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#! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
"""
Package setup and installation.
"""
import sys
import os
### "highly-discouraged" workaround to deal with Python 2.8+ and 3.4+ verifying
### certificates by default; this breaks PyPI uploads ...
import ssl
if hasattr(ssl, '_create_unverified_context'):
ssl._create_default_https_context = ssl._create_unverified_context
###############################################################################
# Identification
from dendropy import __version__, revision_description, description
sys.stderr.write("-setup.py: {}\n".format(description()))
###############################################################################
# setuptools/distutils/etc. import and configuration
try:
import ez_setup
try:
ez_setup_path = " ('" + os.path.abspath(ez_setup.__file__) + "')"
except OSError:
ez_setup_path = ""
sys.stderr.write("-setup.py: using ez_setup{}\n".format(ez_setup_path))
ez_setup.use_setuptools()
import setuptools
try:
setuptools_path = " ('" + os.path.abspath(setuptools.__file__) + "')"
except OSError:
setuptools_path = ""
sys.stderr.write("-setup.py: using setuptools{}\n".format(setuptools_path))
from setuptools import setup, find_packages
except ImportError as e:
sys.stderr.write("-setup.py: using distutils\n")
from distutils.core import setup
sys.stderr.write("-setup.py: using canned package list\n")
PACKAGES = [
"dendropy",
"dendropy.calculate",
"dendropy.dataio",
"dendropy.datamodel",
"dendropy.interop",
"dendropy.legacy",
"dendropy.mathlib",
"dendropy.model",
"dendropy.simulate",
"dendropy.test",
"dendropy.utility",
"dendropy.utility.libexec",
]
else:
sys.stderr.write("-setup.py: searching for packages\n")
PACKAGES = find_packages()
EXTRA_KWARGS = dict(
install_requires = ['setuptools'],
include_package_data = True,
test_suite = "dendropy.test",
zip_safe = True,
)
PACKAGE_DIRS = [p.replace(".", os.path.sep) for p in PACKAGES]
PACKAGE_INFO = [("{p[0]:>40} : {p[1]}".format(p=p)) for p in zip(PACKAGES, PACKAGE_DIRS)]
sys.stderr.write("-setup.py: packages identified:\n{}\n".format("\n".join(PACKAGE_INFO)))
ENTRY_POINTS = {}
###############################################################################
# Script paths
SCRIPT_SUBPATHS = [
['applications', 'sumtrees', 'sumtrees.py'],
# ['scripts', 'sumtrees', 'cattrees.py'],
# ['scripts', 'sumtrees', 'sumlabels.py'],
# ['scripts', 'calculators', 'strict_consensus_merge.py'],
# ['scripts', 'calculators', 'long_branch_symmdiff.py'],
]
SCRIPTS = [os.path.join(*i) for i in SCRIPT_SUBPATHS]
sys.stderr.write("\n-setup.py: scripts identified: {}\n".format(", ".join(SCRIPTS)))
###############################################################################
# setuptools/distuils command extensions
try:
from setuptools import Command
except ImportError:
sys.stderr.write("-setup.py: setuptools.Command could not be imported: setuptools extensions not available\n")
else:
sys.stderr.write("-setup.py: setuptools command extensions are available\n")
command_hook = "distutils.commands"
ENTRY_POINTS[command_hook] = []
###########################################################################
# coverage
from dendropy.test.support import coverage_analysis
if coverage_analysis.DENDROPY_COVERAGE_ANALYSIS_AVAILABLE:
sys.stderr.write("-setup.py: coverage analysis available ('python setup.py coverage')\n")
ENTRY_POINTS[command_hook].append("coverage = dendropy.test.support.coverage_analysis:CoverageAnalysis")
else:
sys.stderr.write("-setup.py: coverage analysis not available\n")
###############################################################################
# Main setup
### compose long description ###
long_description = open('README.rst').read()
long_description = long_description.replace("DendroPy-4.x.x", "DendroPy-{}".format(__version__))
long_description = long_description.replace("""download the source code archive""",
"""`download the source code archive <http://pypi.python.org/packages/source/D/DendroPy/DendroPy-{}.tar.gz>`_""".format(__version__))
revision_text = revision_description()
long_description = long_description + ("""\
Current Release
===============
The current release of DendroPy is version {}{}.
""".format(__version__, revision_text))
setup(name='DendroPy',
version=__version__,
author='Jeet Sukumaran and Mark T. Holder',
author_email='jeetsukumaran@gmail.com and mtholder@ku.edu',
url='http://packages.python.org/DendroPy/',
description="A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.",
license='BSD',
packages=PACKAGES,
package_dir=dict(zip(PACKAGES, PACKAGE_DIRS)),
# not needed?
# package_data={
# # "dendropy.utility" : ["libexec/*"],
# },
scripts = SCRIPTS,
long_description=long_description,
entry_points = ENTRY_POINTS,
classifiers = [
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: BSD License",
"Natural Language :: English",
"Operating System :: OS Independent",
"Programming Language :: Python :: 2.7",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.1",
"Programming Language :: Python :: 3.2",
"Programming Language :: Python :: 3.3",
"Programming Language :: Python :: 3.4",
"Programming Language :: Python",
"Topic :: Scientific/Engineering :: Bio-Informatics",
],
keywords='phylogenetics phylogeny phylogenies phylogeography evolution evolutionary biology systematics coalescent population genetics phyloinformatics bioinformatics',
**EXTRA_KWARGS
)
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