packages.py

#@title
# Install rdkit # Enforce pytorch version 1.6.0   while True:pass  # saver  import pdb; pdb.set_trace()

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")),
        rdkit_version=None,
        add_python_path=True,
        force=False):
    """install rdkit from miniconda
    ```
    import rdkit_installer
    rdkit_installer.install()
    ```
    """
 
    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, "rdkit")):
        logger.info("rdkit 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 rdkit")
    subprocess.check_call([
        os.path.join(conda_path, "bin", "conda"),
        "install",
        "--yes",
        "-c", "rdkit",
        "python==3.7.3",
        "rdkit" if rdkit_version is None else "rdkit=={}".format(rdkit_version)])
    logger.info("done")
 
    import rdkit
    logger.info("rdkit-{} installation finished!".format(rdkit.__version__))
 
 
if __name__ == "__main__":
    install()

# If something breaks in the notebook it is probably related to a mismatch between the Python version, CUDA or torch
import torch
pytorch_version = f"torch-{torch.__version__}+cu{torch.version.cuda.replace('.', '')}.html"
!pip install --no-index torch-scatter -f https://pytorch-geometric.com/whl/$pytorch_version
!pip install --no-index torch-sparse -f https://pytorch-geometric.com/whl/$pytorch_version
!pip install --no-index torch-cluster -f https://pytorch-geometric.com/whl/$pytorch_version
!pip install --no-index torch-spline-conv -f https://pytorch-geometric.com/whl/$pytorch_version
!pip install torch-geometric


! pip install torch-scatter -f https://data.pyg.org/whl/torch-1.10.0+cu111.html
! pip install torch-sparse -f https://data.pyg.org/whl/torch-1.10.0+cu111.html
! pip install torch-geometric

! pip install pubchempy
! pip install molvs