✨ add colabe install script

"""

Original code by @philopon

https://gist.github.com/philopon/a75a33919d9ae41dbed5bc6a39f5ede2

"""

import sys

import os

import requests

import subprocess

import shutil

from logging import getLogger, StreamHandler, INFO

logger = getLogger(__name__)

logger.addHandler(StreamHandler())

logger.setLevel(INFO)

def install(

        chunk_size=4096,

        file_name="Miniconda3-latest-Linux-x86_64.sh",

        url_base="https://repo.continuum.io/miniconda/",

        conda_path=os.path.expanduser(os.path.join("~", "miniconda")),

        version=None,

        gpu=True,

        add_python_path=True,

        force=False):

    """install deepchem from miniconda on Google Colab

    For GPU notebook

    (if you don't set the version, this script installs the latest package)

    ```

    import deepchem_installer

    deepchem_installer.install()

    ```

    For CPU notebook

    ```

    import deepchem_installer

    deepchem_installer.install(version="2.3.0", gpu=False)

    ```

    """

    python_path = os.path.join(

        conda_path,

        "lib",

        "python{0}.{1}".format(*sys.version_info),

        "site-packages",

    )

    if add_python_path and python_path not in sys.path:

        logger.info("add {} to PYTHONPATH".format(python_path))

        sys.path.append(python_path)

    if os.path.isdir(os.path.join(python_path, "deepchem")):

        logger.info("deepchem is already installed")

        if not force:

            return

        logger.info("force re-install")

    url = url_base + file_name

    python_version = "{0}.{1}.{2}".format(*sys.version_info)

    logger.info("python version: {}".format(python_version))

    if os.path.isdir(conda_path):

        logger.warning("remove current miniconda")

        shutil.rmtree(conda_path)

    elif os.path.isfile(conda_path):

        logger.warning("remove {}".format(conda_path))

        os.remove(conda_path)

    logger.info('fetching installer from {}'.format(url))

    res = requests.get(url, stream=True)

    res.raise_for_status()

    with open(file_name, 'wb') as f:

        for chunk in res.iter_content(chunk_size):

            f.write(chunk)

    logger.info('done')

    logger.info('installing miniconda to {}'.format(conda_path))

    subprocess.check_call(["bash", file_name, "-b", "-p", conda_path])

    logger.info('done')

    logger.info("installing deepchem")

    deepchem_package = "deepchem-gpu" if gpu else "deepchem"

    subprocess.check_call([

        os.path.join(conda_path, "bin", "conda"),

        "install",

        "--yes",

        "-c", "deepchem",

        "-c", "rdkit",

        "-c", "conda-forge",

        "-c", "omnia",

        "python=={}".format(python_version),

        deepchem_package if version is None else "{}=={}".format(deepchem_package, version)])

    logger.info("done")

    import deepchem

    logger.info("deepchem-{} installation finished!".format(deepchem.__version__))

if __name__ == "__main__":

    install()