two version of R2R are here HEAD master

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diff --git a/.venv/lib/python3.12/site-packages/markdown/extensions/codehilite.py b/.venv/lib/python3.12/site-packages/markdown/extensions/codehilite.py
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+# CodeHilite Extension for Python-Markdown
+# ========================================
+
+# Adds code/syntax highlighting to standard Python-Markdown code blocks.
+
+# See https://Python-Markdown.github.io/extensions/code_hilite
+# for documentation.
+
+# Original code Copyright 2006-2008 [Waylan Limberg](http://achinghead.com/).
+
+# All changes Copyright 2008-2014 The Python Markdown Project
+
+# License: [BSD](https://opensource.org/licenses/bsd-license.php)
+
+"""
+Adds code/syntax highlighting to standard Python-Markdown code blocks.
+
+See the [documentation](https://Python-Markdown.github.io/extensions/code_hilite)
+for details.
+"""
+
+from __future__ import annotations
+
+from . import Extension
+from ..treeprocessors import Treeprocessor
+from ..util import parseBoolValue
+from typing import TYPE_CHECKING, Callable, Any
+
+if TYPE_CHECKING:  # pragma: no cover
+    import xml.etree.ElementTree as etree
+
+try:  # pragma: no cover
+    from pygments import highlight
+    from pygments.lexers import get_lexer_by_name, guess_lexer
+    from pygments.formatters import get_formatter_by_name
+    from pygments.util import ClassNotFound
+    pygments = True
+except ImportError:  # pragma: no cover
+    pygments = False
+
+
+def parse_hl_lines(expr: str) -> list[int]:
+    """Support our syntax for emphasizing certain lines of code.
+
+    `expr` should be like '1 2' to emphasize lines 1 and 2 of a code block.
+    Returns a list of integers, the line numbers to emphasize.
+    """
+    if not expr:
+        return []
+
+    try:
+        return list(map(int, expr.split()))
+    except ValueError:  # pragma: no cover
+        return []
+
+
+# ------------------ The Main CodeHilite Class ----------------------
+class CodeHilite:
+    """
+    Determine language of source code, and pass it on to the Pygments highlighter.
+
+    Usage:
+
+    ```python
+    code = CodeHilite(src=some_code, lang='python')
+    html = code.hilite()
+    ```
+
+    Arguments:
+        src: Source string or any object with a `.readline` attribute.
+
+    Keyword arguments:
+        lang (str): String name of Pygments lexer to use for highlighting. Default: `None`.
+        guess_lang (bool): Auto-detect which lexer to use.
+            Ignored if `lang` is set to a valid value. Default: `True`.
+        use_pygments (bool): Pass code to Pygments for code highlighting. If `False`, the code is
+            instead wrapped for highlighting by a JavaScript library. Default: `True`.
+        pygments_formatter (str): The name of a Pygments formatter or a formatter class used for
+            highlighting the code blocks. Default: `html`.
+        linenums (bool): An alias to Pygments `linenos` formatter option. Default: `None`.
+        css_class (str): An alias to Pygments `cssclass` formatter option. Default: 'codehilite'.
+        lang_prefix (str): Prefix prepended to the language. Default: "language-".
+
+    Other Options:
+
+    Any other options are accepted and passed on to the lexer and formatter. Therefore,
+    valid options include any options which are accepted by the `html` formatter or
+    whichever lexer the code's language uses. Note that most lexers do not have any
+    options. However, a few have very useful options, such as PHP's `startinline` option.
+    Any invalid options are ignored without error.
+
+    * **Formatter options**: <https://pygments.org/docs/formatters/#HtmlFormatter>
+    * **Lexer Options**: <https://pygments.org/docs/lexers/>
+
+    Additionally, when Pygments is enabled, the code's language is passed to the
+    formatter as an extra option `lang_str`, whose value being `{lang_prefix}{lang}`.
+    This option has no effect to the Pygments' builtin formatters.
+
+    Advanced Usage:
+
+    ```python
+    code = CodeHilite(
+        src = some_code,
+        lang = 'php',
+        startinline = True,      # Lexer option. Snippet does not start with `<?php`.
+        linenostart = 42,        # Formatter option. Snippet starts on line 42.
+        hl_lines = [45, 49, 50], # Formatter option. Highlight lines 45, 49, and 50.
+        linenos = 'inline'       # Formatter option. Avoid alignment problems.
