Simulation logging can't distinguish between unique simulation contexts

[collijk]

vivarium is structured to allow multiple simulation contexts to live in a single python process, but logging is done in interactive settings with global loggers. This means log messages can't distinguish between simulations if they're run from the same Python process. E.g.

>>> from vivarium.examples.disease_model import get_disease_model_simulation
>>> sim1 = get_disease_model_simulation()
2023-02-25 14:54:45.034 | DEBUG    | vivarium.framework.values:register_value_modifier:392 - Registering metrics.1.results_manager.get_results as modifier to metrics
2023-02-25 14:54:45.035 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline mortality_rate
2023-02-25 14:54:45.035 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline lower_respiratory_infections.cause_specific_mortality_rate
2023-02-25 14:54:45.035 | DEBUG    | vivarium.framework.values:register_value_modifier:392 - Registering mortality_rate.1.diseasemodel.lower_respiratory_infections.delete_cause_specific_mortality as modifier to mortality_rate
2023-02-25 14:54:45.035 | DEBUG    | vivarium.framework.values:register_value_modifier:392 - Registering metrics.2.diseasemodel.lower_respiratory_infections.metrics as modifier to metrics
2023-02-25 14:54:45.035 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline susceptible_to_lower_respiratory_infections.excess_mortality_rate
2023-02-25 14:54:45.035 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline susceptible_to_lower_respiratory_infections.excess_mortality_rate.population_attributable_fraction
2023-02-25 14:54:45.035 | DEBUG    | vivarium.framework.values:register_value_modifier:392 - Registering mortality_rate.2.diseasestate.susceptible_to_lower_respiratory_infections.add_in_excess_mortality as modifier to mortality_rate
2023-02-25 14:54:45.036 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline infected_with_lower_respiratory_infections.incidence_rate
2023-02-25 14:54:45.036 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline infected_with_lower_respiratory_infections.incidence_rate.population_attributable_fraction
2023-02-25 14:54:45.036 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline infected_with_lower_respiratory_infections.excess_mortality_rate
2023-02-25 14:54:45.036 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline infected_with_lower_respiratory_infections.excess_mortality_rate.population_attributable_fraction
2023-02-25 14:54:45.036 | DEBUG    | vivarium.framework.values:register_value_modifier:392 - Registering mortality_rate.3.diseasestate.infected_with_lower_respiratory_infections.add_in_excess_mortality as modifier to mortality_rate
2023-02-25 14:54:45.036 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline infected_with_lower_respiratory_infections.remission_rate
2023-02-25 14:54:45.037 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline infected_with_lower_respiratory_infections.remission_rate.population_attributable_fraction
2023-02-25 14:54:45.037 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline child_wasting.base_proportion_exposed
2023-02-25 14:54:45.037 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline child_wasting.proportion_exposed
2023-02-25 14:54:45.037 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline child_wasting.exposure
2023-02-25 14:54:45.037 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline effect_of_child_wasting_on_infected_with_lower_respiratory_infections.incidence_rate.relative_risk
2023-02-25 14:54:45.038 | DEBUG    | vivarium.framework.values:register_value_modifier:392 - Registering infected_with_lower_respiratory_infections.incidence_rate.population_attributable_fraction.1.effect_of_child_wasting_on_infected_with_lower_respiratory_infections.incidence_rate.population_attributable_fraction as modifier to infected_with_lower_respiratory_infections.incidence_rate.population_attributable_fraction
2023-02-25 14:54:45.038 | DEBUG    | vivarium.framework.values:register_value_modifier:392 - Registering infected_with_lower_respiratory_infections.incidence_rate.1.effect_of_child_wasting_on_infected_with_lower_respiratory_infections.incidence_rate.rate_adjustment as modifier to infected_with_lower_respiratory_infections.incidence_rate
2023-02-25 14:54:45.038 | DEBUG    | vivarium.framework.values:register_value_modifier:392 - Registering child_wasting.proportion_exposed.1.sqlns.intervention_effect as modifier to child_wasting.proportion_exposed
2023-02-25 14:54:45.038 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline sqlns.effect_size
2023-02-25 14:54:45.038 | DEBUG    | vivarium.framework.values:register_value_modifier:392 - Registering metrics.3.observer.metrics as modifier to metrics
2023-02-25 14:54:45.038 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline metrics
>>> sim2 = get_disease_model_simulation()
