Commit ⋅ lingpy/lingpy

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src/lingpy/evaluate/acd.py changed.

84.28% 100.00% +0.18%

src/lingpy/thirdparty/cogent/tree.py changed.

100.00% 100.00% ø

src/lingpy/__init__.py changed.

97.93% 100.00% ø

src/lingpy/algorithm/cython/_calign.py changed.

Other files ignored by Codecov

setup.py has changed.

@@ -188,10 +188,10 @@

    def get_scores(one, other):
        scores = []
        multiple_items = []
        for k,v in wordlist.get_etymdict(ref=one).items():
        for k, v in wordlist.get_etymdict(ref=one).items():
            _idxs = [val for val in v if val != 0]
            # now we need to get the position in the index
            poss,idxs = [],[]
            poss, idxs = [], []
            for val in _idxs:
                if len(val) > 1:
                    multiple_items += [len(val)]

@@ -201,7 +201,7 @@

                    idxs += [idx for x in new_pos]
                    poss += new_pos
            if len(idxs) > 1:
                other_idxs = [wordlist[idx,other][pos] for pos,idx in zip(poss,idxs)]
                other_idxs = [wordlist[idx, other][pos] for pos, idx in zip(poss, idxs)]
                for idx in other_idxs:
                    scores += [other_idxs.count(idx) / len(idxs)]
            else: 

@@ -607,10 +607,10 @@

        
        Always tests by identity.
        """
        my_lineage = set([id(node) for node in [self] + self.ancestors()])
        my_lineage = set([str(node) for node in [self] + self.ancestors()])
        curr = other
        while curr is not None:
            if id(curr) in my_lineage:
            if str(curr) in my_lineage:
                return curr
            curr = curr._parent
        return None

@@ -722,10 +722,10 @@

        if self is other:
            return 0
        #otherwise, check the list of ancestors
        my_ancestors = dict.fromkeys(map(id, [self] + self.ancestors()))
        my_ancestors = dict.fromkeys(map(str, [self] + self.ancestors()))
        count = 0
        while other is not None:
            if id(other) in my_ancestors:
            if str(other) in my_ancestors:
                #need to figure out how many steps there were back from self
                curr = self
                while not(curr is None or curr is other):

@@ -1188,7 +1188,7 @@

                    shared_params = [n for (n,v) in self.params.items()
                        if v is not None
                        and child.params.get(n) is not None
                        and n is not "length"]
                        and n != "length"]
                    length = self.Length + child.Length
                    if length:
                        params = dict([(n,

@@ -1238,7 +1238,7 @@

        """"The number of edges beyond 'parent' in the direction of 'self',
        unrooted"""
        neighbours = self._getNeighboursExcept(parent)
        key = (id(parent), id(self))
        key = (str(parent), str(self))
        if key not in cache:
            cache[key] = 1 + sum([child._edgecount(self, cache)
                    for child in neighbours])

@@ -1555,12 +1555,12 @@

        #otherwise, find self's ancestors and find the first ancestor of
        #other that is in the list
        self_anc = self.ancestors()
        self_anc_dict = dict([(id(n),n) for n in self_anc])
        self_anc_dict[id(self)] = self
        self_anc_dict = dict([(str(n),n) for n in self_anc])
        self_anc_dict[str(self)] = self
        
        count = 0
        while other is not None:
            if id(other) in self_anc_dict:
            if str(other) in self_anc_dict:
                #found the first shared ancestor -- need to sum other branch
                curr = self
                while curr is not other:

@@ -2041,7 +2041,7 @@

                NameLoaded = nameLoaded and (name is not None),
                Params = params,
                )
        self._known_edges[id(node)] = node
        self._known_edges[str(node)] = node
        return node



@@ -20,8 +20,8 @@

"""

__author__ = "Johann-Mattis List, and Robert Forkel (with contributions by Simon J. Greenhill, Tiago Tresoldi, Gereon Kaiping, Steven Moran, Taraka Rama, Johannes Dellert, Frank Nagel, and Peter Bouda, and Taraka Rama)"
__date__ = "2021-03-22"
__version__ = "2.6.8.dev0"
__date__ = "2021-06-07"
__version__ = "2.6.8"

# We exempt this module from QA, because it only provides import shortcuts.
# flake8: noqa

@@ -454,14 +454,14 @@


    # modify matrix and traceback
    traceback[0][0] = 1
    for i in range(1,M+1):
    for i in range(1, M+1):
        traceback[0][i] = 2
    for i in range(1,N+1):
    for i in range(1, N+1):
        traceback[i][0] = 3

    # start the loop
    for i in range(1,N+1):
        for j in range(1,M+1):
    for i in range(1, N+1):
        for j in range(1, M+1):

            # calculate costs for gapA
            if j == M:

Files		•	•	Coverage
src/lingpy	14,156	12,400	1,756	87.60%
tests	2,456	2,428	28	98.86%
Project Totals (123 files)	16,612	14,828	1,784	89.26%

