def test_renumber(self):
from lingpy.basic.ops import renumber
tmp = Wordlist(test_data('good_file.tsv'))
tmp.renumber('cogid', 'newcogid')
assert 'newcogid' in tmp.header
tmp.renumber('mock')
assert 'mockid' in tmp.header
def test_renumber(self):
from lingpy.basic.ops import renumber
tmp = Wordlist(test_data('good_file.tsv'))
tmp.renumber('cogid', 'newcogid')
assert 'newcogid' in tmp.header
tmp.renumber('mock')
assert 'mockid' in tmp.header
class TestWordlist(WithTempDir):
def setUp(self):
WithTempDir.setUp(self)
self.wordlist = Wordlist(test_data('KSL.qlc'))
self.wordlist2 = Wordlist(test_data('good_file.tsv'))
def test___len__(self):
assert len(self.wordlist) == 1400
def test_calculate(self):
self.wordlist.calculate('dst')
assert hasattr(self.wordlist, 'distances')
assert sum([
self.wordlist.distances[x][x] for x in range(self.wordlist.width)
]) == 0
self.wordlist.calculate('tree')
assert str(self.wordlist.tree).endswith(';')
assert sorted(self.wordlist.tree.taxa) == sorted(self.wordlist.cols)
self.wordlist.calculate('groups')
assert hasattr(self.wordlist, 'groups')
assert type(self.wordlist.groups) == dict
def test_coverage(self):
self.wordlist.coverage()
self.wordlist.coverage(stats='ratio')
self.wordlist.coverage(stats='mean')
def test_get_list(self):
ger_l = self.wordlist.get_list(doculect='German',
entry='ipa',
flat=True)
ger_d = self.wordlist.get_dict(col='German', entry='ipa')
ger_t = self.wordlist.get_list(doculect='German', entry="ipa")
assert sorted(ger_l) == sorted([v[0] for v in ger_d.values()])
assert sorted(ger_t) == sorted(ger_l)
hand1 = self.wordlist.get_list(concept="hand", entry="ipa", flat=True)
hand2 = self.wordlist.get_dict(row="hand", entry="ipa")
assert sorted(hand1) == sorted([v[0] for v in hand2.values()])
# test for synonym lines, which are flattened
assert self.wordlist2.get_list(concept='hand',
entry="language",
flat=True).count('l6') == 2
nonflat = self.wordlist2.get_list(concept="hand", entry="language")
assert nonflat[0][-1] == nonflat[1][-1]
assert len(self.wordlist2.get_list(col="l1", entry="concept")) == 3
assert len(
self.wordlist2.get_list(col="l1", flat=True, entry="concept")) == 2
assert_raises(ValueError,
self.wordlist2.get_list,
col="l1",
row="hand")
assert_raises(ValueError, self.wordlist2.get_list)
assert_raises(ValueError, self.wordlist.get_list, **{"row": "Hand"})
def test_get_dict(self):
ger_d = self.wordlist.get_dict(col='German')
assert sorted(ger_d.keys()) == sorted(self.wordlist.rows)
assert_raises(ValueError, self.wordlist.get_dict, **{"row": "Hand"})
def test_renumber(self):
self.wordlist.renumber('cogid', 'dummy')
ger1 = self.wordlist.get_list(col='German', entry='cogid', flat=True)
ger2 = self.wordlist.get_list(col='German', entry='dummy', flat=True)
assert len(set(ger1)) == len(set(ger2))
assert sum([1 for x in ger2 if type(x) == int]) == len(ger2)
def test_get_entries(self):
ger = self.wordlist.get_entries('cogid')
assert len(ger) == self.wordlist.height
assert len(ger[0]) == self.wordlist.width
def test_get_etymdict(self):
etd1 = self.wordlist.get_etymdict(ref='cogid',
entry='ipa',
modify_ref=False)
etd2 = self.wordlist.get_etymdict(ref='cogid',
entry='ipa',
modify_ref=abs)
assert (len(etd1) > len(etd2)
and len(set([abs(x) for x in etd1])) == len(etd2))
assert len([x for x in etd2 if x < 0]) == 0
# make "fuzzy" cognate sets
self.wordlist.add_entries('fuzzyid', 'cogid', lambda x: [x])
etd3 = self.wordlist.get_etymdict(ref='fuzzyid',
entry='ipa',
modify_ref=False)
etd4 = self.wordlist.get_etymdict(ref='fuzzyid',
entry='ipa',
modify_ref=abs)
for key in etd1:
assert etd1[key] == etd3[key]
for key in etd2:
self.assertEqual(etd2[key], etd4[key])
