feat: ngen_cal_model_configure model hook

[aaraney]

Add model hook: ngen_cal_model_configure hook that mirrors the existing ngen_cal_configure hook.

    @hookspec
    def ngen_cal_model_configure(self, config: ngen.cal.model.ModelExec) -> None:
        """
        Called before calibration begins.
        This allow plugins to perform initial configuration.

        Plugins' configuration data should be provided using the
        `plugins_settings` field in the `model` section of an `ngen.cal`
        configuration file.
        By convention, the name of the plugin should be used as top level key in
        the `plugin_settings` dictionary.
        """

Additions

• ngen_cal_model_configure model hook; Called before calibration begins. This allow plugins to perform initial configuration.
• unwrap method added to ngen.cal.ngen.Ngen. Returns the instance's __root__ attribute.

Changes

• Agent now takes a Model instance as a parameter. Previously, the raw config was passed.

[hellkite500]

The change in behavior of the Agent and its interaction with the model config is quite likely to break.

[hellkite500]

These steps are minutely important to the use of the Agent, and I don't think they can be dropped...The agent manipulates the configs to ensure root/workdirs are set appropriately under the automatically created agent working dirs.

[aaraney]

I don't think they are dropped? I was just pulling them from the pydantic model instance now instead of the dictionary. Probably missing something thought.

[hellkite500]

Sorry, this comment ended up being unclear, it was intended for lines 81-83 where workdir and binary are configured relative to the Agent's dynamically created workdir. These are critical for correct operation of agents especially in PSO where multiple agents are running simultaneously.

As noted in disscussion with @aaraney the current resolved_binary isn't actually working as intended, and is its own bug which can be resolved in this context.

[aaraney]

Opened #167 to track this.

[hellkite500]

I think we are still missing the updated model workdir. An agent has a job which nests information and job/model files under a dynamically created workdir job.workdir. Any model instance associated with that job must have its workdir aligned with the job.workdir, so we need to update the model reference like such

Suggested change

	self._job = JobMeta(ngen_model.type, workdir, log=log)
	self._job = JobMeta(ngen_model.type, workdir, log=log)
	ngen_model.workdir = self.job.workdir

[hellkite500]

An agent effectively side effects the Model it associates with, particularly setting the workdir for that model run. Because of this, we probably need to initialize the Agent before passing the Model to anything else, including plugins.

Suggested change

	model_inner._plugin_manager.hook.ngen_cal_model_configure(config=model_inner)
	# Initialize the starting agent
	# WARNING: Agent sets the model workdir, so initialize it before using the model object for anything that may require an accurate workdir
	agent = Agent(model, general.workdir, general.log, general.restart, general.strategy.parameters)
	model_inner._plugin_manager.hook.ngen_cal_model_configure(config=model_inner)

[hellkite500]

Suggested change

	# Initialize the starting agent
	agent = Agent(model, general.workdir, general.log, general.restart, general.strategy.parameters)