myst.yaml

# See docs at: https://mystmd.org/guide/frontmatter
version: 1
project:
  plugins:
    - type: executable
      path: table-plugin.py
site:
  template: book-theme

table-plugin.py

#!/usr/bin/env python3
import argparse
import json
import sys


plugin = {
    "name": "Strong to emphasis",
    "transforms": [
        {
            "name": "transform-typography",
            "doc": "An example transform that rewrites bold text as text with emphasis.",
            "stage": "document",
        }
    ],
}


def find_all_by_type(node: dict, type_: str):
    """Simple node visitor that matches a particular node type

    :param parent: starting node
    :param type_: type of the node to search for
    """
    if node["type"] == type_:
        yield node

    if "children" not in node:
        return
    for next_node in node["children"]:
        yield from find_all_by_type(next_node, type_)


def declare_result(content):
    """Declare result as JSON to stdout

    :param content: content to declare as the result
    """

    # Format result and write to stdout
    json.dump(content, sys.stdout, indent=2)
    # Successfully exit
    raise SystemExit(0)


def to_text(node):
    if "children" in node:
        return "".join(to_text(c) for c in node["children"])
    elif "value" in node:
        return node["value"]
    else:
        return ""


###### Custom part of the plugin

colours = {
    "positively charged": "#CBE4F9",
    "negatively charged": "#CDF5F6",
    "polar uncharged": "#EFF9DA",
    "hydrophobic": "#F9EBDF",
    "hydrophobic and aromatic": "#F9D8D6",
    "special": "#D6CDEA",
}


def find_colour(row):
    for col in row["children"]:
        body = to_text(col)

        for pattern, colour in colours.items():
            if body.lower().startswith(pattern):
                return colour


def run_transform(name, data):
    """Execute a transform with the given name and data

    :param name: name of the transform to run
    :param data: AST of the document upon which the transform is being run
    """
    assert name == "transform-typography"
    for container_node in find_all_by_type(data, "container"):
        classes = {*container_node.get("class", "").split()}
        if "amino-acids" not in classes:
            continue

        for table_node in find_all_by_type(container_node, "table"):
            for row in table_node["children"]:
                # Skip header rows
                if any(child.get("header") for child in row["children"]):
                    continue

                colour = find_colour(row)
                if colour is not None:
                    row["style"] = {"background-color": colour}

    return data


if __name__ == "__main__":
    parser = argparse.ArgumentParser()
    group = parser.add_mutually_exclusive_group()
    group.add_argument("--role")
    group.add_argument("--directive")
    group.add_argument("--transform")
    args = parser.parse_args()

    if args.directive:
        raise NotImplementedError
    elif args.transform:
        data = json.load(sys.stdin)
        declare_result(run_transform(args.transform, data))
    elif args.role:
        raise NotImplementedError
    else:
        declare_result(plugin)