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❯ flake8 Tests/test_Phylo_igraph.py Tests/test_Phylo_igraph.py:34:34: E226 missing whitespace around arithmetic operator Perhaps we should explicitly add E226 to our flake8 ignore? Ruff didn't mind either way.
57 lines
2.0 KiB
Python
57 lines
2.0 KiB
Python
# Copyright (C) 2023 by Fabio Zanini (fabio.zanini@unsw.edu.au)
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# This code is part of the Biopython distribution and governed by its
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# license. Please see the LICENSE file that should have been included
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# as part of this package.
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"""Unit tests for Bio.Phylo functions with external dependencies."""
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import unittest
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from io import StringIO
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# Check for any missing dependencies at the top level so we can skip
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from Bio import MissingExternalDependencyError
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from Bio import Phylo
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try:
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import igraph as ig
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except ImportError:
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raise MissingExternalDependencyError(
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"Install igraph if you wish to use it with Bio.Phylo"
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) from None
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# Example PhyloXML file
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EX_DOLLO = "PhyloXML/o_tol_332_d_dollo.xml"
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EX_APAF = "PhyloXML/apaf.xml"
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class UtilTests(unittest.TestCase):
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"""Tests for various utility functions."""
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def test_to_igraph_simple(self):
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"""Tree to Graph conversion, simple tree."""
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tree = Phylo.read(StringIO("()()"), format="newick")
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for i, elem in enumerate(tree.find_clades()):
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elem.name = f"elem_{i + 1}"
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elem.width = f"width_{i}"
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graph = Phylo.to_igraph(tree, vertex_attributes=["name"])
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self.assertEqual(graph.vs["name"], ["elem_1", "elem_2", "elem_3"])
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self.assertEqual(graph.es["width"], ["width_1", "width_2"])
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def test_to_igraph_exd_ollo(self):
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"""Tree to Graph conversion, if networkx is available."""
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tree = Phylo.read(EX_DOLLO, "phyloxml")
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graph = Phylo.to_igraph(tree)
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self.assertEqual(graph.vcount(), 659)
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self.assertEqual(graph.ecount(), graph.vcount() - 1)
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def test_to_igraph_ex_dollo_with_attributes(self):
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tree = Phylo.read(EX_DOLLO, "phyloxml")
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graph = Phylo.to_igraph(tree, vertex_attributes=["name"])
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self.assertEqual(graph.vcount(), 659)
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self.assertEqual(graph.ecount(), graph.vcount() - 1)
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if __name__ == "__main__":
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runner = unittest.TextTestRunner(verbosity=2)
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unittest.main(testRunner=runner)
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