Merge pull request #1917 from nd-02110114/update-docker-doc

  - [Install latest package with conda](#install-via-conda-recommendation)

  - [Install latest package with pip (WIP)](#install-via-pip-wip)

  - [Install from source](#install-from-source)

  - [Install using a Docker (WIP)](#install-using-a-docker-wip)

  - [Install using a Docker](#install-using-a-docker)

- [FAQ and Troubleshooting](#faq-and-troubleshooting)

- [Getting Started](#getting-started)

- [Contributing to DeepChem](/CONTRIBUTING.md)

Check [this link](https://conda.io/projects/conda/en/latest/user-guide/install/index.html) for more information about the installation of conda environments.

### Install using a Docker (WIP)

### Install using a Docker

### Build the image from Dockerfile

If you want to install using a docker, you can pull two kinds of images.  

DockerHub : https://hub.docker.com/repository/docker/deepchemio/deepchem

We created [sample Dockerfiles](https://github.com/deepchem/deepchem/tree/master/docker) based on the `nvidia/cuda:10.1-cudnn7-devel` image.  

If you want to build your own deepchem environment, these files may be helpful.  

- `docker/x.x.x` : build an image by using conda package manager (x.x.x is a version of deepchem)  

- `docker/master` : build an image from master branch of deepchem source codes

- `deepchemio/deepchem:x.x.x`

  - Image built by using a conda package manager (x.x.x is a version of deepchem)

  - The x.x.x image is built when we push x.x.x. tag

  - Dockerfile is put in `docker/conda-forge` directory

- `deepchemio/deepchem:latest`

  - Image built by the master branch of deepchem source codes

  - The latest image is built every time we commit to the master branch

  - Dockerfile is put in `docker/master` directory

### Use the official deepchem image (WIP)

We couldn't check if this introduction works well or not.

First, you pull the latest stable deepchem docker image.

First, you pull the image you want to use.

```bash

docker pull deepchemio/deepchem

docker pull deepchemio/deepchem:2.3.0

```

Then, you create a container based on our latest image.

Then, you create a container based on the image.

```bash

docker run -it deepchemio/deepchem

docker run --rm -it deepchemio/deepchem:2.3.0

```

If you want GPU support:

```bash

# If nvidia-docker is installed

nvidia-docker run -it deepchemio/deepchem

docker run --runtime nvidia -it deepchemio/deepchem

nvidia-docker run --rm -it deepchemio/deepchem:2.3.0

docker run --runtime nvidia --rm -it deepchemio/deepchem:2.3.0

# If nvidia-container-toolkit is installed

docker run --gpus all -it deepchemio/deepchem

docker run --gpus all --rm -it deepchemio/deepchem:2.3.0

```

You are now in a docker container which deepchem was installed. You can start playing with it in the command line.

```

(deepchem) root@xxxxxxxxxxxxx:~/mydir# python

Python 3.6.10 |Anaconda, Inc.| (default, May  8 2020, 02:54:21)

[GCC 7.3.0] on linux

Type "help", "copyright", "credits" or "license" for more information.

>>> import deepchem as dc

```

You are now in a docker container whose python has deepchem installed.

If you want to check the tox21 benchmark:

```bash

# you can start playing with it in the command line

pip install jupyter

ipython

import deepchem as dc

# you can run our tox21 benchmark

cd /deepchem/examples

python benchmark.py -d tox21

(deepchem) root@xxxxxxxxxxxxx:~/mydir# wget https://raw.githubusercontent.com/deepchem/deepchem/master/examples/benchmark.py

(deepchem) root@xxxxxxxxxxxxx:~/mydir# python benchmark.py -d tox21 -m graphconv -s random

```

## FAQ and Troubleshooting

import unittest

import deepchem as dc

class TestInit(unittest.TestCase):

  def test_version(self):

    assert dc.__version__

FROM nvidia/cuda:10.1-cudnn7-devel

FROM nvidia/cuda:10.0-cudnn7-devel

# Install some utilities

RUN apt-get update && \

    import deepchem

Pip and Docker Installation

Pip Installation

---------------------------

We are working on improving our pip and docker installation

We are working on improving our pip installation

capabilities. We'll update our docs once we have more information on

how to do this well.

Docker Installation

------------------

If you want to install using a docker, you can pull two kinds of images from `DockerHub`_.

- **deepchemio/deepchem:x.x.x**

  - Image built by using a conda package manager (x.x.x is a version of deepchem)

  - This image is built when we push x.x.x. tag

  - Dockerfile is put in `docker/conda-forge`_ directory

- **deepchemio/deepchem:latest**

  - Image built by the master branch of deepchem source codes

  - This image is built every time we commit to the master branch

  - Dockerfile is put in `docker/master`_ directory

First, you pull the image you want to use.

.. code-block:: bash

    docker pull deepchemio/deepchem:2.3.0

Then, you create a container based on the image.

.. code-block:: bash

    docker run --rm -it deepchemio/deepchem:2.3.0

If you want GPU support:

.. code-block:: bash

    # If nvidia-docker is installed

    nvidia-docker run --rm -it deepchemio/deepchem:2.3.0

    docker run --runtime nvidia --rm -it deepchemio/deepchem:2.3.0

    # If nvidia-container-toolkit is installed

    docker run --gpus all --rm -it deepchemio/deepchem:2.3.0

You are now in a docker container which deepchem was installed.

You can start playing with it in the command line.

.. code-block:: bash

    (deepchem) root@xxxxxxxxxxxxx:~/mydir# python

    Python 3.6.10 |Anaconda, Inc.| (default, May  8 2020, 02:54:21)

    [GCC 7.3.0] on linux

    Type "help", "copyright", "credits" or "license" for more information.

    >>> import deepchem as dc

If you want to check the tox21 benchmark:

.. code-block:: bash

    # you can run our tox21 benchmark

    (deepchem) root@xxxxxxxxxxxxx:~/mydir# wget https://raw.githubusercontent.com/deepchem/deepchem/master/examples/benchmark.py

    (deepchem) root@xxxxxxxxxxxxx:~/mydir# python benchmark.py -d tox21 -m graphconv -s random

Installing from Source

----------------------

.. _`DeepChem Tutorials`: https://github.com/deepchem/deepchem/tree/master/examples/tutorials

.. _`forum post`: https://forum.deepchem.io/t/getting-deepchem-running-in-colab/81

.. _`install from source`: https://github.com/deepchem/deepchem/blob/master/README.md#linux-64-bit-installation-from-source

.. _`DockerHub`: https://hub.docker.com/repository/docker/deepchemio/deepchem

.. _`docker/conda-forge`: https://github.com/deepchem/deepchem/tree/master/docker/conda-forge

.. _`docker/master`: https://github.com/deepchem/deepchem/tree/master/docker/master

.. _`install from source`: https://github.com/deepchem/deepchem/blob/master/README.md#install-from-source

    pytest-cov `

    flaky

pip install -U tensorflow tensorflow-probability

pip install -U tensorflow==2.2 tensorflow-probability==0.10