<commit_before>#! /usr/bin/env python

##############################################################################
##  Phylogenomic tools package.
##
##  Copyright 2015 <NAME>
##  All rights reserved.
##
##  See "LICENSE.txt" for terms and conditions of usage.
##
##  If you use this work or any portion thereof in published work,
##  please cite it as:
##
##     REF
##
##############################################################################

import sys
import os

#HACK OF DENDROPY setup.py BELOW

###############################################################################
# setuptools/distutils/etc. import and configuration

try:
    import ez_setup
    try:
        ez_setup_path = " ('" + os.path.abspath(ez_setup.__file__) + "')"
    except OSError:
        ez_setup_path = ""
    sys.stderr.write("using ez_setup%s\n" %  ez_setup_path)
    ez_setup.use_setuptools()
    import setuptools
    try:
        setuptools_path = " ('" +  os.path.abspath(setuptools.__file__) + "')"
    except OSError:
        setuptools_path = ""
    sys.stderr.write("using setuptools%s\n" % setuptools_path)
    from setuptools import setup, find_packages
except ImportError, e:
    sys.stderr.write("using distutils\n")
    from distutils.core import setup
    sys.stderr.write("using canned package list\n")
    PACKAGES = ['terraphy']
    EXTRA_KWARGS = {}
else:
    sys.stderr.write("searching for packages\n")
    PACKAGES = find_packages()
    EXTRA_KWARGS = dict(
        install_requires = ['setuptools', 'dendropy', ], 
        include_package_data=True
    )

PACKAGE_DIRS = [p.replace(".", os.path.sep) for p in PACKAGES]
PACKAGE_INFO = [("% 40s : %s" % p) for p in zip(PACKAGES, PACKAGE_DIRS)]
sys.stderr.write("packages identified:\n%s\n" % ("\n".join(PACKAGE_INFO)))
ENTRY_POINTS = {}

###############################################################################
# Script paths

SCRIPT_SUBPATHS = [
    ['scripts', 'terraphy.main.py'],
]
SCRIPTS = [os.path.join(*i) for i in SCRIPT_SUBPATHS]
sys.stderr.write("\nscripts identified: %s\n" % "\n\t".join(SCRIPTS))

###############################################################################
# setuptools/distuils command extensions

try:
    from setuptools import Command
except ImportError:
    sys.stderr.write("setuptools.Command could not be imported: setuptools extensions not available\n")
else:
    sys.stderr.write("setuptools command extensions are available\n")
    command_hook = "distutils.commands"
    ENTRY_POINTS[command_hook] = []

    ###########################################################################

###############################################################################
# Main setup

__version__ = 1.0
EXTRA_KWARGS["zip_safe"] = True

### compose long description ###
long_description = open('README.txt').read()

setup(name='terraphy',
      version=__version__,
      author='<NAME>',
      author_email='<EMAIL>',
      url='https://github.com/zwickl/terraphy',
      description='Scripts for analyzing phylogenetic terraces.',
      license='GPL3',
      packages=PACKAGES,
      package_dir=dict(zip(PACKAGES, PACKAGE_DIRS)),
      scripts = SCRIPTS,
      long_description=long_description,
      entry_points = ENTRY_POINTS,<commit_msg>properly install dependencies<commit_after>#! /usr/bin/env python

##############################################################################
##  Phylogenomic tools package.
##
##  Copyright 2015 <NAME>
##  All rights reserved.
##
##  See "LICENSE.txt" for terms and conditions of usage.
##
##  If you use this work or any portion thereof in published work,
##  please cite it as:
##
##     REF
##
##############################################################################

import sys
import os

#HACK OF DENDROPY setup.py BELOW

###############################################################################
# setuptools/distutils/etc. import and configuration

from setuptools import setup, find_packages

sys.stderr.write("searching for packages\n")
PACKAGES = find_packages()
EXTRA_KWARGS = dict(
    install_requires = ['dendropy', ], 
    include_package_data=True,
    zip_safe=True
    )


PACKAGE_DIRS = [p.replace(".", os.path.sep) for p in PACKAGES]
PACKAGE_INFO = [("% 40s : %s" % p) for p in zip(PACKAGES, PACKAGE_DIRS)]
sys.stderr.write("packages identified:\n%s\n" % ("\n".join(PACKAGE_INFO)))
ENTRY_POINTS = {}

###############################################################################
# Script paths

SCRIPT_SUBPATHS = [
    ['scripts', 'terraphy.main.py'],
]
SCRIPTS = [os.path.join(*i) for i in SCRIPT_SUBPATHS]
sys.stderr.write("\nscripts identified: %s\n" % "\n\t".join(SCRIPTS))

###############################################################################
# setuptools/distuils command extensions

try:
    from setuptools import Command
except ImportError:
    sys.stderr.write("setuptools.Command could not be imported: setuptools extensions not available\n")
else:
    sys.stderr.write("setuptools command extensions are available\n")
    command_hook = "distutils.commands"
    ENTRY_POINTS[command_hook] = []

    ###########################################################################

###############################################################################
# Main setup

__version__ = 1.0

### compose long description ###
long_description = open('README.txt').read()

setup(name='terraphy',
      version=__version__,
      author='<NAME>',
      author_email='<EMAIL>',
      url='https://github.com/zwickl/terraphy',
      description='Scripts for analyzing phylogenetic terraces.',
      license='GPL3',
      packages=PACKAGES,
      package_dir=dict(zip(PACKAGES, PACKAGE_DIRS)),
      scripts = SCRIPTS,
      long_description=long_description,
      entry_points = ENTRY_POINTS,
{'fraction_non_alphanumeric': 0.29507066528783177, 'fraction_numerical': 0.0031023784901758012, 'mean_word_length': 4.861616161616162, 'pattern_counts': {'":': 0, '<': 9, '<?xml version=': 0, '>': 9, 'https://': 2, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3642406', 'n_tokens_mistral': 1759, 'n_tokens_neox': 1672, 'n_words': 358}