add docs, refactor

  hooks:

    - id: mypy

      name: mypy

      entry: poetry run mypy src

      entry: poetry run mypy .

      language: system

      types: [python]

      verbose: true

.. automodule:: nova.galaxy.tool

   :members:

.. automodule:: nova.galaxy.tool_runner

   :members:

   interactive_tools

   outputs

   parameters

   tool_runner

.. _tool_runner:

Tool Runner

--------------

The `ToolRunner` is a helper class to run Galaxy tools using Blinker signals. This allows connect to connect

Galaxy with GUI in a decoupled way.

.. code-block:: python

   import blinker

   from nova.galaxy import ToolRunner

   from nova.common.signals import Signal, ToolCommand, get_signal_id

   # create tool runner

   ToolRunner("runner_id", SomeTool(), lambda: "store_name", GALAXY_URL, GALAXY_API_KEY)

   # from somewhere else, e.g. reacting to a button click:

   async def start_tool():

       execution_signal = blinker.signal(get_signal_id("runner_id", Signal.TOOL_COMMAND))

       await execution_signal.send_async("sender_id", command=ToolCommand.START)

The ToolRunner needs a Tool class which it will manage. This class should inherit from the `BasicTool` and define

functions specific to the tool. For example:

.. code-block:: python

    from nova.galaxy import BasicTool

    from nova.galaxy import Connection, Parameters, Tool

    class RemoteCommandTool(BasicTool):

        """Class that prepares RemoteCommandTool tool."""

        def __init__(self) -> None:

            super().__init__()

        def prepare_tool(self) -> Tool:

            tool_params = Parameters()

            tool = Tool(id="neutrons_remote_command")

            return tool, tool_params

        def get_results(self, tool: Tool) -> bytes:

            outputs = tool.get_results()

            data = outputs.get_dataset("output1")

            return data.get_content()