Bugfixes for composability.

[michaeldeistler]

Bug 1

At the network level, we had a bug with what initialize() is doing. E.g. the following failed:

cell1 = jx.Cell([branch for _ in range(num_branches)], parents=parents).initialize()
cell1.insert(HHChannel())
cell2 = jx.Cell([branch for _ in range(num_branches)], parents=parents).initialize()

net = jx.Network([cell1, cell2], []).initialize()
_ = jx.integrate(net)

whereas the same code, but with

net = jx.Network([cell1, cell2], [])

worked. The reason was that channels get appended to the current channels upon calling initialize(). In the new version, this appending only happens in the __init__() of Network, thereby fixing the issue.

Bug 2

Also, I found a bug that compartments were assembled into branches in the wrong order.

comp1 = jx.Compartment()
comp1.insert(HHChannel())
comp2 = jx.Compartment()
branch1 = jx.Branch([comp1, comp2])

comp = jx.Compartment()
branch2 = jx.Branch(comp, nseg=2)
branch2.comp(0.0).insert(HHChannel())  # Previously needed 1.0 indexing!