Website Update

#!/usr/bin/env bash

echo '$TRAVIS_PULL_REQUEST $TRAVIS_BRANCH'

echo $TRAVIS_PULL_REQUEST $TRAVIS_BRANCH

if [[ "$TRAVIS_PULL_REQUEST" != "false" ]]; then

    echo "This is a pull request. No deployment will be done."; exit 0

fi

if [[ "$TRAVIS_BRANCH" != "master" ]]; then

    echo "No deployment on BRANCH='$TRAVIS_BRANCH'"; exit 0

fi

# Create the docs and push them to S3

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

envname=`cat /dev/urandom | tr -dc 'a-zA-Z0-9' | fold -w 16 | head -n 1`

sed -i -- 's/tensorflow$/tensorflow-gpu/g' scripts/install_deepchem_conda.sh

bash scripts/install_deepchem_conda.sh $envname

source activate $envname

python setup.py install

echo "About to install numpydoc, s3cmd"

pip install -I sphinx==1.3.5 sphinx_bootstrap_theme

pip install numpydoc s3cmd msmb_theme sphinx_rtd_theme nbsphinx

conda list -e

pip install numpydoc s3cmd msmb_theme sphinx_rtd_theme nbsphinx delegator.py

conda install -y -q jupyter

conda install -y -q matplotlib

cd examples/notebooks

python ../../devtools/jenkins/convert_to_rst.py

cd ../..

mkdir -p docs/_build

echo "About to build docs"

sphinx-apidoc -f -o docs/source deepchem

# Copy 

cp -r docs/_build/ website/docs/

echo "About to push docs to s3"

python devtools/travis-ci/push-docs-to-s3.py

python devtools/jenkins/push-docs-to-s3.py

 No newline at end of file

import os

import delegator

import shutil

target_dir = "../../docs/source/notebooks/"

def convert_to_rst(fname):

    cmd = "jupyter-nbconvert --to rst %s" % fname

    c = delegator.run(cmd)

    base_name = os.path.splitext(fname)[0]

    image_files = "%s_files" % base_name

    new_path = os.path.join(target_dir, image_files)

    if os.path.isdir(new_path):

        shutil.rmtree(new_path)

    if os.path.isdir(image_files):

        shutil.move(image_files, target_dir)

    rst_file = '%s.rst' % base_name

    new_path = os.path.join(target_dir, rst_file)

    if os.path.isfile(new_path):

        os.remove(new_path)

    shutil.move(rst_file, target_dir)

def main():

    fnames = os.listdir('./')

    fnames = [x for x in filter(lambda x: x.endswith('ipynb') > 0, fnames)]

    for fname in fnames:

        convert_to_rst(fname)

if __name__ == "__main__":

    main()

extensions = [

    'sphinx.ext.autodoc', 'sphinx.ext.autosummary', 'sphinx.ext.doctest',

    'sphinx.ext.intersphinx', 'sphinx.ext.coverage', 'sphinx.ext.mathjax',

    'sphinx.ext.ifconfig', 'numpydoc', 'sphinx.ext.viewcode',

    'notebook_sphinxext'

    'sphinx.ext.ifconfig', 'numpydoc', 'sphinx.ext.viewcode'

]

autosummary_generate = True

# built documents.

#

# The short X.Y version.

version = '1.2'

version = '1.3.1'

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

release = '1.2'

release = '1.3.1'

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

# for a list of supported languages.

Modeling Inhibitors of BACE-1

=============================

.. notebook:: BACE