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fixed docstrings
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@IngoScholtes
IngoScholtes committed Oct 4, 2018
1 parent a58a127 commit dc550cc
Showing 1 changed file with 51 additions and 63 deletions.
114 changes: 51 additions & 63 deletions pathpy/classes/network.py
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Expand Up @@ -35,17 +35,16 @@


class Network:
"""
A graph or network that can be directed, undirected, unweighted or weighted
r"""A graph or network that can be directed, undirected, unweighted or weighted
and whose edges can contain arbitrary attributes. This is the base class for
HigherOrderNetwork.
HigherOrderNetwork
Attributes:
-----------
Attributes
----------
nodes: list
nodes : list
A list of (string) nodes.
edges: dictionary
edges : dictionary
A dictionary containing edges (as tuple-valued keys) and their attributes (as value)
"""

Expand Down Expand Up @@ -74,8 +73,7 @@ def __init__(self, directed=False):


def __add__(self, other):
"""
Add two networks and return the union of both
r"""Add two networks and return the union of both
Parameters
----------
Expand All @@ -97,8 +95,7 @@ def __add__(self, other):

@classmethod
def read_file(cls, filename, separator=',', weighted=False, directed=False, header=False):
"""
Reads a network from an edge list file
r"""Reads a network from an edge list file.
Reads data from a file containing multiple lines of *edges* of the
form "v,w,frequency,X" (where frequency is optional and X are
Expand All @@ -118,12 +115,12 @@ def read_file(cls, filename, separator=',', weighted=False, directed=False, head
(i.e. ``a,b,2``)
directed : bool
are the edges directed or undirected
header: bool
header : bool
if true skip the first row, useful if header row in file
Returns
-------
Network:
Network
a ``Network`` object obtained from the edgelist
"""
net = cls(directed)
Expand Down Expand Up @@ -152,9 +149,7 @@ def read_file(cls, filename, separator=',', weighted=False, directed=False, head


def write_file(self, filename, separator=',', weighted=False, header=False):
"""
Writes a network to an edge file
"""
r"""Writes a network to an edge file"""
with open(filename, 'w+') as f:
if header:
if weighted:
Expand All @@ -169,7 +164,7 @@ def write_file(self, filename, separator=',', weighted=False, header=False):

@classmethod
def from_sqlite(cls, cursor, directed=True):
"""Returns a new Network instance generated from links obtained
r"""Returns a new Network instance generated from links obtained
from an SQLite cursor. The cursor must refer to a table with at least
two columns
Expand All @@ -184,14 +179,14 @@ def from_sqlite(cls, cursor, directed=True):
Parameters
----------
cursor:
cursor :
The SQLite cursor to fetch rows from.
directed: bool
directed : bool
Whether or not links should be interpreted as directed. Default is True.
Returns
-------
Network:
Network
A Network instance created from the SQLite database.
"""
Expand All @@ -211,7 +206,9 @@ def from_sqlite(cls, cursor, directed=True):

@classmethod
def from_paths(cls, paths):

r"""Gemerates a weighted directed network from a Paths
object. The weight of directed links will correspond
to the statistics of (sub)-paths of length one"""
network = cls(directed=True)

# check all sub-paths of length one
Expand All @@ -222,8 +219,7 @@ def from_paths(cls, paths):

@classmethod
def from_temporal_network(cls, tempnet):
"""
Returns a time-aggregated directed network representation
r"""Returns a time-aggregated directed network representation
of a temporal network. The number of occurrences of
the same edge at different time stamps is captured
by edge weights.
Expand All @@ -240,8 +236,7 @@ def from_temporal_network(cls, tempnet):


def to_unweighted(self):
"""
Returns an unweighted copy of a directed or undirected network.
r"""Returns an unweighted copy of a directed or undirected network.
In this copy all edge and node properties of the original network
are removed, but the directionality of links is retained.
"""
Expand All @@ -253,8 +248,7 @@ def to_unweighted(self):


def to_undirected(self):
"""
Returns an undirected copy of the network, in which all
r"""Returns an undirected copy of the network, in which all
node and edge properties are removed.
"""
n = Network(directed = False)
Expand All @@ -266,13 +260,12 @@ def to_undirected(self):


