okstra 0.108.0 → 0.109.0

package/runtime/python/okstra_vendor/networkx/linalg/tests/test_modularity.py

@@ -0,0 +1,86 @@
+import pytest
+
+import networkx as nx
+
+np = pytest.importorskip("numpy")
+pytest.importorskip("scipy")
+
+
+class TestModularity:
+    @classmethod
+    def setup_class(cls):
+        deg = [3, 2, 2, 1, 0]
+        cls.G = nx.havel_hakimi_graph(deg)
+        # Graph used as an example in Sec. 4.1 of Langville and Meyer,
+        # "Google's PageRank and Beyond". (Used for test_directed_laplacian)
+        cls.DG = nx.DiGraph()
+        cls.DG.add_edges_from(
+            (
+                (1, 2),
+                (1, 3),
+                (3, 1),
+                (3, 2),
+                (3, 5),
+                (4, 5),
+                (4, 6),
+                (5, 4),
+                (5, 6),
+                (6, 4),
+            )
+        )
+
+    def test_modularity(self):
+        "Modularity matrix"
+        # fmt: off
+        B = np.array([[-1.125,  0.25,  0.25,  0.625,  0.],
+                      [0.25, -0.5,  0.5, -0.25,  0.],
+                      [0.25,  0.5, -0.5, -0.25,  0.],
+                      [0.625, -0.25, -0.25, -0.125,  0.],
+                      [0.,  0.,  0.,  0.,  0.]])
+        # fmt: on
+
+        permutation = [4, 0, 1, 2, 3]
+        np.testing.assert_equal(nx.modularity_matrix(self.G), B)
+        np.testing.assert_equal(
+            nx.modularity_matrix(self.G, nodelist=permutation),
+            B[np.ix_(permutation, permutation)],
+        )
+
+    def test_modularity_weight(self):
+        "Modularity matrix with weights"
+        # fmt: off
+        B = np.array([[-1.125,  0.25,  0.25,  0.625,  0.],
+                      [0.25, -0.5,  0.5, -0.25,  0.],
+                      [0.25,  0.5, -0.5, -0.25,  0.],
+                      [0.625, -0.25, -0.25, -0.125,  0.],
+                      [0.,  0.,  0.,  0.,  0.]])
+        # fmt: on
+
+        G_weighted = self.G.copy()
+        for n1, n2 in G_weighted.edges():
+            G_weighted.edges[n1, n2]["weight"] = 0.5
+        # The following test would fail in networkx 1.1
+        np.testing.assert_equal(nx.modularity_matrix(G_weighted), B)
+        # The following test that the modularity matrix get rescaled accordingly
+        np.testing.assert_equal(
+            nx.modularity_matrix(G_weighted, weight="weight"), 0.5 * B
+        )
+
+    def test_directed_modularity(self):
+        "Directed Modularity matrix"
+        # fmt: off
+        B = np.array([[-0.2,  0.6,  0.8, -0.4, -0.4, -0.4],
+                      [0.,  0.,  0.,  0.,  0.,  0.],
+                      [0.7,  0.4, -0.3, -0.6,  0.4, -0.6],
+                      [-0.2, -0.4, -0.2, -0.4,  0.6,  0.6],
+                      [-0.2, -0.4, -0.2,  0.6, -0.4,  0.6],
+                      [-0.1, -0.2, -0.1,  0.8, -0.2, -0.2]])
+        # fmt: on
+        node_permutation = [5, 1, 2, 3, 4, 6]
+        idx_permutation = [4, 0, 1, 2, 3, 5]
+        mm = nx.directed_modularity_matrix(self.DG, nodelist=sorted(self.DG))
+        np.testing.assert_equal(mm, B)
+        np.testing.assert_equal(
+            nx.directed_modularity_matrix(self.DG, nodelist=node_permutation),
+            B[np.ix_(idx_permutation, idx_permutation)],
+        )

