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- """
- ********************
- Bipartite Edge Lists
- ********************
- Read and write NetworkX graphs as bipartite edge lists.
- Format
- ------
- You can read or write three formats of edge lists with these functions.
- Node pairs with no data::
- 1 2
- Python dictionary as data::
- 1 2 {'weight':7, 'color':'green'}
- Arbitrary data::
- 1 2 7 green
- For each edge (u, v) the node u is assigned to part 0 and the node v to part 1.
- """
- __all__ = ["generate_edgelist", "write_edgelist", "parse_edgelist", "read_edgelist"]
- import networkx as nx
- from networkx.utils import not_implemented_for, open_file
- @open_file(1, mode="wb")
- def write_edgelist(G, path, comments="#", delimiter=" ", data=True, encoding="utf-8"):
- """Write a bipartite graph as a list of edges.
- Parameters
- ----------
- G : Graph
- A NetworkX bipartite graph
- path : file or string
- File or filename to write. If a file is provided, it must be
- opened in 'wb' mode. Filenames ending in .gz or .bz2 will be compressed.
- comments : string, optional
- The character used to indicate the start of a comment
- delimiter : string, optional
- The string used to separate values. The default is whitespace.
- data : bool or list, optional
- If False write no edge data.
- If True write a string representation of the edge data dictionary..
- If a list (or other iterable) is provided, write the keys specified
- in the list.
- encoding: string, optional
- Specify which encoding to use when writing file.
- Examples
- --------
- >>> G = nx.path_graph(4)
- >>> G.add_nodes_from([0, 2], bipartite=0)
- >>> G.add_nodes_from([1, 3], bipartite=1)
- >>> nx.write_edgelist(G, "test.edgelist")
- >>> fh = open("test.edgelist", "wb")
- >>> nx.write_edgelist(G, fh)
- >>> nx.write_edgelist(G, "test.edgelist.gz")
- >>> nx.write_edgelist(G, "test.edgelist.gz", data=False)
- >>> G = nx.Graph()
- >>> G.add_edge(1, 2, weight=7, color="red")
- >>> nx.write_edgelist(G, "test.edgelist", data=False)
- >>> nx.write_edgelist(G, "test.edgelist", data=["color"])
- >>> nx.write_edgelist(G, "test.edgelist", data=["color", "weight"])
- See Also
- --------
- write_edgelist
- generate_edgelist
- """
- for line in generate_edgelist(G, delimiter, data):
- line += "\n"
- path.write(line.encode(encoding))
- @not_implemented_for("directed")
- def generate_edgelist(G, delimiter=" ", data=True):
- """Generate a single line of the bipartite graph G in edge list format.
- Parameters
- ----------
- G : NetworkX graph
- The graph is assumed to have node attribute `part` set to 0,1 representing
- the two graph parts
- delimiter : string, optional
- Separator for node labels
- data : bool or list of keys
- If False generate no edge data. If True use a dictionary
- representation of edge data. If a list of keys use a list of data
- values corresponding to the keys.
- Returns
- -------
- lines : string
- Lines of data in adjlist format.
- Examples
- --------
- >>> from networkx.algorithms import bipartite
- >>> G = nx.path_graph(4)
- >>> G.add_nodes_from([0, 2], bipartite=0)
- >>> G.add_nodes_from([1, 3], bipartite=1)
- >>> G[1][2]["weight"] = 3
- >>> G[2][3]["capacity"] = 12
- >>> for line in bipartite.generate_edgelist(G, data=False):
- ... print(line)
- 0 1
- 2 1
- 2 3
- >>> for line in bipartite.generate_edgelist(G):
- ... print(line)
- 0 1 {}
- 2 1 {'weight': 3}
- 2 3 {'capacity': 12}
- >>> for line in bipartite.generate_edgelist(G, data=["weight"]):
- ... print(line)
- 0 1
- 2 1 3
- 2 3
- """
- try:
- part0 = [n for n, d in G.nodes.items() if d["bipartite"] == 0]
- except BaseException as err:
- raise AttributeError("Missing node attribute `bipartite`") from err
- if data is True or data is False:
- for n in part0:
- for edge in G.edges(n, data=data):
- yield delimiter.join(map(str, edge))
- else:
- for n in part0:
- for u, v, d in G.edges(n, data=True):
- edge = [u, v]
- try:
- edge.extend(d[k] for k in data)
- except KeyError:
- pass # missing data for this edge, should warn?
- yield delimiter.join(map(str, edge))
- def parse_edgelist(
- lines, comments="#", delimiter=None, create_using=None, nodetype=None, data=True
- ):
- """Parse lines of an edge list representation of a bipartite graph.
- Parameters
- ----------
- lines : list or iterator of strings
- Input data in edgelist format
- comments : string, optional
- Marker for comment lines
- delimiter : string, optional
- Separator for node labels
- create_using: NetworkX graph container, optional
- Use given NetworkX graph for holding nodes or edges.
- nodetype : Python type, optional
- Convert nodes to this type.
- data : bool or list of (label,type) tuples
- If False generate no edge data or if True use a dictionary
- representation of edge data or a list tuples specifying dictionary
- key names and types for edge data.
