Merge pull request #1870 from nd-02110114/add-colab-install-script

install script for Google Colab

scripts/colab_install.py

@@ -0,0 +1,99 @@
+"""
+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()