okstra 0.107.2 → 0.109.0

package/runtime/python/okstra_vendor/networkx/readwrite/json_graph/tests/test_adjacency.py

@@ -0,0 +1,78 @@
+import copy
+import json
+
+import pytest
+
+import networkx as nx
+from networkx.readwrite.json_graph import adjacency_data, adjacency_graph
+from networkx.utils import graphs_equal
+
+
+class TestAdjacency:
+    def test_graph(self):
+        G = nx.path_graph(4)
+        H = adjacency_graph(adjacency_data(G))
+        assert graphs_equal(G, H)
+
+    def test_graph_attributes(self):
+        G = nx.path_graph(4)
+        G.add_node(1, color="red")
+        G.add_edge(1, 2, width=7)
+        G.graph["foo"] = "bar"
+        G.graph[1] = "one"
+
+        H = adjacency_graph(adjacency_data(G))
+        assert graphs_equal(G, H)
+        assert H.graph["foo"] == "bar"
+        assert H.nodes[1]["color"] == "red"
+        assert H[1][2]["width"] == 7
+
+        d = json.dumps(adjacency_data(G))
+        H = adjacency_graph(json.loads(d))
+        assert graphs_equal(G, H)
+        assert H.graph["foo"] == "bar"
+        assert H.graph[1] == "one"
+        assert H.nodes[1]["color"] == "red"
+        assert H[1][2]["width"] == 7
+
+    def test_digraph(self):
+        G = nx.DiGraph()
+        nx.add_path(G, [1, 2, 3])
+        H = adjacency_graph(adjacency_data(G))
+        assert H.is_directed()
+        assert graphs_equal(G, H)
+
+    def test_multidigraph(self):
+        G = nx.MultiDiGraph()
+        nx.add_path(G, [1, 2, 3])
+        H = adjacency_graph(adjacency_data(G))
+        assert H.is_directed()
+        assert H.is_multigraph()
+        assert graphs_equal(G, H)
+
+    def test_multigraph(self):
+        G = nx.MultiGraph()
+        G.add_edge(1, 2, key="first")
+        G.add_edge(1, 2, key="second", color="blue")
+        H = adjacency_graph(adjacency_data(G))
+        assert graphs_equal(G, H)
+        assert H[1][2]["second"]["color"] == "blue"
+
+    def test_input_data_is_not_modified_when_building_graph(self):
+        G = nx.path_graph(4)
+        input_data = adjacency_data(G)
+        orig_data = copy.deepcopy(input_data)
+        # Ensure input is unmodified by deserialisation
+        assert graphs_equal(G, adjacency_graph(input_data))
+        assert input_data == orig_data
+
+    def test_adjacency_form_json_serialisable(self):
+        G = nx.path_graph(4)
+        H = adjacency_graph(json.loads(json.dumps(adjacency_data(G))))
+        assert graphs_equal(G, H)
+
+    def test_exception(self):
+        with pytest.raises(nx.NetworkXError):
+            G = nx.MultiDiGraph()
+            attrs = {"id": "node", "key": "node"}
+            adjacency_data(G, attrs)

package/runtime/python/okstra_vendor/networkx/readwrite/json_graph/tests/test_cytoscape.py

