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$ ruff check --fix --select=I \ --config=lint.isort.force-single-line=true \ --config=lint.isort.order-by-type=false \ BioSQL/ Bio/ Tests/ Scripts/ Doc/ setup.py Using ruff version 0.4.10
39 lines
1.1 KiB
Python
39 lines
1.1 KiB
Python
# Copyright (C) 2009 by Eric Talevich (eric.talevich@gmail.com)
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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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# 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 networkx
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except ImportError:
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raise MissingExternalDependencyError(
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"Install networkx 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_networkx(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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G = Phylo.to_networkx(tree)
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self.assertEqual(len(G.nodes()), 659)
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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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