def test_get_paps(self):
paps = self.wordlist.get_paps(ref="cogid", modify_ref=abs)
cogs = self.wordlist.get_etymdict(ref="cogid", modify_ref=abs)
for key in cogs:
if abs(key) in paps:
assert True
else:
print(key)
assert False
def test_output(self):
fn = text_type(self.tmp_path('test'))
for fmt in 'tsv taxa tre dst starling paps.nex paps.csv' \
'separated multistate.nex groups'.split():
kw = {'ref': 'word'} if fmt == 'starling' else {}
self.wordlist.output(fmt, filename=fn, **kw)
if fmt == 'starling':
self.wordlist.output(fmt, filename=fn, cognates='cogid', **kw)
if fmt == 'tsv':
kw['subset'] = True
self.wordlist.output(fmt, filename=fn, cols=[], rows={}, **kw)
self.wordlist.output(fmt,
filename=fn,
cols=sorted(self.wordlist.header)[:2],
rows=dict(ID=" > 10"),
**kw)
def test_export(self):
fn = text_type(self.tmp_path('test'))
for fmt in 'txt tex html'.split():
self.wordlist.export(fmt, filename=fn)
def test_get_wordlist(self):
from lingpy.basic.wordlist import get_wordlist
wl1 = get_wordlist(test_data('mycsvwordlist.csv'))
wl2 = get_wordlist(test_data('mycsvwordlistwithoutids.csv'))
assert wl1.height == wl2.height
for k in wl1:
assert wl1[k, 'concept'] == wl2[k, 'concept']
def test_renumber(self):
tmp = Wordlist(test_data('good_file.tsv'))
tmp.renumber('cogid', 'newcogid')
assert 'newcogid' in tmp.header
tmp.renumber('mock')
assert 'mockid' in tmp.header
def test_renumber(self):
tmp = Wordlist(test_data('good_file.tsv'))
tmp.renumber('cogid', 'newcogid')
assert 'newcogid' in tmp.header
tmp.renumber('mock')
assert 'mockid' in tmp.header
class TestWordlist(WithTempDir):
def setUp(self):
WithTempDir.setUp(self)
self.wordlist = Wordlist(test_data('KSL.qlc'))
def test___len__(self):
assert len(self.wordlist) == 1400
def test_calculate(self):
self.wordlist.calculate('dst')
assert hasattr(self.wordlist,'distances')
assert sum([self.wordlist.distances[x][x] for x in
range(self.wordlist.width)]) == 0
self.wordlist.calculate('tree')
assert sorted(self.wordlist.tree.taxa) == sorted(self.wordlist.cols)
self.wordlist.calculate('groups')
assert hasattr(self.wordlist,'groups')
assert type(self.wordlist.groups) == dict
def test_get_list(self):
gerL = self.wordlist.get_list(col='German', entry='ipa', flat=True)
gerD = self.wordlist.get_dict(col='German',entry='ipa')
assert sorted(gerL) == sorted([v[0] for v in gerD.values()])
def test_get_dict(self):
gerD = self.wordlist.get_dict(col='German')
assert sorted(gerD.keys()) == sorted(self.wordlist.rows)
def test_renumber(self):
self.wordlist.renumber('cogid','dummy')
ger1 = self.wordlist.get_list(col='German', entry='cogid', flat=True)
ger2 = self.wordlist.get_list(col='German', entry='dummy', flat=True)
assert len(set(ger1)) == len(set(ger2))
assert sum([1 for x in ger2 if type(x) == int]) == len(ger2)
def test_get_entries(self):
ger = self.wordlist.get_entries('cogid')
assert len(ger) == self.wordlist.height
assert len(ger[0]) == self.wordlist.width
def get_etymdict(self):
etd1 = self.wordlist.get_etymdict(ref='cogid', entry='ipa',
loans=False)
etd2 = self.wordlist.get_etymdict(ref='cogid', entry='ipa',
loans=True)
assert len(etd1) > len(etd2) and len(set([abs(x) for x in etd1])) == \
len(etd2)
assert len([x for x in etd2 if x < 0]) == 0
# make "fuzzy" cognate sets
self.wordlist.add_entries(
'fuzzyid',
'cogid',
lambda x: [x]
)
etd3 = self.wordlist.get_etymdict(ref='fuzzyid', entry='ipa',
loans=False, fuzzy=True)
etd4 = self.wordlist.get_etymdict(ref='fuzzyid', entry='ipa',
loans=True, fuzzy=True)
for key in etd1:
assert etd1[key] == etd3[key]
for key in etd2:
assert etd2[key] == etd4[key]
def test_get_paps(self):
paps = self.wordlist.get_paps(ref="cogid", loans=True)