@@ -0,0 +1,78 @@
+import copy
+import json
+
+import pytest
+
+import networkx as nx
+from networkx.readwrite.json_graph import cytoscape_data, cytoscape_graph
+
+
+def test_graph():
+    G = nx.path_graph(4)
+    H = cytoscape_graph(cytoscape_data(G))
+    assert nx.is_isomorphic(G, H)
+
+
+def test_input_data_is_not_modified_when_building_graph():
+    G = nx.path_graph(4)
+    input_data = cytoscape_data(G)
+    orig_data = copy.deepcopy(input_data)
+    # Ensure input is unmodified by cytoscape_graph (gh-4173)
+    cytoscape_graph(input_data)
+    assert input_data == orig_data
+
+
+def test_graph_attributes():
+    G = nx.path_graph(4)
+    G.add_node(1, color="red")
+    G.add_edge(1, 2, width=7)
+    G.graph["foo"] = "bar"
+    G.graph[1] = "one"
+    G.add_node(3, name="node", id="123")
+
+    H = cytoscape_graph(cytoscape_data(G))
+    assert H.graph["foo"] == "bar"
+    assert H.nodes[1]["color"] == "red"
+    assert H[1][2]["width"] == 7
+    assert H.nodes[3]["name"] == "node"
+    assert H.nodes[3]["id"] == "123"
+
+    d = json.dumps(cytoscape_data(G))
+    H = cytoscape_graph(json.loads(d))
+    assert H.graph["foo"] == "bar"
+    assert H.graph[1] == "one"
+    assert H.nodes[1]["color"] == "red"
+    assert H[1][2]["width"] == 7
+    assert H.nodes[3]["name"] == "node"
+    assert H.nodes[3]["id"] == "123"
+
+
+def test_digraph():
+    G = nx.DiGraph()
+    nx.add_path(G, [1, 2, 3])
+    H = cytoscape_graph(cytoscape_data(G))
+    assert H.is_directed()
+    assert nx.is_isomorphic(G, H)
+
+
+def test_multidigraph():
+    G = nx.MultiDiGraph()
+    nx.add_path(G, [1, 2, 3])
+    H = cytoscape_graph(cytoscape_data(G))
+    assert H.is_directed()
+    assert H.is_multigraph()
+
+
+def test_multigraph():
+    G = nx.MultiGraph()
+    G.add_edge(1, 2, key="first")
+    G.add_edge(1, 2, key="second", color="blue")
+    H = cytoscape_graph(cytoscape_data(G))
+    assert nx.is_isomorphic(G, H)
+    assert H[1][2]["second"]["color"] == "blue"
+
+
+def test_exception():
+    with pytest.raises(nx.NetworkXError):
+        G = nx.MultiDiGraph()
+        cytoscape_data(G, name="foo", ident="foo")

package/runtime/python/okstra_vendor/networkx/readwrite/json_graph/tests/test_node_link.py

