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Track internal dendropy reorganization #126

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merged 2 commits into from
Feb 12, 2024
Merged

Track internal dendropy reorganization #126

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3e8e9ff
Track internal dendropy reorganization
mmore500 May 19, 2023
72a8b30
Bump dendropy version pin
mmore500 May 19, 2023
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4 changes: 1 addition & 3 deletions sepp/tree.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,8 +22,6 @@

from dendropy import Tree, Taxon, treecalc
from dendropy import DataSet as Dataset
from dendropy.datamodel.treemodel import _convert_node_to_root_polytomy as \
convert_node_to_root_polytomy
from sepp import get_logger, sort_by_value
from sepp.alignment import get_pdistance
from sepp.decompose_tree import decompose_by_diameter
Expand Down Expand Up @@ -258,7 +256,7 @@ def bipartition_by_edge(self, e):

nr.edge.length = None
nr.parent_node = None
convert_node_to_root_polytomy(nr)
nr._convert_node_to_root_polytomy()
t1 = PhylogeneticTree(Tree(seed_node=nr))
# temp we could speed this up,
# by telling the Phylogenetic tree how many leaves it has
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2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -162,7 +162,7 @@ def run(self):
author_email="[email protected], [email protected]",

license="General Public License (GPL)",
install_requires=["dendropy >= 4.0.0"],
install_requires=["dendropy >= 4.6.0"],
provides=["sepp"],
scripts=["run_sepp.py", 'run_upp.py', "split_sequences.py"],
cmdclass={"config": ConfigSepp, "upp": ConfigUPP},
Expand Down