"""
**************
Adjacency List
**************
Read and write NetworkX graphs as adjacency lists.
Adjacency list format is useful for graphs without data associated
with nodes or edges and for nodes that can be meaningfully represented
as strings.
Format
------
The adjacency list format consists of lines with node labels. The
first label in a line is the source node. Further labels in the line
are considered target nodes and are added to the graph along with an edge
between the source node and target node.
The graph with edges a-b, a-c, d-e can be represented as the following
adjacency list (anything following the # in a line is a comment)::
a b c # source target target
d e
"""
__all__ = ["generate_adjlist", "write_adjlist", "parse_adjlist", "read_adjlist"]
import networkx as nx
from networkx.utils import open_file
[docs]
def generate_adjlist(G, delimiter=" "):
"""Generate lines representing a graph in adjacency list format.
Parameters
----------
G : NetworkX graph
delimiter : str, default=" "
Separator for node labels.
Yields
------
str
Adjacency list for a node in `G`. The first item is the node label,
followed by the labels of its neighbors.
Examples
--------
>>> G = nx.lollipop_graph(4, 3)
>>> for line in nx.generate_adjlist(G):
... print(line)
0 1 2 3
1 2 3
2 3
3 4
4 5
5 6
6
When `G` is undirected, each edge is only listed once. For directed graphs,
edges appear once for each direction.
>>> G = nx.complete_graph(3, create_using=nx.DiGraph)
>>> for line in nx.generate_adjlist(G):
... print(line)
0 1 2
1 0 2
2 0 1
Node labels are shown multiple times for multiedges, but edge data (including keys)
are not included in the output.
>>> G = nx.MultiGraph([(0, 1, {"weight": 1}), (0, 1, {"weight": 2})])
>>> for line in nx.generate_adjlist(G):
... print(line)
0 1 1
1
See Also
--------
write_adjlist, read_adjlist
Notes
-----
The default `delimiter=" "` will result in unexpected results if node names contain
whitespace characters. To avoid this problem, specify an alternate delimiter when spaces are
valid in node names.
NB: This option is not available for data that isn't user-generated.
"""
seen = set()
directed = G.is_directed()
multigraph = G.is_multigraph()
for s, nbrs in G.adjacency():
nodes = [str(s)]
for t, data in nbrs.items():
if t in seen:
continue
if multigraph and len(data) > 1:
nodes.extend((str(t),) * len(data))
else:
nodes.append(str(t))
if not directed:
seen.add(s)
yield delimiter.join(nodes)
[docs]
@open_file(1, mode="wb")
def write_adjlist(G, path, comments="#", delimiter=" ", encoding="utf-8"):
"""Write graph G in single-line adjacency-list format to path.
Parameters
----------
G : NetworkX graph
path : string or file
Filename or file handle for data output.
Filenames ending in .gz or .bz2 will be compressed.
comments : string, optional
Marker for comment lines
delimiter : string, optional
Separator for node labels
encoding : string, optional
Text encoding.
Examples
--------
>>> from pathlib import Path
>>> import tempfile
>>> tmp_path = Path(tempfile.gettempdir())
>>> G = nx.path_graph(4)
>>> fpath = tmp_path / "path4.adjlist"
>>> nx.write_adjlist(G, fpath)
View the data as stored in file, ignoring header lines which start with the
comment character ("#" by default):
>>> with open(fpath) as fh:
... lines_from_file = fh.readlines()
>>> print("".join(l for l in lines_from_file if not l.startswith("#")))
0 1
1 2
2 3
3
<BLANKLINE>
The path can be a filehandle or a string with the name of the file. If a
filehandle is provided, it has to be opened in 'wb' mode.
>>> with open(tmp_path / "path4.adjlist2", "wb") as fh:
... nx.write_adjlist(G, fh)
>>> with open(tmp_path / "path4.adjlist2") as fh:
... lines_from_file = fh.readlines()
>>> print("".join(l for l in lines_from_file if not l.startswith("#")))
0 1
1 2
2 3
3
<BLANKLINE>
Notes
-----
The default ``delimiter=" "`` will result in unexpected results if node names contain
whitespace characters. To avoid this problem, specify an alternate delimiter when spaces are
valid in node names.
NB: This option is not available for data that isn't user-generated.
This format does not store graph, node, or edge data.
See Also
--------
read_adjlist, generate_adjlist
"""
import sys
import time
pargs = comments + " ".join(sys.argv) + "\n"
header = (
pargs
+ comments
+ f" GMT {time.asctime(time.gmtime())}\n"
+ comments
+ f" {G.name}\n"
)
path.write(header.encode(encoding))
for line in generate_adjlist(G, delimiter):
line += "\n"
path.write(line.encode(encoding))
[docs]
@nx._dispatchable(graphs=None, returns_graph=True)
def parse_adjlist(
lines, comments="#", delimiter=None, create_using=None, nodetype=None
):
"""Parse lines of a graph adjacency list representation.
