Merge pull request #406 from lilleswing/394-Format-Tests-cr

[style]

based_on_style = google

indent_width = 2

- conda install -c conda-forge protobuf=3.1.0

- conda install -c omnia mdtraj

- pip install tensorflow==0.12.1

- pip install yapf==0.16.0

- python setup.py install

script:

- nosetests -v deepchem --nologcapture

- bash devtools/travis-ci/test_format_code.sh

after_success:

- echo $TRAVIS_SECURE_ENV_VARS

- source devtools/travis-ci/after_sucess.sh

Once you've got a sense of how the package works, we encourage the use of Github issues to discuss more complex changes,  raise requests for new features or propose changes to the global architecture of DeepChem. Once consensus is reached on the issue, please submit a PR with proposed modifications. All contributed code to DeepChem will be reviewed by a member of the DeepChem team, so please make sure your code style and documentation style match our guidelines!

### Code Style Guidelines

DeepChem broadly follows the [Google Python Style Guide](https://google.github.io/styleguide/pyguide.html). In terms of practical changes, the biggest effect is that all code uses 2-space indents instead of 4-space indents. We encourage new contributors to make use of [pylint](https://www.pylint.org/) with the following command

```

pylint --disable=invalid-name --indent-string "  " --extension-pkg-whitelist=numpy [file.py]

DeepChem uses [yapf](https://github.com/google/yapf) to autoformat code.  We created a git pre-commit hook to make this process easier.

``` bash

cp devtools/travis-ci/pre-commit .git/hooks

pip install yapf==0.16.0

```

Aim for a score of at least 8/10 on contributed files.

### Documentation Style Guidelines

DeepChem uses [NumPy style documentation](https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt). Please follow these conventions when documenting code, since we use [Sphinx+Napoleon](http://www.sphinx-doc.org/en/stable/ext/napoleon.html) to automatically generate docs on [deepchem.io](deepchem.io).

#!/bin/sh

CHANGED_FILES=`git diff --cached --name-only | grep .py`

if [ -z $CHANGED_FILES ]

then

    echo "No Python Files Changed"

else

    echo $CHANGED_FILES

    yapf -i $CHANGED_FILES

    git diff --name-only --cached | xargs -l git add

fi

#!/bin/bash -e

CHANGED_FILES=`git diff --name-only $TRAVIS_COMMIT_RANGE | grep .py$`

exit_success () {

    echo "Passed Formatting Test"

    exit 0

}

if [ -z $CHANGED_FILES ]

then

    echo "No Python Files Changed"

    exit_success

fi

yapf -d $CHANGED_FILES > diff.txt

if [ -s diff.txt ]

then

    cat diff.txt

    echo ""

    echo "Failing Formatting Test"

    echo "Please run yapf over the files changed"

    echo "pip install yapf"

    echo "yapf -i $CHANGED_FILES"

    exit 1

else

    exit_success

fi

exit 1