- Returns
- -------
- G: NetworkX Graph
- The bipartite graph corresponding to lines
- Examples
- --------
- Edgelist with no data:
- >>> from networkx.algorithms import bipartite
- >>> lines = ["1 2", "2 3", "3 4"]
- >>> G = bipartite.parse_edgelist(lines, nodetype=int)
- >>> sorted(G.nodes())
- [1, 2, 3, 4]
- >>> sorted(G.nodes(data=True))
- [(1, {'bipartite': 0}), (2, {'bipartite': 0}), (3, {'bipartite': 0}), (4, {'bipartite': 1})]
- >>> sorted(G.edges())
- [(1, 2), (2, 3), (3, 4)]
- Edgelist with data in Python dictionary representation:
- >>> lines = ["1 2 {'weight':3}", "2 3 {'weight':27}", "3 4 {'weight':3.0}"]
- >>> G = bipartite.parse_edgelist(lines, nodetype=int)
- >>> sorted(G.nodes())
- [1, 2, 3, 4]
- >>> sorted(G.edges(data=True))
- [(1, 2, {'weight': 3}), (2, 3, {'weight': 27}), (3, 4, {'weight': 3.0})]
- Edgelist with data in a list:
- >>> lines = ["1 2 3", "2 3 27", "3 4 3.0"]
- >>> G = bipartite.parse_edgelist(lines, nodetype=int, data=(("weight", float),))
- >>> sorted(G.nodes())
- [1, 2, 3, 4]
- >>> sorted(G.edges(data=True))
- [(1, 2, {'weight': 3.0}), (2, 3, {'weight': 27.0}), (3, 4, {'weight': 3.0})]
- See Also
- --------
- """
- from ast import literal_eval
- 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
- # split line, should have 2 or more
- s = line.strip().split(delimiter)
- if len(s) < 2:
- continue
- u = s.pop(0)
- v = s.pop(0)
- d = s
- if nodetype is not None:
- try:
- u = nodetype(u)
- v = nodetype(v)
- except BaseException as err:
- raise TypeError(
- f"Failed to convert nodes {u},{v} " f"to type {nodetype}."
- ) from err
- if len(d) == 0 or data is False:
- # no data or data type specified
- edgedata = {}
- elif data is True:
- # no edge types specified
- try: # try to evaluate as dictionary
- edgedata = dict(literal_eval(" ".join(d)))
- except BaseException as err:
- raise TypeError(
- f"Failed to convert edge data ({d})" f"to dictionary."
- ) from err
- else:
- # convert edge data to dictionary with specified keys and type
- if len(d) != len(data):
- raise IndexError(
- f"Edge data {d} and data_keys {data} are not the same length"
- )
- edgedata = {}
- for (edge_key, edge_type), edge_value in zip(data, d):
- try:
- edge_value = edge_type(edge_value)
- except BaseException as err:
- raise TypeError(
- f"Failed to convert {edge_key} data "
- f"{edge_value} to type {edge_type}."
- ) from err
- edgedata.update({edge_key: edge_value})
- G.add_node(u, bipartite=0)
- G.add_node(v, bipartite=1)
- G.add_edge(u, v, **edgedata)
- return G
- @open_file(0, mode="rb")
- def read_edgelist(
- path,
- comments="#",
- delimiter=None,
- create_using=None,
- nodetype=None,
- data=True,
- edgetype=None,
- encoding="utf-8",
- ):
- """Read a bipartite graph from a list of edges.
- Parameters
- ----------
- path : file or string
- File or filename to read. If a file is provided, it must be
- opened in 'rb' mode.
- Filenames ending in .gz or .bz2 will be uncompressed.
- comments : string, optional
- The character used to indicate the start of a comment.
- delimiter : string, optional
- The string used to separate values. The default is whitespace.
- create_using : Graph container, optional,
- Use specified container to build graph. The default is networkx.Graph,
- an undirected graph.
- nodetype : int, float, str, Python type, optional
- Convert node data from strings to specified type
- data : bool or list of (label,type) tuples
- Tuples specifying dictionary key names and types for edge data
- edgetype : int, float, str, Python type, optional OBSOLETE
- Convert edge data from strings to specified type and use as 'weight'
- encoding: string, optional
- Specify which encoding to use when reading file.
- Returns
- -------
- G : graph
- A networkx Graph or other type specified with create_using
- Examples
- --------
- >>> from networkx.algorithms import bipartite
- >>> G = nx.path_graph(4)
- >>> G.add_nodes_from([0, 2], bipartite=0)
- >>> G.add_nodes_from([1, 3], bipartite=1)
- >>> bipartite.write_edgelist(G, "test.edgelist")
- >>> G = bipartite.read_edgelist("test.edgelist")
- >>> fh = open("test.edgelist", "rb")
- >>> G = bipartite.read_edgelist(fh)
- >>> fh.close()
- >>> G = bipartite.read_edgelist("test.edgelist", nodetype=int)
- Edgelist with data in a list:
- >>> textline = "1 2 3"
- >>> fh = open("test.edgelist", "w")
- >>> d = fh.write(textline)
- >>> fh.close()
- >>> G = bipartite.read_edgelist(
- ... "test.edgelist", nodetype=int, data=(("weight", float),)
- ... )
- >>> list(G)
- [1, 2]
- >>> list(G.edges(data=True))
- [(1, 2, {'weight': 3.0})]
- See parse_edgelist() for more examples of formatting.
- See Also
- --------
- parse_edgelist
- Notes
- -----
- Since nodes must be hashable, the function nodetype must return hashable
- types (e.g. int, float, str, frozenset - or tuples of those, etc.)
- """
- lines = (line.decode(encoding) for line in path)
- return parse_edgelist(
- lines,
- comments=comments,
- delimiter=delimiter,
- create_using=create_using,
- nodetype=nodetype,
- data=data,
- )
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