cogs = self.wordlist.get_etymdict(ref="cogid", loans=True)
for key in cogs:
if abs(key) in paps:
assert True
else:
print(key)
assert False
def test_output(self):
fn = text_type(self.tmp_path('test'))
for fmt in 'taxa tre dst starling paps.nex paps.csv'.split():
kw = {'ref': 'word'} if fmt == 'starling' else {}
self.wordlist.output(fmt, filename=fn, **kw)
class TestWordlist(WithTempDir):
def setUp(self):
WithTempDir.setUp(self)
self.wordlist = Wordlist(test_data('KSL.qlc'))
self.wordlist2 = Wordlist(test_data('good_file.tsv'))
def test___len__(self):
assert len(self.wordlist) == 1400
def test_calculate(self):
self.wordlist.calculate('dst')
assert hasattr(self.wordlist, 'distances')
assert sum([self.wordlist.distances[x][x] for x in
range(self.wordlist.width)]) == 0
self.wordlist.calculate('tree')
assert str(self.wordlist.tree).endswith(';')
assert sorted(self.wordlist.tree.taxa) == sorted(self.wordlist.cols)
self.wordlist.calculate('groups')
assert hasattr(self.wordlist, 'groups')
assert type(self.wordlist.groups) == dict
def test_coverage(self):
self.wordlist.coverage()
self.wordlist.coverage(stats='ratio')
self.wordlist.coverage(stats='mean')
def test_get_list(self):
gerL = self.wordlist.get_list(doculect='German', entry='ipa', flat=True)
gerD = self.wordlist.get_dict(col='German', entry='ipa')
gerT = self.wordlist.get_list(doculect='German', entry="ipa")
assert sorted(gerL) == sorted([v[0] for v in gerD.values()])
assert sorted(gerT) == sorted(gerL)
hand1 = self.wordlist.get_list(concept="hand", entry="ipa", flat=True)
hand2 = self.wordlist.get_dict(row="hand", entry="ipa")
hand3 = self.wordlist.get_list(concept="hand", flat=True)
assert sorted(hand1) == sorted([v[0] for v in hand2.values()])
# test for synonym lines, which are flattened
assert self.wordlist2.get_list(concept='hand', entry="language",
flat=True).count('l6') == 2
nonflat = self.wordlist2.get_list(concept="hand", entry="language")
assert nonflat[0][-1] == nonflat[1][-1]
assert len(self.wordlist2.get_list(col="l1", entry="concept")) == 3
assert len(self.wordlist2.get_list(col="l1", flat=True, entry="concept")) == 2
assert_raises(ValueError, self.wordlist2.get_list, col="l1",
row="hand")
assert_raises(ValueError, self.wordlist2.get_list)
assert_raises(ValueError, self.wordlist.get_list, **{"row" : "Hand"})
def test_get_dict(self):
gerD = self.wordlist.get_dict(col='German')
assert sorted(gerD.keys()) == sorted(self.wordlist.rows)
assert_raises(ValueError, self.wordlist.get_dict, **{"row" : "Hand"})
def test_renumber(self):
self.wordlist.renumber('cogid', 'dummy')
ger1 = self.wordlist.get_list(col='German', entry='cogid', flat=True)
ger2 = self.wordlist.get_list(col='German', entry='dummy', flat=True)
assert len(set(ger1)) == len(set(ger2))
assert sum([1 for x in ger2 if type(x) == int]) == len(ger2)
def test_get_entries(self):
ger = self.wordlist.get_entries('cogid')
assert len(ger) == self.wordlist.height
assert len(ger[0]) == self.wordlist.width
def test_get_etymdict(self):
etd1 = self.wordlist.get_etymdict(ref='cogid', entry='ipa', modify_ref=False)
etd2 = self.wordlist.get_etymdict(ref='cogid', entry='ipa',
modify_ref=abs)
assert len(etd1) > len(etd2) and len(set([abs(x) for x in etd1])) == \
len(etd2)
assert len([x for x in etd2 if x < 0]) == 0
# make "fuzzy" cognate sets
self.wordlist.add_entries('fuzzyid', 'cogid', lambda x: [x])
etd3 = self.wordlist.get_etymdict(
ref='fuzzyid', entry='ipa', modify_ref=False)
etd4 = self.wordlist.get_etymdict(
ref='fuzzyid', entry='ipa', modify_ref=abs)
for key in etd1:
assert etd1[key] == etd3[key]
for key in etd2:
self.assertEquals(etd2[key], etd4[key])
