setup.py

"""Setup tu build  panISa program

Derived from setuptools based setup module 
See:
https://packaging.python.org/en/latest/distributing.html
https://github.com/pypa/sampleproject
"""

# 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__))

# Get the long description from the README file
with open(path.join(here, 'README.rst'), encoding='utf-8') as f:
    long_description = f.read()

# Arguments marked as "Required" below must be included for upload to PyPI.
# Fields marked as "Optional" may be commented out.

setup(
    # This is the name of your project. The first time you publish this
    # package, this name will be registered for you. It will determine how
    # users can install this project, e.g.:
    #
    # $ pip install sampleproject
    #
    # And where it will live on PyPI: https://pypi.org/project/sampleproject/
    #
    # There are some restrictions on what makes a valid project name
    # specification here:
    # https://packaging.python.org/specifications/core-metadata/#name
    name='panisa',  # Required

    # Versions should comply with PEP 440:
    # https://www.python.org/dev/peps/pep-0440/
    #
    # For a discussion on single-sourcing the version across setup.py and the
    # project code, see
    # https://packaging.python.org/en/latest/single_source_version.html
    version='0.1.7',  # Required

    # This is a one-line description or tagline of what your project does. This
    # corresponds to the "Summary" metadata field:
    # https://packaging.python.org/specifications/core-metadata/#summary
    description='panISa is a software to search insertion sequence (IS) on resequencing data (bam file)',  # Required

    # This is an optional longer description of your project that represents
    # the body of text which users will see when they visit PyPI.
    #
    # Often, this is the same as your README, so you can just read it in from
    # that file directly (as we have already done above)
    #
    # This field corresponds to the "Description" metadata field:
    # https://packaging.python.org/specifications/core-metadata/#description-optional
    long_description=long_description,  # Optional
    long_description_content_type='text/x-rst',

    # This should be a valid link to your project's main homepage.
    #
    # This field corresponds to the "Home-Page" metadata field:
    # https://packaging.python.org/specifications/core-metadata/#home-page-optional
    url='https://github.com/bvalot/panISa',  # Optional

    # This should be your name or the name of the organization which owns the
    # project.
    author='Benoit Valot',  # Optional

    # This should be a valid email address corresponding to the author listed
    # above.
    author_email='benoit.valot@univ-fcomte.fr',  # Optional

    # Classifiers help users find your project by categorizing it.
    #
    # For a list of valid classifiers, see
    # https://pypi.python.org/pypi?%3Aaction=list_classifiers
    classifiers=[  # Optional
        # How mature is this project? Common values are
        #   3 - Alpha
        #   4 - Beta
        #   5 - Production/Stable
        'Development Status :: 5 - Production/Stable',

        # Indicate who your project is intended for
        'Intended Audience :: Science/Research',
        'Topic :: Scientific/Engineering :: Bio-Informatics',

        # Pick your license as you wish
        'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',

        # 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 :: 3.7',
    ],

    # This field adds keywords for your project which will appear on the
    # project page. What does your project relate to?
    #
    # Note that this is a string of words separated by whitespace, not a list.
    keywords='bioinformatic IS bacteria',  # Optional

    # You can just specify package directories manually here if your project is
    # simple. Or you can use find_packages().
    #
    # Alternatively, if you just want to distribute a single Python file, use
    # the `py_modules` argument instead as follows, which will expect a file
    # called `my_module.py` to exist:
    #
    #   py_modules=["my_module"],
    #
    packages=find_packages('.', exclude=['script', 'validate']),  # Required

    # This field lists other packages that your project depends on to run.
    # Any package you put here will be installed by pip when your project is
    # installed, so they must be valid existing projects.
    #
    # For an analysis of "install_requires" vs pip's requirements files see:
    # https://packaging.python.org/en/latest/requirements.html
    install_requires=['pysam>=0.9', 'requests>=2.12'],  # Optional

    # List additional groups of dependencies here (e.g. development
    # dependencies). Users will be able to install these using the "extras"
    # syntax, for example:
    #
    #   $ pip install sampleproject[dev]
    #
    # Similar to `install_requires` above, these must be valid existing
    # projects.
    # extras_require={  # Optional
    #     'dev': ['check-manifest'],
    #     'test': ['coverage'],
    # },

    # If there are data files included in your packages that need to be
    # installed, specify them here.
    #
    # If using Python 2.6 or earlier, then these have to be included in
    # MANIFEST.in as well.
    package_data={  # Optional
        'sample': ['test.bam'],
    },

    # Although 'package_data' is the preferred approach, in some case you may
    # need to place data files outside of your packages. See:
    # http://docs.python.org/3.4/distutils/setupscript.html#installing-additional-files
    #
    # In this case, 'data_file' will be installed into '<sys.prefix>/my_data'
    # data_files=[('my_data', ['test/test.bam'])],  # Optional

    # 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.
    scripts=['panISa.py', 'ISFinder_search.py']
    # For example, the following would provide a command called `sample` which
    # executes the function `main` from this package when invoked:
    # entry_points={  # Optional
    #     'console_scripts': [
    #         'sample=sample:main',
    #     ],
    # },
)