#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Trailblazer is a tool to manage and track state of analyses.

You can install it from PyPI as follows::
    pip install trailblazer

For more detailed instructions, run :code:`trailblazer --help`

See the GitHub repo for documentation:
`Clinical-Genomics/analysis <https://github.com/Clinical-Genomics/analysis>`_
"""
# To use a consistent encoding
import codecs
import os
# Always prefer setuptools over distutils
from setuptools import setup, find_packages
from setuptools.command.test import test as TestCommand
import sys

# Shortcut for building/publishing to Pypi
if sys.argv[-1] == 'publish':
    os.system('python setup.py sdist bdist_wheel upload')
    sys.exit()


def parse_reqs(req_path='./requirements.txt'):
    """Recursively parse requirements from nested pip files."""
    install_requires = []
    with codecs.open(req_path, 'r') as handle:
        # remove comments and empty lines
        lines = (line.strip() for line in handle
                 if line.strip() and not line.startswith('#'))
        for line in lines:
            # check for nested requirements files
            if line.startswith('-r'):
                # recursively call this function
                install_requires += parse_reqs(req_path=line[3:])
            else:
                # add the line as a new requirement
                install_requires.append(line)
    return install_requires


# This is a plug-in for setuptools that will invoke py.test
# when you run python setup.py test
class PyTest(TestCommand):

    """Set up the py.test test runner."""

    def finalize_options(self):
        """Set options for the command line."""
        TestCommand.finalize_options(self)
        self.test_args = []
        self.test_suite = True

    def run_tests(self):
        """Execute the test runner command."""
        # Import here, because outside the required eggs aren't loaded yet
        import pytest
        sys.exit(pytest.main(self.test_args))


setup(
    name='trailblazer',

    # Versions should comply with PEP440. For a discussion on
    # single-sourcing the version across setup.py and the project code,
    # see http://packaging.python.org/en/latest/tutorial.html#version
    version='3.1.0',

    description=('Track MIP analyses.'),
    long_description=__doc__,
    # What does your project relate to? Separate with spaces.
    keywords='analysis development',
    author='<NAME>',
    author_email='<EMAIL>',
    license='MIT',

    # The project's main homepage
    url='https://github.com/Clinical-Genomics/analysis',

    packages=find_packages(exclude=('tests*', 'docs', 'examples')),

    # If there are data files included in your packages that need to be
    # installed, specify them here.
    include_package_data=True,
    # package_data={
    #     'taboo': [
    #         'server/genotype/templates/genotype/*.html',
    #     ]
    # },
    zip_safe=False,

    # Although 'package_data' is the preferred approach, in some case you
    # may need to place data files outside of your packages.
    # In this case, 'data_file' will be installed into:
    # '<sys.prefix>/my_data'
    # data_files=[('my_data', ['data/data_file'])],

    # Install requirements loaded from ``requirements.txt``
    install_requires=parse_reqs(),
    tests_require=[
        'pytest',
    ],
    cmdclass=dict(
        test=PyTest,
    ),

    # To provide executable scripts, use entry points in preference to the
    # "scripts" keyword. Entry points provide cross-platform support and
    # allow pip to create the appropriate form of executable for the
    # target platform.
    entry_points={
        'console_scripts': [
            'trailblazer = trailblazer.cli:base',
        ]
    },

    # See: http://pypi.python.org/pypi?%3Aaction=list_classifiers
    classifiers=[
        # Pick your license as you wish (should match "license" above)
        'License :: OSI Approved :: MIT License',

        # Specify the Python versions you support here. In particular, ensure
        # that you indicate whether you support Python 2, Python 3 or both.
        'Programming Language :: Python :: 3',
        'Programming Language :: Python :: 3.6',

        'Environment :: Console',
    ],
)

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Trailblazer is a tool to manage and track state of analyses.

You can install it from PyPI as follows::
    pip install trailblazer

For more detailed instructions, run :code:`trailblazer --help`

See the GitHub repo for documentation:
`Clinical-Genomics/analysis <https://github.com/Clinical-Genomics/analysis>`_
"""
# To use a consistent encoding
import codecs
import os
# Always prefer setuptools over distutils
from setuptools import setup, find_packages
from setuptools.command.test import test as TestCommand
import sys

# Shortcut for building/publishing to Pypi
if sys.argv[-1] == 'publish':
    os.system('python setup.py sdist bdist_wheel upload')
    sys.exit()


def parse_reqs(req_path='./requirements.txt'):
    """Recursively parse requirements from nested pip files."""
    install_requires = []
    with codecs.open(req_path, 'r') as handle:
        # remove comments and empty lines
        lines = (line.strip() for line in handle
                 if line.strip() and not line.startswith('#'))
        for line in lines:
            # check for nested requirements files
            if line.startswith('-r'):
                # recursively call this function
                install_requires += parse_reqs(req_path=line[3:])
            else:
                # add the line as a new requirement
                install_requires.append(line)
    return install_requires


