#! /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. ## ############################################################################## """ 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 '
' (for
            'pre-formatted') will not be reformatted, e.g.::

            parser.add_argument("-f", "--frobble",
                help="\n".join([
                "
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('
'):
           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("
"):
                preamble = preamble
            else:
                preamble = re.sub(r'\s+', ' ', preamble)
                preamble = "
" + textwrap.fill(preamble, width=54)
            parts.append(preamble)
        else:
            parts.append("
")
        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("
"):
                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