def compose_citation_for_program(
prog_name,
prog_version,
additional_citations=None,
dendropy_description=None,
width=70,
include_preamble=True,
include_epilog=True):
if dendropy_description is None:
dendropy_description = dendropy.description()
citation_lines = []
citation_lines.extend(dendropy.citation_info(include_preamble=include_preamble, width=width))
if additional_citations:
# citation_lines.append("")
# citation_lines.append("You should also cite the following")
for additional_citation in additional_citations:
citation_lines.append("")
c = textwrap.wrap(
additional_citation,
width=width,
initial_indent=" ",
subsequent_indent=" ",
)
citation_lines.extend(c)
if include_epilog:
citation_lines.append("")
extra = (
"Note that, in the interests of scientific reproducibility, you "
"should describe in the text of your publications not only the "
"specific version of the {prog_name} program, but also the "
"DendroPy library used in your analysis. "
"For your information, you are running {dendropy_desc}."
).format( prog_name=prog_name,
prog_version=prog_version,
dendropy_desc=dendropy_description,
python_version=sys.version)
citation_lines.extend(textwrap.wrap(extra))
return citation_lines
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__) + "')"
#! /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.
##
##############################################################################
import sys
import dendropy
if __name__ == "__main__":
dendropy.description(sys.stdout)
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
"""
Package setup and installation.
"""
import sys
import os
###############################################################################
# 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__) + "')"