Change

.readthedocs.yml

@@ -0,0 +1,23 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+    - requirements: docs/requirements.txt

README.md

@@ -5,8 +5,9 @@
 [![PyPI version](https://badge.fury.io/py/deepchem.svg)](https://badge.fury.io/py/deepchem)
 
 
-DeepChem aims to provide a high quality open-source toolchain that
-democratizes the use of deep-learning in drug discovery, materials science, quantum chemistry, and biology.
+DeepChem aims to provide a high quality open-source toolchain
+that democratizes the use of deep-learning in drug discovery,
+materials science, quantum chemistry, and biology.
 
 ### Table of contents:
 
@@ -128,20 +129,15 @@ via this installation procedure.
    ```
 
 ## Getting Started
-Two good tutorials to get started are [Graph Convolutional Networks](https://deepchem.io/docs/notebooks/graph_convolutional_networks_for_tox21.html) and [Multitask_Networks_on_MUV](https://deepchem.io/docs/notebooks/Multitask_Networks_on_MUV.html). Follow along with the tutorials to see how to predict properties on molecules using neural networks.
+The DeepChem project maintains an extensive colelction of [tutorials](https://github.com/deepchem/deepchem/tree/master/examples/tutorials). All tutorials are designed to be run on Google colab (or locally if you prefer). Tutorials are arranged in a suggested learning sequence which will take you from beginner to proficient at molecular machine learning and computational biology more broadly.
 
-Afterwards you can go through other [tutorials](https://deepchem.io/docs/notebooks/index.html), and look through our examples in the `examples` directory. To apply `deepchem` to a new problem, try starting from one of the existing examples or tutorials and modifying it step by step to work with your new use-case. If you have questions or comments you can raise them on our [gitter](https://gitter.im/deepchem/Lobby).
-
-### Benchmarks
-In depth benchrmarking tables for DeepChem models are available on [MoleculeNet.ai](https://moleculenet.ai)
+After working through the tutorials, you can also go through other [examples](https://github.com/deepchem/deepchem/tree/master/examples). To apply `deepchem` to a new problem, try starting from one of the existing examples or tutorials and modifying it step by step to work with your new use-case. If you have questions or comments you can raise them on our [gitter](https://gitter.im/deepchem/Lobby).
 
 ### Gitter
 Join us on gitter at [https://gitter.im/deepchem/Lobby](https://gitter.im/deepchem/Lobby). Probably the easiest place to ask simple questions or float requests for new features.
 
 ## About Us
-DeepChem is possible due to notable contributions from many people including Peter Eastman, Evan Feinberg, Joe Gomes, Karl Leswing, Vijay Pande, Aneesh Pappu, Bharath Ramsundar and Michael Wu (alphabetical ordering).  DeepChem was originally created by [Bharath Ramsundar](http://rbharath.github.io/) with encouragement and guidance from [Vijay Pande](https://pande.stanford.edu/).
-
-DeepChem started as a [Pande group](https://pande.stanford.edu/) project at Stanford, and is now developed by many academic and industrial collaborators. DeepChem actively encourages new academic and industrial groups to contribute!
+DeepChem is managed by a team of open source contributors. Anyone is free to join and contribute!
 
 ## Citing DeepChem
 

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/conf.py

@@ -0,0 +1,59 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'deepchem'
+copyright = '2020, deepchem-contributors'
+author = 'deepchem-contributors'
+
+# The full version, including alpha/beta/rc tags
+release = '2.3.0'
+
+
+# -- General configuration ---------------------------------------------------
+
+master_doc = 'index'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ['sphinx.ext.autodoc'
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+import sphinx_rtd_theme
+html_theme = 'sphinx_rtd_theme'
+html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']

docs/index.rst

@@ -0,0 +1,63 @@
+.. deepchem documentation master file, created by
+   sphinx-quickstart on Sat Mar  7 12:21:39 2020.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+deepchem
+=========
+
+
+.. raw:: html
+
+  <embed>
+    <a href="https://github.com/deepchem/deepchem"><img style="position: absolute; top: 0; right: 0; border: 0;" src="https://camo.githubusercontent.com/365986a132ccd6a44c23a9169022c0b5c890c387/68747470733a2f2f73332e616d617a6f6e6177732e636f6d2f6769746875622f726962626f6e732f666f726b6d655f72696768745f7265645f6161303030302e706e67" alt="Fork me on GitHub" data-canonical-src="https://s3.amazonaws.com/github/ribbons/forkme_right_red_aa0000.png"></a>
+  </embed>
+
+
+**DeepChem is a python deep learning framework for molecular machine learning.**
+
+
+Star us on `on GitHub`_. You can also get started by visiting our `Tutorials <https://github.com/deepchem/deepchem/tree/master/examples/tutorials>`_
+
+.. _`on GitHub`: https://github.com/deepchem/deepchem
+
+.. important:: Join our `community gitter <https://forms.gle/9TSdDYUgxYs8SA9e8>`_ to discuss DeepChem 
+
+Quick Start
+-----------
+
+First, install deepchem with: ``pip install deepchem``
+
+
+.. code-block:: python
+
+    import deepchem 
+
+
+Getting Involved
+----------------
+
+- `https://forum.deepchem.io`_: For discussions about research, development or any general questions.
+
+.. _`GitHub Issues`: https://github.com/deepchem/torchchem/issues
+.. _`Pull Requests`: https://github.com/deepchem/torchchem/pulls
+
+
+
+.. toctree::
+   :maxdepth: -1
+   :caption: Installation
+
+   installation.rst
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/requirements.txt

@@ -0,0 +1 @@
+sphinx_rtd_theme