<commit_before>#!/usr/bin/env python3

from setuptools import setup
import setuptools
from setuptools.command.install_lib import install_lib
import os
import sys


executable_list = [
    'makeblastdb',
    'tandem',
    'tandem.exe',
    'qvality',
    'percolator',
    'percolator_2_08',
    'omssacl',
    'myrimatch_2_1_138',
    'myrimatch.exe',
    'MSAmanda.exe',
    'PepNovo_bin',
    'novor.bat',
    'novor.sh',
    'PepNovo.exe',
]

if sys.platform in ['win32']:
    class my_install_lib(setuptools.command.install_lib.install_lib):
        pass
else:
    class my_install_lib(setuptools.command.install_lib.install_lib):
        def run(self):
            setuptools.command.install_lib.install_lib.run(self)
            for fn in self.get_outputs():
                print('>>>>>>>>>>>>>>>>>>>', fn )
                if os.path.basename(fn) in executable_list:
                    # copied from setuptools source - make the binaries executable
                    mode = ((os.stat(fn).st_mode) | 0o555) & 0o7777
                    setuptools.log.info("changing mode of %s to %o", fn, mode)
                    os.chmod(fn, mode)


# We store our version number in a simple text file:
version_path = os.path.join(
    os.path.dirname(__file__),
    'ursgal', 'version.txt'
)
with open(version_path, 'r') as version_file:
    ursgal_version = version_file.read().strip()


setup(
    name='ursgal',
    version = ursgal_version,
    packages = ['ursgal'],
    package_dir = {'ursgal': 'ursgal'},
    description='ursgal',
    package_data = {
        'ursgal' : [
            'version.txt',
            'wrappers/*.py',
            'resources/*/*/*',
            'resources/*/*/*/*',
            'resources/*/*/*/*/*',
        ]
    },
    install_requires = [
        'pymzml',
        'regex',
        'pyqms',
        "pyahocorasick >= 1.1.4;sys_platform!='win32'"
    ],
    long_description = 'Universal Python module combining common bottom-up proteomics tools for large-scale analysis',
    author = '<NAME>, <NAME>, <NAME>, <NAME> and <NAME>',
    author_email = '<EMAIL>',
    url = 'http://ursgal.github.com',
    license = 'Lesser GNU General Public License (LGPL)',
    platforms = 'any that supports python 3.4',
    classifiers = [
        'Development Status :: 4 - Beta',
        'Environment :: Console',
        'Intended Audience :: Education',
        'Intended Audience :: Science/Research',
        'Intended Audience :: Developers',
        'Operating System :: MacOS :: MacOS X',
        'Operating System :: Microsoft :: Windows',
        'Operating System :: POSIX',
        'Operating System :: POSIX :: SunOS/Solaris',
        'Operating System :: Unix',
        'Programming Language :: Python :: 3',
        'Programming Language :: Python :: 3.4',
        'Topic :: Scientific/Engineering :: Bio-Informatics',
        'Topic :: Scientific/Engineering :: Chemistry',
        'Topic :: Scientific/Engineering :: Medical Science Apps.',
        'Topic :: Scientific/Engineering :: Education',
        'Topic :: Software Development :: Libraries :: Python Modules'
    ],
    cmdclass= {'install_lib':my_install_lib }
)

<commit_msg>remove unnecessary print function<commit_after>#!/usr/bin/env python3

from setuptools import setup
import setuptools
from setuptools.command.install_lib import install_lib
import os
import sys


executable_list = [
    'makeblastdb',
    'tandem',
    'tandem.exe',
    'qvality',
    'percolator',
    'percolator_2_08',
    'omssacl',
    'myrimatch_2_1_138',
    'myrimatch.exe',
    'MSAmanda.exe',
    'PepNovo_bin',
    'novor.bat',
    'novor.sh',
    'PepNovo.exe',
]

if sys.platform in ['win32']:
    class my_install_lib(setuptools.command.install_lib.install_lib):
        pass
else:
    class my_install_lib(setuptools.command.install_lib.install_lib):
        def run(self):
            setuptools.command.install_lib.install_lib.run(self)
            for fn in self.get_outputs():
                if os.path.basename(fn) in executable_list:
                    # copied from setuptools source - make the binaries executable
                    mode = ((os.stat(fn).st_mode) | 0o555) & 0o7777
                    setuptools.log.info("changing mode of %s to %o", fn, mode)
                    os.chmod(fn, mode)


# We store our version number in a simple text file:
version_path = os.path.join(
    os.path.dirname(__file__),
    'ursgal', 'version.txt'
)
with open(version_path, 'r') as version_file:
    ursgal_version = version_file.read().strip()


setup(
    name='ursgal',
    version = ursgal_version,
    packages = ['ursgal'],
    package_dir = {'ursgal': 'ursgal'},
    description='ursgal',
    package_data = {
        'ursgal' : [
            'version.txt',
            'wrappers/*.py',
            'resources/*/*/*',
            'resources/*/*/*/*',
            'resources/*/*/*/*/*',
        ]
    },
    install_requires = [
        'pymzml',
        'regex',
        'pyqms',
        "pyahocorasick >= 1.1.4;sys_platform!='win32'"
    ],
    long_description = 'Universal Python module combining common bottom-up proteomics tools for large-scale analysis',
    author = '<NAME>, <NAME>, <NAME>, <NAME> and <NAME>',
    author_email = '<EMAIL>',
    url = 'http://ursgal.github.com',
    license = 'Lesser GNU General Public License (LGPL)',
    platforms = 'any that supports python 3.4',
    classifiers = [
        'Development Status :: 4 - Beta',
        'Environment :: Console',
        'Intended Audience :: Education',
        'Intended Audience :: Science/Research',
        'Intended Audience :: Developers',
        'Operating System :: MacOS :: MacOS X',
        'Operating System :: Microsoft :: Windows',
        'Operating System :: POSIX',
        'Operating System :: POSIX :: SunOS/Solaris',
        'Operating System :: Unix',
        'Programming Language :: Python :: 3',
        'Programming Language :: Python :: 3.4',
        'Topic :: Scientific/Engineering :: Bio-Informatics',
        'Topic :: Scientific/Engineering :: Chemistry',
        'Topic :: Scientific/Engineering :: Medical Science Apps.',
        'Topic :: Scientific/Engineering :: Education',
        'Topic :: Software Development :: Libraries :: Python Modules'
    ],
    cmdclass= {'install_lib':my_install_lib }
)


{'fraction_non_alphanumeric': 0.14122862571247624, 'fraction_numerical': 0.009816339455351488, 'mean_word_length': 2.4881281060187743, 'pattern_counts': {'":': 0, '<': 15, '<?xml version=': 0, '>': 36, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 6, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1575709', 'n_tokens_mistral': 2031, 'n_tokens_neox': 1920, 'n_words': 445}