+    )
+    html = code.hilite()
+    ```
+
+    """
+
+    def __init__(self, src: str, **options):
+        self.src = src
+        self.lang: str | None = options.pop('lang', None)
+        self.guess_lang: bool = options.pop('guess_lang', True)
+        self.use_pygments: bool = options.pop('use_pygments', True)
+        self.lang_prefix: str = options.pop('lang_prefix', 'language-')
+        self.pygments_formatter: str | Callable = options.pop('pygments_formatter', 'html')
+
+        if 'linenos' not in options:
+            options['linenos'] = options.pop('linenums', None)
+        if 'cssclass' not in options:
+            options['cssclass'] = options.pop('css_class', 'codehilite')
+        if 'wrapcode' not in options:
+            # Override Pygments default
+            options['wrapcode'] = True
+        # Disallow use of `full` option
+        options['full'] = False
+
+        self.options = options
+
+    def hilite(self, shebang: bool = True) -> str:
+        """
+        Pass code to the [Pygments](https://pygments.org/) highlighter with
+        optional line numbers. The output should then be styled with CSS to
+        your liking. No styles are applied by default - only styling hooks
+        (i.e.: `<span class="k">`).
+
+        returns : A string of html.
+
+        """
+
+        self.src = self.src.strip('\n')
+
+        if self.lang is None and shebang:
+            self._parseHeader()
+
+        if pygments and self.use_pygments:
+            try:
+                lexer = get_lexer_by_name(self.lang, **self.options)
+            except ValueError:
+                try:
+                    if self.guess_lang:
+                        lexer = guess_lexer(self.src, **self.options)
+                    else:
+                        lexer = get_lexer_by_name('text', **self.options)
+                except ValueError:  # pragma: no cover
+                    lexer = get_lexer_by_name('text', **self.options)
+            if not self.lang:
+                # Use the guessed lexer's language instead
+                self.lang = lexer.aliases[0]
+            lang_str = f'{self.lang_prefix}{self.lang}'
+            if isinstance(self.pygments_formatter, str):
+                try:
+                    formatter = get_formatter_by_name(self.pygments_formatter, **self.options)
+                except ClassNotFound:
+                    formatter = get_formatter_by_name('html', **self.options)
+            else:
+                formatter = self.pygments_formatter(lang_str=lang_str, **self.options)
+            return highlight(self.src, lexer, formatter)
+        else:
+            # just escape and build markup usable by JavaScript highlighting libraries
+            txt = self.src.replace('&', '&amp;')
+            txt = txt.replace('<', '&lt;')
+            txt = txt.replace('>', '&gt;')
+            txt = txt.replace('"', '&quot;')
+            classes = []
+            if self.lang:
+                classes.append('{}{}'.format(self.lang_prefix, self.lang))
+            if self.options['linenos']:
+                classes.append('linenums')
+            class_str = ''
+            if classes:
+                class_str = ' class="{}"'.format(' '.join(classes))
+            return '<pre class="{}"><code{}>{}\n</code></pre>\n'.format(
+                self.options['cssclass'],
+                class_str,
+                txt
+            )
+
+    def _parseHeader(self) -> None:
+        """
+        Determines language of a code block from shebang line and whether the
+        said line should be removed or left in place. If the shebang line
+        contains a path (even a single /) then it is assumed to be a real
+        shebang line and left alone. However, if no path is given
+        (e.i.: `#!python` or `:::python`) then it is assumed to be a mock shebang
+        for language identification of a code fragment and removed from the
+        code block prior to processing for code highlighting. When a mock
+        shebang (e.i: `#!python`) is found, line numbering is turned on. When
+        colons are found in place of a shebang (e.i.: `:::python`), line
+        numbering is left in the current state - off by default.
+
+        Also parses optional list of highlight lines, like:
+
+            :::python hl_lines="1 3"
+        """
+
+        import re
+
+        # split text into lines
+        lines = self.src.split("\n")
+        # pull first line to examine
+        fl = lines.pop(0)
+
+        c = re.compile(r'''
+            (?:(?:^::+)|(?P<shebang>^[#]!)) # Shebang or 2 or more colons
+            (?P<path>(?:/\w+)*[/ ])?        # Zero or 1 path
+            (?P<lang>[\w#.+-]*)             # The language
+            \s*                             # Arbitrary whitespace
+            # Optional highlight lines, single- or double-quote-delimited
+            (hl_lines=(?P<quot>"|')(?P<hl_lines>.*?)(?P=quot))?
