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.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.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.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.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.alm = Alignments(test_data('KSL2.qlc'), loans=False, _interactive=False)
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')
def setUp(self):
WithTempDir.setUp(self)
self.wordlist = Wordlist(test_data('KSL.qlc'))
def setUp(self):
WithTempDir.setUp(self)
self.cfg = os.path.join(self.tmp, '.config')
def setUp(self):
WithTempDir.setUp(self)
self.wordlist = Wordlist(test_data('KSL.qlc'))
self.wordlist2 = Wordlist(test_data('good_file.tsv'))
def setUp(self):
WithTempDir.setUp(self)
self.inputfile = os.path.join(os.path.dirname(lingpy.__file__),
'tests', 'test_data', 'phybo.qlc')
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.lex = LexStat(test_data('KSL.qlc'))
def setUp(self):
WithTempDir.setUp(self)
self.wordlist = Wordlist(test_data('KSL.qlc'))
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.inputfile = os.path.join(
os.path.dirname(lingpy.__file__), 'tests', 'test_data', 'phybo.qlc')
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 = LexStat(test_data('KSL.qlc'))
self.log = get_log()
self.get_scorer_kw = dict(runs=10, rands=10, limit=100)
def setUp(self):
WithTempDir.setUp(self)
self.alm = Alignments(test_data('KSL2.qlc'),
loans=False,
_interactive=False)