@@ -0,0 +1,109 @@
+import json
+
+import pytest
+
+import networkx as nx
+from networkx.readwrite.json_graph import node_link_data, node_link_graph
+
+
+class TestNodeLink:
+    def test_exception_dep(self):
+        G = nx.MultiDiGraph()
+        with pytest.raises(nx.NetworkXError):
+            node_link_data(G, name="node", source="node", target="node", key="node")
+
+    def test_graph(self):
+        G = nx.path_graph(4)
+        H = node_link_graph(node_link_data(G))
+        assert nx.is_isomorphic(G, H)
+
+    def test_graph_attributes(self):
+        G = nx.path_graph(4)
+        G.add_node(1, color="red")
+        G.add_edge(1, 2, width=7)
+        G.graph[1] = "one"
+        G.graph["foo"] = "bar"
+
+        H = node_link_graph(node_link_data(G))
+        assert H.graph["foo"] == "bar"
+        assert H.nodes[1]["color"] == "red"
+        assert H[1][2]["width"] == 7
+
+        d = json.dumps(node_link_data(G))
+        H = node_link_graph(json.loads(d))
+        assert H.graph["foo"] == "bar"
+        assert H.graph["1"] == "one"
+        assert H.nodes[1]["color"] == "red"
+        assert H[1][2]["width"] == 7
+
+    def test_digraph(self):
+        G = nx.DiGraph()
+        H = node_link_graph(node_link_data(G))
+        assert H.is_directed()
+
+    def test_multigraph(self):
+        G = nx.MultiGraph()
+        G.add_edge(1, 2, key="first")
+        G.add_edge(1, 2, key="second", color="blue")
+        H = node_link_graph(node_link_data(G))
+        assert nx.is_isomorphic(G, H)
+        assert H[1][2]["second"]["color"] == "blue"
+
+    def test_graph_with_tuple_nodes(self):
+        G = nx.Graph()
+        G.add_edge((0, 0), (1, 0), color=[255, 255, 0])
+        d = node_link_data(G)
+        dumped_d = json.dumps(d)
+        dd = json.loads(dumped_d)
+        H = node_link_graph(dd)
+        assert H.nodes[(0, 0)] == G.nodes[(0, 0)]
+        assert H[(0, 0)][(1, 0)]["color"] == [255, 255, 0]
+
+    def test_unicode_keys(self):
+        q = "qualité"
+        G = nx.Graph()
+        G.add_node(1, **{q: q})
+        s = node_link_data(G)
+        output = json.dumps(s, ensure_ascii=False)
+        data = json.loads(output)
+        H = node_link_graph(data)
+        assert H.nodes[1][q] == q
+
+    def test_exception(self):
+        G = nx.MultiDiGraph()
+        attrs = {"name": "node", "source": "node", "target": "node", "key": "node"}
+        with pytest.raises(nx.NetworkXError):
+            node_link_data(G, **attrs)
+
+    def test_string_ids(self):
+        q = "qualité"
+        G = nx.DiGraph()
+        G.add_node("A")
+        G.add_node(q)
+        G.add_edge("A", q)
+        data = node_link_data(G)
+        assert data["edges"][0]["source"] == "A"
+        assert data["edges"][0]["target"] == q
+        H = node_link_graph(data)
+        assert nx.is_isomorphic(G, H)
+
+    def test_custom_attrs(self):
+        G = nx.path_graph(4)
+        G.add_node(1, color="red")
+        G.add_edge(1, 2, width=7)
+        G.graph[1] = "one"
+        G.graph["foo"] = "bar"
+
+        attrs = {
+            "source": "c_source",
+            "target": "c_target",
+            "name": "c_id",
+            "key": "c_key",
+            "edges": "c_links",
+        }
+
+        H = node_link_graph(node_link_data(G, **attrs), multigraph=False, **attrs)
+        assert nx.is_isomorphic(G, H)
+        assert H.graph["foo"] == "bar"
+        assert H.nodes[1]["color"] == "red"
+        assert H[1][2]["width"] == 7

package/runtime/python/okstra_vendor/networkx/readwrite/json_graph/tests/test_tree.py

@@ -0,0 +1,48 @@
+import json
+
+import pytest
+
+import networkx as nx
+from networkx.readwrite.json_graph import tree_data, tree_graph
+
+
+def test_graph():
+    G = nx.DiGraph()
+    G.add_nodes_from([1, 2, 3], color="red")
+    G.add_edge(1, 2, foo=7)
+    G.add_edge(1, 3, foo=10)
+    G.add_edge(3, 4, foo=10)
+    H = tree_graph(tree_data(G, 1))
+    assert nx.is_isomorphic(G, H)
+
+
+def test_graph_attributes():
+    G = nx.DiGraph()
+    G.add_nodes_from([1, 2, 3], color="red")
+    G.add_edge(1, 2, foo=7)
+    G.add_edge(1, 3, foo=10)
+    G.add_edge(3, 4, foo=10)
+    H = tree_graph(tree_data(G, 1))
+    assert H.nodes[1]["color"] == "red"
+
+    d = json.dumps(tree_data(G, 1))
+    H = tree_graph(json.loads(d))
+    assert H.nodes[1]["color"] == "red"
+
+
+def test_exceptions():
+    with pytest.raises(TypeError, match="is not a tree."):
+        G = nx.complete_graph(3)
+        tree_data(G, 0)
+    with pytest.raises(TypeError, match="is not directed."):
+        G = nx.path_graph(3)
+        tree_data(G, 0)
+    with pytest.raises(TypeError, match="is not weakly connected."):
+        G = nx.path_graph(3, create_using=nx.DiGraph)
+        G.add_edge(2, 0)
+        G.add_node(3)
+        tree_data(G, 0)
+    with pytest.raises(nx.NetworkXError, match="must be different."):
+        G = nx.MultiDiGraph()
+        G.add_node(0)
+        tree_data(G, 0, ident="node", children="node")

