diff env/lib/python3.9/site-packages/networkx/linalg/graphmatrix.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/networkx/linalg/graphmatrix.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,156 @@
+"""
+Adjacency matrix and incidence matrix of graphs.
+"""
+import networkx as nx
+
+__all__ = ["incidence_matrix", "adj_matrix", "adjacency_matrix"]
+
+
+def incidence_matrix(G, nodelist=None, edgelist=None, oriented=False, weight=None):
+    """Returns incidence matrix of G.
+
+    The incidence matrix assigns each row to a node and each column to an edge.
+    For a standard incidence matrix a 1 appears wherever a row's node is
+    incident on the column's edge.  For an oriented incidence matrix each
+    edge is assigned an orientation (arbitrarily for undirected and aligning to
+    direction for directed).  A -1 appears for the source (tail) of an edge and
+    1 for the destination (head) of the edge.  The elements are zero otherwise.
+
+    Parameters
+    ----------
+    G : graph
+       A NetworkX graph
+
+    nodelist : list, optional   (default= all nodes in G)
+       The rows are ordered according to the nodes in nodelist.
+       If nodelist is None, then the ordering is produced by G.nodes().
+
+    edgelist : list, optional (default= all edges in G)
+       The columns are ordered according to the edges in edgelist.
+       If edgelist is None, then the ordering is produced by G.edges().
+
+    oriented: bool, optional (default=False)
+       If True, matrix elements are +1 or -1 for the head or tail node
+       respectively of each edge.  If False, +1 occurs at both nodes.
+
+    weight : string or None, optional (default=None)
+       The edge data key used to provide each value in the matrix.
+       If None, then each edge has weight 1.  Edge weights, if used,
+       should be positive so that the orientation can provide the sign.
+
+    Returns
+    -------
+    A : SciPy sparse matrix
+      The incidence matrix of G.
+
+    Notes
+    -----
+    For MultiGraph/MultiDiGraph, the edges in edgelist should be
+    (u,v,key) 3-tuples.
+
+    "Networks are the best discrete model for so many problems in
+    applied mathematics" [1]_.
+
+    References
+    ----------
+    .. [1] Gil Strang, Network applications: A = incidence matrix,
+       http://academicearth.org/lectures/network-applications-incidence-matrix
+    """
+    import scipy.sparse
+
+    if nodelist is None:
+        nodelist = list(G)
+    if edgelist is None:
+        if G.is_multigraph():
+            edgelist = list(G.edges(keys=True))
+        else:
+            edgelist = list(G.edges())
+    A = scipy.sparse.lil_matrix((len(nodelist), len(edgelist)))
+    node_index = {node: i for i, node in enumerate(nodelist)}
+    for ei, e in enumerate(edgelist):
+        (u, v) = e[:2]
+        if u == v:
+            continue  # self loops give zero column
+        try:
+            ui = node_index[u]
+            vi = node_index[v]
+        except KeyError as e:
+            raise nx.NetworkXError(
+                f"node {u} or {v} in edgelist " f"but not in nodelist"
+            ) from e
+        if weight is None:
+            wt = 1
+        else:
+            if G.is_multigraph():
+                ekey = e[2]
+                wt = G[u][v][ekey].get(weight, 1)
+            else:
+                wt = G[u][v].get(weight, 1)
+        if oriented:
+            A[ui, ei] = -wt
+            A[vi, ei] = wt
+        else:
+            A[ui, ei] = wt
+            A[vi, ei] = wt
+    return A.asformat("csc")
+
+
+def adjacency_matrix(G, nodelist=None, weight="weight"):
+    """Returns adjacency matrix of G.
+
+    Parameters
+    ----------
+    G : graph
+       A NetworkX graph
+
+    nodelist : list, optional
+       The rows and columns are ordered according to the nodes in nodelist.
+       If nodelist is None, then the ordering is produced by G.nodes().
+
+    weight : string or None, optional (default='weight')
+       The edge data key used to provide each value in the matrix.
+       If None, then each edge has weight 1.
+
+    Returns
+    -------
+    A : SciPy sparse matrix
+      Adjacency matrix representation of G.
+
+    Notes
+    -----
+    For directed graphs, entry i,j corresponds to an edge from i to j.
+
+    If you want a pure Python adjacency matrix representation try
+    networkx.convert.to_dict_of_dicts which will return a
+    dictionary-of-dictionaries format that can be addressed as a
+    sparse matrix.
+
+    For MultiGraph/MultiDiGraph with parallel edges the weights are summed.
+    See `to_numpy_array` for other options.
+
+    The convention used for self-loop edges in graphs is to assign the
+    diagonal matrix entry value to the edge weight attribute
+    (or the number 1 if the edge has no weight attribute).  If the
+    alternate convention of doubling the edge weight is desired the
+    resulting Scipy sparse matrix can be modified as follows:
+
+    >>> import scipy as sp
+    >>> G = nx.Graph([(1, 1)])
+    >>> A = nx.adjacency_matrix(G)
+    >>> print(A.todense())
+    [[1]]
+    >>> A.setdiag(A.diagonal() * 2)
+    >>> print(A.todense())
+    [[2]]
+
+    See Also
+    --------
+    to_numpy_array
+    to_scipy_sparse_matrix
+    to_dict_of_dicts
+    adjacency_spectrum
+    """
+    return nx.to_scipy_sparse_matrix(G, nodelist=nodelist, weight=weight)
+
+
+adj_matrix = adjacency_matrix