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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/guides/distributing-packages-using-setuptools/
https://github.com/pypa/sampleproject
"""
# Always prefer setuptools over distutils
# from distutils.core import setup, Extension
from setuptools.command.install import install as DistutilsInstall
from setuptools import find_packages
from setuptools import setup # pylint: disable=no-name-in-module,import-error
#from setuptools.command.build_ext import build_ext
from urllib.request import urlopen
import subprocess
import io
from os import path
import os
import sys
here = path.abspath(path.dirname(__file__))
# Get the long description from the README file
with open(path.join(here, 'README.md'), encoding='utf-8') as f:
long_description = f.read()
# Get the requirements of the packages
with open('dependencies.txt') as f:
requirements = f.read().splitlines()
class git_clone_external(DistutilsInstall):
def internet_on(self):
try:
urlopen('http://python.org/', timeout=1)
return True
except urlopen.URLError as err:
return False
# def run_command(self, command, cwd):
# # print("about to execute command `{0}`. sources = {1}"
# # .format(command, sources))
# proc = subprocess.Popen(command,cwd = cwd, stderr=subprocess.STDOUT, shell=True)
# output, stderr = proc.communicate(input)
# status = proc.wait()
# if status:
# raise Exception("command = {0} failed with output = {1} status {2:d}\n"
# .format(command, output, status))
def run(self):
#connection = self.internet_on()
#if connection is True:
d = os.path.dirname(os.path.realpath(__file__))
bcftools_dir = os.path.dirname(
os.path.realpath(__file__)) + "/bcftools"
htslib_dir = os.path.dirname(os.path.realpath(__file__))+" /htslib"
verina_dir = os.path.dirname(os.path.realpath(__file__))+ "/verina"
if not os.path.exists(htslib_dir):
cmd1 = ['git', 'clone',
'https://github.com/samtools/htslib.git']
#self.run_command( cmd1, d)
subprocess.call(cmd1, cwd=os.path.dirname(
os.path.realpath(__file__)))
if not os.path.exists(path.join(bcftools_dir, 'bcftools')):
cmd2 = ['git', 'clone',
'https://github.com/samtools/bcftools.git']
#self.run_command(self, cmd2, d)
subprocess.call(
cmd2, cwd=os.path.dirname(os.path.realpath(__file__)))
# if not os.path.exists(verina_dir):
# cmd3 = ['git','clone',
# 'https://mmb.irbbarcelona.org/gitlab/dgallego/veriNA3d-dev.git']
# #self.run_command( cmd1, d)
# subprocess.call(cmd3, cwd=os.path.dirname(
# os.path.realpath(__file__)))
#self.run_command(self, ["make", "clean"], bcftools_dir)
#self.run_command(self, ["make"], bcftools_dir)
subprocess.call(
["make", "clean"], cwd=bcftools_dir)
subprocess.call(['make'], cwd=bcftools_dir)
#self.run_command(self, ["cp", "bcftools", "%s/bin/" % os.environ.get('VIRTUAL_ENV', '/usr/local/')], bcftools_dir)
#self.run_command(self, ["cp", "plugins/split-vep.so", "%s/bin/" % os.environ.get('VIRTUAL_ENV', '/usr/local/')], bcftools_dir)
subprocess.call(
["cp", "bcftools", "%s/bin/" % os.environ.get('VIRTUAL_ENV', '/usr/local/')], cwd=bcftools_dir)
subprocess.call(
["cp", "plugins/split-vep.so", "%s/bin/" % os.environ.get('VIRTUAL_ENV', '/usr/local/')], cwd=bcftools_dir)
# subprocess.call(
# ["R","CMD", "build", "%s" % os.environ.get('VIRTUAL_ENV', '/usr/local/') , "--no-build-vignettes"], cwd=verina_dir)
# subprocess.call(
# ["R","CMD", "build", "%s" % os.environ.get('VIRTUAL_ENV', '/usr/local/') , "--no-build-vignettes"], cwd=verina_dir)
#subprocess.call(
# ["tar", "-zxf" ,"stride.tar.gz"], cwd=os.path.dirname(
# os.path.realpath(__file__)))
#subprocess.call(
# ["make"], cwd=stride_dir)
DistutilsInstall.run(self)
# 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='3dmapper', # 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='1.0.0', # Required
