Daedalus is a novel dynamic spatial microsimulation prototype being developed at the Leeds Institute for Institute Data Analytics. Currently, the main goal is to a create a proof of concept component as part of the SPENSER (Synthetic Population Estimation and Scenario Projection Model) project. In this we hope to demonstrate a potential for a highly integrated system that allows users to produce (custom) population projections for policy intervention analysis.
Trying to implement #17 I found a problem running the pipeline. This happens after all the rate registrations (which take around an hour), so it has been difficult to quickly iterate for a fix.
To reproduce the error in branch feature/17-internal-migration
Traceback (most recent call last):
File "/Users/crangelsmith/PycharmProjects/daedalus/scripts/run.py", line 123, in <module>
main(configuration=utils.get_config())
File "/Users/crangelsmith/PycharmProjects/daedalus/scripts/run.py", line 104, in main
simulation.setup()
File "/anaconda3/envs/daedalus/lib/python3.6/site-packages/vivarium/interface/interactive.py", line 43, in setup
self.initialize_simulants()
File "/anaconda3/envs/daedalus/lib/python3.6/site-packages/vivarium/framework/engine.py", line 136, in initialize_simulants
self.simulant_creator(population_size, population_configuration={'sim_state': 'setup'})
File "/anaconda3/envs/daedalus/lib/python3.6/site-packages/vivarium/framework/population.py", line 506, in _create_simulants
initializer(SimulantData(index, population_configuration, self.clock(), self.step_size()))
File "/anaconda3/envs/daedalus/lib/python3.6/site-packages/vivarium_public_health/population/spenser_population.py", line 59, in generate_test_population
population = _build_population(core_population,self.config.path_to_pop_file)
File "/anaconda3/envs/daedalus/lib/python3.6/site-packages/vivarium/config_tree.py", line 488, in __getattr__
return self.get_from_layer(name)
File "/anaconda3/envs/daedalus/lib/python3.6/site-packages/vivarium/config_tree.py", line 349, in get_from_layer
raise ConfigurationKeyError(f'No value at name {name}.', name)
vivarium.config_tree.ConfigurationKeyError: 'No value at name configuration.path_to_pop_file.'
I think this has to do in how the default_config.yaml is defined where there is a distinct 'path' and 'configuration' filed, which is different to how things were defined in the spenser_population.py class, so I added the 'path_to_pop_file' to the 'configuration' field to see if this fixed the problem but it didn't.
Trying to implement #17 I found a problem running the pipeline. This happens after all the rate registrations (which take around an hour), so it has been difficult to quickly iterate for a fix.
To reproduce the error in branch
feature/17-internal-migrationand the error is
I think this has to do in how the default_config.yaml is defined where there is a distinct 'path' and 'configuration' filed, which is different to how things were defined in the spenser_population.py class, so I added the 'path_to_pop_file' to the 'configuration' field to see if this fixed the problem but it didn't.