package/runtime/python/okstra_vendor/networkx/linalg/tests/test_spectrum.py

@@ -0,0 +1,70 @@
+import pytest
+
+import networkx as nx
+
+np = pytest.importorskip("numpy")
+pytest.importorskip("scipy")
+
+
+class TestSpectrum:
+    @classmethod
+    def setup_class(cls):
+        deg = [3, 2, 2, 1, 0]
+        cls.G = nx.havel_hakimi_graph(deg)
+        cls.P = nx.path_graph(3)
+        cls.WG = nx.Graph(
+            (u, v, {"weight": 0.5, "other": 0.3}) for (u, v) in cls.G.edges()
+        )
+        cls.WG.add_node(4)
+        cls.DG = nx.DiGraph()
+        nx.add_path(cls.DG, [0, 1, 2])
+
+    def test_laplacian_spectrum(self):
+        "Laplacian eigenvalues"
+        evals = np.array([0, 0, 1, 3, 4])
+        e = sorted(nx.laplacian_spectrum(self.G))
+        np.testing.assert_almost_equal(e, evals)
+        e = sorted(nx.laplacian_spectrum(self.WG, weight=None))
+        np.testing.assert_almost_equal(e, evals)
+        e = sorted(nx.laplacian_spectrum(self.WG))
+        np.testing.assert_almost_equal(e, 0.5 * evals)
+        e = sorted(nx.laplacian_spectrum(self.WG, weight="other"))
+        np.testing.assert_almost_equal(e, 0.3 * evals)
+
+    def test_normalized_laplacian_spectrum(self):
+        "Normalized Laplacian eigenvalues"
+        evals = np.array([0, 0, 0.7712864461218, 1.5, 1.7287135538781])
+        e = sorted(nx.normalized_laplacian_spectrum(self.G))
+        np.testing.assert_almost_equal(e, evals)
+        e = sorted(nx.normalized_laplacian_spectrum(self.WG, weight=None))
+        np.testing.assert_almost_equal(e, evals)
+        e = sorted(nx.normalized_laplacian_spectrum(self.WG))
+        np.testing.assert_almost_equal(e, evals)
+        e = sorted(nx.normalized_laplacian_spectrum(self.WG, weight="other"))
+        np.testing.assert_almost_equal(e, evals)
+
+    def test_adjacency_spectrum(self):
+        "Adjacency eigenvalues"
+        evals = np.array([-np.sqrt(2), 0, np.sqrt(2)])
+        e = sorted(nx.adjacency_spectrum(self.P))
+        np.testing.assert_almost_equal(e, evals)
+
+    def test_modularity_spectrum(self):
+        "Modularity eigenvalues"
+        evals = np.array([-1.5, 0.0, 0.0])
+        e = sorted(nx.modularity_spectrum(self.P))
+        np.testing.assert_almost_equal(e, evals)
+        # Directed modularity eigenvalues
+        evals = np.array([-0.5, 0.0, 0.0])
+        e = sorted(nx.modularity_spectrum(self.DG))
+        np.testing.assert_almost_equal(e, evals)
+
+    def test_bethe_hessian_spectrum(self):
+        "Bethe Hessian eigenvalues"
+        evals = np.array([0.5 * (9 - np.sqrt(33)), 4, 0.5 * (9 + np.sqrt(33))])
+        e = sorted(nx.bethe_hessian_spectrum(self.P, r=2))
+        np.testing.assert_almost_equal(e, evals)
+        # Collapses back to Laplacian:
+        e1 = sorted(nx.bethe_hessian_spectrum(self.P, r=1))
+        e2 = sorted(nx.laplacian_spectrum(self.P))
+        np.testing.assert_almost_equal(e1, e2)

package/runtime/python/okstra_vendor/networkx/readwrite/__init__.py

@@ -0,0 +1,17 @@
+"""
+A package for reading and writing graphs in various formats.
+
+"""
+
+from networkx.readwrite.adjlist import *
+from networkx.readwrite.multiline_adjlist import *
+from networkx.readwrite.edgelist import *
+from networkx.readwrite.pajek import *
+from networkx.readwrite.leda import *
+from networkx.readwrite.sparse6 import *
+from networkx.readwrite.graph6 import *
+from networkx.readwrite.gml import *
+from networkx.readwrite.graphml import *
+from networkx.readwrite.gexf import *
+from networkx.readwrite.json_graph import *
+from networkx.readwrite.text import *

package/runtime/python/okstra_vendor/networkx/readwrite/adjlist.py

@@ -0,0 +1,330 @@
+"""
+**************
+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
+
+
+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)
+
+
+@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
+    --------
+    >>> G = nx.path_graph(4)
+    >>> nx.write_adjlist(G, "path4.adjlist")
+
+    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.
+
+    >>> fh = open("path4.adjlist2", "wb")
+    >>> nx.write_adjlist(G, fh)
+
+    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))
+
+
+@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
+
+
+@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
+    --------
+    >>> G = nx.path_graph(4)
+    >>> nx.write_adjlist(G, "test.adjlist")
+    >>> G = nx.read_adjlist("test.adjlist")
+
+    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.
+
+    >>> fh = open("test.adjlist", "rb")
+    >>> G = nx.read_adjlist(fh)
+
+    Filenames ending in .gz or .bz2 will be compressed.
+
+    >>> nx.write_adjlist(G, "test.adjlist.gz")
+    >>> G = nx.read_adjlist("test.adjlist.gz")
+
+    The optional nodetype is a function to convert node strings to nodetype.
+
+    For example
+
+    >>> G = nx.read_adjlist("test.adjlist", nodetype=int)
+
+    will attempt to convert all nodes to integer type.
+
+    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
+
+    >>> G = nx.read_adjlist("test.adjlist", create_using=nx.DiGraph)
+
+    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,
+    )