'ToyTree' object has no attribute 'get_node_descendant_idxs'

[lucia-ramirez]

Hello, I'm trying to run the tutorial and I'm getting the following error. I think toytree might have changed its attributes as now I'm getting an error.

tree_mod= ana.CompositionalAnalysisTree(
...             data_LP_hn.copy(),
...             reference_cell_type="automatic",
...             formula="Health",
...             reg="scaled_3",
...             pen_args={"phi": 0}
...         )
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/software/hgi/envs/conda/team152/lr23/single_cell/lib/python3.12/site-packages/tasccoda/tree_ana.py", line 85, in __new__
    phy_tree = util.collapse_singularities(data.uns["phylo_tree"])
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/software/hgi/envs/conda/team152/lr23/single_cell/lib/python3.12/site-packages/tasccoda/tree_utils.py", line 78, in collapse_singularities
    A, _ = get_A(tree)
           ^^^^^^^^^^^
  File "/software/hgi/envs/conda/team152/lr23/single_cell/lib/python3.12/site-packages/tasccoda/tree_utils.py", line 41, in get_A
    leaves_i = list(set(tree.get_node_descendant_idxs(i)) & set(np.arange(n_tips)))
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'ToyTree' object has no attribute 'get_node_descendant_idxs'

I'm using tasccoda 0.1.3, toytree 3.0.5 and python 3.12.2

Thanks

[johannesostner]

Hi @lucia-ramirez !
can you try to uninstall toytree and ete3 and install an older version with pip install toytree<3.0?
We don't actively maintain this repository anymore, but there is an active implementation in the pertpy package: https://github.com/scverse/pertpy