See https://github.com/executablebooks/rst-to-myst instead. https://github.com/readthedocs/recommonmark/issues/221

convert_recommonmark_to_myst.py

import json
import os
import re
import sys
from textwrap import dedent

replacements = {
    r'.. markdown *::': '',
    r'\.\. admonition:: Hint\n *:class: hint': '.. hint::',
    r'\.\. admonition:: Note\n *:class: note': '.. note::',
    r'\.\. admonition:: Warning\n *:class: warning': '.. warning::',
}


def repl(matchobj):
    content = matchobj.group(1)
    for old, new in replacements.items():
        content = re.sub(old, new, content)

    contents = []
    for text in re.split(r'\n *(?=\.\.)', content)[1:]:
        text = text.strip()

        match = re.search(r'\A\.\. ([^:]+)::(.*)', text)
        directive = match.group(1).strip()
        arguments = match.group(2).strip()

        if directive == 'codelisttable':
            directive = 'csv-table'

        options = []
        body = []
        for line in dedent(text[match.end(0):]).splitlines():
            line = line.rstrip()
            if line.startswith(':'):
                options.append(line)
            else:
                body.append(line)

        options = '\n'.join(options)
        body = '\n'.join(body)

        if body.lstrip().startswith('{'):
            body = json.dumps(json.loads(body), ensure_ascii=False, indent=2)
        else:
            body = dedent(body).lstrip('\n')

        parts = [f'```{{{directive}}}']
        if arguments:
            parts.append(f' {arguments}')
        if options or body:
            parts.append('\n')
        if options:
            parts.append(f'{options}')
        if options and body:
            parts.append('\n\n')
        parts.append(f'{body}\n```')

        contents.append(''.join(parts))

    return '\n\n'.join(contents)


for root, dirs, files in os.walk(sys.argv[1]):
    for file in files:
        if not file.endswith('.md'):
            continue

        with open(os.path.join(root, file)) as f:
            content = f.read()

        content = re.sub(r'```{eval-rst}(.+?)```', repl, content, flags=re.DOTALL)
        content = content.replace('\n\n\n', '\n\n')

        with open(os.path.join(root, file), 'w') as f:
            f.write(content)