Setup basic package structure.

AUTHORS.rst

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+
+Authors
+=======
+
+* Youngjune Park - https://github.com/iron-lion
+* Dohoon Lee - https://github.com/dohlee

CHANGELOG.rst

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+
+Changelog
+=========
+
+0.1.0 (2018-07-15)
+------------------
+
+* First release on PyPI.

LICENSE

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+BSD 2-Clause License
+
+Copyright (c) 2018, Dohoon Lee
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following
+conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this list of conditions and the following
+  disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following
+  disclaimer in the documentation and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

MANIFEST.in

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+graft docs
+graft src
+graft ci
+graft tests
+
+include .bumpversion.cfg
+include .coveragerc
+include .cookiecutterrc
+include .editorconfig
+
+include AUTHORS.rst
+include CHANGELOG.rst
+include CONTRIBUTING.rst
+include LICENSE
+include README.rst
+
+include tox.ini .travis.yml appveyor.yml
+
+global-exclude *.py[cod] __pycache__ *.so *.dylib

Pipfile

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+[[source]]
+url = "https://pypi.org/simple"
+verify_ssl = true
+name = "pypi"
+
+[packages]
+numpy = "*"
+networkx = "*"
+
+[dev-packages]
+
+[requires]
+python_version = "3.6"

docs/authors.rst

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+.. include:: ../AUTHORS.rst

docs/changelog.rst

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+.. include:: ../CHANGELOG.rst

docs/conf.py

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+# -*- coding: utf-8 -*-
+from __future__ import unicode_literals
+
+import os
+
+
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.coverage',
+    'sphinx.ext.doctest',
+    'sphinx.ext.extlinks',
+    'sphinx.ext.ifconfig',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.todo',
+    'sphinx.ext.viewcode',
+]
+if os.getenv('SPELLCHECK'):
+    extensions += 'sphinxcontrib.spelling',
+    spelling_show_suggestions = True
+    spelling_lang = 'en_US'
+
+source_suffix = '.rst'
+master_doc = 'index'
+project = 'njsd'
+year = '2018'
+author = 'Dohoon Lee'
+copyright = '{0}, {1}'.format(year, author)
+version = release = '0.1.0'
+
+pygments_style = 'trac'
+templates_path = ['.']
+extlinks = {
+    'issue': ('https://github.com/dohlee/python-njsd/issues/%s', '#'),
+    'pr': ('https://github.com/dohlee/python-njsd/pull/%s', 'PR #'),
+}
+# on_rtd is whether we are on readthedocs.org
+on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
+
+if not on_rtd:  # only set the theme if we're building docs locally
+    html_theme = 'sphinx_rtd_theme'
+
+html_use_smartypants = True
+html_last_updated_fmt = '%b %d, %Y'
+html_split_index = False
+html_sidebars = {
+   '**': ['searchbox.html', 'globaltoc.html', 'sourcelink.html'],
+}
+html_short_title = '%s-%s' % (project, version)
+
+napoleon_use_ivar = True
+napoleon_use_rtype = False
+napoleon_use_param = False

docs/contributing.rst

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+.. include:: ../CONTRIBUTING.rst

docs/index.rst

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+========
+Contents
+========
+
+.. toctree::
+   :maxdepth: 2
+
+   readme
+   installation
+   usage
+   reference/index
+   contributing
+   authors
+   changelog
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+

docs/installation.rst

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+============
+Installation
+============
+
+At the command line::
+
+    pip install njsd

docs/readme.rst

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+.. include:: ../README.rst

docs/reference/index.rst

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+Reference
+=========
+
+.. toctree::
+    :glob:
+
+    njsd*

docs/reference/njsd.rst

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+njsd
+====
+
+.. testsetup::
+
+    from njsd import *
+
+.. automodule:: njsd
+    :members:

docs/requirements.txt

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+sphinx>=1.3
+sphinx-rtd-theme
+-e .

docs/spelling_wordlist.txt

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+builtin
+builtins
+classmethod
+staticmethod
+classmethods
+staticmethods
+args
+kwargs
+callstack
+Changelog
+Indices

docs/usage.rst

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+=====
+Usage
+=====
+
+To use njsd in a project::
+
+	import njsd

setup.cfg

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+[bdist_wheel]
+universal = 1
+
+
+[flake8]
+max-line-length = 140
+exclude = */migrations/*
+
+[nosetests]
+verbosity = 2
+
+[isort]
+force_single_line = True
+line_length = 120
+known_first_party = njsd
+default_section = THIRDPARTY
+forced_separate = test_njsd
+not_skip = __init__.py
+skip = migrations

setup.py

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+#!/usr/bin/env python
+# -*- encoding: utf-8 -*-
+from __future__ import absolute_import
+from __future__ import print_function
+
+import io
+import re
+from glob import glob
+from os.path import basename
+from os.path import dirname
+from os.path import join
+from os.path import splitext
+
+from setuptools import find_packages
+from setuptools import setup
+
+
+def read(*names, **kwargs):
+    return io.open(
+        join(dirname(__file__), *names),
+        encoding=kwargs.get('encoding', 'utf8')
+    ).read()
+
+
+setup(
+    name='njsd',
+    version='0.1.0',
+    license='BSD 2-Clause License',
+    description='Calculate Jensen-Shannon Divergence between two gene expression profiles to measure transcriptome-based intratumor heterogeneity(tITH).',
+    # long_description='%s\n%s' % (
+    #     re.compile('^.. start-badges.*^.. end-badges', re.M | re.S).sub('', read('README.rst')),
+    #     re.sub(':[a-z]+:`~?(.*?)`', r'``\1``', read('CHANGELOG.rst'))
+    # ),
+    long_description=read('README.md'),
+    url='https://github.com/iron-lion/nJSD',
+    packages=find_packages('src'),
+    package_dir={'': 'src'},
+    py_modules=[splitext(basename(path))[0] for path in glob('src/*.py')],
+    include_package_data=True,
+    zip_safe=False,
+    classifiers=[
+        # complete classifier list: http://pypi.python.org/pypi?%3Aaction=list_classifiers
+        'Development Status :: 5 - Production/Stable',
+        'Intended Audience :: Developers',
+        'License :: OSI Approved :: BSD License',
+        'Operating System :: Unix',
+        'Operating System :: POSIX',
+        'Operating System :: Microsoft :: Windows',
+        'Programming Language :: Python',
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.4',
+        'Programming Language :: Python :: 3.5',
+        'Programming Language :: Python :: 3.6',
+        'Topic :: Utilities',
+        'Topic :: Bioinformatics',
+    ],
+    keywords=[
+        # eg: 'keyword1', 'keyword2', 'keyword3',
+    ],
+    install_requires=[
+        # eg: 'aspectlib==1.1.1', 'six>=1.7',
+        'numpy>=1.14.5',
+        'networkx>=2.1',
+    ],
+    extras_require={
+        # eg:
+        #   'rst': ['docutils>=0.11'],
+        #   ':python_version=="2.6"': ['argparse'],
+    },
+    entry_points={
+        'console_scripts': [
+            'njsd = njsd.cli:main',
+        ]
+    },
+)