<gh_stars>0
import unittest

from nexusmaker import Record, NexusMaker, NexusMakerAscertained
from nexusmaker import NexusMakerAscertainedWords
from nexusmaker import CognateParser

RECORDS = """
Aiwoo-501	132312	five	vili	1
Aiwoo-501	133751	leg	nyike	86
Aiwoo-501	133752	leg	nuku	86
Aiwoo-501	208804	hand	nyime	1,66
Aiwoo-501	208805	hand	nyimä	1,66
Banoni-4	1075	leg	rapinna		
Banoni-4	250221	five	ghinima	1
Banoni-4	4	hand	numa-	1,64
Dehu-196	129281	five	tripi	1
Dehu-196	196	hand	wanakoim	
Eton-1088	265408	five	e-lim	1
Eton-1088	278627	leg	tua-ŋ	95
Hiw-639	164951	hand	mja-	1,78
Hiw-639	164952	leg	ᶢʟoŋo-	17
Hiw-639	165135	five	təβɔjimə	1
Iaai-471	125656	hand	beñi-	14
Iaai-471	125657	hand	HAND	
Iaai-471	125659	leg	ca	
Iaai-471	125853	five	baa|xaca	
Iaai-471	125865	five	thabyŋ	
Lamogai-67	83796	five	elmé	1
Lamogai-67	83881	hand	mulǵu	45
Lamogai-67	83882	hand	melsé	45
Lamogai-67	83883	hand	milpí	45
Lamogai-67	83884	hand	melép	45
Lamogai-67	83885	hand	milpú	45
Lamogai-67	83886	hand	meylá	45
Lamogai-67	83887	hand	melsék	45
Lamogai-67	83942	leg	kaip	1
Lamogai-67	83943	leg	kaŋgú	1
"""

RECORDS = [r.split("\t") for r in RECORDS.split("\n") if len(r)]
COMPLEX_TESTDATA = [
    Record(Language=r[0], Word=r[2], Item=r[3], Cognacy=r[4])
    for r in RECORDS
]

EXPECTED_COGNATES = {
    ('five', '1'): {
        'Aiwoo-501', 'Banoni-4', 'Dehu-196', 'Eton-1088', 'Hiw-639',
        'Lamogai-67'
    },
    ('leg', '86'): {'Aiwoo-501'},
    ('hand', '1'): {'Aiwoo-501', 'Banoni-4', 'Hiw-639'},
    ('hand', '64'): {'Banoni-4'},
    ('hand', '66'): {'Aiwoo-501'},
    ('leg', '95'): {'Eton-1088'},
    ('hand', '78'): {'Hiw-639'},
    ('leg', '17'): {'Hiw-639'},
    ('hand', '14'): {'Iaai-471'},
    ('hand', '45'): {'Lamogai-67'},
    ('leg', '1'): {'Lamogai-67'},
}

EXPECTED_UNIQUES = [
    ('leg', 'Banoni-4'),
    ('hand', 'Dehu-196'),
    ('leg', 'Iaai-471'),
    ('five', 'Iaai-471'),
]




class TestNexusMaker(unittest.TestCase):
    model = NexusMaker
    # number of cognate sets expected
    expected_ncog = len(EXPECTED_COGNATES) + len(EXPECTED_UNIQUES)
    # number of characters expected in the nexus file
    expected_nchar = len(EXPECTED_COGNATES) + len(EXPECTED_UNIQUES)
    
    def setUp(self):
        self.maker = self.model(data=COMPLEX_TESTDATA)
        self.nex = self.maker.make()

    def test_languages(self):
        self.assertEqual(self.maker.languages, {
            'Aiwoo-501', 'Banoni-4', 'Dehu-196', 'Eton-1088', 'Hiw-639',
            'Iaai-471', 'Lamogai-67'
        })

    def test_words(self):
        self.assertEqual(self.maker.words, {'hand', 'leg', 'five'})
    
    def test_ncognates(self):
        self.assertEqual(len(self.maker.cognates), self.expected_ncog)
    
    def test_cognate_sets(self):  # pragma: no cover
        errors = []
        for ecog in EXPECTED_COGNATES:
            if ecog not in self.maker.cognates:
                errors.append("Missing %s" % (ecog, ))
            elif self.maker.cognates.get(ecog, set()) != EXPECTED_COGNATES[ecog]:
                errors.append("Cognate set %s incorrect %r != %r" % (
                    ecog,
                    EXPECTED_COGNATES[ecog],
                    self.maker.cognates.get(ecog, set())
                ))

