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#! /usr/bin/env python
# -*- coding: utf-8 -*-
##############################################################################
## 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 re
import os
import io
###############################################################################
### "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
###############################################################################
## Utility
def _read(names, **kwargs):
path = os.path.join(os.path.dirname(__file__), *names)
if sys.version_info.major < 3:
return open(path, "rU").read()
else:
with open(path, encoding=kwargs.get('encoding', 'utf8')) as src:
s = src.read()
return s
def _compose_list(values, prefix=None):
if prefix is None:
prefix = ""
s = []
max_len = max(len(i) for i in values)
template = "{}{{value:<{}}}".format(prefix,max_len)
for v in values:
s.append(template.format(value=v))
return "\n".join(s)
###############################################################################
# Identification
__version__ = re.match(r".*^__version__\s*=\s*['\"](.*?)['\"]\s*$.*", _read(["src", "dendropy", "__init__.py"]), re.S | re.M).group(1)
sys.stderr.write("-setup.py: DendroPy version {}\n".format(__version__))
###############################################################################
# setuptools/distutils/etc. import and configuration
try:
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.utility",
"dendropy.utility.libexec",
]
else:
sys.stderr.write("-setup.py: searching for packages\n")
PACKAGES = find_packages("src")
EXTRA_KWARGS = dict(
include_package_data = True,
# test_suite = "tests",
zip_safe = True,
)
sys.stderr.write("-setup.py: packages identified:\n{}\n".format(_compose_list(PACKAGES, prefix=" - ")))
ENTRY_POINTS = {}
###############################################################################
# Script paths
SCRIPT_SUBPATHS = [
['applications', 'sumtrees', 'sumtrees.py'],
['applications', 'sumlabels', 'sumlabels.py'],
['applications', 'dendropy-format', 'dendropy-format'],
# ['scripts', 'sumtrees', 'cattrees.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("-setup.py: scripts identified:\n{}\n".format(_compose_list(SCRIPTS, prefix=" - ")))
###############################################################################
# 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 = _read(["README.rst"])
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__))
long_description = long_description + ("""\
Current Release
===============
The current release of DendroPy is version {}.
""".format(__version__))
setup(name='DendroPy',
version=__version__,
author='Jeet Sukumaran and Mark T. Holder',
author_email='jeetsukumaran@gmail.com, mtholder@ku.edu',
url='http://pypi.org/project/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={"": "src"},
# 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 :: 3.6",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"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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