diff planemo/lib/python3.7/site-packages/networkx/generators/atlas.py @ 1:56ad4e20f292 draft

"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"

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+++ b/planemo/lib/python3.7/site-packages/networkx/generators/atlas.py	Fri Jul 31 00:32:28 2020 -0400
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+#    Copyright (C) 2004-2019 by
+#    Aric Hagberg <[e-mail]>
+#    Dan Schult <[e-mail]>
+#    Pieter Swart <[e-mail]>
+#    All rights reserved.
+#    BSD license.
+#
+# Author:
+#     Pieter Swart <[e-mail]>
+"""
+Generators for the small graph atlas.
+"""
+import gzip
+from itertools import islice
+import os
+import os.path
+
+import networkx as nx
+
+__all__ = ['graph_atlas', 'graph_atlas_g']
+
+#: The total number of graphs in the atlas.
+#:
+#: The graphs are labeled starting from 0 and extending to (but not
+#: including) this number.
+NUM_GRAPHS = 1253
+
+#: The absolute path representing the directory containing this file.
+THIS_DIR = os.path.dirname(os.path.abspath(__file__))
+
+#: The path to the data file containing the graph edge lists.
+#:
+#: This is the absolute filename of the gzipped text file containing the
+#: edge list for each graph in the atlas. The file contains one entry
+#: per graph in the atlas, in sequential order, starting from graph
+#: number 0 and extending through graph number 1252 (see
+#: :data:`NUM_GRAPHS`). Each entry looks like
+#:
+#: .. sourcecode:: text
+#:
+#:    GRAPH 6
+#:    NODES 3
+#:    0 1
+#:    0 2
+#:
+#: where the first two lines are the graph's index in the atlas and the
+#: number of nodes in the graph, and the remaining lines are the edge
+#: list.
+#:
+#: This file was generated from a Python list of graphs via code like
+#: the following::
+#:
+#:     import gzip
+#:     from networkx.generators.atlas import graph_atlas_g
+#:     from networkx.readwrite.edgelist import write_edgelist
+#:
+#:     with gzip.open('atlas.dat.gz', 'wb') as f:
+#:         for i, G in enumerate(graph_atlas_g()):
+#:             f.write(bytes('GRAPH {}\n'.format(i), encoding='utf-8'))
+#:             f.write(bytes('NODES {}\n'.format(len(G)), encoding='utf-8'))
+#:             write_edgelist(G, f, data=False)
+#:
+ATLAS_FILE = os.path.join(THIS_DIR, 'atlas.dat.gz')
+
+
+def _generate_graphs():
+    """Sequentially read the file containing the edge list data for the
+    graphs in the atlas and generate the graphs one at a time.
+
+    This function reads the file given in :data:`.ATLAS_FILE`.
+
+    """
+    with gzip.open(ATLAS_FILE, 'rb') as f:
+        line = f.readline()
+        while line and line.startswith(b'GRAPH'):
+            # The first two lines of each entry tell us the index of the
+            # graph in the list and the number of nodes in the graph.
+            # They look like this:
+            #
+            #     GRAPH 3
+            #     NODES 2
+            #
+            graph_index = int(line[6:].rstrip())
+            line = f.readline()
+            num_nodes = int(line[6:].rstrip())
+            # The remaining lines contain the edge list, until the next
+            # GRAPH line (or until the end of the file).
+            edgelist = []
+            line = f.readline()
+            while line and not line.startswith(b'GRAPH'):
+                edgelist.append(line.rstrip())
+                line = f.readline()
+            G = nx.Graph()
+            G.name = 'G{}'.format(graph_index)
+            G.add_nodes_from(range(num_nodes))
+            G.add_edges_from(tuple(map(int, e.split())) for e in edgelist)
+            yield G
+
+
+def graph_atlas(i):
+    """Returns graph number `i` from the Graph Atlas.
+
+    For more information, see :func:`.graph_atlas_g`.
+
+    Parameters
+    ----------
+    i : int
+        The index of the graph from the atlas to get. The graph at index
+        0 is assumed to be the null graph.
+
+    Returns
+    -------
+    list
+        A list of :class:`~networkx.Graph` objects, the one at index *i*
+        corresponding to the graph *i* in the Graph Atlas.
+
+    See also
+    --------
+    graph_atlas_g
+
+    Notes
+    -----
+    The time required by this function increases linearly with the
+    argument `i`, since it reads a large file sequentially in order to
+    generate the graph [1]_.
+
+    References
+    ----------
+    .. [1] Ronald C. Read and Robin J. Wilson, *An Atlas of Graphs*.
+           Oxford University Press, 1998.
+
+    """
+    if not (0 <= i < NUM_GRAPHS):
+        raise ValueError('index must be between 0 and {}'.format(NUM_GRAPHS))
+    return next(islice(_generate_graphs(), i, None))
+
+
+def graph_atlas_g():
+    """Returns the list of all graphs with up to seven nodes named in the
+    Graph Atlas.
+
+    The graphs are listed in increasing order by
+
+    1. number of nodes,
+    2. number of edges,
+    3. degree sequence (for example 111223 < 112222),
+    4. number of automorphisms,
+
+    in that order, with three exceptions as described in the *Notes*
+    section below. This causes the list to correspond with the index of
+    the graphs in the Graph Atlas [atlas]_, with the first graph,
+    ``G[0]``, being the null graph.
+
+    Returns
+    -------
+    list
+        A list of :class:`~networkx.Graph` objects, the one at index *i*
+        corresponding to the graph *i* in the Graph Atlas.
+
+    See also
+    --------
+    graph_atlas
+
+    Notes
+    -----
+    This function may be expensive in both time and space, since it
+    reads a large file sequentially in order to populate the list.
+
+    Although the NetworkX atlas functions match the order of graphs
+    given in the "Atlas of Graphs" book, there are (at least) three
+    errors in the ordering described in the book. The following three
+    pairs of nodes violate the lexicographically nondecreasing sorted
+    degree sequence rule:
+
+    - graphs 55 and 56 with degree sequences 001111 and 000112,
+    - graphs 1007 and 1008 with degree sequences 3333444 and 3333336,
+    - graphs 1012 and 1213 with degree sequences 1244555 and 1244456.
+
+    References
+    ----------
+    .. [atlas] Ronald C. Read and Robin J. Wilson,
+               *An Atlas of Graphs*.
+               Oxford University Press, 1998.
+
+    """
+    return list(_generate_graphs())