package/runtime/python/okstra_vendor/networkx/readwrite/json_graph/tree.py

@@ -0,0 +1,137 @@
+from itertools import chain
+
+import networkx as nx
+
+__all__ = ["tree_data", "tree_graph"]
+
+
+def tree_data(G, root, ident="id", children="children"):
+    """Returns data in tree format that is suitable for JSON serialization
+    and use in JavaScript documents.
+
+    Parameters
+    ----------
+    G : NetworkX graph
+       G must be an oriented tree
+
+    root : node
+       The root of the tree
+
+    ident : string
+        Attribute name for storing NetworkX-internal graph data. `ident` must
+        have a different value than `children`. The default is 'id'.
+
+    children : string
+        Attribute name for storing NetworkX-internal graph data. `children`
+        must have a different value than `ident`. The default is 'children'.
+
+    Returns
+    -------
+    data : dict
+       A dictionary with node-link formatted data.
+
+    Raises
+    ------
+    NetworkXError
+        If `children` and `ident` attributes are identical.
+
+    Examples
+    --------
+    >>> from networkx.readwrite import json_graph
+    >>> G = nx.DiGraph([(1, 2)])
+    >>> data = json_graph.tree_data(G, root=1)
+
+    To serialize with json
+
+    >>> import json
+    >>> s = json.dumps(data)
+
+    Notes
+    -----
+    Node attributes are stored in this format but keys
+    for attributes must be strings if you want to serialize with JSON.
+
+    Graph and edge attributes are not stored.
+
+    See Also
+    --------
+    tree_graph, node_link_data, adjacency_data
+    """
+    if G.number_of_nodes() != G.number_of_edges() + 1:
+        raise TypeError("G is not a tree.")
+    if not G.is_directed():
+        raise TypeError("G is not directed.")
+    if not nx.is_weakly_connected(G):
+        raise TypeError("G is not weakly connected.")
+
+    if ident == children:
+        raise nx.NetworkXError("The values for `id` and `children` must be different.")
+
+    def add_children(n, G):
+        nbrs = G[n]
+        if len(nbrs) == 0:
+            return []
+        children_ = []
+        for child in nbrs:
+            d = {**G.nodes[child], ident: child}
+            c = add_children(child, G)
+            if c:
+                d[children] = c
+            children_.append(d)
+        return children_
+
+    return {**G.nodes[root], ident: root, children: add_children(root, G)}
+
+
+@nx._dispatchable(graphs=None, returns_graph=True)
+def tree_graph(data, ident="id", children="children"):
+    """Returns graph from tree data format.
+
+    Parameters
+    ----------
+    data : dict
+        Tree formatted graph data
+
+    ident : string
+        Attribute name for storing NetworkX-internal graph data. `ident` must
+        have a different value than `children`. The default is 'id'.
+
+    children : string
+        Attribute name for storing NetworkX-internal graph data. `children`
+        must have a different value than `ident`. The default is 'children'.
+
+    Returns
+    -------
+    G : NetworkX DiGraph
+
+    Examples
+    --------
+    >>> from networkx.readwrite import json_graph
+    >>> G = nx.DiGraph([(1, 2)])
+    >>> data = json_graph.tree_data(G, root=1)
+    >>> H = json_graph.tree_graph(data)
+
+    See Also
+    --------
+    tree_data, node_link_data, adjacency_data
+    """
+    graph = nx.DiGraph()
+
+    def add_children(parent, children_):
+        for data in children_:
+            child = data[ident]
+            graph.add_edge(parent, child)
+            grandchildren = data.get(children, [])
+            if grandchildren:
+                add_children(child, grandchildren)
+            nodedata = {
+                str(k): v for k, v in data.items() if k != ident and k != children
+            }
+            graph.add_node(child, **nodedata)
+
+    root = data[ident]
+    children_ = data.get(children, [])
+    nodedata = {str(k): v for k, v in data.items() if k != ident and k != children}
+    graph.add_node(root, **nodedata)
+    add_children(root, children_)
+    return graph