Parameters
----------
lines : list or iterator of strings
Input data in adjlist format
create_using : NetworkX graph constructor, optional (default=nx.Graph)
Graph type to create. If graph instance, then cleared before populated.
nodetype : Python type, optional
Convert nodes to this type.
comments : string, optional
Marker for comment lines
delimiter : string, optional
Separator for node labels. The default is whitespace.
Returns
-------
G: NetworkX graph
The graph corresponding to the lines in adjacency list format.
Examples
--------
>>> lines = ["1 2 5", "2 3 4", "3 5", "4", "5"]
>>> G = nx.parse_adjlist(lines, nodetype=int)
>>> nodes = [1, 2, 3, 4, 5]
>>> all(node in G for node in nodes)
True
>>> edges = [(1, 2), (1, 5), (2, 3), (2, 4), (3, 5)]
>>> all((u, v) in G.edges() or (v, u) in G.edges() for (u, v) in edges)
True
See Also
--------
read_adjlist
"""
G = nx.empty_graph(0, create_using)
for line in lines:
p = line.find(comments)
if p >= 0:
line = line[:p]
if not len(line):
continue
vlist = line.rstrip("\n").split(delimiter)
u = vlist.pop(0)
# convert types
if nodetype is not None:
try:
u = nodetype(u)
except BaseException as err:
raise TypeError(
f"Failed to convert node ({u}) to type {nodetype}"
) from err
G.add_node(u)
if nodetype is not None:
try:
vlist = list(map(nodetype, vlist))
except BaseException as err:
raise TypeError(
f"Failed to convert nodes ({','.join(vlist)}) to type {nodetype}"
) from err
G.add_edges_from([(u, v) for v in vlist])
return G
[docs]
@open_file(0, mode="rb")
@nx._dispatchable(graphs=None, returns_graph=True)
def read_adjlist(
path,
comments="#",
delimiter=None,
create_using=None,
nodetype=None,
encoding="utf-8",
):
"""Read graph in adjacency list format from path.
Parameters
----------
path : string or file
Filename or file handle to read.
Filenames ending in .gz or .bz2 will be decompressed.
create_using : NetworkX graph constructor, optional (default=nx.Graph)
Graph type to create. If graph instance, then cleared before populated.
nodetype : Python type, optional
Convert nodes to this type.
comments : string, optional
Marker for comment lines
delimiter : string, optional
Separator for node labels. The default is whitespace.
Returns
-------
G: NetworkX graph
The graph corresponding to the lines in adjacency list format.
Examples
--------
>>> from pathlib import Path
>>> import tempfile
>>> tmp_path = Path(tempfile.gettempdir())
>>> G = nx.path_graph(4)
>>> fpath = tmp_path / "test.adjlist"
>>> nx.write_adjlist(G, fpath)
>>> H = nx.read_adjlist(fpath)
Data read from the file are interpreted as strings by default, regardless of
the node type of the original graph.
>>> G.edges
EdgeView([(0, 1), (1, 2), (2, 3)])
>>> H.edges
EdgeView([('0', '1'), ('1', '2'), ('2', '3')])
The node data can be converted to a specific type with the `nodetype`
parameter.
>>> H = nx.read_adjlist(fpath, nodetype=int)
>>> H.edges
EdgeView([(0, 1), (1, 2), (2, 3)])
>>> nx.utils.edges_equal(G.edges, H.edges)
True
Since nodes must be hashable, the function `nodetype` must return hashable
types (e.g. int, float, str, frozenset - or tuples of those, etc.)
The optional `create_using` parameter indicates the type of NetworkX graph
created. The default is `nx.Graph`, an undirected graph. To read the data
as a directed graph use
>>> H = nx.read_adjlist(fpath, create_using=nx.DiGraph)
>>> H.is_directed()
True
The path can be a filehandle or a string with the name of the file. If a
filehandle is provided, it has to be opened in 'rb' mode.
>>> with open(fpath, "rb") as fh:
... H = nx.read_adjlist(fh, nodetype=int)
>>> H.edges
EdgeView([(0, 1), (1, 2), (2, 3)])
Filenames ending in .gz or .bz2 will be compressed automatically.
>>> fpath = tmp_path / "test_adjlist.gz"
>>> nx.write_adjlist(G, fpath)
Notes
-----
This format does not store graph or node data.
See Also
--------
write_adjlist
"""
lines = (line.decode(encoding) for line in path)
return parse_adjlist(
lines,
comments=comments,
delimiter=delimiter,
create_using=create_using,
nodetype=nodetype,
)
