<commit_before># Always prefer setuptools over distutils
from setuptools import setup, find_packages
# To use a consistent encoding
from codecs import open
from os import path

here = path.abspath(path.dirname(__file__))
exec(open('nanoplot/version.py').read())

setup(
    name='NanoPlot',
    version=__version__,
    description='Plotting suit for Oxford Nanopore sequencing data and alignments',
    long_description='Plotting suit for Oxford Nanopore sequencing data, reading data from fastq and bam files.',
    url='https://github.com/wdecoster/NanoPlot',
    author='Wouter De Coster',
    author_email='decosterwouter@gmail.com',
    license='MIT',
    classifiers=[
        'Development Status :: 4 - Beta',
        'Intended Audience :: Science/Research',
        'Topic :: Scientific/Engineering :: Bio-Informatics',
        'License :: OSI Approved :: MIT License',
        'Programming Language :: Python :: 3',
        'Programming Language :: Python :: 3.3',
        'Programming Language :: Python :: 3.4',
        'Programming Language :: Python :: 3.5',
    ],
    keywords='nanopore sequencing plotting quality control',
    packages=find_packages(),
    install_requires=['biopython',
        'pysam>0.10.0.0',
        'pandas',
        'numpy',
        'scipy',
        'matplotlib',
        'python-dateutil',
        'seaborn',
        'nanoplotter>=0.13.1',
        'nanoget>=0.10.0',
        'nanomath>=0.12.0'
        ],
    package_data={'NanoPlot': []},
    package_dir={'nanoplot': 'nanoplot'},
    include_package_data=True,
    entry_points={
        'console_scripts': [
            'NanoPlot=nanoplot.NanoPlot:main',
        ],
    },
)
<commit_msg>specify minimal nanoget<commit_after># Always prefer setuptools over distutils
from setuptools import setup, find_packages
# To use a consistent encoding
from codecs import open
from os import path

here = path.abspath(path.dirname(__file__))
exec(open('nanoplot/version.py').read())

setup(
    name='NanoPlot',
    version=__version__,
    description='Plotting suit for Oxford Nanopore sequencing data and alignments',
    long_description='Plotting suit for Oxford Nanopore sequencing data, reading data from fastq and bam files.',
    url='https://github.com/wdecoster/NanoPlot',
    author='Wouter De Coster',
    author_email='decosterwouter@gmail.com',
    license='MIT',
    classifiers=[
        'Development Status :: 4 - Beta',
        'Intended Audience :: Science/Research',
        'Topic :: Scientific/Engineering :: Bio-Informatics',
        'License :: OSI Approved :: MIT License',
        'Programming Language :: Python :: 3',
        'Programming Language :: Python :: 3.3',
        'Programming Language :: Python :: 3.4',
        'Programming Language :: Python :: 3.5',
    ],
    keywords='nanopore sequencing plotting quality control',
    packages=find_packages(),
    install_requires=['biopython',
        'pysam>0.10.0.0',
        'pandas',
        'numpy',
        'scipy',
        'matplotlib',
        'python-dateutil',
        'seaborn',
        'nanoplotter>=0.13.1',
        'nanoget>=0.11.0',
        'nanomath>=0.12.0'
        ],
    package_data={'NanoPlot': []},
    package_dir={'nanoplot': 'nanoplot'},
    include_package_data=True,
    entry_points={
        'console_scripts': [
            'NanoPlot=nanoplot.NanoPlot:main',
        ],
    },
)
<|endoftext|>


<commit_before>from setuptools import setup, find_packages
import os

CLASSIFIERS = []

setup(
    author="Christopher Glass",
    author_email="tribaal@gmail.com",
    name='django-shop',
    version='0.0.2',
    description='An Advanced Django Shop',
    long_description=open(os.path.join(os.path.dirname(__file__), 'README.rst')).read(),
    url='http://www.django-shop.org/',
    license='BSD License',
    platforms=['OS Independent'],
    classifiers=CLASSIFIERS,
    install_requires=[
        'Django>=1.2',
        'django-classy-tags>=0.3.3',
        'django-polymorphic>=0.2',
        'south>=0.7.2'
    ],
    packages=find_packages(exclude=["example", "example.*"]),
    include_package_data=True,
    zip_safe = False,
)

<commit_msg>Bumped version<commit_after>from setuptools import setup, find_packages
import os

CLASSIFIERS = []

setup(
    author="Christopher Glass",
    author_email="tribaal@gmail.com",
    name='django-shop',
    version='0.0.3',
    description='An Advanced Django Shop',
    long_description=open(os.path.join(os.path.dirname(__file__), 'README.rst')).read(),
    url='http://www.django-shop.org/',
    license='BSD License',
    platforms=['OS Independent'],
    classifiers=CLASSIFIERS,
    install_requires=[
        'Django>=1.2',
        'django-classy-tags>=0.3.3',
        'django-polymorphic>=0.2',
        'south>=0.7.2'
    ],
    packages=find_packages(exclude=["example", "example.*"]),
    include_package_data=True,
    zip_safe = False,
)

<|endoftext|>


<commit_before>from setuptools import setup
import sys

if sys.version_info < (3, 0):
    sys.exit('Sorry, Python < 3 is not supported')

setup(name='downloads',
      version='0.0.1',
      description='Easy HTTP downloads',
      url='https://github.com/audy/downloads',
      author='Austin Davis-Richardson',
      author_email='harekrishna@gmail.com',
      packages=['downloads'])
<commit_msg>version 0.1.0<commit_after>from setuptools import setup
import sys

if sys.version_info < (3, 0):
    sys.exit('Sorry, Python < 3 is not supported')

setup(name='downloads',
      version='0.1.0',
      description='Easy HTTP downloads',
      url='https://github.com/audy/downloads',
      author='Austin Davis-Richardson',
      author_email='harekrishna@gmail.com',
      packages=['downloads'])
<|endoftext|>


<commit_before>#!/usr/bin/env python
# -*- coding: utf-8 -*-

""" setup.py

Packaging for dax
"""

from glob import glob
import os
from setuptools import setup, find_packages
import subprocess

def git_version():
    def _minimal_ext_cmd(cmd):
        env = {}
        for k in ['SYSTEMROOT', 'PATH', 'HOME']:
            v = os.environ.get(k)
            if v is not None:
                env[k] = v

        out = subprocess.check_output(cmd, stderr=subprocess.STDOUT, env=env)
        return out

    try:
        out = _minimal_ext_cmd(['git', 'rev-parse', 'HEAD'])
        GIT_REVISION = out.strip().decode('ascii')
    except OSError:
        GIT_REVISION = "Unknown"

    return GIT_REVISION

def write_git_revision_py(filename='dax/git_revision.py'):
    cnt = """
# THIS FILE IS GENERATED BY SETUP.PY
git_revision = '%(git_revision)s'
"""

    GIT_REVISION = git_version()

    with open(filename, 'w') as f:
        f.write(cnt % {'git_revision': GIT_REVISION})

def get_version():
    basedir = os.path.dirname(__file__)
    with open(os.path.join(basedir, 'dax/version.py')) as f:
        VERSION = None
        version_ns = {}
        exec(f.read(), version_ns)
        VERSION = version_ns['VERSION']
        return VERSION
    raise RuntimeError("No version found")

def readme():
    with open('README.md') as f:
        return f.read()

description = 'Distributed Automation for XNAT'

# Note: this long_description is actually a copy/paste from the top-level
# README.txt, so that it shows up nicely on PyPI.  So please remember to edit
# it only in one place and sync it correctly.
long_description = """
========================================================
DAX: Distributed Automation for XNAT
========================================================

*DAX*, is a python package developed at Vanderbilt University, Nashville, TN,
USA. It's available on github at: https://github.com/VUIIS/dax.

XNAT provides a flexible imaging informatics software platform to
organize and manage imaging data.

*DAX*, an open-source initiative under the umbrella of Vanderbilt University
Institute of Imaging Science (VUIIS), is a Python project that provides a
uniform interface to run pipelines on a cluster by grabbing data from a XNAT
database via RESTApi Calls.

*DAX* allows you to:

* extract information from XNAT via scripts (bin/Xnat_tools/Xnat...)
* create pipelines (spiders/processors) to run pipelines on your data
* build a project on XNAT with pipelines (assessors)
* launch pipelines on your cluster and upload results back to xnat
* interact with XNAT via python using commands in XnatUtils.
"""

NAME = 'dax'
MAINTAINER = 'VUIIS CCI'
MAINTAINER_EMAIL = 'vuiis-cci@googlegroups.com'
DESCRIPTION = description
LONG_DESCRIPTION = long_description
URL = "http://github.com/VUIIS/dax"
DOWNLOAD_URL = "http://github.com/VUIIS/dax"
LICENSE = 'MIT'
CLASSIFIERS = [
    # As from http://pypi.python.org/pypi?%3Aaction=list_classifiers
    "Development Status :: 5 - Production/Stable",
    "Environment :: Console",
    "Intended Audience :: Science/Research",
    "Operating System :: MacOS :: MacOS X",
    "Operating System :: POSIX",
    "Operating System :: POSIX :: Linux",
    "Operating System :: Unix",
    "Programming Language :: Python :: 3.7",
    "Topic :: Scientific/Engineering",
    "Topic :: Scientific/Engineering :: Information Analysis"]
AUTHOR = MAINTAINER
AUTHOR_EMAIL = MAINTAINER_EMAIL
PLATFORMS = ["MacOs",
             "Linux"]
VERSION = get_version()

# versions
SPHINX_MIN_VERSION = '1.4'
PYXNAT_MIN_VERSION = '1.1.0.2'

REQUIRES = [
    'pyxnat>=%s' % PYXNAT_MIN_VERSION,
    'pyyaml',
    'pycap',
    'nibabel',
    'fpdf2',
    'PyPDF2',
    'cubids-bond-fork',
    'numpy']

DOCS_REQUIRES = ['Sphinx>=%s' % SPHINX_MIN_VERSION]

TESTS_REQUIRES = ['nose']

if __name__ == '__main__':
    write_git_revision_py()

    setup(name=NAME,
          maintainer=MAINTAINER,
          maintainer_email=MAINTAINER_EMAIL,
          version=get_version(),
          description=DESCRIPTION,
          long_description=LONG_DESCRIPTION,
          url=URL,
          download_url=DOWNLOAD_URL,
          author=AUTHOR,
          author_email=AUTHOR_EMAIL,
          platforms=PLATFORMS,
          license=LICENSE,
          packages=find_packages(),
          package_data={},
          test_suite='nose.collector',
          tests_require=TESTS_REQUIRES,
          install_requires=REQUIRES,
          python_requires='~=3.6',
          zip_safe=True,
          scripts=glob(os.path.join('bin', '*', '*')),
          classifiers=CLASSIFIERS,
          extras_require={
              'docs': DOCS_REQUIRES
          })
<commit_msg>pin numpy version, newer requires python 3.8<commit_after>#!/usr/bin/env python
# -*- coding: utf-8 -*-

""" setup.py

Packaging for dax
"""

from glob import glob
import os
from setuptools import setup, find_packages
import subprocess

def git_version():
    def _minimal_ext_cmd(cmd):
        env = {}
        for k in ['SYSTEMROOT', 'PATH', 'HOME']:
            v = os.environ.get(k)
            if v is not None:
                env[k] = v

        out = subprocess.check_output(cmd, stderr=subprocess.STDOUT, env=env)
        return out

    try:
        out = _minimal_ext_cmd(['git', 'rev-parse', 'HEAD'])
        GIT_REVISION = out.strip().decode('ascii')
    except OSError:
        GIT_REVISION = "Unknown"

    return GIT_REVISION

def write_git_revision_py(filename='dax/git_revision.py'):
    cnt = """
# THIS FILE IS GENERATED BY SETUP.PY
git_revision = '%(git_revision)s'
"""

    GIT_REVISION = git_version()

    with open(filename, 'w') as f:
        f.write(cnt % {'git_revision': GIT_REVISION})

def get_version():
    basedir = os.path.dirname(__file__)
    with open(os.path.join(basedir, 'dax/version.py')) as f:
        VERSION = None
        version_ns = {}
        exec(f.read(), version_ns)
        VERSION = version_ns['VERSION']
        return VERSION
    raise RuntimeError("No version found")

def readme():
    with open('README.md') as f:
        return f.read()

description = 'Distributed Automation for XNAT'

# Note: this long_description is actually a copy/paste from the top-level
# README.txt, so that it shows up nicely on PyPI.  So please remember to edit
# it only in one place and sync it correctly.
long_description = """
========================================================
DAX: Distributed Automation for XNAT
========================================================

*DAX*, is a python package developed at Vanderbilt University, Nashville, TN,
USA. It's available on github at: https://github.com/VUIIS/dax.

