Skip to content

Warn for support values as node attributes when rerooting #219

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
mmore500 wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Warn for support values as node attributes when rerooting #219

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
14 changes: 14 additions & 0 deletions src/dendropy/datamodel/treemodel/_tree.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
# -*- coding: utf-8 -*-

import copy
import functools
import warnings
from io import StringIO
from dendropy.utility import terminal
Expand Down Expand Up @@ -2493,6 +2494,19 @@ def reseed_at(
edges_to_invert = []
current_node = new_seed_node
while current_node:

@functools.lru_cache()
def warn_node_support_values_once():
warnings.warn("""Support value detected as a node attribute, which can cause unexpected results when rerooting.

See <https://doi.org/10.1093/molbev/msx055> for details on this issue. Consider
using the `is_assign_internal_labels_to_edges` kwarg when loading data to assign support values to edges instead of nodes.

See <https://docs.python.org/3/library/warnings.html#warning-filter> for information on how to suppress this warning with a using a filter.""")

if any("support" in attr for attr in current_node.__dict__):
warn_node_support_values_once()

if current_node._parent_node is not None:
edges_to_invert.append(current_node.edge)
current_node = current_node._parent_node
Expand Down