setup.py

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


import io
import os
import sys
import csv
from shutil import rmtree

from setuptools import find_packages, setup
from distutils.cmd import Command
from setuptools.command.build_py import build_py

# Package meta-data.
NAME = 'cigar_aligner'
DESCRIPTION = 'CIGAR alignment functionality'
URL = 'https://github.com/foadgr/cigar_aligner'
EMAIL = 'foadgreen@gmail.com'
AUTHOR = 'Foad Green'
REQUIRES_PYTHON = '>=3.7.0'
VERSION = '0.2'

# Required packages
REQUIRED = [
  'pandas'
]


EXTRAS = {}


here = os.path.abspath(os.path.dirname(__file__))

try:
  with io.open(os.path.join(here, 'README.md'), encoding='utf-8') as f:
    long_description = '\n' + f.read()
except FileNotFoundError:
  long_description = DESCRIPTION

# Load the package's __version__.py module as a dict.
about = {}
if not VERSION:
  project_slug = NAME.lower().replace("-", "_").replace(" ", "_")
  with open(os.path.join(here, project_slug, '__version__.py')) as f:
    exec(f.read(), about)
else:
  about['__version__'] = VERSION


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

  description = 'Build and publish the package.'
  user_options = [
    ('only_required=', None, 'Only create required data.'),
    ('all_tests=', None, 'Crate all test data.')
  ]

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

  def initialize_options(self):
    """Set default values for options."""
    pass

  def finalize_options(self):
    """Post-process options."""
    pass

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

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

    self.status('Uploading the package to PyPI via Twine…')
    os.system('twine upload dist/*')

    self.status('Pushing git tags…')
    os.system('git tag v{0}'.format(about['__version__']))
    os.system('git push --tags')

    sys.exit()


class CreateData(Command):
  """A custom setup command to create test data files"""

  description = 'Create test data files'
  user_options = []

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

  def initialize_options(self):
    """Set default values for options."""
    pass

  def finalize_options(self):
    """Post-process options."""
    pass

  def run(self):
    """Run command."""
    self.status('Creating data tables')

    try:
      self.status('Removing previous data files…')
      rmtree(os.path.join(here, 'cigar_aligner/data'))
    except OSError:
      pass

    # Generate data tables for main specification
    req_dir = os.path.join(here, 'cigar_aligner/data/main_spec')
    os.system(f'mkdir -p {req_dir}')
    with open(os.path.join(req_dir,'input_01.tsv'), 'w') as f:
      writer = csv.writer(f, delimiter='\t', quotechar='"')
      writer.writerow(['TR1', 'CHR1', '3', '8M7D6M2I2M11D7M'])
      writer.writerow(['TR2', 'CHR2', '10', '20M'])
    with open(os.path.join(req_dir,'input_02.tsv'), 'w') as f:
      writer = csv.writer(f, delimiter='\t', quotechar='"')
      writer.writerow(['TR1', '4'])
      writer.writerow(['TR2', '0'])
      writer.writerow(['TR1', '13'])
      writer.writerow(['TR2', '10'])
    self.status(f'Data tables created in path: {req_dir}')

    # Generate bells and whistles data tables
    req_dir = os.path.join(here, 'cigar_aligner/data/bells_and_whistles')
    os.system(f'mkdir -p {req_dir}')
    with open(os.path.join(req_dir,'input_01.tsv'), 'w') as f:
      writer = csv.writer(f, delimiter='\t', quotechar='"')
      writer.writerow(['TR1', 'CHR1', '3', '8M7D6M2I2M11D7M'])
      writer.writerow(['TR2', 'CHR2', '5', '13M15I2M8D'])
    with open(os.path.join(req_dir,'input_02.tsv'), 'w') as f:
      writer = csv.writer(f, delimiter='\t', quotechar='"')
      writer.writerow(['TR1', '4', '19', 'R', True])
      writer.writerow(['TR2', '0', '7', 'R', False])
      writer.writerow(['TR1', '13', '18', 'F', False])
      writer.writerow(['TR2', '10', '14', 'F', True])
    self.status(f'Data tables created in path: {req_dir}')

    sys.exit()

# Setup the build:
setup(
  name=NAME,
  version=about['__version__'],
  description=DESCRIPTION,
  long_description=long_description,
  author=AUTHOR,
  author_email=EMAIL,
  python_requires=REQUIRES_PYTHON,
  url=URL,
  packages=find_packages(exclude=('tests',)),
  install_requires=REQUIRED,
  extras_require=EXTRAS,
  include_package_data=True,
  license='MIT',
  classifiers=[
    'License :: OSI Approved :: MIT License',
    'Programming Language :: Python',
    'Programming Language :: Python :: 3',
    'Programming Language :: Python :: 3.6',
    'Programming Language :: Python :: Implementation :: CPython',
    'Programming Language :: Python :: Implementation :: PyPy'
  ],
  cmdclass={
    'upload': UploadCommand,
    'create_data': CreateData
  },
)