XNAT provides a flexible imaging informatics software platform to
organize and manage imaging data.

*DAX*, an open-source initiative under the umbrella of Vanderbilt University
Institute of Imaging Science (VUIIS), is a Python project that provides a
uniform interface to run pipelines on a cluster by grabbing data from a XNAT
database via RESTApi Calls.

*DAX* allows you to:

* extract information from XNAT via scripts (bin/Xnat_tools/Xnat...)
* create pipelines (spiders/processors) to run pipelines on your data
* build a project on XNAT with pipelines (assessors)
* launch pipelines on your cluster and upload results back to xnat
* interact with XNAT via python using commands in XnatUtils.
"""

NAME = 'dax'
MAINTAINER = 'VUIIS CCI'
MAINTAINER_EMAIL = 'vuiis-cci@googlegroups.com'
DESCRIPTION = description
LONG_DESCRIPTION = long_description
URL = "http://github.com/VUIIS/dax"
DOWNLOAD_URL = "http://github.com/VUIIS/dax"
LICENSE = 'MIT'
CLASSIFIERS = [
    # As from http://pypi.python.org/pypi?%3Aaction=list_classifiers
    "Development Status :: 5 - Production/Stable",
    "Environment :: Console",
    "Intended Audience :: Science/Research",
    "Operating System :: MacOS :: MacOS X",
    "Operating System :: POSIX",
    "Operating System :: POSIX :: Linux",
    "Operating System :: Unix",
    "Programming Language :: Python :: 3.7",
    "Topic :: Scientific/Engineering",
    "Topic :: Scientific/Engineering :: Information Analysis"]
AUTHOR = MAINTAINER
AUTHOR_EMAIL = MAINTAINER_EMAIL
PLATFORMS = ["MacOs",
             "Linux"]
VERSION = get_version()

# versions
SPHINX_MIN_VERSION = '1.4'
PYXNAT_MIN_VERSION = '1.1.0.2'

REQUIRES = [
    'pyxnat>=%s' % PYXNAT_MIN_VERSION,
    'pyyaml',
    'pycap',
    'nibabel',
    'fpdf2',
    'PyPDF2',
    'cubids-bond-fork',
    'numpy==1.19.5']

DOCS_REQUIRES = ['Sphinx>=%s' % SPHINX_MIN_VERSION]

TESTS_REQUIRES = ['nose']

if __name__ == '__main__':
    write_git_revision_py()

    setup(name=NAME,
          maintainer=MAINTAINER,
          maintainer_email=MAINTAINER_EMAIL,
          version=get_version(),
          description=DESCRIPTION,
          long_description=LONG_DESCRIPTION,
          url=URL,
          download_url=DOWNLOAD_URL,
          author=AUTHOR,
          author_email=AUTHOR_EMAIL,
          platforms=PLATFORMS,
          license=LICENSE,
          packages=find_packages(),
          package_data={},
          test_suite='nose.collector',
          tests_require=TESTS_REQUIRES,
          install_requires=REQUIRES,
          python_requires='~=3.6',
          zip_safe=True,
          scripts=glob(os.path.join('bin', '*', '*')),
          classifiers=CLASSIFIERS,
          extras_require={
              'docs': DOCS_REQUIRES
          })
<|endoftext|>


<commit_before># import multiprocessing to avoid this bug (http://bugs.python.org/issue15881#msg170215)
import multiprocessing
assert multiprocessing
import re
from setuptools import setup, find_packages

def get_version():
    """
    Extracts the version number from the version.py file.
    """
    VERSION_FILE = 'activatable_model/version.py'
    mo = re.search(r'^__version__ = [\'"]([^\'"]*)[\'"]', open(VERSION_FILE, 'rt').read(), re.M)
    if mo:
        return mo.group(1)
    else:
        raise RuntimeError('Unable to find version string in {0}.'.format(VERSION_FILE))

setup(
    name='django-activatable-model',
    version=get_version(),
    description='Django Activatable Model',
    long_description=open('README.md').read(),
    url='https://github.com/ambitioninc/django-activatable-model',
    author='Wes Kendall',
    author_email='opensource@ambition.com',
    keywords='Django, Model, Activatable',
    packages=find_packages(),
    classifiers=[
        'Programming Language :: Python',
        'Programming Language :: Python :: 2.7',
        'Programming Language :: Python :: 3.4',
        'Intended Audience :: Developers',
        'License :: OSI Approved :: MIT License',
        'Operating System :: OS Independent',
        'Framework :: Django',
        'Framework :: Django :: 1.7',
        'Framework :: Django :: 1.8',
        'Framework :: Django :: 1.9',
    ],
    license='MIT',
    install_requires=[
        'django>=1.7',
        'django-manager-utils>=0.8.2',
    ],
    tests_require=[
        'psycopg2',
        'django-dynamic-fixture',
        'django-nose>=1.4',
        'mock',
    ],
    test_suite='run_tests.run_tests',
    include_package_data=True,
    zip_safe=False,
)
<commit_msg>update manager utils version<commit_after># import multiprocessing to avoid this bug (http://bugs.python.org/issue15881#msg170215)
import multiprocessing
assert multiprocessing
import re
from setuptools import setup, find_packages

def get_version():
    """
    Extracts the version number from the version.py file.
    """
    VERSION_FILE = 'activatable_model/version.py'
    mo = re.search(r'^__version__ = [\'"]([^\'"]*)[\'"]', open(VERSION_FILE, 'rt').read(), re.M)
    if mo:
        return mo.group(1)
    else:
        raise RuntimeError('Unable to find version string in {0}.'.format(VERSION_FILE))

setup(
    name='django-activatable-model',
    version=get_version(),
    description='Django Activatable Model',
    long_description=open('README.md').read(),
    url='https://github.com/ambitioninc/django-activatable-model',
    author='Wes Kendall',
    author_email='opensource@ambition.com',
    keywords='Django, Model, Activatable',
    packages=find_packages(),
    classifiers=[
        'Programming Language :: Python',
        'Programming Language :: Python :: 2.7',
        'Programming Language :: Python :: 3.4',
        'Intended Audience :: Developers',
        'License :: OSI Approved :: MIT License',
        'Operating System :: OS Independent',
        'Framework :: Django',
        'Framework :: Django :: 1.7',
        'Framework :: Django :: 1.8',
        'Framework :: Django :: 1.9',
    ],
    license='MIT',
    install_requires=[
        'django>=1.7',
        'django-manager-utils>=0.9.0',
    ],
    tests_require=[
        'psycopg2',
        'django-dynamic-fixture',
        'django-nose>=1.4',
        'mock',
    ],
    test_suite='run_tests.run_tests',
    include_package_data=True,
    zip_safe=False,
)
<|endoftext|>


<commit_before>"""
The setup package to install SeleniumBase dependencies and plugins
"""

from setuptools import setup, find_packages  # noqa

setup(
    name='seleniumbase',
    version='1.2.7',
    url='http://seleniumbase.com',
    author='Michael Mintz',
    author_email='@mintzworld',
    maintainer='Michael Mintz',
    description='Reliable Browser Automation - http://seleniumbase.com',
    license='The MIT License',
    install_requires=[
        'pip>=8.1.2',
        'setuptools>=24.3.0',
        'selenium>=2.53.6',
        'nose>=1.3.7',
        'pytest>=2.9.2',
        'flake8==2.6.2',
        'requests==2.10.0',
        'urllib3==1.15.1',
        'BeautifulSoup==3.2.1',
        'unittest2==1.1.0',
        'chardet==2.3.0',
        'simplejson==3.8.2',
        'boto==2.40.0',
        'ipdb==0.10.0',
        'pyvirtualdisplay==0.2',
        ],
    packages=['seleniumbase',
              'seleniumbase.core',
              'seleniumbase.plugins',
              'seleniumbase.fixtures',
              'seleniumbase.masterqa',
              'seleniumbase.common',
              'seleniumbase.config'],
    entry_points={
        'nose.plugins': [
            'base_plugin = seleniumbase.plugins.base_plugin:Base',
            'selenium = seleniumbase.plugins.selenium_plugin:SeleniumBrowser',
            'page_source = seleniumbase.plugins.page_source:PageSource',
            'screen_shots = seleniumbase.plugins.screen_shots:ScreenShots',
            'test_info = seleniumbase.plugins.basic_test_info:BasicTestInfo',
            ('db_reporting = '
             'seleniumbase.plugins.db_reporting_plugin:DBReporting'),
            's3_logging = seleniumbase.plugins.s3_logging_plugin:S3Logging',
            ('hipchat_reporting = seleniumbase.plugins'
             '.hipchat_reporting_plugin:HipchatReporting'),
            ]
        }
    )
<commit_msg>Have setup.py reqs match requirements.txt reqs<commit_after>"""
The setup package to install SeleniumBase dependencies and plugins
"""

from setuptools import setup, find_packages  # noqa

setup(
    name='seleniumbase',
    version='1.2.7',
    url='http://seleniumbase.com',
    author='Michael Mintz',
    author_email='@mintzworld',
    maintainer='Michael Mintz',
    description='Reliable Browser Automation - http://seleniumbase.com',
    license='The MIT License',
    install_requires=[
        'pip>=8.1.2',
        'setuptools>=26.0.0',
        'selenium>=2.53.6',
        'nose>=1.3.7',
        'pytest>=3.0.1',
        'flake8==3.0.4',
        'requests==2.11.1',
        'urllib3==1.16',
        'BeautifulSoup==3.2.1',
        'unittest2==1.1.0',
        'chardet==2.3.0',
        'simplejson==3.8.2',
        'boto==2.42.0',
        'ipdb==0.10.1',
        'pyvirtualdisplay==0.2',
        ],
    packages=['seleniumbase',
              'seleniumbase.core',
              'seleniumbase.plugins',
              'seleniumbase.fixtures',
              'seleniumbase.masterqa',
              'seleniumbase.common',
              'seleniumbase.config'],
    entry_points={
        'nose.plugins': [
            'base_plugin = seleniumbase.plugins.base_plugin:Base',
            'selenium = seleniumbase.plugins.selenium_plugin:SeleniumBrowser',
            'page_source = seleniumbase.plugins.page_source:PageSource',
            'screen_shots = seleniumbase.plugins.screen_shots:ScreenShots',
            'test_info = seleniumbase.plugins.basic_test_info:BasicTestInfo',
            ('db_reporting = '
             'seleniumbase.plugins.db_reporting_plugin:DBReporting'),
            's3_logging = seleniumbase.plugins.s3_logging_plugin:S3Logging',
            ('hipchat_reporting = seleniumbase.plugins'
             '.hipchat_reporting_plugin:HipchatReporting'),
            ]
        }
    )
<|endoftext|>


<commit_before>"""Setup for Flask Jsondash."""

import os

from setuptools import setup

SRCDIR = '.'
folder = os.path.abspath(os.path.dirname(__file__))
test_requirements = [
    'pytest==3.10.0',
    'pytest-cov==2.6.0',
    'pyquery==1.4.0',
    'requests_mock',
]
extras_require = {
    'wordcloud-utils': [
        'requests',
        'pyquery',
        'requests-mock',
    ]
}
requirements = [
    'click==7.0',
    'Flask',
    'cerberus',
    'pymongo==3.7.2',
]

def readme():
    """Grab the long README file."""
    try:
        with open('README.md', 'r') as fobj:
            return fobj.read()
    except IOError:
        try:
            with open('README.rst', 'r') as fobj:
                return fobj.read()
        except IOError:
            return 'No README specified.'

