From 3e8e9ffd4b4db2ca559649dc9b4456b8d80f7aff Mon Sep 17 00:00:00 2001 From: Matthew Andres Moreno Date: Fri, 19 May 2023 07:57:00 -0700 Subject: [PATCH 1/2] Track internal dendropy reorganization --- sepp/tree.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/sepp/tree.py b/sepp/tree.py index 71123283..134aaf65 100644 --- a/sepp/tree.py +++ b/sepp/tree.py @@ -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 @@ -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 From 72a8b300983d7c6fba95b81be657cdea46e74c94 Mon Sep 17 00:00:00 2001 From: Matthew Andres Moreno Date: Fri, 19 May 2023 08:01:38 -0700 Subject: [PATCH 2/2] Bump dendropy version pin --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 11d9e5e7..3be73002 100755 --- a/setup.py +++ b/setup.py @@ -162,7 +162,7 @@ def run(self): author_email="smirarab@gmail.com, namphuon@cs.utah.edu", 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},