2023-02-25 14:54:56.029 | DEBUG    | vivarium.framework.values:register_value_modifier:392 - Registering metrics.1.results_manager.get_results as modifier to metrics
2023-02-25 14:54:56.029 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline mortality_rate
2023-02-25 14:54:56.029 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline lower_respiratory_infections.cause_specific_mortality_rate
2023-02-25 14:54:56.030 | DEBUG    | vivarium.framework.values:register_value_modifier:392 - Registering mortality_rate.1.diseasemodel.lower_respiratory_infections.delete_cause_specific_mortality as modifier to mortality_rate
2023-02-25 14:54:56.030 | DEBUG    | vivarium.framework.values:register_value_modifier:392 - Registering metrics.2.diseasemodel.lower_respiratory_infections.metrics as modifier to metrics
2023-02-25 14:54:56.030 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline susceptible_to_lower_respiratory_infections.excess_mortality_rate
2023-02-25 14:54:56.030 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline susceptible_to_lower_respiratory_infections.excess_mortality_rate.population_attributable_fraction
2023-02-25 14:54:56.030 | DEBUG    | vivarium.framework.values:register_value_modifier:392 - Registering mortality_rate.2.diseasestate.susceptible_to_lower_respiratory_infections.add_in_excess_mortality as modifier to mortality_rate
2023-02-25 14:54:56.030 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline infected_with_lower_respiratory_infections.incidence_rate
2023-02-25 14:54:56.030 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline infected_with_lower_respiratory_infections.incidence_rate.population_attributable_fraction
2023-02-25 14:54:56.031 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline infected_with_lower_respiratory_infections.excess_mortality_rate
2023-02-25 14:54:56.031 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline infected_with_lower_respiratory_infections.excess_mortality_rate.population_attributable_fraction
2023-02-25 14:54:56.031 | DEBUG    | vivarium.framework.values:register_value_modifier:392 - Registering mortality_rate.3.diseasestate.infected_with_lower_respiratory_infections.add_in_excess_mortality as modifier to mortality_rate
2023-02-25 14:54:56.031 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline infected_with_lower_respiratory_infections.remission_rate
2023-02-25 14:54:56.031 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline infected_with_lower_respiratory_infections.remission_rate.population_attributable_fraction
2023-02-25 14:54:56.031 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline child_wasting.base_proportion_exposed
2023-02-25 14:54:56.031 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline child_wasting.proportion_exposed
2023-02-25 14:54:56.031 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline child_wasting.exposure
2023-02-25 14:54:56.032 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline effect_of_child_wasting_on_infected_with_lower_respiratory_infections.incidence_rate.relative_risk
2023-02-25 14:54:56.032 | DEBUG    | vivarium.framework.values:register_value_modifier:392 - Registering infected_with_lower_respiratory_infections.incidence_rate.population_attributable_fraction.1.effect_of_child_wasting_on_infected_with_lower_respiratory_infections.incidence_rate.population_attributable_fraction as modifier to infected_with_lower_respiratory_infections.incidence_rate.population_attributable_fraction
2023-02-25 14:54:56.032 | DEBUG    | vivarium.framework.values:register_value_modifier:392 - Registering infected_with_lower_respiratory_infections.incidence_rate.1.effect_of_child_wasting_on_infected_with_lower_respiratory_infections.incidence_rate.rate_adjustment as modifier to infected_with_lower_respiratory_infections.incidence_rate
2023-02-25 14:54:56.032 | DEBUG    | vivarium.framework.values:register_value_modifier:392 - Registering child_wasting.proportion_exposed.1.sqlns.intervention_effect as modifier to child_wasting.proportion_exposed
2023-02-25 14:54:56.032 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline sqlns.effect_size
2023-02-25 14:54:56.032 | DEBUG    | vivarium.framework.values:register_value_modifier:392 - Registering metrics.3.observer.metrics as modifier to metrics
2023-02-25 14:54:56.033 | DEBUG    | vivarium.framework.values:_register_value_producer:338 - Registering value pipeline metrics
>>> sim1.step()
2023-02-25 14:55:04.430 | DEBUG    | vivarium.framework.engine:step:198 - 2022-01-01 00:00:00
>>> sim2.step()
2023-02-25 14:55:09.652 | DEBUG    | vivarium.framework.engine:step:198 - 2022-01-01 00:00:00
>>>

This should be fairly straightforward to fix. Steps:

1. Add a way for SimulationContext objects to generate a unique name
2. Make logging a proper subsystem of vivarium and bind the emitted logs to the simulation context