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#! /usr/bin/env python3
"""A setuptools based setup module.
See:
https://packaging.python.org/en/latest/distributing.html
https://github.com/pypa/sampleproject
"""
# Always prefer setuptools over distutils
from os import path
from setuptools.command.develop import develop
from setuptools.command.install import install
from setuptools import setup, find_packages
import sys
def query_yes_no(question, default="yes"):
"""Ask a yes/no question via raw_input() and return their answer.
"question" is a string that is presented to the user.
"default" is the presumed answer if the user just hits <Enter>.
It must be "yes" (the default), "no" or None (meaning
an answer is required of the user).
The "answer" return value is True for "yes" or False for "no".
"""
valid = {"yes": True, "y": True, "ye": True,
"no": False, "n": False}
if default is None:
prompt = " [y/n] "
elif default == "yes":
prompt = " [Y/n] "
elif default == "no":
prompt = " [y/N] "
else:
raise ValueError("invalid default answer: '%s'" % default)
while True:
print(question + prompt)
choice = input().lower()
if default is not None and choice == '':
return valid[default]
elif choice in valid:
return valid[choice]
else:
print("Please respond with 'yes' or 'no' "
"(or 'y' or 'n').\n")
class PostDevelopCommand(develop):
"""Post-installation for development mode."""
def run(self):
develop.run(self)
class PostInstallCommand(install):
"""Post-installation for installation mode."""
def run(self):
import subprocess
import os
# read the docs does not need any further dependencies, just the doc code
if not os.environ.get('READTHEDOCS') == 'True':
subprocess.check_call(["bash", "scripts/install_create_r_environ.sh"])
subprocess.check_call(["bash", "scripts/install_external.sh"])
subprocess.check_call(["bash", "scripts/install_add_to_bashrc.sh"])
install.run(self)
# place for post install commands
here = path.abspath(path.dirname(__file__))
if sys.version_info.major < 3:
sys.exit('\n'
'Sorry, Python 2 is not supported\n'
'Did you run pip install circtools?\n'
'Try \'pip3 install circtools\'')
elif sys.version_info.minor < 4:
sys.exit('\nSorry, Python < 3.4 is not supported\n')
# Get the long description from the relevant file
with open(path.join(here, 'README.rst')) as f:
long_description = f.read()
setup(
name='circtools',
# 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='1.1.0.7',
description='circtools - a circular RNA toolbox',
long_description=long_description,
# The project's main homepage.
url='https://github.com/dieterich-lab/circtools',
# Author details
author='Tobias Jakobi',
author_email='Tobias.Jakobi@med.Uni-Heidelberg.DE',
# Choose your license
license='GNU General Public License (GPL)',
# See https://pypi.python.org/pypi?%3Aaction=list_classifiers
classifiers=[
# How mature is this project? Common values are
# Development Status :: 1 - Planning
# Development Status :: 2 - Pre-Alpha
# Development Status :: 3 - Alpha
# Development Status :: 4 - Beta
# 'Development Status :: 5 - Production/Stable',
# Development Status :: 6 - Mature
# Development Status :: 7 - Inactive
'Development Status :: 4 - Beta',
# Indicate who your project is intended for
'Intended Audience :: Science/Research',
'Topic :: Scientific/Engineering :: Bio-Informatics',
# Pick your license as you wish (should match "license" above)
'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 :: 2',
# 'Programming Language :: Python :: 2.6',
# 'Programming Language :: Python :: 2.7',
# 'Programming Language :: Python :: 3',
# 'Programming Language :: Python :: 3.2',
# 'Programming Language :: Python :: 3.3',
'Programming Language :: Python :: 3.4',
'Programming Language :: Python :: 3.5',
'Programming Language :: Python :: 3.6',
],
# What does your project relate to?
keywords='circular RNA bioinformatics',
# You can just specify the packages manually here if your project is
# simple. Or you can use find_packages().
packages=find_packages(),
# 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
install_requires=[
'HTSeq>=0.11.0',
'pysam >= 0.13',
'numpy>=1.14.5',
'pybedtools>=0.7.10',
'biopython >= 1.71',
'scipy>=0.19.0'
],
python_requires='>=3.4',
# 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={
'circtools': ['scripts/circtools'],
},
# 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=[('my_data', ['data/data_file'])],
# 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.
zip_safe=False,
# entry_points={
# 'console_scripts': [
# 'circtools=circtools:main'
# ],
# },
# this will be our main "executable"
scripts=[
'scripts/circtools',
'scripts/circtools_detect_write_skip_tracks.pl',
'scripts/circtools_enrich_visualization.R',
'scripts/circtools_quickcheck_wrapper.R',
'scripts/circtools_reconstruct_visualization.R',
'scripts/circtools_primex_wrapper.R',
'scripts/circtools_primex_formatter.R',
'scripts/circtools_exon_wrapper.R',
'scripts/circtools_circtest_wrapper.R',
'scripts/circtools_generate_intron_gtf.sh',
'scripts/circtools_generate_flanking_introns.py',
'scripts/create_igv_script_from_gene_names.py',
'scripts/create_igv_script_from_position_list.py',
'scripts/create_igv_script.py',
'scripts/detect_new_exons_from_fuchs_data.py',
'scripts/get_introns_from_ensembl.pl'
],
# adding support for post install scripts from
# https://stackoverflow.com/questions/20288711/post-install-script-with-python-setuptools
cmdclass={
'develop': PostDevelopCommand,
'install': PostInstallCommand,
},
project_urls={ # Optional
'Bug Reports': 'https://github.com/dieterich-lab/circtools/issues',
'Dieterich Lab': 'https://dieterichlab.org',
'Source': 'https://github.com/dieterich-lab/circtools',
'Documentation': 'http://docs.circ.tools'
},
)