#! /usr/bin/env python

##############################################################################
##  DendroPy Phylogenetic Computing Library.
##
##  Copyright 2010-2015 <NAME> and <NAME>.
##  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:
##
##     <NAME>. and <NAME>. 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

#! /usr/bin/env python

##############################################################################
##  DendroPy Phylogenetic Computing Library.
##
##  Copyright 2010-2015 <NAME> and <NAME>.
##  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:
##
##     <NAME>. and <NAME>. 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

#! /usr/bin/env python ############################################################################## ##  DendroPy Phylogenetic Computing Library. ## ##  Copyright 2010-2015 <NAME> and <NAME>. ##  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: ## ##     <NAME>. and <NAME>. 2010. DendroPy: a Python library ##     for phylogenetic computing. Bioinformatics 26: 1569-1571. ## ############################################################################## Support for CLI operations. # citation_lines.append("") # citation_lines.append("You should also cite the following") # from http://stackoverflow.com/a/22157136/268330 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.")) # this is the RawTextHelpFormatter._split_lines # 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