Commit 4a2ce9d3 authored by nd-02110114's avatar nd-02110114
Browse files

🐛 fix docs bug

parent 546e2db6
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+2 −0
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@@ -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_OS_NAME" != "windows" ]]; then
  cd docs && pip install -r requirements.txt && make clean html; fi
after_success:
- echo $TRAVIS_SECURE_ENV_VARS
- coveralls
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@@ -142,10 +142,10 @@ 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" % (
    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" % (
    return "https://github.com/deepchem/deepchem/blob/%s/%s%s" % (
        deepchem.__version__, fn, linespec)


+27 −13
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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//molnet_pr_template.md
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@@ -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