def setUp(self):
WithTempDir.setUp(self)
self.matrix = [[0.0, 0.5, 0.67, 0.8, 0.2], [0.5, 0.0, 0.4, 0.7, 0.6],
[0.67, 0.4, 0.0, 0.8, 0.8], [0.8, 0.7, 0.8, 0.0, 0.3],
[0.2, 0.6, 0.8, 0.3, 0.0]]
self.taxa = ['German', 'Swedish', 'Icelandic', 'English', 'Dutch']
def setUp(self):
WithTempDir.setUp(self)
self.hlc = link_clustering.HLC(
{
"a": set(["b", "c"]),
"b": set(["c"]),
"c": set(["a"])
}, set([("a", "b"), ("b", "c"), ("a", "c")]))
def setUp(self):
WithTempDir.setUp(self)
self.lex = LexStat(test_data('KSL.qlc'))
self.part = Partial(test_data('partial_cognates.tsv'),
segments='segments')
self.part.add_entries('pid1', 'partial_cognate_sets', lambda x: x)
self.part.add_entries('pid2', 'partialids2',
lambda x: [int(y) for y in x.split(' ')])
def setUp(self):
WithTempDir.setUp(self)
self.repos = self.tmp_path()
self.languoids = self.tmp_path('languoids')
copytree(Path(__file__).parent.joinpath('data', 'languoids'), self.languoids)
self.tree = self.languoids.joinpath('tree')
self.references = self.tmp_path('references')
copytree(Path(__file__).parent.joinpath('data', 'references'), self.references)
self.tmp_path('build').mkdir()
def setUp(self):
WithTempDir.setUp(self)
self.repos = self.tmp_path()
self.languoids = self.tmp_path('languoids')
copytree(
Path(__file__).parent.joinpath('data', 'languoids'),
self.languoids)
self.tree = self.languoids.joinpath('tree')
self.references = self.tmp_path('references')
copytree(
Path(__file__).parent.joinpath('data', 'references'),
self.references)
self.tmp_path('build').mkdir()
def setUp(self):
WithTempDir.setUp(self)
self.tmp_path('_test').mkdir()
with self.tmp_path('_test', 'converter').open(mode='w',
encoding='utf8') as fp:
fp.write("""\
p : p, ɸ, p͡f
b : b, β, b͡v
f : f
v : v
m : m, ɱ
w : w, ɰ, ʋ, ʍ
8 : θ, θ, Ɵ, ð""")
with self.tmp_path('_test', 'scorer').open(mode='w',
encoding='utf8') as fp:
fp.write(SCORER)
def setUp(self):
WithTempDir.setUp(self)
self.gls = [('Haerbin', 0), ('Beijing', 0), ('Xi’an', 0),
('Lanzhou', 0), ('Kunming', 1), ('Tianjin', 0),
('edge.13', 1), ('edge.11', 0)]
self.scenarios = [['p1', self.gls],
[
'p2',
[('Taiyuan', 0), ('Nanning', 0), ('Wenzhou', 0),
('Lanzhou', 0), ('edge.24', 0), ('Pingyao', 0),
('Jinan', 1), ('edge.6', 0), ('Kunming', 0),
('Zhengzhou', 0), ('Xi’an', 0), ('edge.10', 0),
('edge.14', 0), ('Shexian', 0), ('edge.26', 1),
('Suzhou', 0)]
]]
self.tree = "((((((((Taiyuan,Pingyao,Huhehaote),((((Xi’an,Xining,Zhengzhou),(Lanzhou,Yinchuan,Wulumuqi)),(((Tianjin,Jinan),Qingdao),Beijing,Haerbin)),(((Guiyang,Kunming),Chengdu,Wuhan),(Nanjing,Hefei)))),(Xiangtan,Changsha)),Nanchang),(Shexian,Tunxi)),((Shanghai,Suzhou,Hangzhou),Wenzhou)),(((Xianggang,Guangzhou),Nanning),(Meixian,Taoyuan))),((((Xiamen,Taibei),Shantou,Haikou),Fuzhou),Jian’ou));"
def setUp(self):
WithTempDir.setUp(self)
self.alm = Alignments(test_data('KSL2.qlc'),
loans=False,
_interactive=False)
self.alm.align()
def setUp(self):
WithTempDir.setUp(self)
self.wordlist = Wordlist(test_data('KSL.qlc'))
self.wordlist2 = Wordlist(test_data('KSL4.qlc'))
def setUp(self):
WithTempDir.setUp(self)
self.cfg = os.path.join(self.tmp.as_posix(), '.config')
def setUp(self):
WithTempDir.setUp(self)
self.newick = '(((a,b),(c,d)),e);'
self.tree = Tree(self.newick)
def setUp(self):
WithTempDir.setUp(self)
self.lex = self._make_one(test_data('KSL.qlc'))
self.log = get_log()
self.get_scorer_kw = dict(runs=10, rands=10, limit=100)
def tearDown(self):
# Reset the global _logger to make sure, it's recreated with appropriate config
# when the other tests are run.
log._logger = None
WithTempDir.tearDown(self)
def setUp(self):
WithTempDir.setUp(self)
self.repos = self.tmp_path('repos')
copytree(Path(__file__).parent.joinpath('data'), self.repos)
self.api = Glottolog(self.repos)
def tearDown(self):
sys.stdout, sys.stderr = self._stdout, self._stderr
WithTempDir.tearDown(self)
def setUp(self):
WithTempDir.setUp(self)
self._stdout, sys.stdout = sys.stdout, StringIO()
self._stderr, sys.stderr = sys.stderr, StringIO()
def setUp(self):
WithTempDir.setUp(self)
self.inputfile = os.path.join(
os.path.dirname(lingpy.__file__), 'tests', 'test_data', 'phybo.qlc')
def setUp(self):
WithTempDir.setUp(self)
self._stdout, sys.stdout = sys.stdout, StringIO()
self._stderr, sys.stderr = sys.stderr, StringIO()
def tearDown(self):
sys.stdout, sys.stderr = self._stdout, self._stderr
WithTempDir.tearDown(self)
def setUp(self):
WithTempDir.setUp(self)
self.wordlist = Wordlist(test_data('colexification.tsv'))
self.cols = colx._get_colexifications(self.wordlist)
def setUp(self):
WithTempDir.setUp(self)
self.part = Partial(test_data('partial_cognates.tsv'),
segments='segments')
self.part2 = Partial(test_data('partial_cognates-scored.tsv'),
segments='segments')