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

@@ -0,0 +1,108 @@
+"""
+Read graphs in LEDA format.
+
+LEDA is a C++ class library for efficient data types and algorithms.
+
+Format
+------
+See http://www.algorithmic-solutions.info/leda_guide/graphs/leda_native_graph_fileformat.html
+
+"""
+# Original author: D. Eppstein, UC Irvine, August 12, 2003.
+# The original code at http://www.ics.uci.edu/~eppstein/PADS/ is public domain.
+
+__all__ = ["read_leda", "parse_leda"]
+
+import networkx as nx
+from networkx.exception import NetworkXError
+from networkx.utils import open_file
+
+
+@open_file(0, mode="rb")
+@nx._dispatchable(graphs=None, returns_graph=True)
+def read_leda(path, encoding="UTF-8"):
+    """Read graph in LEDA format from path.
+
+    Parameters
+    ----------
+    path : file or string
+       Filename or file handle to read.
+       Filenames ending in .gz or .bz2 will be decompressed.
+
+    Returns
+    -------
+    G : NetworkX graph
+
+    Examples
+    --------
+    >>> G = nx.read_leda("file.leda")  # doctest: +SKIP
+
+    References
+    ----------
+    .. [1] http://www.algorithmic-solutions.info/leda_guide/graphs/leda_native_graph_fileformat.html
+    """
+    lines = (line.decode(encoding) for line in path)
+    G = parse_leda(lines)
+    return G
+
+
+@nx._dispatchable(graphs=None, returns_graph=True)
+def parse_leda(lines):
+    """Read graph in LEDA format from string or iterable.
+
+    Parameters
+    ----------
+    lines : string or iterable
+       Data in LEDA format.
+
+    Returns
+    -------
+    G : NetworkX graph
+
+    Examples
+    --------
+    >>> G = nx.parse_leda(string)  # doctest: +SKIP
+
+    References
+    ----------
+    .. [1] http://www.algorithmic-solutions.info/leda_guide/graphs/leda_native_graph_fileformat.html
+    """
+    if isinstance(lines, str):
+        lines = iter(lines.split("\n"))
+    lines = iter(
+        [
+            line.rstrip("\n")
+            for line in lines
+            if not (line.startswith(("#", "\n")) or line == "")
+        ]
+    )
+    for i in range(3):
+        next(lines)
+    # Graph
+    du = int(next(lines))  # -1=directed, -2=undirected
+    if du == -1:
+        G = nx.DiGraph()
+    else:
+        G = nx.Graph()
+
+    # Nodes
+    n = int(next(lines))  # number of nodes
+    node = {}
+    for i in range(1, n + 1):  # LEDA counts from 1 to n
+        symbol = next(lines).rstrip().strip("|{}|  ")
+        if symbol == "":
+            symbol = str(i)  # use int if no label - could be trouble
+        node[i] = symbol
+
+    G.add_nodes_from([s for i, s in node.items()])
+
+    # Edges
+    m = int(next(lines))  # number of edges
+    for i in range(m):
+        try:
+            s, t, reversal, label = next(lines).split()
+        except BaseException as err:
+            raise NetworkXError(f"Too few fields in LEDA.GRAPH edge {i + 1}") from err
+        # BEWARE: no handling of reversal edges
+        G.add_edge(node[int(s)], node[int(t)], label=label[2:-2])
+    return G