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188	188		def get_scores(one, other):
189	189		scores = []
190	190		multiple_items = []
191		-	for k,v in wordlist.get_etymdict(ref=one).items():
	191	+	for k, v in wordlist.get_etymdict(ref=one).items():
192	192		_idxs = [val for val in v if val != 0]
193	193		# now we need to get the position in the index
194		-	poss,idxs = [],[]
	194	+	poss, idxs = [], []
195	195		for val in _idxs:
196	196		if len(val) > 1:
197	197		multiple_items += [len(val)]

607	607
608	608		Always tests by identity.
609	609		"""
610		-	my_lineage = set([id(node) for node in [self] + self.ancestors()])
	610	+	my_lineage = set([str(node) for node in [self] + self.ancestors()])
611	611		curr = other
612	612		while curr is not None:
613		-	if id(curr) in my_lineage:
	613	+	if str(curr) in my_lineage:
614	614		return curr
615	615		curr = curr._parent
616	616		return None

722	722		if self is other:
723	723		return 0
724	724		#otherwise, check the list of ancestors
725		-	my_ancestors = dict.fromkeys(map(id, [self] + self.ancestors()))
	725	+	my_ancestors = dict.fromkeys(map(str, [self] + self.ancestors()))
726	726		count = 0
727	727		while other is not None:
728		-	if id(other) in my_ancestors:
	728	+	if str(other) in my_ancestors:
729	729		#need to figure out how many steps there were back from self
730	730		curr = self
731	731		while not(curr is None or curr is other):

1188	1188		shared_params = [n for (n,v) in self.params.items()
1189	1189		if v is not None
1190	1190		and child.params.get(n) is not None
1191		-	and n is not "length"]
	1191	+	and n != "length"]
1192	1192		length = self.Length + child.Length
1193	1193		if length:
1194	1194		params = dict([(n,

1238	1238		""""The number of edges beyond 'parent' in the direction of 'self',
1239	1239		unrooted"""
1240	1240		neighbours = self._getNeighboursExcept(parent)
1241		-	key = (id(parent), id(self))
	1241	+	key = (str(parent), str(self))
1242	1242		if key not in cache:
1243	1243		cache[key] = 1 + sum([child._edgecount(self, cache)
1244	1244		for child in neighbours])

201	201		idxs += [idx for x in new_pos]
202	202		poss += new_pos
203	203		if len(idxs) > 1:
204		-	other_idxs = [wordlist[idx,other][pos] for pos,idx in zip(poss,idxs)]
	204	+	other_idxs = [wordlist[idx, other][pos] for pos, idx in zip(poss, idxs)]
205	205		for idx in other_idxs:
206	206		scores += [other_idxs.count(idx) / len(idxs)]
207	207		else:

1555	1555		#otherwise, find self's ancestors and find the first ancestor of
1556	1556		#other that is in the list
1557	1557		self_anc = self.ancestors()
1558		-	self_anc_dict = dict([(id(n),n) for n in self_anc])
1559		-	self_anc_dict[id(self)] = self
	1558	+	self_anc_dict = dict([(str(n),n) for n in self_anc])
	1559	+	self_anc_dict[str(self)] = self
1560	1560
1561	1561		count = 0
1562	1562		while other is not None:
1563		-	if id(other) in self_anc_dict:
	1563	+	if str(other) in self_anc_dict:
1564	1564		#found the first shared ancestor -- need to sum other branch
1565	1565		curr = self
1566	1566		while curr is not other:

2041	2041		NameLoaded = nameLoaded and (name is not None),
2042	2042		Params = params,
2043	2043		)
2044		-	self._known_edges[id(node)] = node
	2044	+	self._known_edges[str(node)] = node
2045	2045		return node
2046	2046
2047	2047

20	20		"""
21	21
22	22		__author__ = "Johann-Mattis List, and Robert Forkel (with contributions by Simon J. Greenhill, Tiago Tresoldi, Gereon Kaiping, Steven Moran, Taraka Rama, Johannes Dellert, Frank Nagel, and Peter Bouda, and Taraka Rama)"
23		-	__date__ = "2021-03-22"
24		-	__version__ = "2.6.8.dev0"
	23	+	__date__ = "2021-06-07"
	24	+	__version__ = "2.6.8"
25	25
26	26		# We exempt this module from QA, because it only provides import shortcuts.
27	27		# flake8: noqa

454	454
455	455		# modify matrix and traceback
456	456		traceback[0][0] = 1
457		-	for i in range(1,M+1):
	457	+	for i in range(1, M+1):
458	458		traceback[0][i] = 2
459		-	for i in range(1,N+1):
	459	+	for i in range(1, N+1):
460	460		traceback[i][0] = 3
461	461
462	462		# start the loop
463		-	for i in range(1,N+1):
464		-	for j in range(1,M+1):
	463	+	for i in range(1, N+1):
	464	+	for j in range(1, M+1):
465	465
466	466		# calculate costs for gapA
467	467		if j == M:

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