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jeetsukumaran / DendroPy

A Python library for phylogenetic scripting, simulation, data processing and manipulation.
https://pypi.org/project/DendroPy/.
BSD 3-Clause "New" or "Revised" License
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`shuffle_taxa` raises `DeprecationWarning` #154

Closed mmore500 closed 1 year ago

mmore500 commented 1 year ago

The shuffle_taxa function passes as set as an operand to random.sample. This was deprecated in Python 3.9.

/usr/local/lib/python3.9/dist-packages/dendropy/datamodel/treemodel.py:5459: DeprecationWarning: Sampling from a set deprecated since Python 3.9 and will be removed in a subsequent version.
    new_taxon = rng.sample(node_taxa, 1)[0]

The relevant line is https://github.com/jeetsukumaran/DendroPy/blob/0b0d8df448d32a8d829b91204b817ce6c98fb6ec/src/dendropy/datamodel/treemodel/_tree.py#L3087.