def test_get_paps(self):
paps = self.wordlist.get_paps(ref="cogid", modify_ref=abs)
cogs = self.wordlist.get_etymdict(ref="cogid", modify_ref=abs)
for key in cogs:
if abs(key) in paps:
assert True
else:
print(key)
assert False
def test_output(self):
fn = text_type(self.tmp_path('test'))
for fmt in 'tsv taxa tre dst starling paps.nex paps.csv separated multistate.nex groups'.split():
kw = {'ref': 'word'} if fmt == 'starling' else {}
self.wordlist.output(fmt, filename=fn, **kw)
if fmt == 'starling':
self.wordlist.output(fmt, filename=fn, cognates='cogid', **kw)
if fmt == 'tsv':
kw['subset'] = True
self.wordlist.output(fmt, filename=fn, cols=[], rows={}, **kw)
self.wordlist.output(fmt, filename=fn,
cols=sorted(self.wordlist.header)[:2], rows=dict(ID=" > 10"),
**kw)
def test_export(self):
fn = text_type(self.tmp_path('test'))
for fmt in 'txt tex html'.split():
self.wordlist.export(fmt, filename=fn)
def test_get_wordlist(self):
from lingpy.basic.wordlist import get_wordlist
wl1 = get_wordlist(test_data('mycsvwordlist.csv'))
wl2 = get_wordlist(test_data('mycsvwordlistwithoutids.csv'))
assert wl1.height == wl2.height
for k in wl1:
assert wl1[k, 'concept'] == wl2[k, 'concept']
class TestWordlist(WithTempDir):
def setUp(self):
WithTempDir.setUp(self)
self.wordlist = Wordlist(test_data('KSL.qlc'))
def test___len__(self):
assert len(self.wordlist) == 1400
def test_calculate(self):
self.wordlist.calculate('dst')
assert hasattr(self.wordlist, 'distances')
assert sum([
self.wordlist.distances[x][x] for x in range(self.wordlist.width)
]) == 0
self.wordlist.calculate('tree')
assert sorted(self.wordlist.tree.taxa) == sorted(self.wordlist.cols)
self.wordlist.calculate('groups')
assert hasattr(self.wordlist, 'groups')
assert type(self.wordlist.groups) == dict
def test_get_list(self):
gerL = self.wordlist.get_list(col='German', entry='ipa', flat=True)
gerD = self.wordlist.get_dict(col='German', entry='ipa')
assert sorted(gerL) == sorted([v[0] for v in gerD.values()])
def test_get_dict(self):
gerD = self.wordlist.get_dict(col='German')
assert sorted(gerD.keys()) == sorted(self.wordlist.rows)
def test_renumber(self):
self.wordlist.renumber('cogid', 'dummy')
ger1 = self.wordlist.get_list(col='German', entry='cogid', flat=True)
ger2 = self.wordlist.get_list(col='German', entry='dummy', flat=True)
assert len(set(ger1)) == len(set(ger2))
assert sum([1 for x in ger2 if type(x) == int]) == len(ger2)
def test_get_entries(self):
ger = self.wordlist.get_entries('cogid')
assert len(ger) == self.wordlist.height
assert len(ger[0]) == self.wordlist.width
def get_etymdict(self):
etd1 = self.wordlist.get_etymdict(ref='cogid',
entry='ipa',
loans=False)
etd2 = self.wordlist.get_etymdict(ref='cogid', entry='ipa', loans=True)
assert len(etd1) > len(etd2) and len(set([abs(x) for x in etd1])) == \
len(etd2)
assert len([x for x in etd2 if x < 0]) == 0
# make "fuzzy" cognate sets
self.wordlist.add_entries('fuzzyid', 'cogid', lambda x: [x])
etd3 = self.wordlist.get_etymdict(ref='fuzzyid',
entry='ipa',
loans=False,
fuzzy=True)
etd4 = self.wordlist.get_etymdict(ref='fuzzyid',
entry='ipa',
loans=True,
fuzzy=True)
for key in etd1:
assert etd1[key] == etd3[key]
for key in etd2:
assert etd2[key] == etd4[key]
def test_get_paps(self):
paps = self.wordlist.get_paps(ref="cogid", loans=True)
cogs = self.wordlist.get_etymdict(ref="cogid", loans=True)
for key in cogs:
if abs(key) in paps:
assert True
else:
print(key)
assert False
def test_output(self):
fn = text_type(self.tmp_path('test'))
for fmt in 'taxa tre dst starling paps.nex paps.csv'.split():
kw = {'ref': 'word'} if fmt == 'starling' else {}
self.wordlist.output(fmt, filename=fn, **kw)