Network Classes

The neet module provides the following abstract network classes from which all concrete Neet networks inherit:

Network	The Network class is the core base class for all Neet networks.
UniformNetwork	The UnformNetwork class represents a network in which every node has the same number of discrete states.

These classes provide an abstract interface which algorithms can leverage for generic implementation of various network-theoretic analyses.

Network

class neet.Network(shape, names=None, metadata=None)

The Network class is the core base class for all Neet networks. It provides an interface for describing network state updating and simple graph-theoretic analyses.

names	Get or set the names of the nodes of the network.
metadata	Any metadata associated with the network.
_unsafe_update	Unsafely update the state of a network in place.
update	Update the state of a network in place.
neighbors_in	Get a set of all incoming neighbors of the node at index.
neighbors_out	Get a set of all outgoing neighbors of the node at index.
neighbors	Get a set of the neighbors of the node at index.
network_graph	The graph of the network as a networkx.DiGraph.
draw_network_graph	Draw network’s networkx graph using PyGraphviz.

Network is an abstract class, meaning it cannot be instantiated, and inherits from neet.LandscapeMixin and neet.StateSpace. Initialization of the Network requires, at a minimum, a specification of the shape of the network’s state space, and optionally allows the user to specify a list of names for the nodes of the network and a metadata dictionary for the network as a whole (e.g. citation information).

Any concrete deriving class must overload the following methods:

• _unsafe_update()
• neighbors_in()
• neighbors_out()

Parameters:

• shape (list) – the base of each node of the network
• names (seq) – an iterable object of the names of the nodes in the network
• metadata (dict) – metadata dictionary for the network

metadata

Any metadata associated with the network.

names

Get or set the names of the nodes of the network.

Raises:

• TypeError – if the assigned value is not convertable to a list
• ValueError – if the length fo the assigned values does not match the networks’s size

_unsafe_update(state, index, pin, values, *args, **kwargs)

Unsafely update the state of a network in place.

This function accepts three optional arguments by default:

• index - update only the specified node (by index)
• pin - do not update the state of any node in a list
• values - set the state of some subset of nodes to specified values

Note

As an abstract method, every concrete class derving from Network must overload this method. The overload should not perform no ensurance checks on the arguments to maximize performance, as those check are performed in the update() method. Further, it is assumed that this method modifies the state argument in-place and no others.

Parameters:

• state (list, numpy.ndarray) – the state of the network to update
• index (int or None) – the index to update
• pin (list, numpy.ndarray or None) – which nodes to pin to their current state
• values (dict or None) – a dictionary mapping nodes to a state to which to reset the node to

Returns:

the updated state

neighbors_in(index, *args, **kwargs)

Get a set of all incoming neighbors of the node at index.

All concrete network classes must overload this method.

Parameters:index (int) – the index of the node target node Returns:a set of incoming neighbor indices

neighbors_out(index, *args, **kwargs)

Get a set of all outgoing neighbors of the node at index.

All concrete network classes must overload this method.

Parameters:index (int) – the index of the node source node Returns:a set of outgoing neighbor indices

update(state, index=None, pin=None, values=None, *args, **kwargs)

Update the state of a network in place.

This function accepts three optional arguments by default:

• index - update only the specified node (by index)
• pin - do not update the state of any node in a list
• values - set the state of some subset of nodes to specified values

Examples

Updates States In-Place:

>>> rule = ECA(30, size=5)
>>> state = [0, 0, 1, 0, 0]
>>> rule.update(state)
[0, 1, 1, 1, 0]
>>> state
[0, 1, 1, 1, 0]

Updating A Single Node:

>>> rule = ECA(30, size=5)
>>> rule.update([0, 0, 1, 0, 0])
[0, 1, 1, 1, 0]
>>> rule.update([0, 0, 1, 0, 0], index=1)
[0, 1, 1, 0, 0]

Pinning States:

>>> rule = ECA(30, size=5)
>>> rule.update([0, 0, 1, 0, 0])
[0, 1, 1, 1, 0]
>>> rule.update([0, 0, 1, 0, 0], pin=[1])
[0, 0, 1, 1, 0]

Overriding States:

>>> rule = ECA(30, size=5)
>>> rule.update([0, 0, 1, 0, 0])
[0, 1, 1, 1, 0]
>>> rule.update([0, 0, 1, 0, 0], values={0: 1, 2: 0})
[1, 1, 0, 1, 0]

This function ensures that:

1. If index is provided, then neither pin nor values is provided.
2. If pin and values are both provided, then they do not affect the same nodes.
3. If values is provided, then the overriding states specified in it are consistent with the state space of the network.

Note

Typically, this method should not be overloaded unless the particular deriving class makes use of the args or kwargs arguments. In that case, it should first ensure that those arguments are well-behaved, and and the delegate subsequent checks and the call to _unsafe_update() to a call to this neet.Network.update().

Parameters:

• state (list or numpy.ndarray) – the state of the network to update
• index (int or None) – the index to update
• pin (list, numpy.ndarray or None) – which nodes to pin to their current state
• values (dict or None) – a dictionary mapping nodes to a state to which to reset the node to

Returns:

the updated state

neighbors(index, direction='both', *args, **kwargs)

Get a set of the neighbors of the node at index. Optionally, specify the directionality of the neighboring edges, e.g. 'in', 'out' or 'both'.

Examples

All Neighbors:

>>> s_pombe.neighbors(7)
{1, 5, 7, 8}

Incoming Neighbors:

>>> s_pombe.neighbors(7, direction='in')
{8, 1, 7}

Outgoing Neighbors:

>>> s_pombe.neighbors(7, direction='out')
{5, 7}

Parameters:

• index (int) – the index of the node
• direction (str) – the directionality of the neighboring edges

Returns:

a set of neighboring node indices, respecting direction.

network_graph(labels='indices', **kwargs)

The graph of the network as a networkx.DiGraph.

This method should only be overloaded by derived classes if additional metadata is to be added to the graph by default.

Examples

>>> s_pombe.network_graph()
<networkx.classes.digraph.DiGraph object at 0x...>

Parameters:

• labels – label to be applied to graph nodes (either 'indices' or 'names')
• kwargs – kwargs to pass to the networkx.DiGraph constructor

Returns:

a networkx.DiGraph object

draw_network_graph(graphkwargs={}, pygraphkwargs={})

Draw network’s networkx graph using PyGraphviz.

Note

This method requires Graphviz and pygraphviz. The former requires manual installation (see https://graphviz.gitlab.io/download/), while the latter can be installed via pip.

Parameters:

• graphkwargs – kwargs to pass to network_graph()
• pygraphkwargs – kwargs to pass to neet.draw.view_pygraphviz()

UniformNetwork

class neet.UniformNetwork(size, base, names=None, metadata=None)

The UnformNetwork class represents a network in which every node has the same number of discrete states. This allows for more efficient default implementations of several methods. If your particular concrete network type meets this condition, then you should derive from UniformNetwork rather than Network.

In addition to the methods provided by Network, UniformNetwork also provides the following attribute:

base	Get the number of states each node can take.

UniformNetwork derives from Network, but is still abstract, meaning it cannot be instantiated. Initialization of the UniformNetwork requires, at a minimum, the number of nodes in the network (size) and the number of states the nodes can take (base). As with Network, the user can optionally specify a list of names for the nodes of the network and a metadata dictionary for the network as a whole (e.g. citation information).

Any concrete deriving class must overload the following methods:

• _unsafe_update()
• neighbors_in()
• neighbors_out()

Parameters:

• size (int) – the number of nodes in the network
• base (int) – the number of states each node can take
• names (seq) – an interable object of the names of the nodes in the network
• metadata (dict) – metadata dictionary for the network

base

Get the number of states each node can take.

Examples

>>> ECA(30, size=5).base
2

Returns:the base of nodes of the network