        if errors:
            raise AssertionError("Errors: %s" % "\n".join(errors))

    def test_uniques(self):  # pragma: no cover
        errors = []
        obtained = [c for c in self.maker.cognates if 'u' in c[1]]
        expected = {e: 0 for e in EXPECTED_UNIQUES}
        # check what has been identified as unique
        for cog in obtained:
            if len(self.maker.cognates[cog]) != 1:
                errors.append("Unique cognate %s should only have one member" % (cog, ))
            # make key to look up EXPECTED_UNIQUES as (word, language)
            key = (cog[0], list(self.maker.cognates[cog])[0])
            # error on anything that is not expected
            if key not in expected:
                errors.append("%s unexpectedly seen as unique" % (key, ))
            else:
                expected[key] += 1

        # the counts for each expected cognate should be max 1.
        for e in expected:
            if expected[e] != 1:
                errors.append("Expected 1 cognate for %s, but got %d" % (e, expected[e]))

        if errors:
            raise AssertionError("Errors: %s" % "\n".join(errors))

    def test_dehu_is_all_missing_for_leg(self):
        for cog in [cog for cog in self.nex.data if cog.startswith('leg_')]:
            assert self.nex.data[cog]['Dehu-196'] == '?'

    def test_eton_is_all_missing_for_hand(self):
        for cog in [cog for cog in self.nex.data if cog.startswith('hand_')]:
            assert self.nex.data[cog]['Eton-1088'] == '?'

    def test_only_one_unique_for_Iaai471(self):
        iaai = 0
        for cog in [cog for cog in self.nex.data if cog.startswith('five_u_')]:
            present = [t for t in self.nex.data[cog] if self.nex.data[cog][t] == '1']
            if present == ['Iaai-471']:
                iaai += 1

        if iaai != 1:  # pragma: no cover
            raise AssertionError("Should only have one unique site for Iaai-471-five")

    def test_nexus_symbols(self):
        assert sorted(self.nex.symbols) == sorted(['0', '1'])

    def test_nexus_taxa(self):
        self.assertEqual(self.maker.languages, self.nex.taxa)

    def test_nexus_characters_expected_cognates(self):
        for e in EXPECTED_COGNATES:
            assert "_".join(e) in self.nex.characters

    def test_nexus_characters_expected_uniques(self):
        uniques = [
            c for c in self.nex.characters if
            CognateParser().is_unique_cognateset(c, labelled=True)
        ]
        assert len(uniques) == len(EXPECTED_UNIQUES)

    def test_nexus_nchar(self):
        assert len(self.nex.characters) == self.expected_nchar
    
    def test_entries_with_a_cognate_word_arenot_added_as_unique(self):
        hand = [c for c in self.nex.characters if c.startswith('hand_')]
        hand = [c for c in hand if CognateParser().is_unique_cognateset(c, labelled=True)]
        assert len(hand) == 1, 'Only expecting one unique character for hand'
        assert self.nex.data['hand_u_2']['Iaai-471'] in ('0', '?'), \
            'Iaai-471 should not be unique for `hand`'
    

class TestNexusMakerAscertained(TestNexusMaker):
    model = NexusMakerAscertained
    expected_nchar = len(EXPECTED_COGNATES) + len(EXPECTED_UNIQUES) + 1


class TestNexusMakerAscertainedWords(TestNexusMaker):
    model = NexusMakerAscertainedWords
    expected_nchar = len(EXPECTED_COGNATES) + len(EXPECTED_UNIQUES) + 3



import unittest

from nexusmaker import Record, NexusMaker, NexusMakerAscertained
from nexusmaker import NexusMakerAscertainedWords
from nexusmaker import CognateParser