# This is a plug-in for setuptools that will invoke py.test
# when you run python setup.py test
class PyTest(TestCommand):

    """Set up the py.test test runner."""

    def finalize_options(self):
        """Set options for the command line."""
        TestCommand.finalize_options(self)
        self.test_args = []
        self.test_suite = True

    def run_tests(self):
        """Execute the test runner command."""
        # Import here, because outside the required eggs aren't loaded yet
        import pytest
        sys.exit(pytest.main(self.test_args))


setup(
    name='trailblazer',

    # Versions should comply with PEP440. For a discussion on
    # single-sourcing the version across setup.py and the project code,
    # see http://packaging.python.org/en/latest/tutorial.html#version
    version='3.1.0',

    description=('Track MIP analyses.'),
    long_description=__doc__,
    # What does your project relate to? Separate with spaces.
    keywords='analysis development',
    author='<NAME>',
    author_email='<EMAIL>',
    license='MIT',

    # The project's main homepage
    url='https://github.com/Clinical-Genomics/analysis',

    packages=find_packages(exclude=('tests*', 'docs', 'examples')),

    # If there are data files included in your packages that need to be
    # installed, specify them here.
    include_package_data=True,
    # package_data={
    #     'taboo': [
    #         'server/genotype/templates/genotype/*.html',
    #     ]
    # },
    zip_safe=False,

    # Although 'package_data' is the preferred approach, in some case you
    # may need to place data files outside of your packages.
    # In this case, 'data_file' will be installed into:
    # '<sys.prefix>/my_data'
    # data_files=[('my_data', ['data/data_file'])],

    # Install requirements loaded from ``requirements.txt``
    install_requires=parse_reqs(),
    tests_require=[
        'pytest',
    ],
    cmdclass=dict(
        test=PyTest,
    ),

    # To provide executable scripts, use entry points in preference to the
    # "scripts" keyword. Entry points provide cross-platform support and
    # allow pip to create the appropriate form of executable for the
    # target platform.
    entry_points={
        'console_scripts': [
            'trailblazer = trailblazer.cli:base',
        ]
    },

    # See: http://pypi.python.org/pypi?%3Aaction=list_classifiers
    classifiers=[
        # Pick your license as you wish (should match "license" above)
        'License :: OSI Approved :: MIT License',

        # Specify the Python versions you support here. In particular, ensure
        # that you indicate whether you support Python 2, Python 3 or both.
        'Programming Language :: Python :: 3',
        'Programming Language :: Python :: 3.6',

        'Environment :: Console',
    ],
)

#!/usr/bin/env python # -*- coding: utf-8 -*- Trailblazer is a tool to manage and track state of analyses.  You can install it from PyPI as follows::     pip install trailblazer  For more detailed instructions, run :code:`trailblazer --help`  See the GitHub repo for documentation: `Clinical-Genomics/analysis <https://github.com/Clinical-Genomics/analysis>`_ # To use a consistent encoding # Always prefer setuptools over distutils # Shortcut for building/publishing to Pypi Recursively parse requirements from nested pip files. # remove comments and empty lines # check for nested requirements files # recursively call this function # add the line as a new requirement # This is a plug-in for setuptools that will invoke py.test # when you run python setup.py test Set up the py.test test runner. Set options for the command line. Execute the test runner command. # Import here, because outside the required eggs aren't loaded yet # Versions should comply with PEP440. For a discussion on # single-sourcing the version across setup.py and the project code, # see http://packaging.python.org/en/latest/tutorial.html#version # What does your project relate to? Separate with spaces. # The project's main homepage # If there are data files included in your packages that need to be # installed, specify them here. # package_data={ #     'taboo': [ #         'server/genotype/templates/genotype/*.html', #     ] # }, # Although 'package_data' is the preferred approach, in some case you # may need to place data files outside of your packages. # In this case, 'data_file' will be installed into: # '<sys.prefix>/my_data' # data_files=[('my_data', ['data/data_file'])], # Install requirements loaded from ``requirements.txt`` # To provide executable scripts, use entry points in preference to the # "scripts" keyword. Entry points provide cross-platform support and # allow pip to create the appropriate form of executable for the # target platform. # See: http://pypi.python.org/pypi?%3Aaction=list_classifiers # Pick your license as you wish (should match "license" above) # Specify the Python versions you support here. In particular, ensure # that you indicate whether you support Python 2, Python 3 or both.