Website Update

vsag96 · Nov 8, 2017 · bd92e5c · bd92e5c
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Showing 24 changed files with 211 additions and 345 deletions.
diff --git a/devtools/jenkins/build_and_upload_docs.sh b/devtools/jenkins/build_and_upload_docs.sh
@@ -0,0 +1,27 @@
+#!/usr/bin/env bash
+# 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 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
+sphinx-build -b html docs/source docs/_build
+# Copy 
+cp -r docs/_build/ website/docs/
+echo "About to push docs to s3"
+python devtools/jenkins/push-docs-to-s3.py
diff --git a/devtools/jenkins/convert_to_rst.py b/devtools/jenkins/convert_to_rst.py
@@ -0,0 +1,35 @@
+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()
diff --git a/devtools/travis-ci/push-docs-to-s3.py → devtools/jenkins/push-docs-to-s3.py b/devtools/travis-ci/push-docs-to-s3.py → devtools/jenkins/push-docs-to-s3.py
diff --git a/devtools/travis-ci/after_sucess.sh b/devtools/travis-ci/after_sucess.sh
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -34,8 +34,7 @@
 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
@@ -65,9 +64,9 @@
 # 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.

diff --git a/docs/source/notebooks/BACE.rst b/docs/source/notebooks/BACE.rst
diff --git a/docs/source/notebooks/Multitask_Networks_on_MUV.rst b/docs/source/notebooks/Multitask_Networks_on_MUV.rst
diff --git a/docs/source/notebooks/dataset_preparation.rst b/docs/source/notebooks/dataset_preparation.rst
diff --git a/docs/source/notebooks/graph_convolutional_networks_for_tox21.rst b/docs/source/notebooks/graph_convolutional_networks_for_tox21.rst
diff --git a/docs/source/notebooks/index.rst b/docs/source/notebooks/index.rst
diff --git a/docs/source/notebooks/mnist.rst b/docs/source/notebooks/mnist.rst