RECORDS = """
Aiwoo-501	132312	five	vili	1
Aiwoo-501	133751	leg	nyike	86
Aiwoo-501	133752	leg	nuku	86
Aiwoo-501	208804	hand	nyime	1,66
Aiwoo-501	208805	hand	nyimä	1,66
Banoni-4	1075	leg	rapinna		
Banoni-4	250221	five	ghinima	1
Banoni-4	4	hand	numa-	1,64
Dehu-196	129281	five	tripi	1
Dehu-196	196	hand	wanakoim	
Eton-1088	265408	five	e-lim	1
Eton-1088	278627	leg	tua-ŋ	95
Hiw-639	164951	hand	mja-	1,78
Hiw-639	164952	leg	ᶢʟoŋo-	17
Hiw-639	165135	five	təβɔjimə	1
Iaai-471	125656	hand	beñi-	14
Iaai-471	125657	hand	HAND	
Iaai-471	125659	leg	ca	
Iaai-471	125853	five	baa|xaca	
Iaai-471	125865	five	thabyŋ	
Lamogai-67	83796	five	elmé	1
Lamogai-67	83881	hand	mulǵu	45
Lamogai-67	83882	hand	melsé	45
Lamogai-67	83883	hand	milpí	45
Lamogai-67	83884	hand	melép	45
Lamogai-67	83885	hand	milpú	45
Lamogai-67	83886	hand	meylá	45
Lamogai-67	83887	hand	melsék	45
Lamogai-67	83942	leg	kaip	1
Lamogai-67	83943	leg	kaŋgú	1
"""

RECORDS = [r.split("\t") for r in RECORDS.split("\n") if len(r)]
COMPLEX_TESTDATA = [
    Record(Language=r[0], Word=r[2], Item=r[3], Cognacy=r[4])
    for r in RECORDS
]

EXPECTED_COGNATES = {
    ('five', '1'): {
        'Aiwoo-501', 'Banoni-4', 'Dehu-196', 'Eton-1088', 'Hiw-639',
        'Lamogai-67'
    },
    ('leg', '86'): {'Aiwoo-501'},
    ('hand', '1'): {'Aiwoo-501', 'Banoni-4', 'Hiw-639'},
    ('hand', '64'): {'Banoni-4'},
    ('hand', '66'): {'Aiwoo-501'},
    ('leg', '95'): {'Eton-1088'},
    ('hand', '78'): {'Hiw-639'},
    ('leg', '17'): {'Hiw-639'},
    ('hand', '14'): {'Iaai-471'},
    ('hand', '45'): {'Lamogai-67'},
    ('leg', '1'): {'Lamogai-67'},
}

EXPECTED_UNIQUES = [
    ('leg', 'Banoni-4'),
    ('hand', 'Dehu-196'),
    ('leg', 'Iaai-471'),
    ('five', 'Iaai-471'),
]




class TestNexusMaker(unittest.TestCase):
    model = NexusMaker
    # number of cognate sets expected
    expected_ncog = len(EXPECTED_COGNATES) + len(EXPECTED_UNIQUES)
    # number of characters expected in the nexus file
    expected_nchar = len(EXPECTED_COGNATES) + len(EXPECTED_UNIQUES)
    
    def setUp(self):
        self.maker = self.model(data=COMPLEX_TESTDATA)
        self.nex = self.maker.make()

    def test_languages(self):
        self.assertEqual(self.maker.languages, {
            'Aiwoo-501', 'Banoni-4', 'Dehu-196', 'Eton-1088', 'Hiw-639',
            'Iaai-471', 'Lamogai-67'
        })

    def test_words(self):
        self.assertEqual(self.maker.words, {'hand', 'leg', 'five'})
    
    def test_ncognates(self):
        self.assertEqual(len(self.maker.cognates), self.expected_ncog)
    
    def test_cognate_sets(self):  # pragma: no cover
        errors = []
        for ecog in EXPECTED_COGNATES:
            if ecog not in self.maker.cognates:
                errors.append("Missing %s" % (ecog, ))
            elif self.maker.cognates.get(ecog, set()) != EXPECTED_COGNATES[ecog]:
                errors.append("Cognate set %s incorrect %r != %r" % (
                    ecog,
                    EXPECTED_COGNATES[ecog],
                    self.maker.cognates.get(ecog, set())
                ))

        if errors:
            raise AssertionError("Errors: %s" % "\n".join(errors))

    def test_uniques(self):  # pragma: no cover
        errors = []
        obtained = [c for c in self.maker.cognates if 'u' in c[1]]
        expected = {e: 0 for e in EXPECTED_UNIQUES}
        # check what has been identified as unique
        for cog in obtained:
            if len(self.maker.cognates[cog]) != 1:
                errors.append("Unique cognate %s should only have one member" % (cog, ))
            # make key to look up EXPECTED_UNIQUES as (word, language)
            key = (cog[0], list(self.maker.cognates[cog])[0])
            # error on anything that is not expected
            if key not in expected:
                errors.append("%s unexpectedly seen as unique" % (key, ))
            else:
                expected[key] += 1

