MSTIS Networks - #227

@jhprinz: I think I need your help finishing up the storage here. I thought storage was supposed to recursively save things; however, it doesn't seem to save the transitions in the MSTIS.from_state dictionary.

You'll be able to see very quickly if you've got it working by running the multistate_system_setup notebook followed by the mstis_analysis notebook. The output from the last cell in the latter should give information on all the transitions.

I tried to model the storage based on what we did for RETISTransition; that doesn't seem to be enough.

If you can issue a fix PR to my networks branch, then I'm only a few tests from calling this PR ready for review. Analysis aspects can come later.

on it...

@jhprinz : Still a small problem in storage. It looks like .name attributes aren't being saved if they're added separately.

All objects should have an optional .name attribute. If the user overrides the automatically-defined .name, then the name given by the user should be reconstructed (assuming the changed name was what was saved).

In principle, I know how to fix this class-by-class, but I'm hoping you can come up with a simpler global fix for this.

In the particular case I'm seeing, name isn't being saved for UnionVolume:

import openpathsampling as paths
storage = paths.storage.Storage("mstis.nc", mode="r")
mstis = storage.networks.load(0)
print mstis

errors with:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-3-84477e647a0d> in <module>()
----> 1 print mstis

/Users/dwhs/Dropbox/msm-tis/openpathsampling/analysis/network.pyc in __str__(self)
    209         mystr = "Multiple State TIS Network:\n"
    210         for state in self.from_state.keys():
--> 211             mystr += str(self.from_state[state])
    212         return mystr
    213 

/Users/dwhs/Dropbox/msm-tis/openpathsampling/analysis/tis_analysis.pyc in __str__(self)
    329         mystr = str(self.__class__.__name__) + ": " + str(self.name) + "\n"
    330         mystr += (str(self.stateA.name) + " -> " + str(self.stateA.name) 
--> 331                   + " or " + str(self.stateB.name) + "\n")
    332         for iface in self.interfaces:
    333             mystr += "Interface: " + str(iface.name) + "\n"

AttributeError: 'UnionVolume' object has no attribute 'name'

Whereas, if I run this in on the object before storage, I get the expected:

Multiple State TIS Network:
RETISTransition: Out C
C -> C or all states except C
Interface: 0.0<opC<0.04
Interface: 0.0<opC<0.09
Interface: 0.0<opC<0.16
RETISTransition: Out A
A -> A or all states except A
Interface: 0.0<opA<0.04
Interface: 0.0<opA<0.09
Interface: 0.0<opA<0.16
RETISTransition: Out B
B -> B or all states except B
Interface: 0.0<opB<0.04
Interface: 0.0<opB<0.09
Interface: 0.0<opB<0.16

Having this implemented properly will also help later when we get to #233.

Correct, the current handling of the .name attribute is not the best and I will find a better way and submit a PR today to get this working...

Everything seems to be saving and loading now! Let's call this one ready for review and merge; I'll start on the analysis aspects later.

great. merging...