Source code for dosma.utils.collect_env

import os
import sys

import h5py
import nibabel
import nipype
import numpy as np
import pandas as pd
import pydicom
import scipy as sp
import skimage
from tabulate import tabulate

__all__ = ["collect_env_info"]


def collect_env_info():
    """Collect environment information for reporting issues.

    Run this function when reporting issues on Github.
    """
    data = []
    data.append(("sys.platform", sys.platform))
    data.append(("Python", sys.version.replace("\n", "")))
    data.append(("numpy", np.__version__))

    try:
        import dosma  # noqa

        data.append(("dosma", dosma.__version__ + " @" + os.path.dirname(dosma.__file__)))
    except ImportError:
        data.append(("dosma", "failed to import"))

    # Required packages
    data.append(("h5py", h5py.__version__))
    data.append(("nibabel", nibabel.__version__))
    data.append(("nipype", nipype.__version__))
    data.append(("pandas", pd.__version__))
    data.append(("pydicom", pydicom.__version__))
    data.append(("scipy", sp.__version__))
    data.append(("skimage", skimage.__version__))

    # Optional packages
    try:
        import cupy

        data.append(("cupy", cupy.__version__))
    except ImportError:
        pass

    try:
        import tensorflow

        data.append(("tensorflow", tensorflow.__version__))
    except ImportError:
        pass

    try:
        import keras

        data.append(("keras", keras.__version__))
    except ImportError:
        pass

    try:
        import SimpleITK as sitk

        data.append(("SimpleITK", sitk.__version__))
    except ImportError:
        pass

    try:
        import sigpy

        data.append(("sigpy", sigpy.__version__))
    except ImportError:
        pass

    env_str = tabulate(data)
    return env_str