Changed Network to conform to API

- Removed run(), make_theano_tick(), write_to_hdf5
- Changed make to make_ensemble
- Removed theano references
- Added lists for different network objects
- Updated probe, removed compute_tranform
- Updated "func" to "function" in Network.connect.
- Renamed the "func" parameter to "function" for clairity.
- Moved the pre-node get routine before it is used
- Wrote Network.connect_neurons function.
- Fixed up the documentation for this function
- Made Network.connect and Network.connect_neurons return connection
- Added metadata and properties properties
- Added remove function to network
- Alias added to network, network.probe stripped