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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.
##
##############################################################################
"""
Support for CLI operations.
"""
import re
import argparse
import os
import sys
if sys.hexversion < 0x03000000:
input_str = raw_input
else:
input_str = input
import textwrap
import dendropy
def confirm_overwrite(filepath,
replace_without_asking=False,
file_desc="Output",
out=sys.stdout):
if os.path.realpath(filepath) == os.devnull:
return True
if os.path.exists(filepath):
if replace_without_asking:
overwrite = 'y'
else:
out.write('%s file already exists: "%s"\n' % (file_desc, filepath))
overwrite = input_str("Overwrite (y/N)? ")
if not overwrite.lower().startswith("y"):
return False
else:
return True
else:
return True
def show_splash(
prog_name,
prog_subtitle,
prog_version,
prog_author,
prog_copyright,
include_citation=True,
include_copyright=False,
additional_citations=None,
width=76,
dest=sys.stderr,
):
wrap_width = width - 2
dendropy_description = dendropy.name()
lines = []
lines.append("^"+prog_name)
lines.append("^"+prog_subtitle)
lines.append("^Version {}".format(prog_version))
lines.append("^By {}".format(prog_author))
lines.append("^Using: {}".format(dendropy_description))
if include_copyright:
copyright_lines = []
copyright_lines.append("{sub_bar1}")
copyright_text = textwrap.wrap(
prog_copyright,
width=wrap_width,
)
copyright_lines.extend(copyright_text)
lines.extend(copyright_lines)
if include_citation:
lines.append("{sub_bar1}")
lines.append("^Citation")
lines.append("^~~~~~~~~")
lines.extend(compose_citation_for_program(
prog_name=prog_name,
prog_version=prog_version,
additional_citations=additional_citations,
dendropy_description=dendropy_description,
width=wrap_width-2,
))
max_splash_text_width = max(len(i) for i in lines)
top_bar = "/{}\\".format("=" * (max_splash_text_width + 2))
bottom_bar = "\\{}/".format("=" * (max_splash_text_width + 2))
sub_bar1 = "-" * (max_splash_text_width + 2)
dest.write(top_bar + "\n")
for line in lines:
if line == "{sub_bar1}":
dest.write("+{}+\n".format(sub_bar1))
else:
if line.startswith("^"):
line = line[1:]
align_char = "^"
else:
align_char = "<"
dest.write("| {:{align_char}{width}} |\n".format(line, align_char=align_char, width=max_splash_text_width))
dest.write(bottom_bar + "\n")
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_text()
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
# from http://stackoverflow.com/a/22157136/268330
class CustomFormatter(argparse.HelpFormatter):
"""
Provides special help formatting:
(1) Any format help text that begins with the token '<pre>' (for
'pre-formatted') will not be reformatted, e.g.::
parser.add_argument("-f", "--frobble",
help="\n".join([
"<pre>Sets the frobble specification:",
"",
"(1) 'foo bar'",
" bar foo bar foo bar foo bar foo bar",
" bar foo bar foo bar foo bar foo bar",
"(1) 'foo baz'",
" baz foo baz foo baz foo baz foo baz",
" baz foo baz foo baz foo baz foo baz",
"(1) 'foo boo'",
" boo foo boo foo boo foo boo foo boo",
" boo foo boo foo boo foo boo foo boo",
]))
(2) A definition list:
parser.add_argument("-f", "--frobble",
help=CustomFormatter.format_definition_list_help(
preamble="Sets the frobble specification:"
definitions=(
('foo-bar', "bar foo bar foo bar foo bar foo bar"),
('foo-baz', "baz foo baz foo baz foo baz foo baz"),
('foo-boo', "boo foo boo foo boo foo boo foo boo"),
)
coda="And so, have a nice day."))
"""
def _split_lines(self, text, width):
# this is the RawTextHelpFormatter._split_lines
if text.startswith('<pre>'):
return text[5:].splitlines()
return argparse.HelpFormatter._split_lines(self, text, width)
@staticmethod
def format_definition_list_help(
preamble,
definitions,
coda=None):
parts = []
if preamble:
if preamble.startswith("<pre>"):
preamble = preamble
else:
preamble = re.sub(r'\s+', ' ', preamble)
preamble = "<pre>" + textwrap.fill(preamble, width=54)
parts.append(preamble)
else:
parts.append("<pre>")
for term, term_definition in definitions:
parts.append("- {}".format(term))
body = textwrap.fill(
re.sub(r'\s+', ' ', term_definition),
width=54,
initial_indent=" ",
subsequent_indent=" ",
replace_whitespace=True,
drop_whitespace=True,
)
parts.append(body)
if coda:
if coda.startswith("<pre>"):
coda = coda[5:]
else:
coda = re.sub(r'\s+', ' ', coda)
coda = textwrap.fill(coda, width=54)
parts.append(coda)
return "\n".join(parts)
# for debugging: prints the name of the argument being processed
# def _format_action_invocation(self, *args, **kwargs):
# s = argparse.HelpFormatter._format_action_invocation(self, *args, **kwargs)
# print(s)
# return s
# Wrap long invocation
# def _format_action_invocation(self, *args, **kwargs):
# s = argparse.HelpFormatter._format_action_invocation(self, *args, **kwargs)
# if len(s) > 72:
# parts = s.split(", -")
# s = "\n -".join(parts)
# return s
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