# This should be your name or the name of the organization which owns the
# project.
author='Victoria Ruiz-Serra', # Optional
# This should be a valid email address corresponding to the author listed
# above.
author_email='[email protected]', # Optional
# This should be a valid link to your project's main homepage.
#
# This field corresponds to the "Home-Page" metadata field:
url="https://github.com/vicruiser/3Dmapper", # Optional
# You have previously uploaded your project to your github repository. Now,
# we create a new release version of your project on github. This release
# will then be downloaded by anyone that runs the “pip install YourPackage” command.
# download_url='https://github.com/vicruiser/PDBmapper/archive/v_01.tar.gz',
# This is a one-line description or tagline of what your project does. This
# corresponds to the "Summary" metadata field:
description='Map annotated genomic positions to protein interfaces data in 3D.', # Optional
# This field corresponds to the "Description" metadata field:
# https://packaging.python.org/specifications/core-metadata/#description-optional
long_description=long_description, # Optional
# Denotes that our long_description is in Markdown; valid values are
# text/plain, text/x-rst, and text/markdown
#
# Optional if long_description is written in reStructuredText (rst) but
# required for plain-text or Markdown; if unspecified, "applications should
# attempt to render [the long_description] as text/x-rst; charset=UTF-8 and
# fall back to text/plain if it is not valid rst" (see link below)
#
# This field corresponds to the "Description-Content-Type" metadata field:
# https://packaging.python.org/specifications/core-metadata/#description-content-type-optional
# Optional (see note above)
long_description_content_type='text/markdown',
# For a list of valid classifiers, see https://pypi.org/classifiers/
classifiers=[ # Optional
# How mature is this project? Common values are
# 3 - Alpha
# 4 - Beta
# 5 - Production/Stable
'Development Status :: 3 - Alpha',
# Indicate who your project is intended for
'Intended Audience :: Science/Research',
'Topic :: Scientific/Engineering :: Bio-Informatics',
# Pick your license as you wish
'License :: GPLv3',
# Specify the Python versions you support here. In particular, ensure
# that you indicate whether you support Python 2, Python 3 or both.
# These classifiers are *not* checked by 'pip install'. See instead
# 'python_requires' below.
'Programming Language :: Python :: 3.6',
'Programming Language :: Python :: 3.7',
'Programming Language :: Python :: 3.8',
'Programming Language :: Python :: 3.9',
],
# 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=["mapping","CLI", "genetic positions", "protein structure", "PDB"], # Optional
# When your source code is in a subdirectory under the project root, e.g.
# `src/`, it is necessary to specify the `package_dir` argument.
# package_dir={'': 'pdbmapper'}, # 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=['mapper', #'makepsdb',
'makevariantsdb', 'makeinterfacedb', 'makechimera' ], # Required!!!!!
# Specify which Python versions you support. In contrast to the
# 'Programming Language' classifiers above, 'pip install' will check this
# and refuse to install the project if the version does not match. If you
# do not support Python 2, you can simplify this to '>=3.5' or similar, see
# https://packaging.python.org/guides/distributing-packages-using-setuptools/#python-requires
python_requires='>=3.6, <4', # Optional
# 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=requirements,
setup_requires=['wheel'],
# External requirements
cmdclass={'install': git_clone_external},
# ext_modules=[module1],
# Data requirements
package_data={
# And include any *.dat files found in the 'data' subdirectory
# of the 'mypkg' package, also:
'': ['data/*','rscripts/*']
},
include_package_data = True,
# If your project depends on packages that don’t exist on PyPI, you may
# still be able to depend on them, as long as they are available for
# download as:
# an egg, in the standard distutils sdist format,
# a single .py file, or
# a VCS repository(Subversion, Mercurial, or Git).
# The dependency_links option takes the form of a list of URL strings. For
# example, this will cause a search of the specified page for eggs or
# source distributions, if the package’s dependencies aren’t already
# installed
# dependency_links=[ # Optional
# 'https://github.com/samtools/bcftools@develop#egg=bcftools-1.8.0'
# ],
# 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={
"console_scripts": ['mapper=mapper.__main__:main',
#'makepsdb=makepsdb.__main__:main',
'makevariantsdb=makevariantsdb.__main__:main',
'makevisualization=makechimera.__main__:main',
'makestructuraldb=makeinterfacedb.__main__:main']
},
# 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/vicruiser/3Dmapper/issues',
# 'Funding': 'https://donate.pypi.org',
# 'Say Thanks!': 'http://saythanks.io/to/example',
'Source': 'https://github.com/vicruiser/3Dmapper/',
},
)