Initial website change

# -----------------------------------

echo "About to install numpydoc, s3cmd"

pip install numpydoc s3cmd msmb_theme sphinx_rtd_theme

pip install -I sphinx==1.3.5 sphinx_bootstrap_theme

conda list -e

mkdir -p docs/_build

echo "About to build docs"

import sys

import os

import shlex

import sphinx_bootstrap_theme

# 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.

#sys.path.insert(0, os.path.abspath('.'))

sys.path.insert(0, os.path.abspath("../../deepchem"))

sys.path.insert(0, os.path.abspath("../sphinxext"))

# -- General configuration ------------------------------------------------

    'sphinx.ext.ifconfig',

    'numpydoc',

    'sphinx.ext.viewcode',

    'notebook_sphinxext'

]

autosummary_generate = True

# built documents.

#

# The short X.Y version.

version = '0.1'

version = '1.2'

# The full version, including alpha/beta/rc tags.

release = '0.1'

release = '1.2'

# The language for content autogenerated by Sphinx. Refer to documentation

# for a list of supported languages.

# List of patterns, relative to source directory, that match files and

# directories to ignore when looking for source files.

exclude_patterns = []

exclude_patterns = ['_build', '**.ipynb_checkpoints']

# The reST default role (used for this markup: `text`) to use for all

# documents.

# a list of builtin themes.

import msmb_theme

html_theme = 'msmb_theme'

html_theme = 'bootstrap'

# Theme options are theme-specific and customize the look and feel of a theme

# further.  For a list of options available for each theme, see the

# documentation.

#html_theme_options = {}

html_theme_options = {

    'source_link_position': "footer",

    'bootswatch_theme': "flatly",

    'navbar_sidebarrel': False,

    'bootstrap_version': "3",

    'navbar_links': [("Notebooks", "notebooks/index")],

}

# Add any paths that contain custom themes here, relative to this directory.

html_theme_path = [

  msmb_theme.get_html_theme_path()

]

#print("sphinx_bootstrap_theme.get_html_theme_path()")

html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()

#html_theme_path = [

#  #msmb_theme.get_html_theme_path(),

#  sphinx_bootstrap_theme.get_html_theme_path()

#]

# The name for this set of Sphinx documents.  If None, it defaults to

# "<project> v<release> documentation".

# The name of an image file (relative to this directory) to place at the top

# of the sidebar.

html_logo = '_static/logo.png' 

#html_logo = '../website/static/img/logo.png' 

# The name of an image file (within the static path) to use as favicon of the

# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32

# 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']

#html_static_path = ['../website/static/']

# Add any extra paths that contain custom files (such as robots.txt or

# .htaccess) here, relative to this directory. These files are copied

BACE

====

.. notebook:: BACE 

.. _notebooks:

Tutorials

========

The following tutorials show off various aspects or capabilities of

DeepChem. They can be run interactively in Jupyter (IPython) notebook.

Download the `notebook files

<https://github.com/deepchem/deepchem/tree/master/examples/notebooks>`_ and open

them in Jupyter::

    $ jupyter notebook

.. To make the ipython rendered images show up, each rst file must be

   in its own directory.

.. toctree::

   :maxdepth: 2

   :titlesonly:

   BACE 

Contributing tutorials 

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

Do you have a neat example of using DeepChem? Format your code

into an IPython notebook and submit a pull request!

.. vim: tw=75

# Copied from the yt_project, commit e8fb57e

# yt/doc/extensions/notebook_sphinxext.py

#  https://bitbucket.org/yt_analysis/yt/src/e8fb57e66ca42e26052dadf054a5c782740abec9/doc/extensions/notebook_sphinxext.py?at=yt

# Almost completely re-written by Matthew Harrigan to use nbconvert v4

from __future__ import print_function

import os

import shutil

from sphinx.util.compat import Directive

from docutils import nodes

from docutils.parsers.rst import directives

import nbformat

from nbconvert import HTMLExporter, PythonExporter

from nbconvert.preprocessors import ExecutePreprocessor

def export_html(nb, f):

    config = {

        'Exporter': {'template_file': 'basic',

                     'template_path': ['./sphinxext/']},

        'ExtractOutputPreprocessor': {'enabled': True},

        'CSSHTMLHeaderPreprocessor': {'enabled': True}

    }

    exporter = HTMLExporter(config)

    body, resources = exporter.from_notebook_node(

        nb, resources={'output_files_dir': f['nbname']})

    for fn, data in resources['outputs'].items():

        bfn = os.path.basename(fn)

        with open("{destdir}/{fn}".format(fn=bfn, **f), 'wb') as res_f:

            res_f.write(data)

    return body

def export_python(nb, destfn):

    exporter = PythonExporter()

    body, resources = exporter.from_notebook_node(nb)

    with open(destfn, 'w') as f:

        f.write(body)

class NotebookDirective(Directive):

    """Insert an evaluated notebook into a document

    """

    required_arguments = 1

    optional_arguments = 1

    option_spec = {'skip_exceptions': directives.flag}

    final_argument_whitespace = True

    def run(self):

        f = {

            'docdir': setup.confdir,

            'builddir': setup.app.builder.outdir,

            'nbname': self.arguments[0],

        }

        f['nbpath'] = "{docdir}/../../examples/notebooks/{nbname}.ipynb".format(**f)

        f['destdir'] = "{builddir}/notebooks/{nbname}".format(**f)

        if not os.path.exists(f['destdir']):

            os.makedirs(f['destdir'])

        f['uneval'] = "{destdir}/{nbname}.ipynb".format(**f)

        f['eval'] = "{destdir}/{nbname}.eval.ipynb".format(**f)

        f['py'] = "{destdir}/{nbname}.py".format(**f)

        # 1. Uneval notebook

        shutil.copyfile(f['nbpath'], f['uneval'])

        with open(f['nbpath']) as nb_f:

            nb = nbformat.read(nb_f, as_version=4)

        # 2. Python

        export_python(nb, f['py'])

        # 3. HTML (execute first)

        executer = ExecutePreprocessor()

        executer.preprocess(nb, {})

        html = export_html(nb, f)

        # 4. Eval'd notebook

        with open(f['eval'], 'w') as eval_f:

            nbformat.write(nb, eval_f)

        # Create link to notebook and script files

        link_rst = "({uneval}; {eval}; {py})".format(

            uneval=formatted_link(f['uneval']),

            eval=formatted_link(f['eval']),

            py=formatted_link(f['py']),

        )

        rst_file = self.state_machine.document.attributes['source']

        self.state_machine.insert_input([link_rst], rst_file)

        # create notebook node

        nb_node = notebook_node('', html, format='html', source='nb_path')

        nb_node.source, nb_node.line = (self.state_machine

                                        .get_source_and_line(self.lineno))

        # add dependency

        self.state.document.settings.record_dependencies.add(f['nbpath'])

        return [nb_node]

class notebook_node(nodes.raw):

    pass

def formatted_link(path):

    return "`%s <%s>`__" % (os.path.basename(path), path)

def visit_notebook_node(self, node):

    self.visit_raw(node)

def depart_notebook_node(self, node):

    self.depart_raw(node)

def setup(app):

    setup.app = app

    setup.config = app.config

    setup.confdir = app.confdir

    app.add_node(notebook_node,

                 html=(visit_notebook_node, depart_notebook_node))

    app.add_directive('notebook', NotebookDirective)