setup(
    name='flask_jsondash',
    version='6.3.3',
    description=('Easily configurable, chart dashboards from any '
                 'arbitrary API endpoint. JSON config only. Ready to go.'),
    long_description=readme(),
    author='Chris Tabor',
    author_email='dxdstudio@gmail.com',
    url='https://github.com/christabor/flask_jsondash',
    license='MIT',
    classifiers=[
        'Environment :: Web Environment',
        'Intended Audience :: Developers',
        'License :: OSI Approved :: BSD License',
        'Operating System :: OS Independent',
        'Programming Language :: Python :: 2.7',
        'Topic :: Internet :: WWW/HTTP :: Dynamic Content',
        'Topic :: Software Development :: Libraries :: Python Modules'
    ],
    extras_require=extras_require,
    tests_require=test_requirements,
    install_requires=requirements,
    package_dir={'flask_jsondash': 'flask_jsondash'},
    packages=['flask_jsondash'],
    zip_safe=False,
    include_package_data=True,
)
<commit_msg>Bump pytest from 3.10.0 to 3.10.1 (#195)<commit_after>"""Setup for Flask Jsondash."""

import os

from setuptools import setup

SRCDIR = '.'
folder = os.path.abspath(os.path.dirname(__file__))
test_requirements = [
    'pytest==3.10.1',
    'pytest-cov==2.6.0',
    'pyquery==1.4.0',
    'requests_mock',
]
extras_require = {
    'wordcloud-utils': [
        'requests',
        'pyquery',
        'requests-mock',
    ]
}
requirements = [
    'click==7.0',
    'Flask',
    'cerberus',
    'pymongo==3.7.2',
]

def readme():
    """Grab the long README file."""
    try:
        with open('README.md', 'r') as fobj:
            return fobj.read()
    except IOError:
        try:
            with open('README.rst', 'r') as fobj:
                return fobj.read()
        except IOError:
            return 'No README specified.'

setup(
    name='flask_jsondash',
    version='6.3.3',
    description=('Easily configurable, chart dashboards from any '
                 'arbitrary API endpoint. JSON config only. Ready to go.'),
    long_description=readme(),
    author='Chris Tabor',
    author_email='dxdstudio@gmail.com',
    url='https://github.com/christabor/flask_jsondash',
    license='MIT',
    classifiers=[
        'Environment :: Web Environment',
        'Intended Audience :: Developers',
        'License :: OSI Approved :: BSD License',
        'Operating System :: OS Independent',
        'Programming Language :: Python :: 2.7',
        'Topic :: Internet :: WWW/HTTP :: Dynamic Content',
        'Topic :: Software Development :: Libraries :: Python Modules'
    ],
    extras_require=extras_require,
    tests_require=test_requirements,
    install_requires=requirements,
    package_dir={'flask_jsondash': 'flask_jsondash'},
    packages=['flask_jsondash'],
    zip_safe=False,
    include_package_data=True,
)
<|endoftext|>


<commit_before>#!/usr/bin/env python
# -*- coding: utf-8 -*-
#/*##########################################################################
#
# The fisx library for X-Ray Fluorescence
#
# Copyright (c) 2014-2016 V. Armando Sole
#
# This file is part of the fisx X-ray developed by V.A. Sole
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
#############################################################################*/
import glob
import os
import sys
if "bdist_wheel" in sys.argv:
    from setuptools import setup, Extension
    from setuptools.command.build_py import build_py
    from distutils.command.install_data import install_data
else:
    try:
        from setuptools import setup, Extension
        from setuptools.command.build_py import build_py
        from distutils.command.install_data import install_data
    except ImportError:
        from distutils.core import setup, Extension
        from distutils.sysconfig import get_python_lib
        from distutils.command.build_py import build_py
        from distutils.command.install_data import install_data

# check if cython is not to be used despite being present
def use_cython():
    """
    Check if cython is disabled from the command line or the environment.
    """
    if "WITH_CYTHON" in os.environ:
        if os.environ["WITH_CYTHON"] == "False":
            print("No Cython requested by environment")
            return False

    if ("--no-cython" in sys.argv):
        sys.argv.remove("--no-cython")
        os.environ["WITH_CYTHON"] = "False"
        print("No Cython requested by command line")
        return False
    return True

if use_cython():
    try:
        from Cython.Distutils import build_ext
        from Cython.Compiler.Version import version
        if version < "0.17":
            build_ext = None
    except:
        build_ext = None
else:
    build_ext = None

import numpy
# deal with required data

#for the time being there is no doc directory
FISX_DATA_DIR = os.getenv("FISX_DATA_DIR")
FISX_DOC_DIR = os.getenv("FISX_DOC_DIR")

if FISX_DATA_DIR is None:
    FISX_DATA_DIR = os.path.join('fisx', 'fisx_data')
if FISX_DOC_DIR is None:
    FISX_DOC_DIR = os.path.join('fisx', 'fisx_data')

def getFisxVersion():
    cppDir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "src")
    content = open(os.path.join(cppDir, "fisx_version.h"), "r").readlines()
    for line in content:
        if "FISX_VERSION_STR" in line:
            version = line.split("FISX_VERSION_STR")[-1].replace("\n","")
            version = version.replace(" ","")
            return version[1:-1]

__version__ = getFisxVersion()

print("fisx X-Ray Fluorescence Toolkit %s\n" % __version__)

class smart_build_py(build_py):
    def run (self):
        toReturn = build_py.run(self)
        global FISX_DATA_DIR
        global FISX_DOC_DIR
        global INSTALL_DIR
        defaultDataPath = os.path.join('fisx', 'fisx_data')
        defaultDocPath = os.path.join('fisx', 'fisx_data')
        if (FISX_DATA_DIR == defaultDataPath) or\
           (FISX_DOC_DIR == defaultDocPath):
            #default, just make sure the complete path is there
            install_cmd = self.get_finalized_command('install')
            INSTALL_DIR = getattr(install_cmd, 'install_lib')

        #packager should have given the complete path
        #in other cases
        if FISX_DATA_DIR == defaultDataPath:
            FISX_DATA_DIR = os.path.join(INSTALL_DIR, FISX_DATA_DIR)
        if FISX_DOC_DIR == defaultDocPath:
            #default, just make sure the complete path is there
            FISX_DOC_DIR = os.path.join(INSTALL_DIR, FISX_DOC_DIR)
        target = os.path.join(self.build_lib, "fisx", "DataDir.py")
        fid = open(target,'r')
        content = fid.readlines()
        fid.close()
        fid = open(target,'w')
        for line in content:
            lineToBeWritten = line
            if lineToBeWritten.startswith("FISX_DATA_DIR"):
                lineToBeWritten = "FISX_DATA_DIR = r'%s'\n" % FISX_DATA_DIR
            if line.startswith("FISX_DOC_DIR"):
                lineToBeWritten = "FISX_DOC_DIR = r'%s'\n" % FISX_DOC_DIR
            fid.write(lineToBeWritten)
        fid.close()
        return toReturn

class smart_install_data(install_data):
    def run(self):
        global INSTALL_DIR
        global FISX_DATA_DIR
        global FISX_DOC_DIR
        #need to change self.install_dir to the library dir
        install_cmd = self.get_finalized_command('install')
        self.install_dir = getattr(install_cmd, 'install_lib')
        INSTALL_DIR = self.install_dir
        print("fisx to be installed in %s" %  self.install_dir)
        return install_data.run(self)

topLevel = os.path.dirname(os.path.abspath(__file__))
fileList = glob.glob(os.path.join(topLevel, "fisx_data", "*.dat"))
fileList.append(os.path.join(topLevel, "changelog.txt"))
fileList.append(os.path.join(topLevel, "LICENSE"))
fileList.append(os.path.join(topLevel, "README.rst"))
fileList.append(os.path.join(topLevel, "TODO"))
data_files = [(FISX_DATA_DIR, fileList)]

# actual build stuff
FORCE = False
cython_dir = os.path.join(os.getcwd(), "python", "cython")
if build_ext:
    #make sure everything is totally clean?
    fileList  = glob.glob(os.path.join(cython_dir, "*.cpp"))
    fileList += glob.glob(os.path.join(cython_dir, "*.h"))
    if FORCE:
        for fname in fileList:
            if os.path.exists(fname):
                os.remove(fname)
    #this does not work:
    #src = glob.glob(os.path.join(cython_dir, "*pyx"))
    multiple_pyx = os.path.join(cython_dir, "_fisx.pyx")
    if os.path.exists(multiple_pyx):
        try:
            os.remove(multiple_pyx)
        except:
            print("WARNING: Could not delete file. Assuming up-to-date.")
    if not os.path.exists(multiple_pyx):
        pyx = glob.glob(os.path.join(cython_dir, "*pyx"))
        pyx = sorted(pyx, key=str.lower)
        f = open(multiple_pyx, 'wb')
        for fname in pyx:
            inFile = open(fname, 'rb')
            lines = inFile.readlines()
            inFile.close()
            for line in lines:
                f.write(line)
        f.close()
    src = [multiple_pyx]
else:
    src_files = glob.glob(os.path.join(cython_dir, 'default', '*.cpp'))
    src = []
    for fname in src_files:
        inFile = open(fname, 'rb')
        lines = inFile.readlines()
        inFile.close()
        f = open(os.path.join(cython_dir, os.path.basename(fname), 'wb')
        for line in lines:
            f.write(line)
        f.close()
        src.append(f)

src += glob.glob(os.path.join(os.path.dirname(os.path.abspath(__file__)),
                'src', 'fisx_*.cpp'))

include_dirs = [numpy.get_include(),
                os.path.join(os.path.dirname(os.path.abspath(__file__)), "src")]

if sys.platform == 'win32':
    extra_compile_args = ['/EHsc']
    extra_link_args = []
else:
    extra_compile_args = []
    extra_link_args = []

def buildExtension():
    module = Extension(name="fisx._fisx",
                    sources=src,
                    include_dirs=include_dirs,
                    extra_compile_args=extra_compile_args,
                    extra_link_args=extra_link_args,
                    language="c++",
                    )
    return module

ext_modules = [buildExtension()]

cmdclass = {'install_data':smart_install_data,
            'build_py':smart_build_py}
if build_ext:
    cmdclass['build_ext'] = build_ext

description = "Quantitative X-Ray Fluorescence Analysis Support Library"
long_description = open("README.rst").read()

# tell distutils where to find the packages
package_dir = {"":"python"}
packages = ['fisx', 'fisx.tests']

classifiers = ["Development Status :: 5 - Production/Stable",
               "Programming Language :: C++",
               "Programming Language :: Python :: 2",
               "Programming Language :: Python :: 3",
               "Programming Language :: Cython",
               "Environment :: Console",
               "Intended Audience :: Developers",
               "Intended Audience :: End Users/Desktop",
               "Intended Audience :: Science/Research",
               "License :: OSI Approved :: MIT License",
               "Topic :: Software Development :: Libraries :: Python Modules",
               "Operating System :: Microsoft :: Windows",
               "Operating System :: Unix",
               "Operating System :: MacOS :: MacOS X",
               "Operating System :: POSIX",
               "Topic :: Scientific/Engineering :: Chemistry",
               "Topic :: Scientific/Engineering :: Physics"
               ]

install_requires = ["numpy"]

