Merge pull request #2002 from nd-02110114/fix-dos

Fix docs bug

.travis.yml

@@ -32,6 +32,8 @@ script:
 - if [ $TRAVIS_PYTHON_VERSION == '3.7' ]; then
   find ./deepchem -name "*.py" ! -name '*load_dataset_template.py' | xargs python -m doctest -v; fi
 - bash devtools/travis-ci/test_format_code.sh
+- if [ $TRAVIS_PYTHON_VERSION == '3.7' ]; then
+  cd docs && pip install -r requirements.txt && make clean html && cd ..; fi
 after_success:
 - echo $TRAVIS_SECURE_ENV_VARS
 - coveralls

deepchem/models/layers.py

@@ -447,10 +447,14 @@ class AttnLSTMEmbedding(tf.keras.layers.Layer):
   metric that allows a network to modify its internal notion of
   distance.
 
+  See references [1]_ [2]_ for more details.
+
   References
   ----------
-  .. [1] Matching Networks for One Shot Learning, https://arxiv.org/abs/1606.04080
-  .. [2] Order Matters: Sequence to sequence for sets, https://arxiv.org/abs/1511.06391
+  .. [1] Vinyals, Oriol, et al. "Matching networks for one shot learning." 
+         Advances in neural information processing systems. 2016.
+  .. [2] Vinyals, Oriol, Samy Bengio, and Manjunath Kudlur. "Order matters:
+         Sequence to sequence for sets." arXiv preprint arXiv:1511.06391 (2015).
   """
 
   def __init__(self, n_test, n_support, n_feat, max_depth, **kwargs):

deepchem/utils/conformers.py

@@ -21,7 +21,7 @@ class ConformerGenerator(object):
   3. Prune conformers using an RMSD threshold.
 
   Note that pruning is done _after_ minimization, which differs from the
-  protocol described in the references.
+  protocol described in the references [1]_ [2]_.
 
   References
   ----------

docs/conf.py

@@ -142,11 +142,11 @@ def linkcode_resolve(domain, info):
       fn, start=os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
 
   if 'dev' in deepchem.__version__:
-    return "https://github.com/deepchem/deepchem/blob/master/deepchem/%s%s" % (
-        fn, linespec)
+    return "https://github.com/deepchem/deepchem/blob/master/%s%s" % \
+      (fn, linespec)
   else:
-    return "https://github.com/deepchem/deepchem/blob/v%s/deepchem/%s%s" % (
-        deepchem.__version__, fn, linespec)
+    return "https://github.com/deepchem/deepchem/blob/%s/%s%s" % \
+      (deepchem.__version__, fn, linespec)
 
 
 # Document __init__ methods

docs/moleculenet.rst

@@ -1,31 +1,35 @@
 MoleculeNet
 ===========
-The DeepChem library is packaged alongside the MoleculeNet suite of datasets. One of the most important parts of machine learning applications is finding a suitable dataset. The MoleculeNet suite has curated a whole range of datasets and loaded them into DeepChem :code:`dc.data.Dataset` objects for convenience.
+The DeepChem library is packaged alongside the MoleculeNet suite of datasets.
+One of the most important parts of machine learning applications is finding a suitable dataset.
+The MoleculeNet suite has curated a whole range of datasets and loaded them into DeepChem
+:code:`dc.data.Dataset` objects for convenience.
 
 Contributing a new dataset to MoleculeNet
 -----------------------------------------
 
-If you are proposing a new dataset to be included in the MoleculeNet benchmarking suite, 
-please follow the instructions below. Please review the `datasets already available in MolNet <http://moleculenet.ai/datasets-1>`_ before contributing.
+If you are proposing a new dataset to be included in the 
+MoleculeNet benchmarking suite, please follow the instructions below. 
+Please review the `datasets already available in MolNet`_ before contributing.
 
-0. Read the `Contribution guidelines <https://github.com/deepchem/deepchem/blob/master/CONTRIBUTING.md>`_.
+0. Read the `Contribution guidelines`_.
 
-1. Open an `issue <https://github.com/deepchem/deepchem/issues>`_ to discuss the dataset you want to add to MolNet.
+1. Open an `issue`_ to discuss the dataset you want to add to MolNet.
 
-2. Implement a function in the `deepchem.molnet.load_function <https://github.com/deepchem/deepchem/tree/master/deepchem/molnet/load_function>`_ module following the template function `deepchem.molnet.load_function.load_mydataset <https://github.com/deepchem/deepchem/blob/master/deepchem/molnet/load_function/load_mydataset.py>`_. Specify which featurizers, transformers, and splitters (available from `deepchem.molnet.defaults <https://github.com/deepchem/deepchem/tree/master/deepchem/molnet/defaults.py>`_) are supported for your dataset. 
+2. Implement a function in the `deepchem.molnet.load_function`_ 
+   module following the template function `deepchem.molnet.load_function.load_dataset_template`_.
+   Specify which featurizers, transformers, and splitters (available from
+   `deepchem.molnet.defaults`_) are supported for your dataset. 
 
-3. Add your load function to `deepchem.molnet.__init__.py <https://github.com/deepchem/deepchem/blob/master/deepchem/molnet/__init__.py>`_ for easy importing.
+3. Add your load function to `deepchem.molnet.__init__.py`_ for easy importing.
 
 4. Prepare your dataset as a .tar.gz or .zip file. Accepted filetypes include CSV, JSON, and SDF.
 
-5. Ask a member of the technical steering committee to add your .tar.gz or .zip file to the DeepChem AWS bucket. Modify your load function to pull down the dataset from AWS.
+5. Ask a member of the technical steering committee to add your .tar.gz or .zip file 
+   to the DeepChem AWS bucket. Modify your load function to pull down the dataset from AWS.
 
-6. Submit a [WIP] PR (Work in progress pull request) following the PR `template <https://github.com/deepchem/deepchem/blob/master/docs/molnet_pr_template.md>`_.  
+6. Submit a [WIP] PR (Work in progress pull request) following the PR `template`_.
 
-Load Dataset Template
----------------------
-
-.. autofunction:: deepchem.molnet.load_function.load_dataset_template.load_mydataset
 
 BACE Dataset
 ------------
@@ -197,3 +201,13 @@ UV Datasets
 -----------
 
 .. autofunction:: deepchem.molnet.load_uv
+
+
+.. _`datasets already available in MolNet`: http://moleculenet.ai/datasets-1
+.. _`Contribution guidelines`: https://github.com/deepchem/deepchem/blob/master/CONTRIBUTING.md
+.. _`issue`: https://github.com/deepchem/deepchem/issues
+.. _`deepchem.molnet.load_function`: https://github.com/deepchem/deepchem/tree/master/deepchem/molnet/load_function
+.. _`deepchem.molnet.load_function.load_dataset_template`: https://github.com/deepchem/deepchem/blob/master/deepchem/molnet/load_function/load_dataset_template.py
+.. _`deepchem.molnet.defaults`: https://github.com/deepchem/deepchem/tree/master/deepchem/molnet/defaults.py
+.. _`deepchem.molnet.__init__.py`: https://github.com/deepchem/deepchem/blob/master/deepchem/molnet/__init__.py
+.. _`template`: https://github.com/deepchem/deepchem/blob/master/.github/PULL_REQUEST_TEMPLATE/molnet_pr_template.md

docs/tutorial.rst

@@ -40,7 +40,7 @@ DeepChem is under very active development at present, so we recommend using our
 
 .. code-block:: bash
 
-    conda install -y -c rdkit rdkit
+    conda install -y -c conda-forge rdkit