Feature/11 refactor spenser population and mortality

alan-turing-institute / vivarium_population_spenser

Vivarium microsimulation tools used to model population evolution with the SPENSER project

GNU General Public License v3.0

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Feature/11 refactor spenser population and mortality #12

Closed crangelsmith closed 4 years ago

crangelsmith commented 4 years ago

Closes #11

Some refactoring to remove code that is not used in the SPENSER case (we discussed some of this in the hack session of 17 June)

[x] Removed the NonCRNTestPopulation class, and refactored the TestPopulation class.
[x] Refactor mortality class, removing specific causes of deaths and only keeping the general all causes.
[x] Fixed the years of life lost calculation in the mortality class (it was broken).
[x] Adjusted the year on the configuration to 2011.

crangelsmith commented 4 years ago

I tried to refactor the conftest.base_config to our data, but this breaks some test from other components in VPH, i'll leave it like this until we have finished the development and know that we don't need those components anymore.