# cython is not mandatory to build because generated code is supplied
setup_requires = ["numpy"]

if __name__ == "__main__":
    setup(
        name='fisx',
        version=__version__,
        author="V. Armando Solé",
        author_email="sole@esrf.fr",
        description=description,
        long_description=long_description,
        license="MIT",
        url="https://github.com/vasole/fisx",
        download_url="https://github.com/vasole/fisx/archive/v%s.tar.gz" % __version__,
        package_dir=package_dir,
        packages=packages,
        ext_modules=ext_modules,
        data_files=data_files,
        cmdclass=cmdclass,
        classifiers=classifiers,
        install_requires=install_requires,
        setup_requires=setup_requires,
    )
<commit_msg>Correct syntax error.<commit_after>#!/usr/bin/env python
# -*- coding: utf-8 -*-
#/*##########################################################################
#
# The fisx library for X-Ray Fluorescence
#
# Copyright (c) 2014-2016 V. Armando Sole
#
# This file is part of the fisx X-ray developed by V.A. Sole
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
#############################################################################*/
import glob
import os
import sys
if "bdist_wheel" in sys.argv:
    from setuptools import setup, Extension
    from setuptools.command.build_py import build_py
    from distutils.command.install_data import install_data
else:
    try:
        from setuptools import setup, Extension
        from setuptools.command.build_py import build_py
        from distutils.command.install_data import install_data
    except ImportError:
        from distutils.core import setup, Extension
        from distutils.sysconfig import get_python_lib
        from distutils.command.build_py import build_py
        from distutils.command.install_data import install_data

# check if cython is not to be used despite being present
def use_cython():
    """
    Check if cython is disabled from the command line or the environment.
    """
    if "WITH_CYTHON" in os.environ:
        if os.environ["WITH_CYTHON"] == "False":
            print("No Cython requested by environment")
            return False

    if ("--no-cython" in sys.argv):
        sys.argv.remove("--no-cython")
        os.environ["WITH_CYTHON"] = "False"
        print("No Cython requested by command line")
        return False
    return True

if use_cython():
    try:
        from Cython.Distutils import build_ext
        from Cython.Compiler.Version import version
        if version < "0.17":
            build_ext = None
    except:
        build_ext = None
else:
    build_ext = None

import numpy
# deal with required data

#for the time being there is no doc directory
FISX_DATA_DIR = os.getenv("FISX_DATA_DIR")
FISX_DOC_DIR = os.getenv("FISX_DOC_DIR")

if FISX_DATA_DIR is None:
    FISX_DATA_DIR = os.path.join('fisx', 'fisx_data')
if FISX_DOC_DIR is None:
    FISX_DOC_DIR = os.path.join('fisx', 'fisx_data')

def getFisxVersion():
    cppDir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "src")
    content = open(os.path.join(cppDir, "fisx_version.h"), "r").readlines()
    for line in content:
        if "FISX_VERSION_STR" in line:
            version = line.split("FISX_VERSION_STR")[-1].replace("\n","")
            version = version.replace(" ","")
            return version[1:-1]

__version__ = getFisxVersion()

print("fisx X-Ray Fluorescence Toolkit %s\n" % __version__)

class smart_build_py(build_py):
    def run (self):
        toReturn = build_py.run(self)
        global FISX_DATA_DIR
        global FISX_DOC_DIR
        global INSTALL_DIR
        defaultDataPath = os.path.join('fisx', 'fisx_data')
        defaultDocPath = os.path.join('fisx', 'fisx_data')
        if (FISX_DATA_DIR == defaultDataPath) or\
           (FISX_DOC_DIR == defaultDocPath):
            #default, just make sure the complete path is there
            install_cmd = self.get_finalized_command('install')
            INSTALL_DIR = getattr(install_cmd, 'install_lib')

        #packager should have given the complete path
        #in other cases
        if FISX_DATA_DIR == defaultDataPath:
            FISX_DATA_DIR = os.path.join(INSTALL_DIR, FISX_DATA_DIR)
        if FISX_DOC_DIR == defaultDocPath:
            #default, just make sure the complete path is there
            FISX_DOC_DIR = os.path.join(INSTALL_DIR, FISX_DOC_DIR)
        target = os.path.join(self.build_lib, "fisx", "DataDir.py")
        fid = open(target,'r')
        content = fid.readlines()
        fid.close()
        fid = open(target,'w')
        for line in content:
            lineToBeWritten = line
            if lineToBeWritten.startswith("FISX_DATA_DIR"):
                lineToBeWritten = "FISX_DATA_DIR = r'%s'\n" % FISX_DATA_DIR
            if line.startswith("FISX_DOC_DIR"):
                lineToBeWritten = "FISX_DOC_DIR = r'%s'\n" % FISX_DOC_DIR
            fid.write(lineToBeWritten)
        fid.close()
        return toReturn

class smart_install_data(install_data):
    def run(self):
        global INSTALL_DIR
        global FISX_DATA_DIR
        global FISX_DOC_DIR
        #need to change self.install_dir to the library dir
        install_cmd = self.get_finalized_command('install')
        self.install_dir = getattr(install_cmd, 'install_lib')
        INSTALL_DIR = self.install_dir
        print("fisx to be installed in %s" %  self.install_dir)
        return install_data.run(self)

topLevel = os.path.dirname(os.path.abspath(__file__))
fileList = glob.glob(os.path.join(topLevel, "fisx_data", "*.dat"))
fileList.append(os.path.join(topLevel, "changelog.txt"))
fileList.append(os.path.join(topLevel, "LICENSE"))
fileList.append(os.path.join(topLevel, "README.rst"))
fileList.append(os.path.join(topLevel, "TODO"))
data_files = [(FISX_DATA_DIR, fileList)]

# actual build stuff
FORCE = False
cython_dir = os.path.join(os.getcwd(), "python", "cython")
if build_ext:
    #make sure everything is totally clean?
    fileList  = glob.glob(os.path.join(cython_dir, "*.cpp"))
    fileList += glob.glob(os.path.join(cython_dir, "*.h"))
    if FORCE:
        for fname in fileList:
            if os.path.exists(fname):
                os.remove(fname)
    #this does not work:
    #src = glob.glob(os.path.join(cython_dir, "*pyx"))
    multiple_pyx = os.path.join(cython_dir, "_fisx.pyx")
    if os.path.exists(multiple_pyx):
        try:
            os.remove(multiple_pyx)
        except:
            print("WARNING: Could not delete file. Assuming up-to-date.")
    if not os.path.exists(multiple_pyx):
        pyx = glob.glob(os.path.join(cython_dir, "*pyx"))
        pyx = sorted(pyx, key=str.lower)
        f = open(multiple_pyx, 'wb')
        for fname in pyx:
            inFile = open(fname, 'rb')
            lines = inFile.readlines()
            inFile.close()
            for line in lines:
                f.write(line)
        f.close()
    src = [multiple_pyx]
else:
    src_files = glob.glob(os.path.join(cython_dir, 'default', '*.cpp'))
    src = []
    for fname in src_files:
        inFile = open(fname, 'rb')
        lines = inFile.readlines()
        inFile.close()
        f = open(os.path.join(cython_dir, os.path.basename(fname), 'wb'))
        for line in lines:
            f.write(line)
        f.close()
        src.append(f)

src += glob.glob(os.path.join(os.path.dirname(os.path.abspath(__file__)),
                'src', 'fisx_*.cpp'))

include_dirs = [numpy.get_include(),
                os.path.join(os.path.dirname(os.path.abspath(__file__)), "src")]

if sys.platform == 'win32':
    extra_compile_args = ['/EHsc']
    extra_link_args = []
else:
    extra_compile_args = []
    extra_link_args = []

def buildExtension():
    module = Extension(name="fisx._fisx",
                    sources=src,
                    include_dirs=include_dirs,
                    extra_compile_args=extra_compile_args,
                    extra_link_args=extra_link_args,
                    language="c++",
                    )
    return module

ext_modules = [buildExtension()]

cmdclass = {'install_data':smart_install_data,
            'build_py':smart_build_py}
if build_ext:
    cmdclass['build_ext'] = build_ext

description = "Quantitative X-Ray Fluorescence Analysis Support Library"
long_description = open("README.rst").read()

# tell distutils where to find the packages
package_dir = {"":"python"}
packages = ['fisx', 'fisx.tests']

classifiers = ["Development Status :: 5 - Production/Stable",
               "Programming Language :: C++",
               "Programming Language :: Python :: 2",
               "Programming Language :: Python :: 3",
               "Programming Language :: Cython",
               "Environment :: Console",
               "Intended Audience :: Developers",
               "Intended Audience :: End Users/Desktop",
               "Intended Audience :: Science/Research",
               "License :: OSI Approved :: MIT License",
               "Topic :: Software Development :: Libraries :: Python Modules",
               "Operating System :: Microsoft :: Windows",
               "Operating System :: Unix",
               "Operating System :: MacOS :: MacOS X",
               "Operating System :: POSIX",
               "Topic :: Scientific/Engineering :: Chemistry",
               "Topic :: Scientific/Engineering :: Physics"
               ]

install_requires = ["numpy"]

# cython is not mandatory to build because generated code is supplied
setup_requires = ["numpy"]

if __name__ == "__main__":
    setup(
        name='fisx',
        version=__version__,
        author="V. Armando Solé",
        author_email="sole@esrf.fr",
        description=description,
        long_description=long_description,
        license="MIT",
        url="https://github.com/vasole/fisx",
        download_url="https://github.com/vasole/fisx/archive/v%s.tar.gz" % __version__,
        package_dir=package_dir,
        packages=packages,
        ext_modules=ext_modules,
        data_files=data_files,
        cmdclass=cmdclass,
        classifiers=classifiers,
        install_requires=install_requires,
        setup_requires=setup_requires,
    )
<|endoftext|>


<commit_before># Copyright 2016 Uri Laserson
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

from setuptools import setup, find_packages

def readme():
    with open('README.md', 'r') as ip:
        return ip.read()

setup(
    name='pepsyn',
    version='0.1.0',
    description='Peptide library design',
    long_description=readme(),
    url='https://github.com/lasersonlab/pepsyn',
    author='Laserson Lab',
    license='Apache License, Version 2.0',
    classifiers=['Programming Language :: Python :: 3'],
    packages=find_packages(),
    install_requires=['click', 'biopython'],
    entry_points={'console_scripts': ['pepsyn = pepsyn.cli:cli']}
)
<commit_msg>Changed to 0.0.0 for initial PyPI registration<commit_after># Copyright 2016 Uri Laserson
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

from setuptools import setup, find_packages

def readme():
    with open('README.md', 'r') as ip:
        return ip.read()

setup(
    name='pepsyn',
    version='0.0.0',
    description='Peptide library design',
    long_description=readme(),
    url='https://github.com/lasersonlab/pepsyn',
    author='Laserson Lab',
    license='Apache License, Version 2.0',
    classifiers=['Programming Language :: Python :: 3'],
    packages=find_packages(),
    install_requires=['click', 'biopython'],
    entry_points={'console_scripts': ['pepsyn = pepsyn.cli:cli']}
)
<|endoftext|>


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

from __future__ import print_function
import os
import sys
import re
from setuptools import setup
from setuptools.extension import Extension

extension = 'wsgi_boost'

