Pass initial population to EpiSystem, not EpiEnv

[sdl1]

This is a pre-cursor to #54

This removes the initial_population member from the EpiEnv struct. Instead, the initial_population can be passed to an EpiSystem constructor, where it is used to initialise the abundances.

There are a few reasons for this:

• It is conceptually cleaner and means we can easily support constructing an EpiSystem without an initial_population
• It means that in WIP: Use AxisArray for abundances.grid #54, we don't have to make any changes to EpiEnv, instead, we just have some small changes in EpiLandscape and EpiSystem
• Also in WIP: Use AxisArray for abundances.grid #54, it will be possible to make EpiLandscape.grid the appropriate AxisArray in the EpiSystem constructor if initial_population is not passed in. This is hard to do in the current code, because initial_population is set to a default matrix of zeros in EpiEnv, which does not match with the actual shape of the classes

So basically with this PR the workflow is

total_pop = # load population
total_pop.data[total_pop .≈ 0.0] .= NaN
# Explicitly call the shrink function, which shrinks based on the NaNs
# We could easily wrap all this in a separate function
total_pop = shrink_to_active(total_pop)
...

# Just pass in the size here, like it used to be
epienv = simplehabitatAE(298.0K, size(total_pop), area, NoControl())
...

# Pass in the total_pop here. This will also take care of modifying the active region based on the NaNs in total_pop
epi = EpiSystem(epilist, epienv, rel, total_pop, UInt16(1))

Some of the diffs are large but this is mostly just moving around code

[claireh93]

This looks great @sdl1! Ready to merge