error passing in Tree object to treesim.birth_death_tree

[August Guang]

I get an Attribute error when I try to pass in a Tree object to treesim.birth_death_tree using almost the exact code as described here in Building a tree in multiple stages under different conditions. Error is below:

>>> tree = treesim.birth_death_tree(birth_rate=0.2,death_rate=0.2,max_time=6,assign_taxa=False,repeat_until_success=True,tree=tree)

Traceback (most recent call last):

  File "<stdin>", line 1, in <module>

  File "/Users/august/anaconda/envs/HIV/lib/python3.4/site-packages/dendropy/model/birthdeath.py", line 237, in birth_death_tree

    extinct_tips.append(nd)

AttributeError: 'set' object has no attribute 'append'

This occurs whether I pass in an empty tree, a tree with assigned taxa, or a tree without assigned taxa. I believe it to be a bug with the birth_death_tree function, as additionally the sample code provided in the 'Building a tree in multiple stages under different conditions' gives the same error.

[August Guang]

Oh, I should add that I am using Dendropy 4.3.0 and Python 3.4.5.

[Jeet Sukumaran]

Hi August,

This is a bug. Thank you for bringing it to our attention. It has been
fixed in the latest development-master tip, 9d2352e .


-- jeet

On 10/23/17 8:09 PM, August Guang wrote:
> Oh, I should add that I am using Dendropy 4.3.0 and Python 3.4.5.
>
> On Monday, October 23, 2017 at 8:07:47 PM UTC-4, August Guang wrote:
>
> I get an Attribute error when I try to pass in a Tree object to
> treesim.birth_death_tree using almost the exact code as described
> here in Building a tree in multiple stages under different
> conditions

> <https://pythonhosted.org/DendroPy/primer/treesims.html#building-a-tree-in-multiple-stages-under-different-conditions>.

> Error is below:
>
> >>> tree = treesim.birth_death_tree(birth_rate=0.2,death_rate=0.2,max_time=6,assign_taxa=False,repeat_until_success=True,tree=tree)
>
> Traceback (most recent call last):
>
> File "<stdin>", line 1, in <module>
>
> File
> "/Users/august/anaconda/envs/HIV/lib/python3.4/site-packages/dendropy/model/birthdeath.py",
> line 237, in birth_death_tree
>
> extinct_tips.append(nd)
>
> AttributeError: 'set' object has no attribute 'append'
>
>
> This occurs whether I pass in an empty tree, a tree with assigned
> taxa, or a tree without assigned taxa. I believe it to be a bug with
> the birth_death_tree function, as additionally the sample code
> provided in the 'Building a tree in multiple stages under different
> conditions' gives the same error.
>

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