SUPPORTED_MSVC_COMPILERS = [14.0]

cwd = os.path.dirname(os.path.abspath(__file__))
src = os.path.join(cwd, extension)

class BuildError(Exception):
    pass

def get_msvc_compiler():
    """
    Returns environment path for a supported MS Visual C++ compiler
    """
    for vc_version in SUPPORTED_MSVC_COMPILERS:
        compiler = 'VS{0}COMNTOOLS'.format(int(vc_version * 10))
        if compiler in os.environ:
            return os.environ[compiler]
    raise BuildError('Compatible MS Visual C++ compiler not found! Only v. {0} are supported.'.format(str(SUPPORTED_MSVC_COMPILERS)))

def get_version():
    with open(os.path.join(src, 'response.h'), 'r') as fo:
        response_h = fo.read()
    return re.search(r'#define WSGI_BOOST_VERSION "(\d+\.\d+\.\d+)"', response_h).group(1)

def get_long_description():
    with open(os.path.join(cwd, 'Readme.rst'), 'r') as fo:
        return fo.read()

sources = [os.path.join(src, file) for file in os.listdir(src) if os.path.splitext(file)[1] == '.cpp']
include_dirs = [src]
libraries = []
library_dirs=[]

define_macros = [('BOOST_PYTHON_STATIC_LIB', None)]
extra_compile_args = []
extra_link_args = []

if sys.platform == 'win32':
    from distutils.msvc9compiler import get_build_version
    # Monkey-patching the default distutils compliler to a supported MS Visual C++ version
    vs_comntools = 'VS{0}COMNTOOLS'.format(int(get_build_version() * 10))
    os.environ[vs_comntools] = get_msvc_compiler()

    try:
        boost_root = os.environ['BOOST_ROOT']
    except KeyError:
        raise BuildError('BOOST_ROOT environment variable is not defined!')
    include_dirs.append(boost_root)
    try:
        boost_librarydir = os.environ['BOOST_LIBRARYDIR']
    except KeyError:
        raise BuildError('BOOST_LIBRARYDIR environment variable is not defined!')
    library_dirs.append(boost_librarydir)

    boost_python = 'boost_python{0}.*?-mt-s[\.-]'
    if sys.version_info.major >= 3:
        boost_python = boost_python.format(sys.version_info.major)
    else:
        boost_python = boost_python.format('')
    boost_py_re = re.compile(boost_python, re.IGNORECASE)
    for lib in os.listdir(boost_librarydir):
        if re.search(boost_py_re, lib) is not None:
            libraries.append(os.path.splitext(lib)[0])
            break
    else:
        raise BuildError('Unable to find boost_python library!')

    extra_compile_args.append('/EHsk')
    extra_compile_args.append('/MT')
    extra_link_args.append('/SAFESEH:NO')
else:
    try:
        include_dirs.append(os.environ['BOOST_ROOT'])
    except KeyError:
        pass
    try:
        library_dirs.append(os.environ['BOOST_LIBRARYDIR'])
    except KeyError:
        libraries.append(
            'boost_python-py{major}{minor}'.format(
                major=sys.version_info.major,
                minor=sys.version_info.minor
                ))
    else:
        libraries.append('boost_python')
    libraries += [
            'boost_regex',
            'boost_system',
            'boost_coroutine',
            'boost_context',
            'boost_filesystem',
            'boost_iostreams',
            'boost_date_time',
            'z',
        ]

    extra_compile_args.append('-std=c++11')

setup(
    name='WsgiBoostServer',
    version=get_version(),
    description='Multithreaded WSGI server based on C++ Boost.Asio',
    long_description=get_long_description(),
    author='Roman Miroshnychenko',
    author_email='romanvm@yandex.ua',
    url='https://github.com/romanvm/WsgiBoostServer',
    license='MIT',
    keywords='boost asio wsgi server http',
    classifiers=[
        'Development Status :: 4 - Beta',
        'Environment :: Web Environment',
        'Intended Audience :: Developers',
        'License :: OSI Approved :: MIT License',
        'Operating System :: Microsoft',
        'Operating System :: Microsoft :: Windows',
        'Operating System :: POSIX',
        'Operating System :: POSIX :: Linux',
        'Programming Language :: C++',
        'Programming Language :: Python',
        'Programming Language :: Python :: 2',
        'Programming Language :: Python :: 3',
        'Topic :: Internet :: WWW/HTTP',
        'Topic :: Internet :: WWW/HTTP :: WSGI',
        'Topic :: Internet :: WWW/HTTP :: WSGI :: Server',
        ],
    platforms=['win32', 'posix'],
    zip_safe=False,
    ext_modules=[
        Extension(
            name=extension,
            sources=sources,
            library_dirs=library_dirs,
            libraries=libraries,
            include_dirs=include_dirs,
            define_macros=define_macros,
            extra_compile_args=extra_compile_args,
            extra_link_args=extra_link_args,
            depends=[]
            )
        ]
    )
<commit_msg>Refactors setup.py: changes patching msvc compiler version, adds nose tests<commit_after>#!/usr/bin/env python

from __future__ import print_function
import os
import sys
import re
import distutils.msvc9compiler
from setuptools import setup
from setuptools.extension import Extension

NAME = 'wsgi_boost'

SUPPORTED_MSVC_COMPILERS = [14.0]

cwd = os.path.dirname(os.path.abspath(__file__))
src = os.path.join(cwd, NAME)

class BuildError(Exception):
    pass

def patch_msvc_compiler():
    """
    Monkey-patch distutils to use MS Visual C++ 2015 compiler
    """
    for vc_version in SUPPORTED_MSVC_COMPILERS:
        vcvarsall = distutils.msvc9compiler.find_vcvarsall(vc_version)
        if vcvarsall is not None:
            distutils.msvc9compiler.get_build_version = lambda: vc_version
            distutils.msvc9compiler.find_vcvarsall = lambda version: vcvarsall
            break
    else:
        raise BuildError('Compatible MS Visual C++ compiler not found! Only v. {0} are supported.'.format(str(SUPPORTED_MSVC_COMPILERS)))

def get_version():
    with open(os.path.join(src, 'response.h'), 'r') as fo:
        response_h = fo.read()
    return re.search(r'#define WSGI_BOOST_VERSION "(\d+\.\d+\.\d+)"', response_h).group(1)

def get_long_description():
    with open(os.path.join(cwd, 'Readme.rst'), 'r') as fo:
        return fo.read()

sources = [os.path.join(src, file) for file in os.listdir(src) if os.path.splitext(file)[1] == '.cpp']
include_dirs = [src]
libraries = []
library_dirs=[]

define_macros = []
extra_compile_args = []
extra_link_args = []

if sys.platform == 'win32':
    patch_msvc_compiler()

    try:
        boost_root = os.environ['BOOST_ROOT']
    except KeyError:
        raise BuildError('BOOST_ROOT environment variable is not defined!')
    include_dirs.append(boost_root)
    try:
        boost_librarydir = os.environ['BOOST_LIBRARYDIR']
    except KeyError:
        raise BuildError('BOOST_LIBRARYDIR environment variable is not defined!')
    library_dirs.append(boost_librarydir)

    define_macros.append(('BOOST_PYTHON_STATIC_LIB', None))
    extra_compile_args.append('/EHsk')
    extra_compile_args.append('/MT')
    extra_link_args.append('/SAFESEH:NO')
else:
    try:
        include_dirs.append(os.environ['BOOST_ROOT'])
    except KeyError:
        pass
    try:
        library_dirs.append(os.environ['BOOST_LIBRARYDIR'])
    except KeyError:
        libraries.append(
            'boost_python-py{major}{minor}'.format(
                major=sys.version_info.major,
                minor=sys.version_info.minor
                ))
    else:
        libraries.append('boost_python')
    libraries += [
            'boost_regex',
            'boost_system',
            'boost_coroutine',
            'boost_context',
            'boost_filesystem',
            'boost_iostreams',
            'boost_date_time',
            'z',
        ]

    extra_compile_args.append('-std=c++11')

setup(
    name='WsgiBoostServer',
    version=get_version(),
    description='Multithreaded WSGI server based on C++ Boost.Asio',
    long_description=get_long_description(),
    author='Roman Miroshnychenko',
    author_email='romanvm@yandex.ua',
    url='https://github.com/romanvm/WsgiBoostServer',
    license='MIT',
    keywords='boost asio wsgi server http',
    classifiers=[
        'Development Status :: 4 - Beta',
        'Environment :: Web Environment',
        'Intended Audience :: Developers',
        'License :: OSI Approved :: MIT License',
        'Operating System :: Microsoft',
        'Operating System :: Microsoft :: Windows',
        'Operating System :: POSIX',
        'Operating System :: POSIX :: Linux',
        'Programming Language :: C++',
        'Programming Language :: Python',
        'Programming Language :: Python :: 2',
        'Programming Language :: Python :: 3',
        'Topic :: Internet :: WWW/HTTP',
        'Topic :: Internet :: WWW/HTTP :: WSGI',
        'Topic :: Internet :: WWW/HTTP :: WSGI :: Server',
        ],
    platforms=['win32', 'posix'],
    zip_safe=False,
    test_suite = 'nose.collector',
    tests_require=['nose'],
    ext_modules=[
        Extension(
            name=NAME,
            sources=sources,
            library_dirs=library_dirs,
            libraries=libraries,
            include_dirs=include_dirs,
            define_macros=define_macros,
            extra_compile_args=extra_compile_args,
            extra_link_args=extra_link_args,
            depends=[]
            )
        ]
    )
<|endoftext|>


<commit_before>"""
   Copyright 2013 nilmtk authors

   Licensed under the Apache License, Version 2.0 (the "License");
   you may not use this file except in compliance with the License.
   You may obtain a copy of the License at

       http://www.apache.org/licenses/LICENSE-2.0

   Unless required by applicable law or agreed to in writing, software
   distributed under the License is distributed on an "AS IS" BASIS,
   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   See the License for the specific language governing permissions and
   limitations under the License.
"""

from setuptools import setup, find_packages, Extension
from os.path import join
import os
import sys
import warnings
import numpy

"""
CYTHON_DIR = 'nilmtk/disaggregate/feature_detectors'

try:
    # This trick adapted from
    # http://stackoverflow.com/a/4515279/732596
    from Cython.Build import cythonize
except ImportError:
    use_cython = False
else:
    use_cython = True

if use_cython:
    sources = [join(CYTHON_DIR, '_feature_detectors.pyx')]
    extensions = [Extension("nilmtk.disaggregate._feature_detectors",
                            sources=sources,
                            include_dirs=[numpy.get_include()])]
    ext_modules = cythonize(extensions)
else:
    ext_modules = [
        Extension("nilmtk.disaggregate._feature_detectors",
                  [join(CYTHON_DIR, '_feature_detectors.c')],
                  include_dirs=[numpy.get_include()]),
    ]

"""

"""
Following Segment of this file was taken from the pandas project(https://github.com/pydata/pandas)
"""
#Version Check

MAJOR = 0
MINOR = 1
MICRO = 0
ISRELEASED = False
VERSION = '%d.%d.%d' % (MAJOR, MINOR, MICRO)
QUALIFIER = ''

FULLVERSION = VERSION
if not ISRELEASED:
    FULLVERSION += '.dev'
    try:
        import subprocess
        try:
            pipe = subprocess.Popen(["git", "rev-parse", "--short", "HEAD"],
                                    stdout=subprocess.PIPE).stdout
        except OSError:
            # msysgit compatibility
            pipe = subprocess.Popen(["git.cmd", "rev-parse", "--short", "HEAD"],
                                    stdout=subprocess.PIPE).stdout
        rev = pipe.read().strip()
        # makes distutils blow up on Python 2.7
        if sys.version_info[0] >= 3:
            rev = rev.decode('ascii')

        FULLVERSION += "-%s" % rev
    except:
        warnings.warn("WARNING: Couldn't get git revision")
else:
    FULLVERSION += QUALIFIER

def write_version_py(filename=None):
    cnt = """\
version = '%s'
short_version = '%s'
"""
    if not filename:
        filename = os.path.join(os.path.dirname(__file__), 'nilmtk', 'version.py')

    a = open(filename, 'w')
    try:
        a.write(cnt % (FULLVERSION, VERSION))
    finally:
        a.close()
write_version_py()
#End of Version Check

setup(
    name='nilmtk',
    version=FULLVERSION,
    packages = find_packages(),
    ext_modules = ext_modules,
    install_requires = [],
    description='Estimate the energy consumed by individual appliances from '
                'whole-house power meter readings',
    author='nilmtk authors',
    author_email='',
    url='https://github.com/nilmtk/nilmtk',
    download_url = "https://github.com/nilmtk/nilmtk/tarball/master#egg=nilmtk-dev",
    long_description=open('README.md').read(),
    license='Apache 2.0',
    classifiers=[
        'Development Status :: 3 - Alpha',
        'Intended Audience :: Developers',
        'License :: OSI Approved :: Apache 2.0',
        'Programming Language :: Python',
        'Topic :: Scientific/Engineering :: Mathematics',
    ],
    keywords='smartmeters power electricity energy analytics redd '
             'disaggregation nilm nialm'
)
<commit_msg>removed ext modules from setup.py<commit_after>"""
   Copyright 2013 nilmtk authors

