""" Unit tests for bipartite edgelists. """ import io import pytest import networkx as nx from networkx.algorithms import bipartite from networkx.utils import edges_equal, graphs_equal, nodes_equal class TestEdgelist: @classmethod def setup_class(cls): cls.G = nx.Graph(name="test") e = [("a", "b"), ("b", "c"), ("c", "d"), ("d", "e"), ("e", "f"), ("a", "f")] cls.G.add_edges_from(e) cls.G.add_nodes_from(["a", "c", "e"], bipartite=0) cls.G.add_nodes_from(["b", "d", "f"], bipartite=1) cls.G.add_node("g", bipartite=0) cls.DG = nx.DiGraph(cls.G) cls.MG = nx.MultiGraph() cls.MG.add_edges_from([(1, 2), (1, 2), (1, 2)]) cls.MG.add_node(1, bipartite=0) cls.MG.add_node(2, bipartite=1) def test_read_edgelist_1(self): s = b"""\ # comment line 1 2 # comment line 2 3 """ bytesIO = io.BytesIO(s) G = bipartite.read_edgelist(bytesIO, nodetype=int) assert edges_equal(G.edges(), [(1, 2), (2, 3)]) def test_read_edgelist_3(self): s = b"""\ # comment line 1 2 {'weight':2.0} # comment line 2 3 {'weight':3.0} """ bytesIO = io.BytesIO(s) G = bipartite.read_edgelist(bytesIO, nodetype=int, data=False) assert edges_equal(G.edges(), [(1, 2), (2, 3)]) bytesIO = io.BytesIO(s) G = bipartite.read_edgelist(bytesIO, nodetype=int, data=True) assert edges_equal( G.edges(data=True), [(1, 2, {"weight": 2.0}), (2, 3, {"weight": 3.0})] ) def test_write_edgelist_1(self): fh = io.BytesIO() G = nx.Graph() G.add_edges_from([(1, 2), (2, 3)]) G.add_node(1, bipartite=0) G.add_node(2, bipartite=1) G.add_node(3, bipartite=0) bipartite.write_edgelist(G, fh, data=False) fh.seek(0) assert fh.read() == b"1 2\n3 2\n" def test_write_edgelist_2(self): fh = io.BytesIO() G = nx.Graph() G.add_edges_from([(1, 2), (2, 3)]) G.add_node(1, bipartite=0) G.add_node(2, bipartite=1) G.add_node(3, bipartite=0) bipartite.write_edgelist(G, fh, data=True) fh.seek(0) assert fh.read() == b"1 2 {}\n3 2 {}\n" def test_write_edgelist_3(self): fh = io.BytesIO() G = nx.Graph() G.add_edge(1, 2, weight=2.0) G.add_edge(2, 3, weight=3.0) G.add_node(1, bipartite=0) G.add_node(2, bipartite=1) G.add_node(3, bipartite=0) bipartite.write_edgelist(G, fh, data=True) fh.seek(0) assert fh.read() == b"1 2 {'weight': 2.0}\n3 2 {'weight': 3.0}\n" def test_write_edgelist_4(self): fh = io.BytesIO() G = nx.Graph() G.add_edge(1, 2, weight=2.0) G.add_edge(2, 3, weight=3.0) G.add_node(1, bipartite=0) G.add_node(2, bipartite=1) G.add_node(3, bipartite=0) bipartite.write_edgelist(G, fh, data=[("weight")]) fh.seek(0) assert fh.read() == b"1 2 2.0\n3 2 3.0\n" def test_unicode(self, tmp_path): G = nx.Graph() name1 = chr(2344) + chr(123) + chr(6543) name2 = chr(5543) + chr(1543) + chr(324) G.add_edge(name1, "Radiohead", **{name2: 3}) G.add_node(name1, bipartite=0) G.add_node("Radiohead", bipartite=1) fname = tmp_path / "edgelist.txt" bipartite.write_edgelist(G, fname) H = bipartite.read_edgelist(fname) assert graphs_equal(G, H) def test_latin1_issue(self, tmp_path): G = nx.Graph() name1 = chr(2344) + chr(123) + chr(6543) name2 = chr(5543) + chr(1543) + chr(324) G.add_edge(name1, "Radiohead", **{name2: 3}) G.add_node(name1, bipartite=0) G.add_node("Radiohead", bipartite=1) fname = tmp_path / "edgelist.txt" with pytest.raises(UnicodeEncodeError): bipartite.write_edgelist(G, fname, encoding="latin-1") def test_latin1(self, tmp_path): G = nx.Graph() name1 = "Bj" + chr(246) + "rk" name2 = chr(220) + "ber" G.add_edge(name1, "Radiohead", **{name2: 3}) G.add_node(name1, bipartite=0) G.add_node("Radiohead", bipartite=1) fname = tmp_path / "edgelist.txt" bipartite.write_edgelist(G, fname, encoding="latin-1") H = bipartite.read_edgelist(fname, encoding="latin-1") assert graphs_equal(G, H) def test_edgelist_graph(self, tmp_path): G = self.G fname = tmp_path / "edgelist.txt" bipartite.write_edgelist(G, fname) H = bipartite.read_edgelist(fname) H2 = bipartite.read_edgelist(fname) assert H is not H2 # they should be different graphs G.remove_node("g") # isolated nodes are not written in edgelist assert nodes_equal(list(H), list(G)) assert edges_equal(list(H.edges()), list(G.edges())) def test_edgelist_integers(self, tmp_path): G = nx.convert_node_labels_to_integers(self.G) fname = tmp_path / "edgelist.txt" bipartite.write_edgelist(G, fname) H = bipartite.read_edgelist(fname, nodetype=int) # isolated nodes are not written in edgelist G.remove_nodes_from(list(nx.isolates(G))) assert nodes_equal(list(H), list(G)) assert edges_equal(list(H.edges()), list(G.edges())) def test_edgelist_multigraph(self, tmp_path): G = self.MG fname = tmp_path / "edgelist.txt" bipartite.write_edgelist(G, fname) H = bipartite.read_edgelist(fname, nodetype=int, create_using=nx.MultiGraph()) H2 = bipartite.read_edgelist(fname, nodetype=int, create_using=nx.MultiGraph()) assert H is not H2 # they should be different graphs assert nodes_equal(list(H), list(G)) assert edges_equal(list(H.edges()), list(G.edges())) def test_empty_digraph(self): with pytest.raises(nx.NetworkXNotImplemented): bytesIO = io.BytesIO() bipartite.write_edgelist(nx.DiGraph(), bytesIO) def test_raise_attribute(self): with pytest.raises(AttributeError): G = nx.path_graph(4) bytesIO = io.BytesIO() bipartite.write_edgelist(G, bytesIO) def test_parse_edgelist(self): """Tests for conditions specific to parse_edge_list method""" # ignore strings of length less than 2 lines = ["1 2", "2 3", "3 1", "4", " "] G = bipartite.parse_edgelist(lines, nodetype=int) assert list(G.nodes) == [1, 2, 3] # Exception raised when node is not convertible # to specified data type with pytest.raises(TypeError, match=".*Failed to convert nodes"): lines = ["a b", "b c", "c a"] G = bipartite.parse_edgelist(lines, nodetype=int) # Exception raised when format of data is not # convertible to dictionary object with pytest.raises(TypeError, match=".*Failed to convert edge data"): lines = ["1 2 3", "2 3 4", "3 1 2"] G = bipartite.parse_edgelist(lines, nodetype=int) # Exception raised when edge data and data # keys are not of same length with pytest.raises(IndexError): lines = ["1 2 3 4", "2 3 4"] G = bipartite.parse_edgelist( lines, nodetype=int, data=[("weight", int), ("key", int)] ) # Exception raised when edge data is not # convertible to specified data type with pytest.raises(TypeError, match=".*Failed to convert key data"): lines = ["1 2 3 a", "2 3 4 b"] G = bipartite.parse_edgelist( lines, nodetype=int, data=[("weight", int), ("key", int)] ) def test_bipartite_edgelist_consistent_strip_handling(): """See gh-7462 Input when printed looks like: A B interaction 2 B C interaction 4 C A interaction Note the trailing \\t in the last line, which indicates the existence of an empty data field. """ lines = io.StringIO( "A\tB\tinteraction\t2\nB\tC\tinteraction\t4\nC\tA\tinteraction\t" ) descr = [("type", str), ("weight", str)] # Should not raise G = nx.bipartite.parse_edgelist(lines, delimiter="\t", data=descr) expected = [("A", "B", "2"), ("A", "C", ""), ("B", "C", "4")] assert sorted(G.edges(data="weight")) == expected