histopath/tool/support_tools.py

import sys
from io import StringIO

# Create a persistent namespace that will be shared across all executions
_persistent_namespace = {}

def run_python_repl(command: str) -> str:
    """Executes the provided Python command in a persistent environment and returns the output.
    Variables defined in one execution will be available in subsequent executions.
    """

    def execute_in_repl(command: str) -> str:
        """Helper function to execute the command in the persistent environment."""
        old_stdout = sys.stdout
        sys.stdout = mystdout = StringIO()

        # Use the persistent namespace
        global _persistent_namespace

        try:
            # Execute the command in the persistent namespace
            exec(command, _persistent_namespace)
            output = mystdout.getvalue()
        except Exception as e:
            output = f"Error: {str(e)}"
        finally:
            sys.stdout = old_stdout
        return output

    command = command.strip("```").strip()
    return execute_in_repl(command)


def read_function_source_code(function_name: str) -> str:
    """Read the source code of a function from any module path.

    Parameters
    ----------
        function_name (str): Fully qualified function name (e.g., 'bioagentos.tool.support_tools.write_python_code')

    Returns
    -------
        str: The source code of the function

    """
    import importlib
    import inspect

    # Split the function name into module path and function name
    parts = function_name.split(".")
    module_path = ".".join(parts[:-1])
    func_name = parts[-1]

    try:
        # Import the module
        module = importlib.import_module(module_path)

        # Get the function object from the module
        function = getattr(module, func_name)

        # Get the source code of the function
        source_code = inspect.getsource(function)

        return source_code
    except (ImportError, AttributeError) as e:
        return f"Error: Could not find function '{function_name}'. Details: {str(e)}"