   Licensed under the Apache License, Version 2.0 (the "License");
   you may not use this file except in compliance with the License.
   You may obtain a copy of the License at

       http://www.apache.org/licenses/LICENSE-2.0

   Unless required by applicable law or agreed to in writing, software
   distributed under the License is distributed on an "AS IS" BASIS,
   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   See the License for the specific language governing permissions and
   limitations under the License.
"""

from setuptools import setup, find_packages, Extension
from os.path import join
import os
import sys
import warnings
import numpy

"""
CYTHON_DIR = 'nilmtk/disaggregate/feature_detectors'

try:
    # This trick adapted from
    # http://stackoverflow.com/a/4515279/732596
    from Cython.Build import cythonize
except ImportError:
    use_cython = False
else:
    use_cython = True

if use_cython:
    sources = [join(CYTHON_DIR, '_feature_detectors.pyx')]
    extensions = [Extension("nilmtk.disaggregate._feature_detectors",
                            sources=sources,
                            include_dirs=[numpy.get_include()])]
    ext_modules = cythonize(extensions)
else:
    ext_modules = [
        Extension("nilmtk.disaggregate._feature_detectors",
                  [join(CYTHON_DIR, '_feature_detectors.c')],
                  include_dirs=[numpy.get_include()]),
    ]

"""

"""
Following Segment of this file was taken from the pandas project(https://github.com/pydata/pandas)
"""
# Version Check

MAJOR = 0
MINOR = 1
MICRO = 0
ISRELEASED = False
VERSION = '%d.%d.%d' % (MAJOR, MINOR, MICRO)
QUALIFIER = ''

FULLVERSION = VERSION
if not ISRELEASED:
    FULLVERSION += '.dev'
    try:
        import subprocess
        try:
            pipe = subprocess.Popen(["git", "rev-parse", "--short", "HEAD"],
                                    stdout=subprocess.PIPE).stdout
        except OSError:
            # msysgit compatibility
            pipe = subprocess.Popen(
                ["git.cmd", "rev-parse", "--short", "HEAD"],
                stdout=subprocess.PIPE).stdout
        rev = pipe.read().strip()
        # makes distutils blow up on Python 2.7
        if sys.version_info[0] >= 3:
            rev = rev.decode('ascii')

        FULLVERSION += "-%s" % rev
    except:
        warnings.warn("WARNING: Couldn't get git revision")
else:
    FULLVERSION += QUALIFIER

def write_version_py(filename=None):
    cnt = """\
version = '%s'
short_version = '%s'
"""
    if not filename:
        filename = os.path.join(
            os.path.dirname(__file__), 'nilmtk', 'version.py')

    a = open(filename, 'w')
    try:
        a.write(cnt % (FULLVERSION, VERSION))
    finally:
        a.close()
write_version_py()
# End of Version Check

setup(
    name='nilmtk',
    version=FULLVERSION,
    packages=find_packages(),
    install_requires=[],
    description='Estimate the energy consumed by individual appliances from '
                'whole-house power meter readings',
    author='nilmtk authors',
    author_email='',
    url='https://github.com/nilmtk/nilmtk',
    download_url="https://github.com/nilmtk/nilmtk/tarball/master#egg=nilmtk-dev",
    long_description=open('README.md').read(),
    license='Apache 2.0',
    classifiers=[
        'Development Status :: 3 - Alpha',
        'Intended Audience :: Developers',
        'License :: OSI Approved :: Apache 2.0',
        'Programming Language :: Python',
        'Topic :: Scientific/Engineering :: Mathematics',
    ],
    keywords='smartmeters power electricity energy analytics redd '
             'disaggregation nilm nialm'
)
<|endoftext|>


<commit_before>import os.path

from setuptools import setup

setup(
    name='astroNN',
    version='0.99',
    classifiers=[
        'Development Status :: 3 - Alpha',
        'License :: OSI Approved :: MIT License',
        'Programming Language :: Python :: 3 :: Only',
        'Intended Audience :: Science/Research',
        'License :: OSI Approved :: MIT License',
        'Natural Language :: English',
        'Topic :: Scientific/Engineering :: Artificial Intelligence',
        'Topic:: Scientific / Engineering:: Astronomy'],
    packages=['astroNN',
              os.path.join('astroNN', 'apogee'),
              os.path.join('astroNN', 'gaia'),
              os.path.join('astroNN', 'NN'),
              os.path.join('astroNN', 'models'),
              os.path.join('astroNN', 'datasets'),
              os.path.join('astroNN', 'shared')],
    include_package_data=True,
    package_data={
            '': ['*.npy'],},
    install_requires=[
        'keras','numpy','astropy','h5py','matplotlib', 'astroquery', 'pandas', 'seaborn'],
    extras_require={
        "tensorflow": ["tensorflow>=1.4.0"],
        "tensorflow-gpu": ["tensorflow-gpu>=1.4.0"]},
    url='https://henrysky.github.io/astroNN/',
    license='MIT',
    author='Henry Leung',
    author_email='henrysky.leung@ mail.utoronto.ca',
    description='A python package to do neural network in astronomy using Keras and Tensorflow'
)
<commit_msg>fix setup.py error<commit_after>import os.path

from setuptools import setup

setup(
    name='astroNN',
    version='0.99',
    classifiers=[
        'Development Status :: 3 - Alpha',
        'License :: OSI Approved :: MIT License',
        'Programming Language :: Python :: 3 :: Only',
        'Intended Audience :: Science/Research',
        'License :: OSI Approved :: MIT License',
        'Natural Language :: English',
        'Topic :: Scientific/Engineering :: Artificial Intelligence',
        'Topic:: Scientific / Engineering:: Astronomy'],
    packages=['astroNN',
              os.path.join('astroNN', 'apogee'),
              os.path.join('astroNN', 'gaia'),
              os.path.join('astroNN', 'models'),
              os.path.join('astroNN', 'datasets'),
              os.path.join('astroNN', 'shared')],
    include_package_data=True,
    package_data={
            '': ['*.npy'],},
    install_requires=[
        'keras','numpy','astropy','h5py','matplotlib', 'astroquery', 'pandas', 'seaborn'],
    extras_require={
        "tensorflow": ["tensorflow>=1.4.0"],
        "tensorflow-gpu": ["tensorflow-gpu>=1.4.0"]},
    url='https://henrysky.github.io/astroNN/',
    license='MIT',
    author='Henry Leung',
    author_email='henrysky.leung@ mail.utoronto.ca',
    description='A python package to do neural network in astronomy using Keras and Tensorflow'
)
<|endoftext|>


<commit_before># -*- coding: utf-8 -*-
# License: 3-clause BSD
__revision__ = "$Id: $" # for the SVN Id
import sys
import os
from setuptools import setup, find_packages
import glob

_MAJOR               = 0
_MINOR               = 1
_MICRO               = 13
version              = '%d.%d.%d' % (_MAJOR, _MINOR, _MICRO)
release              = '%d.%d' % (_MAJOR, _MINOR)

metainfo = {
    'authors': {"main": ("yourname", "email@whatever.org")},
    'version': version,
    'license' : 'new BSD',
    'download_url' : ['http://pypi.python.org/pypi/sequana'],
    'url' : ["http://github.com/sequana/"],
    'description': "A set of standalone application and pipelines dedicated to NGS (new generation sequencing) analysis" ,
    'platforms' : ['Linux', 'Unix', 'MacOsX', 'Windows'],
    'keywords' : [''],
    'classifiers' : [
          'Development Status :: 4 - Beta',
          'Intended Audience :: Developers',
          'Intended Audience :: Science/Research',
          'License :: OSI Approved :: BSD License',
          'Operating System :: OS Independent',
          'Programming Language :: Python :: 2.7',
          'Topic :: Software Development :: Libraries :: Python Modules',
          'Topic :: Scientific/Engineering :: Bio-Informatics',
          'Topic :: Scientific/Engineering :: Information Analysis',
          'Topic :: Scientific/Engineering :: Mathematics',
          'Topic :: Scientific/Engineering :: Physics']
    }

packages = find_packages()
packages = [this for this in packages if this.startswith('test.') is False]
packages = [this for this in packages if this not in ['test']]

setup(
    name             = "sequana",
    version          = version,
    maintainer       = metainfo['authors']['main'][0],
    maintainer_email = metainfo['authors']['main'][1],
    author           = metainfo['authors']['main'][0],
    author_email     = metainfo['authors']['main'][1],
    long_description = open("README.rst").read(),
    keywords         = metainfo['keywords'],
    description      = metainfo['description'],
    license          = metainfo['license'],
    platforms        = metainfo['platforms'],
    url              = metainfo['url'],
    download_url     = metainfo['download_url'],
    classifiers      = metainfo['classifiers'],

    # package installation
    packages = packages,

    # pillow, sphinx-gallery and numpydoc are  for the doc only
    # mock is for the test only
    install_requires = ["easydev>=0.9.28", "reports>=0.2.0", "matplotlib",
        "pandas", "cutadapt>=1.9.1", "bioservices>=1.4.14", "biokit>=0.3.2",
        "pysam", "pyVCF", "docutils", "sphinx-gallery", "mock", "numpydoc", "pillow",
        "blist", "sphinx", "pyyaml"],

    # here below '': pattern means include that pattern in all packages
    # so '' :['README.rst'] will include all README.rst recursively
    # required to use python setup.py install

    # This is recursive include of data files
    exclude_package_data = {"": ["__pycache__"]},
    package_data = {
        '': ['Snakefile*', '*html', 'README.rst', 'config*.yaml', '*.css', "*.js",
                "snpEff.config*", "*.fa", "*.rules"],
        'sequana.rules' : ['*/*.rules', "*/*/*.rules"],
        'sequana.pipelines' : ['*/*.rules', "*/*/*.rules", "*/*yaml"],
        'sequana.resources.data' : ['*.*'],  # use *.* for files and not ./adapters
        'sequana.resources.data.adapters' : ['*'],
        'sequana.resources.images' : ['*'],
        'sequana.resources.testing' : ['*'],
        'sequana.resources.js/galleria/themes' : ['*'],
        },

    # thise files do not need to be added in MANIFEST.in since there are python
    # packages that will be copied from sequana/ into sequana/
    # Note, however, that e.g. ./pipelines must be added

    zip_safe=False,
    entry_points = {
        'console_scripts':[
           'fastq_head=sequana.scripts.fastq_head:main',
           'fastq_count=sequana.scripts.fastq_count:main',
           'sequana_fastq_head=sequana.scripts.fastq_head:main',
           'sequana_fastq_count=sequana.scripts.fastq_count:main',
           'sequana=sequana.scripts.main:main',
           'sequana_taxonomy=sequana.scripts.taxonomy:main',
           'sequana_coverage=sequana.scripts.coverage:main',
           'sequana_summary=sequana.scripts.summary:main',
           'sequana_mapping=sequana.scripts.mapping:main',
           'sequana_compressor=sequana.scripts.compressor:main'
        ]
    },

)
<commit_msg>add sequana_gui<commit_after># -*- coding: utf-8 -*-
# License: 3-clause BSD
__revision__ = "$Id: $" # for the SVN Id
import sys
import os
from setuptools import setup, find_packages
import glob

