remove composition.py

[eagmon]

This removes vivarium-core dependence from composition.py, and adds a deprecation warning. This file holds a collection of helper functions for bringing processes together. In the last year composite.merge and Engine have been made much easier to use directly instead of relying on helper functions. Because of this composition.py is no longer helpful and in some cases made upkeep harder.

directories.py now has a few standard directories -- PROCESS_OUT_DIR, COMPOSITE_OUT_DIR, etc.

This will be a breaking change and I expect many dependent libraries will have to update their code to remove the helper functions. Some tips for this:

Instead of simulate_process:

    my_composite = my_process.generate()
    sim = Engine(composite=my_composite)
    sim.update(total_time)
    timeseries = sim.emitter.get_timeseries()

instead of simulate_composer:

    sim = Engine(
        composite=composite,
        initial_state=initial_state
        )
    sim.update(time_total)
    output = sim.emitter.get_timeseries()

adding a timeseries process:

    from vivarium.processes.timeline import TimelineProcess
    # create the processes
    agent = ToyAgent({'agent_id': agent_id})
    timeline_process = TimelineProcess({'timeline': timeline})

    # compose
    composite = agent.generate(path=('agents', agent_id))
    composite.merge(
        processes={'timeline': timeline_process},
        topology={'timeline': {
            'global': ('global',),
            'agents': ('agents',)}},
    )

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[U8NWXD]

Since this is a breaking change, should it go in a 2.0 release? I think there are other breaking changes we've been wanting to make--should those all go in together?

[eagmon]

@U8NWXD -- This could go into a 2.0 release, but it alone would not warrant a 2.0 release. What is the best practice for working on a number of changes and then releasing them all at once as a new version? Maybe this should go into a dev branch?

[U8NWXD]

I looked into this and proposed a workflow in #194 for developing v2 while still maintaining v1

[eagmon]

@U8NWXD -- I'm in support of your proposal for v2. But to put that off for a bit I brought composition.py back in this PR with a deprecation warning. So the main change for this PR is that Vivarium-core no longer uses composition.py, even though it is still available for dependent libraries. This will make it easier to remove when the time comes.