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# -*- coding: utf-8 -*-
#! /usr/bin/env python
from __future__ import absolute_import
from __future__ import print_function
import sys
import os
import ez_setup
import hashlib
import time, random
import re
try:
from urllib2 import quote
from urllib2 import urlopen
from urllib2 import HTTPError
except ImportError:
from urllib.parse import quote
from urllib.request import urlopen
from urllib.error import HTTPError
HERE = os.path.abspath(os.path.split(os.path.realpath(__file__))[0])
if "--donottrackinstall" in sys.argv:
TRACKINSTALL = None
sys.argv.remove("--donottrackinstall")
else:
# Avoids importing self module
orig_path = list(sys.path)
_wd = os.getcwd()
try:
sys.path.remove(_wd)
except ValueError:
pass
try:
sys.path.remove("")
except ValueError:
pass
# Is this and upgrade or a new install?
try:
import ete3
except ImportError:
TRACKINSTALL = "ete-new-installation"
else:
TRACKINSTALL = "ete-upgrade"
sys.path = orig_path
try:
from setuptools import setup, find_packages
except ImportError:
ez_setup.use_setuptools()
from setuptools import setup, find_packages
PYTHON_DEPENDENCIES = [
["numpy", "Numpy is required for the ArrayTable and ClusterTree classes.", 0],
["PyQt", "PyQt4/5 is required for tree visualization and image rendering.", 0],
["lxml", "lxml is required from Nexml and Phyloxml support.", 0]
]
CLASSIFIERS= [
"Development Status :: 6 - Mature",
"Environment :: Console",
"Environment :: X11 Applications :: Qt",
"Intended Audience :: Developers",
"Intended Audience :: Other Audience",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: GNU General Public License (GPL)",
"Natural Language :: English",
"Operating System :: MacOS",
"Operating System :: Microsoft :: Windows",
"Operating System :: POSIX :: Linux",
"Programming Language :: Python",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Scientific/Engineering :: Visualization",
"Topic :: Software Development :: Libraries :: Python Modules",
]
def can_import(mname):
'Test if a module can be imported '
if mname == "PyQt":
try:
__import__("PyQt4.QtCore")
__import__("PyQt4.QtGui")
except ImportError:
try:
__import__("PyQt5.QtCore")
__import__("PyQt5.QtGui")
except ImportError:
return False
else:
return True
else:
return True
else:
try:
__import__(mname)
except ImportError:
return False
else:
return True
try:
ETE_VERSION = open(os.path.join(HERE, "VERSION")).readline().strip()
except IOError:
ETE_VERSION = 'unknown'
print("\nInstalling ETE (%s) \n" %ETE_VERSION)
print()
MOD_NAME = "ete3"
LONG_DESCRIPTION="""
The Environment for Tree Exploration (ETE) is a Python programming
toolkit that assists in the recontruction, manipulation, analysis and
visualization of phylogenetic trees (although clustering trees or any
other tree-like data structure are also supported).
ETE is currently developed as a tool for researchers working in
phylogenetics and genomics. If you use ETE for a published work,
please cite:
::
Jaime Huerta-Cepas, François Serra and Peer Bork. "ETE 3: Reconstruction,
analysis and visualization of phylogenomic data." Mol Biol Evol (2016) doi:
10.1093/molbev/msw046
Visit http://etetoolkit.org for more info.
"""
try:
_s = setup(
include_package_data = True,
name = MOD_NAME,
version = ETE_VERSION,
packages = ["ete3"],
entry_points = {"console_scripts":
["ete3 = %s.tools.ete:main" %MOD_NAME]},
requires = ["six"],
# Project uses reStructuredText, so ensure that the docutils get
# installed or upgraded on the target machine
install_requires = [
],
package_data = {
},
data_files = [("%s/tools" %MOD_NAME, ["%s/tools/ete_build.cfg" %MOD_NAME])],
# metadata for upload to PyPI
author = "Jaime Huerta-Cepas",
author_email = "jhcepas@gmail.com",
maintainer = "Jaime Huerta-Cepas",
maintainer_email = "huerta@embl.de",
platforms = "OS Independent",
license = "GPLv3",
description = "A Python Environment for (phylogenetic) Tree Exploration",
long_description = LONG_DESCRIPTION,
classifiers = CLASSIFIERS,
provides = [MOD_NAME],
keywords = "tree, tree reconstruction, tree visualization, tree comparison, phylogeny, phylogenetics, phylogenomics",
url = "http://etetoolkit.org",
download_url = "http://etetoolkit.org/static/releases/ete3/",
)
except:
print("\033[91m - Errors found! - \033[0m")
raise
else:
print("\033[92m - Done! - \033[0m")
missing = False
for mname, msg, ex in PYTHON_DEPENDENCIES:
if not can_import(mname):
print(" Warning:\033[93m Optional library [%s] could not be found \033[0m" %mname)
print(" ",msg)
missing=True
notwanted = set(["-h", "--help", "-n", "--dry-run"])
seen = set(_s.script_args)
wanted = set(["install", "bdist", "bdist_egg"])
if TRACKINSTALL is not None and (wanted & seen) and not (notwanted & seen):
try:
welcome = quote("New alien in earth! (%s %s)" %(TRACKINSTALL, time.ctime()))
urlopen("http://etetoolkit.org/static/et_phone_home.php?ID=%s&VERSION=%s&MSG=%s"
%(TRACKINSTALL, ETE_VERSION, welcome))
except Exception:
pass
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