def add_node(self, v, **node_attributes):
"""
Adds a node to a network and assigns arbitrary
r"""Adds a node to a network and assigns arbitrary
node attributes.
Parameters:
-----------
node_attributes: dict
Parameters
----------
node_attributes : dict
Key-value pairs that will be stored as
named node attributes in a dictionary. An
attribute set via network.add_node(v, x=42) can be
Expand All @@ -282,18 +275,16 @@ def add_node(self, v, **node_attributes):
default attributes 'indegree', 'outdegree', 'inweight', and 'outweight'.
See examples below.
Example:
Examples
--------
>>> network = pathpy.Network(directed=False)
>>> network.add_node(v)
>>> print(network.nodes[v])
>>> {'inweight': 0.0, 'outweight': 0.0, 'degree': 0}
>>> {'inweight': 0.0, 'outweight': 0.0, 'degree': 0}
>>> network = pathpy.Network(directed=True)
>>> network.add_node(v)
>>> print(network.nodes[v])
>>> {'inweight': 0.0, 'outweight': 0.0, 'indegree': 0, 'outdegree': 0}
"""
if v not in self.nodes:
self.nodes[v] = {**self.nodes[v], **node_attributes}
Expand All @@ -311,9 +302,7 @@ def add_node(self, v, **node_attributes):


def remove_node(self, v):
"""
Removes a node and all of its attributes from the network.
"""
r"""Removes a node and all of its attributes from the network."""
if v in self.nodes:
# remove all incident edges and update neighbors
if not self.directed:
Expand Down Expand Up @@ -342,14 +331,14 @@ def remove_node(self, v):


def remove_edge(self, source, target):
"""
r"""
Remove an edge and all of its attributes from the network.
Parameters
----------
source: str
source : str
Source node of the edge to remove
target: str
target : str
Target node of the edge to remove
"""
if not (source in self.nodes and target in self.nodes):
Expand Down Expand Up @@ -387,17 +376,17 @@ def remove_edge(self, source, target):


def add_edge(self, v, w, **edge_attributes):
"""
r"""
Adds an edge to a network and assigns arbitrary
key-value pairs as edge attribute.
Parameters:
-----------
v: str
Parameters
----------
v : str
String label of the source node
w: str
w : str
String label of the target node
edge_attributes: dict
edge_attributes : dict
Key-value pairs that will be stored as
named edge attributes in a dictionary. An
attribute set via network.add_edge(v, w, x=42) can be
Expand All @@ -407,7 +396,7 @@ def add_edge(self, v, w, **edge_attributes):
if an additional weighted edge is added later
(see example below).
Example:
Examples
--------
>>> network.add_edge('a','b')
>>> print(network.edges[('a', 'b')]['weight'])
Expand Down Expand Up @@ -481,31 +470,32 @@ def add_edge(self, v, w, **edge_attributes):


def find_nodes(self, select_node=lambda v: True):
"""
r"""
Returns all nodes that satisfy a given condition. In the select_node
lambda function, node attributes can be accessed by calling v['attr']
"""
return [n for n in self.nodes if select_node(self.nodes[n])]


def find_edges(self, select_nodes=lambda v, w: True, select_edges=lambda e: True):
"""
r"""
Returns all edges that satisfy a given condition. Edges can be selected based
on attributes of the adjacent nodes as well as attributes of the edge. In the select_edges
lambda function,.
Parameters
----------
select_nodes:
select_nodes : lambda
a lambda function that takes two parameters v, w corresponding to the source and
target node of an edge. All edges for which the lambda function returns True will be
selected. Default is lambda v,w: True.
select_edges:
select_edges : lambda
a lambda function that takes a single parameter e corresponding to an edge tuple.
Edge attributes can be accessed by e['attr']. All edges for which the lambda function
returns True will be selected. Default is lambda e: True.
Example:
Examples
--------
>>> network.find_edges(select_nodes = lambda v,w: if v['desired_node_property'] return True,
select_edges = lambda e: if e['desired_edge_propert'] return True)
"""
Expand All @@ -518,20 +508,19 @@ def ncount(self):


def ecount(self):
""" Returns the number of links """
r"""Returns the number of links """
return len(self.edges)


def total_edge_weight(self):
""" Returns the sum of all edge weights """
r"""Returns the sum of all edge weights """
if self.edges:
return _np.sum(e['weight'] for e in self.edges.values())
return 0


def node_properties(self, prop):
"""
Returns a list of arbitrary node properties in the network,
r"""Returns a list of arbitrary node properties in the network,
where entries have the same order as in network.nodes. If a property
is not present for a given node, None will be added to the list.
"""
Expand All @@ -545,15 +534,14 @@ def node_properties(self, prop):


def degrees(self, mode='degree'):
"""
Returns the sequence of node degrees in the network, where
r"""Returns the sequence of node degrees in the network, where
entries have the same order as in network.nodes. Note that
if mode == 'degree' for a directed network, the degree sequence
of the undirected network will be returned.
Parameters:
-----------
mode: str
Parameters
----------
mode : str
either 'degree', 'indegree', or 'outdegree'
"""
assert mode is 'degree' or mode is 'indegree' or mode is 'outdegree', \
Expand Down

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