setup.py

"""A setuptools based setup module.

See:
https://packaging.python.org/en/latest/distributing.html
https://github.com/pypa/sampleproject
"""
import sys
import os
from os import path
import glob
import shutil
from pathlib import Path
from shutil import rmtree

# Always prefer setuptools over distutils
from setuptools import setup, find_packages, Command
# To use a consistent encoding
from codecs import open

sys.path.append("src")
import pytransit
from pytransit.generic_tools import file_system_py as FS
version =  pytransit.__version__[1:]

package_name = "pytransit"

def file_exclusion_function(file_path):
    """
        Summary:
            this is supposed to return True if the file should be excluded from the pypi upload
            HOWEVER for some reason some files can still be included, partly because of the MANIFEST.in file
            The process is rather mysterious
            
    """
    # no folders
    if os.path.isdir(file_path):
        return True
    
    # no __pycache__ folders
    if (
        '/__pycache__/' in file_path
        or file_path.startswith('__pycache__/')
        or file_path.endswith('/__pycache__')
    ):
        return True
        
    # only .py, .json, and .yaml from the __dependencies__ folders
    if '/__dependencies__/' in file_path and not (file_path.endswith(".py") or file_path.endswith(".json") or file_path.endswith(".yaml")):
        return True
    # no test files
    if "/ruamel/yaml/_test/" in file_path:
        return True
    
    if "/doc/" in file_path:
        return True
    
    
    return False

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

# Get current version
sys.path.insert(1, "src/")

class UploadCommand(Command):
    """Support setup.py upload."""

    description = 'Build and publish the package.'
    user_options = []

    @staticmethod
    def status(s):
        """Prints things in bold."""
        print('\033[1m{0}\033[0m'.format(s))

    def initialize_options(self):
        pass

    def finalize_options(self):
        pass

    def yes_or_no(self, question):
        while True:
            reply = str(input(question +' (y/n): ')).lower().strip()
            if reply == 'y':
                return True
            return False

    def run(self):
        try:
            self.status('Removing previous builds...')
            rmtree(os.path.join(here, 'dist'))
        except OSError:
            pass

        if not self.yes_or_no("Have you done the following? \n" +
                    "- Updated README/Documentation?\n"
                    "- Are in the master branch, and have you merged version branch into master?\n"
                    "- Have you run the tests ('pytest tests/')?\n"
                    "- Have you updated CHANGELOG?\n"
                    "- Have you updated Transit Essentiality page?\n"
                    "- Updated version in src/pytransit/__init__.py (used to set git tag)?\n"
                    "- Is version v{0} correct".format(version)):
            self.status("Exiting...")
            sys.exit()

        self.status('Building Source and Wheel (universal) distribution...')
        #os.system('{0} setup.py sdist bdist_wheel'.format(sys.executable))
        os.system('{0} -m build'.format(sys.executable))

        if self.yes_or_no("Add tag and push to public github? tag:v{0}".format(version)):
            self.status('Adding and pushing git tags to origin and public...')
            os.system('git tag v{0}'.format(version))
            os.system('git push origin --tags')
            os.system('git push https://github.com/mad-lab/transit master')
            os.system('git push https://github.com/mad-lab/transit --tags')
        else:
            self.status("Exiting...")
            sys.exit()

        if self.yes_or_no("Proceed with publish to PyPI? version: v{0}, tag:v{0}".format(version)):
            self.status('Uploading the package to PyPI via Twine...')
            os.system('twine upload dist/*')
        else:
            self.status("Exiting...")
            sys.exit()

        sys.exit()

package_data = {
    # include all files/folders in the module (recursively)
    package_name: sorted(list(set([
        each[len(package_name)+1:]
            for each in FS.iterate_paths_in(package_name, recursively=True)
                if not file_exclusion_function(each)
    ]))),
}

setup(
    #name='tnseq-transit',
    name='transit1',

    # Versions should comply with PEP440.  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=version,

    description='TRANSIT is a tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.',
    long_description=long_description,
    long_description_content_type='text/markdown',

    # The project's main homepage.
    url='https://github.com/mad-lab/transit',
    download_url='https://github.com/mad-lab/transit',

    # Author details
    author='Michael A. DeJesus',
    author_email='mad@cs.tamu.edu',

    # Choose your license
    license='GNU GPL',
    python_requires='>=3.6',
    # See https://pypi.python.org/pypi?%3Aaction=list_classifiers

    classifiers=[
        #'Development Status :: 3 - Alpha',
        'Development Status :: 5 - Production/Stable',
        'Programming Language :: Python',
        'Programming Language :: Python :: 3',
        'Intended Audience :: Science/Research',
        'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
        'Operating System :: OS Independent',
        'Topic :: Scientific/Engineering :: Bio-Informatics',
    ],

    # What does your project relate to?
    keywords=['tnseq', 'analysis', 'biology', 'genome'],

    # You can just specify the packages manually here if your project is
    # simple. Or you can use find_packages().
    #packages = find_packages('src', exclude=['contrib', 'tests']), # any subdir in src/ with __init__.py
    packages = ['pytransit.generic_tools', 'pytpp', 'pytransit', 'pytransit.analysis'],
    package_dir = {'pytransit': 'src/pytransit',  'pytpp': 'src/pytpp'},
    include_package_data=True,
    #py_modules = ['tpp'],

    # Alternatively, if you want to distribute just a my_module.py, uncomment
    # this:
    #   py_modules=["my_module"],

    # List run-time dependencies here.  These will be installed by pip when
    # your project is installed. For an analysis of "install_requires" vs pip's
    # requirements files see:
    # https://packaging.python.org/en/latest/requirements.html
    # 'pypubsub<4.0' and 'wxPython' are needed for GUI only, but go ahead and install them
    # the reason for restriction on pypubsub is that version>=4.0 does not work with python2 - I can probably get rid of this restriction, since everybody must be using python3 by now
    install_requires=['wheel','setuptools', 'numpy~=1.16', 'scipy~=1.2', 'matplotlib~=3.0', 'pillow', 'scikit-learn', 'statsmodels~=0.9', 'pypubsub', 'wxPython'],

    #dependency_links = [
    #	"git+https://github.com/wxWidgets/wxPython.git#egg=wxPython"
	#],

    # List additional groups of dependencies here (e.g. development
    # dependencies). You can install these using the following syntax,
    # for example:
    # $ pip install -e .[dev,test]
    #extras_require={
    #    '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 less, then these
    # have to be included in MANIFEST.in as well.
    package_data=package_data,

    #scripts=['src/tpp.py', 'src/transit.py'],

    # 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 # noqa
    # In this case, 'data_file' will be installed into '<sys.prefix>/my_data'
    #data_files=[('transitdata', ['package_data.dat'])],

    # 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': [
            'transit=pytransit.__main__:run_main',
            'tpp=pytpp.__main__:run_main',
        ],
    },
    cmdclass={
        'upload': UploadCommand,
    },
)