+            ''',  re.VERBOSE)
+        # search first line for shebang
+        m = c.search(fl)
+        if m:
+            # we have a match
+            try:
+                self.lang = m.group('lang').lower()
+            except IndexError:  # pragma: no cover
+                self.lang = None
+            if m.group('path'):
+                # path exists - restore first line
+                lines.insert(0, fl)
+            if self.options['linenos'] is None and m.group('shebang'):
+                # Overridable and Shebang exists - use line numbers
+                self.options['linenos'] = True
+
+            self.options['hl_lines'] = parse_hl_lines(m.group('hl_lines'))
+        else:
+            # No match
+            lines.insert(0, fl)
+
+        self.src = "\n".join(lines).strip("\n")
+
+
+# ------------------ The Markdown Extension -------------------------------
+
+
+class HiliteTreeprocessor(Treeprocessor):
+    """ Highlight source code in code blocks. """
+
+    config: dict[str, Any]
+
+    def code_unescape(self, text: str) -> str:
+        """Unescape code."""
+        text = text.replace("&lt;", "<")
+        text = text.replace("&gt;", ">")
+        # Escaped '&' should be replaced at the end to avoid
+        # conflicting with < and >.
+        text = text.replace("&amp;", "&")
+        return text
+
+    def run(self, root: etree.Element) -> None:
+        """ Find code blocks and store in `htmlStash`. """
+        blocks = root.iter('pre')
+        for block in blocks:
+            if len(block) == 1 and block[0].tag == 'code':
+                local_config = self.config.copy()
+                text = block[0].text
+                if text is None:
+                    continue
+                code = CodeHilite(
+                    self.code_unescape(text),
+                    tab_length=self.md.tab_length,
+                    style=local_config.pop('pygments_style', 'default'),
+                    **local_config
+                )
+                placeholder = self.md.htmlStash.store(code.hilite())
+                # Clear code block in `etree` instance
+                block.clear()
+                # Change to `p` element which will later
+                # be removed when inserting raw html
+                block.tag = 'p'
+                block.text = placeholder
+
+
+class CodeHiliteExtension(Extension):
+    """ Add source code highlighting to markdown code blocks. """
+
+    def __init__(self, **kwargs):
+        # define default configs
+        self.config = {
+            'linenums': [
+                None, "Use lines numbers. True|table|inline=yes, False=no, None=auto. Default: `None`."
+            ],
+            'guess_lang': [
+                True, "Automatic language detection - Default: `True`."
+            ],
+            'css_class': [
+                "codehilite", "Set class name for wrapper <div> - Default: `codehilite`."
+            ],
+            'pygments_style': [
+                'default', 'Pygments HTML Formatter Style (Colorscheme). Default: `default`.'
+            ],
+            'noclasses': [
+                False, 'Use inline styles instead of CSS classes - Default `False`.'
+            ],
+            'use_pygments': [
+                True, 'Highlight code blocks with pygments. Disable if using a JavaScript library. Default: `True`.'
+            ],
+            'lang_prefix': [
+                'language-', 'Prefix prepended to the language when `use_pygments` is false. Default: `language-`.'
+            ],
+            'pygments_formatter': [
+                'html', 'Use a specific formatter for Pygments highlighting. Default: `html`.'
+            ],
+        }
+        """ Default configuration options. """
+
+        for key, value in kwargs.items():
+            if key in self.config:
+                self.setConfig(key, value)
+            else:
+                # manually set unknown keywords.
+                if isinstance(value, str):
+                    try:
+                        # Attempt to parse `str` as a boolean value
+                        value = parseBoolValue(value, preserve_none=True)
+                    except ValueError:
+                        pass  # Assume it's not a boolean value. Use as-is.
+                self.config[key] = [value, '']
+
+    def extendMarkdown(self, md):
+        """ Add `HilitePostprocessor` to Markdown instance. """
+        hiliter = HiliteTreeprocessor(md)
+        hiliter.config = self.getConfigs()
+        md.treeprocessors.register(hiliter, 'hilite', 30)
+
+        md.registerExtension(self)
+
+
+def makeExtension(**kwargs):  # pragma: no cover
+    return CodeHiliteExtension(**kwargs)