_MAJOR               = 0
_MINOR               = 1
_MICRO               = 13
version              = '%d.%d.%d' % (_MAJOR, _MINOR, _MICRO)
release              = '%d.%d' % (_MAJOR, _MINOR)

metainfo = {
    'authors': {"main": ("yourname", "email@whatever.org")},
    'version': version,
    'license' : 'new BSD',
    'download_url' : ['http://pypi.python.org/pypi/sequana'],
    'url' : ["http://github.com/sequana/"],
    'description': "A set of standalone application and pipelines dedicated to NGS (new generation sequencing) analysis" ,
    'platforms' : ['Linux', 'Unix', 'MacOsX', 'Windows'],
    'keywords' : [''],
    'classifiers' : [
          'Development Status :: 4 - Beta',
          'Intended Audience :: Developers',
          'Intended Audience :: Science/Research',
          'License :: OSI Approved :: BSD License',
          'Operating System :: OS Independent',
          'Programming Language :: Python :: 2.7',
          'Topic :: Software Development :: Libraries :: Python Modules',
          'Topic :: Scientific/Engineering :: Bio-Informatics',
          'Topic :: Scientific/Engineering :: Information Analysis',
          'Topic :: Scientific/Engineering :: Mathematics',
          'Topic :: Scientific/Engineering :: Physics']
    }

packages = find_packages()
packages = [this for this in packages if this.startswith('test.') is False]
packages = [this for this in packages if this not in ['test']]

setup(
    name             = "sequana",
    version          = version,
    maintainer       = metainfo['authors']['main'][0],
    maintainer_email = metainfo['authors']['main'][1],
    author           = metainfo['authors']['main'][0],
    author_email     = metainfo['authors']['main'][1],
    long_description = open("README.rst").read(),
    keywords         = metainfo['keywords'],
    description      = metainfo['description'],
    license          = metainfo['license'],
    platforms        = metainfo['platforms'],
    url              = metainfo['url'],
    download_url     = metainfo['download_url'],
    classifiers      = metainfo['classifiers'],

    # package installation
    packages = packages,

    # pillow, sphinx-gallery and numpydoc are  for the doc only
    # mock is for the test only
    install_requires = ["easydev>=0.9.28", "reports>=0.2.0", "matplotlib",
        "pandas", "cutadapt>=1.9.1", "bioservices>=1.4.14", "biokit>=0.3.2",
        "pysam", "pyVCF", "docutils", "sphinx-gallery", "mock", "numpydoc", "pillow",
        "blist", "sphinx", "pyyaml"],

    # here below '': pattern means include that pattern in all packages
    # so '' :['README.rst'] will include all README.rst recursively
    # required to use python setup.py install

    # This is recursive include of data files
    exclude_package_data = {"": ["__pycache__"]},
    package_data = {
        '': ['Snakefile*', '*html', 'README.rst', 'config*.yaml', '*.css', "*.js",
                "snpEff.config*", "*.fa", "*.rules"],
        'sequana.rules' : ['*/*.rules', "*/*/*.rules"],
        'sequana.pipelines' : ['*/*.rules', "*/*/*.rules", "*/*yaml"],
        'sequana.resources.data' : ['*.*'],  # use *.* for files and not ./adapters
        'sequana.resources.data.adapters' : ['*'],
        'sequana.resources.images' : ['*'],
        'sequana.resources.testing' : ['*'],
        'sequana.resources.js/galleria/themes' : ['*'],
        },

    # thise files do not need to be added in MANIFEST.in since there are python
    # packages that will be copied from sequana/ into sequana/
    # Note, however, that e.g. ./pipelines must be added

    zip_safe=False,
    entry_points = {
        'console_scripts':[
           'sequana_gui=sequana.gui.sequana_gui:main',
           'fastq_head=sequana.scripts.fastq_head:main',
           'fastq_count=sequana.scripts.fastq_count:main',
           'sequana_fastq_head=sequana.scripts.fastq_head:main',
           'sequana_fastq_count=sequana.scripts.fastq_count:main',
           'sequana=sequana.scripts.main:main',
           'sequana_taxonomy=sequana.scripts.taxonomy:main',
           'sequana_coverage=sequana.scripts.coverage:main',
           'sequana_summary=sequana.scripts.summary:main',
           'sequana_mapping=sequana.scripts.mapping:main',
           'sequana_compressor=sequana.scripts.compressor:main'
        ]
    },

)
<|endoftext|>


<commit_before>"""
Setup for indico apis
"""
try:
    from setuptools import setup
except ImportError:
    from distutils.core import setup

setup(
    name="IndicoIo",
    version='0.4.4',
    packages=[
        "indicoio",
        "indicoio.text",
        "indicoio.images",
        "indicoio.utils",
        "tests",
    ],
    description="""
        A Python Wrapper for indico.
        Use pre-built state of the art machine learning algorithms with a single line of code.
    """,
    license="MIT License (See LICENSE)",
    long_description=open("README").read(),
    url="https://github.com/IndicoDataSolutions/indicoio-python",
    author="Alec Radford, Slater Victoroff, Aidan McLaughlin",
    author_email="""
        Alec Radford <alec@indicodatasolutions.com>,
        Slater Victoroff <slater@indicodatasolutions.com>,
        Aidan McLaughlin <aidan@indicodatasolutions.com>
    """,
    install_requires=[
        "requests >= 1.2.3",
        "six >= 1.3.0",
        "numpy >= 1.8.1",
        "scikit-image >= 0.10.1"
    ],
)
<commit_msg>Update version number<commit_after>"""
Setup for indico apis
"""
try:
    from setuptools import setup
except ImportError:
    from distutils.core import setup

setup(
    name="IndicoIo",
    version='0.4.5',
    packages=[
        "indicoio",
        "indicoio.text",
        "indicoio.images",
        "indicoio.utils",
        "tests",
    ],
    description="""
        A Python Wrapper for indico.
        Use pre-built state of the art machine learning algorithms with a single line of code.
    """,
    license="MIT License (See LICENSE)",
    long_description=open("README").read(),
    url="https://github.com/IndicoDataSolutions/indicoio-python",
    author="Alec Radford, Slater Victoroff, Aidan McLaughlin",
    author_email="""
        Alec Radford <alec@indicodatasolutions.com>,
        Slater Victoroff <slater@indicodatasolutions.com>,
        Aidan McLaughlin <aidan@indicodatasolutions.com>
    """,
    install_requires=[
        "requests >= 1.2.3",
        "six >= 1.3.0",
        "numpy >= 1.8.1",
        "scikit-image >= 0.10.1"
    ],
)
<|endoftext|>


<commit_before># -*- coding: utf-8 -*-
import os

from setuptools import setup

VERSION = '1.4.0'

def readme(*paths):
    with open(os.path.join(*paths), 'r') as f:
        return f.read()

def requirements(*paths):
    with open(os.path.join(*paths), 'r') as f:
        return list(line.strip() for line in f.readlines() if line.strip() != '')

setup(
    name='slacker_log_handler',
    packages=['slacker_log_handler'],
    version=VERSION,
    description='Posts log events to Slack via API',
    long_description=readme('README.rst'),
    classifiers=[
        'Development Status :: 5 - Production/Stable',
        'Environment :: Web Environment',
        'Framework :: Django',
        'Intended Audience :: Developers',
        'Intended Audience :: System Administrators',
        'License :: OSI Approved :: Apache Software License',
        'Natural Language :: English',
        'Operating System :: OS Independent',
        'Programming Language :: Python',
        'Programming Language :: Python :: 2',
        'Programming Language :: Python :: 3',
        'Topic :: Communications :: Chat',
        'Topic :: Office/Business :: Groupware',
    ],
    url='https://github.com/mathiasose/slacker_log_handler',
    download_url='https://github.com/mathiasose/slacker_log_handler/archive/{v}.tar.gz'.format(v=VERSION),
    author='Mathias Ose',
    author_email='mathias.ose@gmail.com',
    keywords=['slack', 'logging'],
    install_requires=requirements('requirements.txt'),
    include_package_data=True,
    zip_safe=False
)
<commit_msg>Bump version to 1.5.0<commit_after># -*- coding: utf-8 -*-
import os

from setuptools import setup

VERSION = '1.5.0'

def readme(*paths):
    with open(os.path.join(*paths), 'r') as f:
        return f.read()

def requirements(*paths):
    with open(os.path.join(*paths), 'r') as f:
        return list(line.strip() for line in f.readlines() if line.strip() != '')

setup(
    name='slacker_log_handler',
    packages=['slacker_log_handler'],
    version=VERSION,
    description='Posts log events to Slack via API',
    long_description=readme('README.rst'),
    classifiers=[
        'Development Status :: 5 - Production/Stable',
        'Environment :: Web Environment',
        'Framework :: Django',
        'Intended Audience :: Developers',
        'Intended Audience :: System Administrators',
        'License :: OSI Approved :: Apache Software License',
        'Natural Language :: English',
        'Operating System :: OS Independent',
        'Programming Language :: Python',
        'Programming Language :: Python :: 2',
        'Programming Language :: Python :: 3',
        'Topic :: Communications :: Chat',
        'Topic :: Office/Business :: Groupware',
    ],
    url='https://github.com/mathiasose/slacker_log_handler',
    download_url='https://github.com/mathiasose/slacker_log_handler/archive/{v}.tar.gz'.format(v=VERSION),
    author='Mathias Ose',
    author_email='mathias.ose@gmail.com',
    keywords=['slack', 'logging'],
    install_requires=requirements('requirements.txt'),
    include_package_data=True,
    zip_safe=False
)
<|endoftext|>


<commit_before>#!/usr/bin/env python
"""
Sentry
======

Sentry is a realtime event logging and aggregation platform. It specializes
in monitoring errors and extracting all the information needed to do a proper
post-mortem without any of the hassle of the standard user feedback loop.

Sentry is a Server
------------------

The Sentry package, at its core, is just a simple server and web UI. It will
handle authentication clients (such as `Raven
<https://github.com/getsentry/raven-python>`_)
and all of the logic behind storage and aggregation.

That said, Sentry is not limited to Python. The primary implementation is in
Python, but it contains a full API for sending events from any language, in
any application.

:copyright: (c) 2011-2014 by the Sentry Team, see AUTHORS for more details.
:license: BSD, see LICENSE for more details.
"""
from __future__ import absolute_import

# if sys.version_info[:2] != (2, 7):
#     print 'Error: Sentry requires Python 2.7'
#     sys.exit(1)

import os
import os.path
import sys

from distutils.command.build import build as BuildCommand
from setuptools import setup, find_packages
from setuptools.command.sdist import sdist as SDistCommand
from setuptools.command.develop import develop as DevelopCommand

ROOT = os.path.realpath(os.path.join(os.path.dirname(
    sys.modules['__main__'].__file__)))

# Add Sentry to path so we can import distutils
sys.path.insert(0, os.path.join(ROOT, 'src'))

from sentry.utils.distutils import (
    BuildAssetsCommand, BuildIntegrationDocsCommand
)

# The version of sentry
VERSION = '8.18.0.dev0'

# Hack to prevent stupid "TypeError: 'NoneType' object is not callable" error
# in multiprocessing/util.py _exit_function when running `python
# setup.py test` (see
# http://www.eby-sarna.com/pipermail/peak/2010-May/003357.html)
for m in ('multiprocessing', 'billiard'):
    try:
        __import__(m)
    except ImportError:
        pass

IS_LIGHT_BUILD = os.environ.get('SENTRY_LIGHT_BUILD') == '1'

dev_requires = [
    'Babel',
    'flake8>=2.6,<2.7',
    'pycodestyle>=2.0,<2.1',
    'isort>=4.2.2,<4.3.0',
]

tests_require = [
    # cassandra
    'blist',
    # TODO(dcramer): figure out why Travis needs this
    'cassandra-driver<=3.5.0',
    'casscache',
    'cqlsh',
    # /cassandra
    'datadog',
    'msgpack-python<0.5.0',
    'pytest-cov>=1.8.0,<1.9.0',
    'pytest-timeout>=0.5.0,<0.6.0',
    'pytest-xdist>=1.11.0,<1.12.0',
    'python-coveralls',
    'responses',
]

install_requires = [
    'boto3>=1.4.1,<1.5',
    'celery>=3.1.8,<3.1.19',
    'click>=5.0,<7.0',
    # 'cryptography>=1.3,<1.4',
    'cssutils>=0.9.9,<0.10.0',
    'Django>=1.6.0,<1.7',
    'django-crispy-forms>=1.4.0,<1.5.0',
    'django-debug-toolbar>=1.3.2,<1.4.0',
    'django-jsonfield>=0.9.13,<0.9.14',
    'django-picklefield>=0.3.0,<0.4.0',
    'django-sudo>=2.1.0,<3.0.0',
    'django-templatetag-sugar>=0.1.0',
    'djangorestframework>=2.4.8,<2.5.0',
    'email-reply-parser>=0.2.0,<0.3.0',
    'enum34>=0.9.18,<1.2.0',
    'exam>=0.5.1',
    # broken on python3
    'hiredis>=0.1.0,<0.2.0',
    'honcho>=0.7.0,<0.8.0',
    'kombu==3.0.35',
    'lxml>=3.4.1',

