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setup.py
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setup.py
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"""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 setuptools import setup, find_packages
# To use a consistent encoding
from codecs import open
from os import path, remove, mkdir
import shutil
import tarfile
import urllib
import platform
import sys
platform_system = platform.system() # Linux: Linux; Mac:Darwin; Windows: Windows
here = path.abspath(path.dirname(__file__))
blast_path_bin = path.join(here, 'gff3tool', 'lib', 'ncbi-blast+', 'bin')
blast_path = path.join(here, 'gff3tool', 'lib', 'ncbi-blast+')
blast_file = path.join(blast_path, 'blast.tgz')
if not path.exists(blast_path):
mkdir(blast_path)
if path.exists(blast_path_bin):
shutil.rmtree(blast_path_bin)
if platform_system == 'Linux':
urllib.urlretrieve('https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.31/ncbi-blast-2.2.31+-x64-linux.tar.gz', blast_file)
elif platform_system == 'Windows':
urllib.urlretrieve('https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.31/ncbi-blast-2.2.31+-x64-win64.tar.gz', blast_file)
elif platform_system == 'Darwin':
urllib.urlretrieve('https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.31/ncbi-blast-2.2.31+-universal-macosx.tar.gz', blast_file)
else:
sys.error('GFF3 Toolkit currently only supports linux, windows, and MacOS')
tar = tarfile.open(blast_file, 'r:gz')
tar.extractall(blast_path)
tar.close()
extract_path = path.join(blast_path, 'ncbi-blast-2.2.31+')
shutil.move(path.join(extract_path, 'bin'), blast_path)
if path.exists(blast_file):
remove(blast_file)
if path.exists(extract_path):
shutil.rmtree(extract_path)
# Get the long description from the README file
with open(path.join(here, 'README.md'), 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 bcinfo
#
# And where it will live on PyPI: https://pypi.org/project/bcinfo/
#
# There are some restrictions on what makes a valid project name
# specification here:
# https://packaging.python.org/specifications/core-metadata/#name
name='gff3tool', # 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='1.3.0', # 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='Python programs for processing GFF3 files', # 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
# 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/NAL-i5K/GFF3toolkit', # Optional
# This should be your name or the name of the organization which owns the
# project.
author='NAL i5k workspace', # Optional
# This should be a valid email address corresponding to the author listed
# above.
author_email='[email protected]', # 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',
'Operating System :: POSIX :: Linux',
'Operating System :: Microsoft :: Windows',
# Indicate who your project is intended for
'Intended Audience :: Science/Research',
'Topic :: Scientific/Engineering :: Bio-Informatics',
# Pick your license as you wish
'License :: Public Domain',
# 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 :: 2.7',
],
# 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='gff3 gff bioinformatics ', # 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=['contrib', 'docs', 'tests']), # 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=[], # 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
},
# 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
},
# 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=[], # 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.
#
# 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': [
'gff3_fix=gff3tool.bin.gff3_fix:script_main',
'gff3_merge=gff3tool.bin.gff3_merge:script_main',
'gff3_QC=gff3tool.bin.gff3_QC:script_main',
'gff3_sort=gff3tool.bin.gff3_sort:script_main',
'gff3_to_fasta=gff3tool.bin.gff3_to_fasta:script_main'
]
},
include_package_data=True, # include other files
# List additional URLs that are relevant to your project as a dict.
#
# This field corresponds to the "Project-URL" metadata fields:
# https://packaging.python.org/specifications/core-metadata/#project-url-multiple-use
#
# Examples listed include a pattern for specifying where the package tracks
# issues, where the source is hosted, where to say thanks to the package
# maintainers, and where to support the project financially. The key is
# what's used to render the link text on PyPI.
project_urls={ # Optional
'Bug Reports': 'https://github.com/NAL-i5K/GFF3toolkit/issues',
'Source': 'https://github.com/NAL-i5K/GFF3toolkit',
},
)