exposes the C++ implementation as a Python module named deContamination. It is intended for use in scripted workflows and batch experiments without manual compilation.

Installation

Install the wheel file with pip:

python3 -m pip install decontamination-0.1.0-cp310-cp310-linux_x86_64.whl

After installation, verify the module:

python3 -c "import deContamination; print(deContamination.__file__)"

Usage

A minimal test script is shown below.

# test_decontamination.py
from pathlib import Path
import traceback
import deContamination as dc


def main():
    out_dir = Path("./output/")
    out_dir.mkdir(parents=True, exist_ok=True)

    print("Loaded module from:", deContamination.__file__)
    print("Available attributes:")
    print([x for x in dir(deContamination) if not x.startswith("_")])

    params = {
        "G": 300,
        "K": 3,
        "N_nei": 49,
        "N": 10000,
        "N_MB": 50,
        "N_tail": 454,
        "n_record": 3000,
        "seed": 123,
        "output_list": "./output/",
        "data_name": "./data/Y_obs.txt",
        "nei_name": "./data/nei_list.txt",
        "dist_name": "./data/nei_dist.txt",
        "label_name": "./data/Y_label.txt",
        "cell_size_name": "./data/cell_size.txt",
        "MB_dir": "./data/MB/",
    }

    print("Start running...")
    try:
        ret = dc.run(
            params["G"],
            params["K"],
            params["N_nei"],
            params["N"],
            params["N_MB"],
            params["N_tail"],
            params["n_record"],
            params["seed"],
            params["output_list"],
            params["data_name"],
            params["nei_name"],
            params["dist_name"],
            params["label_name"],
            params["cell_size_name"],
            params["MB_dir"],
        )
        print("Finished. Return value:", ret)
    except Exception:
        print("Run failed with exception:")
        traceback.print_exc()


if __name__ == "__main__":
    main()

Run the script with:

python3 test_decontamination.py

Input files

The package expects the same input files used by the original C++ workflow. Update the paths in the Python script to match your local directory layout.

Typical inputs include:

• observed data file
• neighbor list file
• neighbor distance file
• label file
• cell size file
• MB directory
• true Z file, if enabled in your binding

Output

Results are written to the output directory passed to the Python function. In the example above, all outputs are written under ./output/.

Notes

• The module name is deContamination.
• The callable function name depends on the pybind11 binding.
• The argument order must match the C++ binding exactly.
• If the wheel is rebuilt for another Python version or operating system, a new wheel is required.