Merge pull request #1870 from nd-02110114/add-colab-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 will install 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()