    'ipaddress>=1.0.16,<1.1.0',
    'libsourcemap>=0.7.0,<0.8.0',
    'loremipsum>=1.0.5,<1.1.0',
    'mock>=0.8.0,<1.1',
    'mmh3>=2.3.1,<2.4',
    'oauth2>=1.5.167',
    'percy>=0.4.4',
    'petname>=2.0,<2.1',
    'Pillow>=3.2.0,<3.3.0',
    'progressbar2>=3.10,<3.11',
    'psycopg2>=2.6.0,<2.7.0',
    'pytest>=2.8.0,<2.9.0',
    'pytest-django>=2.9.1,<2.10.0',
    'pytest-html>=1.9.0,<1.10.0',
    'python-dateutil>=2.0.0,<3.0.0',
    'python-memcached>=1.53,<2.0.0',
    'python-openid>=2.2',
    'PyYAML>=3.11,<3.12',
    'raven>=5.29.0,<6.0.0',
    'redis>=2.10.3,<2.11.0',
    'requests[security]>=2.9.1,<2.13.0',
    'selenium==3.0.0b3',
    'simplejson>=3.2.0,<3.9.0',
    'six>=1.10.0,<1.11.0',
    'setproctitle>=1.1.7,<1.2.0',
    'statsd>=3.1.0,<3.2.0',
    'structlog==16.1.0',
    'South==1.0.1',
    'symsynd>=3.0.0,<4.0.0',
    'toronado>=0.0.11,<0.1.0',
    'ua-parser>=0.6.1,<0.8.0',
    'urllib3>=1.14,<1.17',
    'uwsgi>2.0.0,<2.1.0',
    'rb>=1.6.0,<2.0.0',
    'qrcode>=5.2.2,<6.0.0',
    'python-u2flib-server>=4.0.1,<4.1.0',
]

class SentrySDistCommand(SDistCommand):
    # If we are not a light build we want to also execute build_assets as
    # part of our source build pipeline.
    if not IS_LIGHT_BUILD:
        sub_commands = SDistCommand.sub_commands + \
            [('build_assets', None), ('build_integration_docs', None)]

class SentryBuildCommand(BuildCommand):

    def run(self):
        BuildCommand.run(self)
        if not IS_LIGHT_BUILD:
            self.run_command('build_assets')
            self.run_command('build_integration_docs')

class SentryDevelopCommand(DevelopCommand):

    def run(self):
        DevelopCommand.run(self)
        if not IS_LIGHT_BUILD:
            self.run_command('build_assets')
            self.run_command('build_integration_docs')

cmdclass = {
    'sdist': SentrySDistCommand,
    'develop': SentryDevelopCommand,
    'build': SentryBuildCommand,
    'build_assets': BuildAssetsCommand,
    'build_integration_docs': BuildIntegrationDocsCommand,
}

setup(
    name='sentry',
    version=VERSION,
    author='Sentry',
    author_email='hello@sentry.io',
    url='https://sentry.io',
    description='A realtime logging and aggregation server.',
    long_description=open(os.path.join(ROOT, 'README.rst')).read(),
    package_dir={'': 'src'},
    packages=find_packages('src'),
    zip_safe=False,
    install_requires=install_requires,
    extras_require={
        'dev': dev_requires,
        'postgres': [],
        'tests': tests_require,
    },
    cmdclass=cmdclass,
    license='BSD',
    include_package_data=True,
    entry_points={
        'console_scripts': [
            'sentry = sentry.runner:main',
        ],
        'flake8.extension': [
        ],
    },
    classifiers=[
        'Framework :: Django',
        'Intended Audience :: Developers',
        'Intended Audience :: System Administrators',
        'Operating System :: POSIX :: Linux',
        'Programming Language :: Python :: 2',
        'Programming Language :: Python :: 2.7',
        'Programming Language :: Python :: 2 :: Only',
        'Topic :: Software Development'
    ],
)
<commit_msg>Revert libsourcemap<commit_after>#!/usr/bin/env python
"""
Sentry
======

Sentry is a realtime event logging and aggregation platform. It specializes
in monitoring errors and extracting all the information needed to do a proper
post-mortem without any of the hassle of the standard user feedback loop.

Sentry is a Server
------------------

The Sentry package, at its core, is just a simple server and web UI. It will
handle authentication clients (such as `Raven
<https://github.com/getsentry/raven-python>`_)
and all of the logic behind storage and aggregation.

That said, Sentry is not limited to Python. The primary implementation is in
Python, but it contains a full API for sending events from any language, in
any application.

:copyright: (c) 2011-2014 by the Sentry Team, see AUTHORS for more details.
:license: BSD, see LICENSE for more details.
"""
from __future__ import absolute_import

# if sys.version_info[:2] != (2, 7):
#     print 'Error: Sentry requires Python 2.7'
#     sys.exit(1)

import os
import os.path
import sys

from distutils.command.build import build as BuildCommand
from setuptools import setup, find_packages
from setuptools.command.sdist import sdist as SDistCommand
from setuptools.command.develop import develop as DevelopCommand

ROOT = os.path.realpath(os.path.join(os.path.dirname(
    sys.modules['__main__'].__file__)))

# Add Sentry to path so we can import distutils
sys.path.insert(0, os.path.join(ROOT, 'src'))

from sentry.utils.distutils import (
    BuildAssetsCommand, BuildIntegrationDocsCommand
)

# The version of sentry
VERSION = '8.18.0.dev0'

# Hack to prevent stupid "TypeError: 'NoneType' object is not callable" error
# in multiprocessing/util.py _exit_function when running `python
# setup.py test` (see
# http://www.eby-sarna.com/pipermail/peak/2010-May/003357.html)
for m in ('multiprocessing', 'billiard'):
    try:
        __import__(m)
    except ImportError:
        pass

IS_LIGHT_BUILD = os.environ.get('SENTRY_LIGHT_BUILD') == '1'

dev_requires = [
    'Babel',
    'flake8>=2.6,<2.7',
    'pycodestyle>=2.0,<2.1',
    'isort>=4.2.2,<4.3.0',
]

tests_require = [
    # cassandra
    'blist',
    # TODO(dcramer): figure out why Travis needs this
    'cassandra-driver<=3.5.0',
    'casscache',
    'cqlsh',
    # /cassandra
    'datadog',
    'msgpack-python<0.5.0',
    'pytest-cov>=1.8.0,<1.9.0',
    'pytest-timeout>=0.5.0,<0.6.0',
    'pytest-xdist>=1.11.0,<1.12.0',
    'python-coveralls',
    'responses',
]

install_requires = [
    'boto3>=1.4.1,<1.5',
    'celery>=3.1.8,<3.1.19',
    'click>=5.0,<7.0',
    # 'cryptography>=1.3,<1.4',
    'cssutils>=0.9.9,<0.10.0',
    'Django>=1.6.0,<1.7',
    'django-crispy-forms>=1.4.0,<1.5.0',
    'django-debug-toolbar>=1.3.2,<1.4.0',
    'django-jsonfield>=0.9.13,<0.9.14',
    'django-picklefield>=0.3.0,<0.4.0',
    'django-sudo>=2.1.0,<3.0.0',
    'django-templatetag-sugar>=0.1.0',
    'djangorestframework>=2.4.8,<2.5.0',
    'email-reply-parser>=0.2.0,<0.3.0',
    'enum34>=0.9.18,<1.2.0',
    'exam>=0.5.1',
    # broken on python3
    'hiredis>=0.1.0,<0.2.0',
    'honcho>=0.7.0,<0.8.0',
    'kombu==3.0.35',
    'lxml>=3.4.1',

    'ipaddress>=1.0.16,<1.1.0',
    'libsourcemap>=0.5.0,<0.6.0',
    'loremipsum>=1.0.5,<1.1.0',
    'mock>=0.8.0,<1.1',
    'mmh3>=2.3.1,<2.4',
    'oauth2>=1.5.167',
    'percy>=0.4.4',
    'petname>=2.0,<2.1',
    'Pillow>=3.2.0,<3.3.0',
    'progressbar2>=3.10,<3.11',
    'psycopg2>=2.6.0,<2.7.0',
    'pytest>=2.8.0,<2.9.0',
    'pytest-django>=2.9.1,<2.10.0',
    'pytest-html>=1.9.0,<1.10.0',
    'python-dateutil>=2.0.0,<3.0.0',
    'python-memcached>=1.53,<2.0.0',
    'python-openid>=2.2',
    'PyYAML>=3.11,<3.12',
    'raven>=5.29.0,<6.0.0',
    'redis>=2.10.3,<2.11.0',
    'requests[security]>=2.9.1,<2.13.0',
    'selenium==3.0.0b3',
    'simplejson>=3.2.0,<3.9.0',
    'six>=1.10.0,<1.11.0',
    'setproctitle>=1.1.7,<1.2.0',
    'statsd>=3.1.0,<3.2.0',
    'structlog==16.1.0',
    'South==1.0.1',
    'symsynd>=3.0.0,<4.0.0',
    'toronado>=0.0.11,<0.1.0',
    'ua-parser>=0.6.1,<0.8.0',
    'urllib3>=1.14,<1.17',
    'uwsgi>2.0.0,<2.1.0',
    'rb>=1.6.0,<2.0.0',
    'qrcode>=5.2.2,<6.0.0',
    'python-u2flib-server>=4.0.1,<4.1.0',
]

class SentrySDistCommand(SDistCommand):
    # If we are not a light build we want to also execute build_assets as
    # part of our source build pipeline.
    if not IS_LIGHT_BUILD:
        sub_commands = SDistCommand.sub_commands + \
            [('build_assets', None), ('build_integration_docs', None)]

class SentryBuildCommand(BuildCommand):

    def run(self):
        BuildCommand.run(self)
        if not IS_LIGHT_BUILD:
            self.run_command('build_assets')
            self.run_command('build_integration_docs')

class SentryDevelopCommand(DevelopCommand):

    def run(self):
        DevelopCommand.run(self)
        if not IS_LIGHT_BUILD:
            self.run_command('build_assets')
            self.run_command('build_integration_docs')

cmdclass = {
    'sdist': SentrySDistCommand,
    'develop': SentryDevelopCommand,
    'build': SentryBuildCommand,
    'build_assets': BuildAssetsCommand,
    'build_integration_docs': BuildIntegrationDocsCommand,
}

setup(
    name='sentry',
    version=VERSION,
    author='Sentry',
    author_email='hello@sentry.io',
    url='https://sentry.io',
    description='A realtime logging and aggregation server.',
    long_description=open(os.path.join(ROOT, 'README.rst')).read(),
    package_dir={'': 'src'},
    packages=find_packages('src'),
    zip_safe=False,
    install_requires=install_requires,
    extras_require={
        'dev': dev_requires,
        'postgres': [],
        'tests': tests_require,
    },
    cmdclass=cmdclass,
    license='BSD',
    include_package_data=True,
    entry_points={
        'console_scripts': [
            'sentry = sentry.runner:main',
        ],
        'flake8.extension': [
        ],
    },
    classifiers=[
        'Framework :: Django',
        'Intended Audience :: Developers',
        'Intended Audience :: System Administrators',
        'Operating System :: POSIX :: Linux',
        'Programming Language :: Python :: 2',
        'Programming Language :: Python :: 2.7',
        'Programming Language :: Python :: 2 :: Only',
        'Topic :: Software Development'
    ],
)
<|endoftext|>