        # the counts for each expected cognate should be max 1.
        for e in expected:
            if expected[e] != 1:
                errors.append("Expected 1 cognate for %s, but got %d" % (e, expected[e]))

        if errors:
            raise AssertionError("Errors: %s" % "\n".join(errors))

    def test_dehu_is_all_missing_for_leg(self):
        for cog in [cog for cog in self.nex.data if cog.startswith('leg_')]:
            assert self.nex.data[cog]['Dehu-196'] == '?'

    def test_eton_is_all_missing_for_hand(self):
        for cog in [cog for cog in self.nex.data if cog.startswith('hand_')]:
            assert self.nex.data[cog]['Eton-1088'] == '?'

    def test_only_one_unique_for_Iaai471(self):
        iaai = 0
        for cog in [cog for cog in self.nex.data if cog.startswith('five_u_')]:
            present = [t for t in self.nex.data[cog] if self.nex.data[cog][t] == '1']
            if present == ['Iaai-471']:
                iaai += 1

        if iaai != 1:  # pragma: no cover
            raise AssertionError("Should only have one unique site for Iaai-471-five")

    def test_nexus_symbols(self):
        assert sorted(self.nex.symbols) == sorted(['0', '1'])

    def test_nexus_taxa(self):
        self.assertEqual(self.maker.languages, self.nex.taxa)

    def test_nexus_characters_expected_cognates(self):
        for e in EXPECTED_COGNATES:
            assert "_".join(e) in self.nex.characters

    def test_nexus_characters_expected_uniques(self):
        uniques = [
            c for c in self.nex.characters if
            CognateParser().is_unique_cognateset(c, labelled=True)
        ]
        assert len(uniques) == len(EXPECTED_UNIQUES)

    def test_nexus_nchar(self):
        assert len(self.nex.characters) == self.expected_nchar
    
    def test_entries_with_a_cognate_word_arenot_added_as_unique(self):
        hand = [c for c in self.nex.characters if c.startswith('hand_')]
        hand = [c for c in hand if CognateParser().is_unique_cognateset(c, labelled=True)]
        assert len(hand) == 1, 'Only expecting one unique character for hand'
        assert self.nex.data['hand_u_2']['Iaai-471'] in ('0', '?'), \
            'Iaai-471 should not be unique for `hand`'
    

class TestNexusMakerAscertained(TestNexusMaker):
    model = NexusMakerAscertained
    expected_nchar = len(EXPECTED_COGNATES) + len(EXPECTED_UNIQUES) + 1


class TestNexusMakerAscertainedWords(TestNexusMaker):
    model = NexusMakerAscertainedWords
    expected_nchar = len(EXPECTED_COGNATES) + len(EXPECTED_UNIQUES) + 3
Aiwoo-501	132312	five	vili	1 Aiwoo-501	133751	leg	nyike	86 Aiwoo-501	133752	leg	nuku	86 Aiwoo-501	208804	hand	nyime	1,66 Aiwoo-501	208805	hand	nyimä	1,66 Banoni-4	1075	leg	rapinna		 Banoni-4	250221	five	ghinima	1 Banoni-4	4	hand	numa-	1,64 Dehu-196	129281	five	tripi	1 Dehu-196	196	hand	wanakoim	 Eton-1088	265408	five	e-lim	1 Eton-1088	278627	leg	tua-ŋ	95 Hiw-639	164951	hand	mja-	1,78 Hiw-639	164952	leg	ᶢʟoŋo-	17 Hiw-639	165135	five	təβɔjimə	1 Iaai-471	125656	hand	beñi-	14 Iaai-471	125657	hand	HAND	 Iaai-471	125659	leg	ca	 Iaai-471	125853	five	baa|xaca	 Iaai-471	125865	five	thabyŋ	 Lamogai-67	83796	five	elmé	1 Lamogai-67	83881	hand	mulǵu	45 Lamogai-67	83882	hand	melsé	45 Lamogai-67	83883	hand	milpí	45 Lamogai-67	83884	hand	melép	45 Lamogai-67	83885	hand	milpú	45 Lamogai-67	83886	hand	meylá	45 Lamogai-67	83887	hand	melsék	45 Lamogai-67	83942	leg	kaip	1 Lamogai-67	83943	leg	kaŋgú	1 # number of cognate sets expected # number of characters expected in the nexus file # pragma: no cover # pragma: no cover # check what has been identified as unique # make key to look up EXPECTED_UNIQUES as (word, language) # error on anything that is not expected # the counts for each expected cognate should be max 1. # pragma: no cover