AttributeError: 'PhyloTree' object has no attribute 'add_properties'

[Mark Blaxter]

I have just installed ete4 [I know, very late to the party] using pip and am getting the following error when trying to run a toy ncbi query which I always used to test ete3 install with:

ete4 ncbiquery --tree --search 9606 9598 10090 7707 8782

this yields:

Traceback (most recent call last):

  File "/opt/homebrew/Caskroom/miniforge/base/bin/ete4", line 8, in <module>

    sys.exit(main())

             ^^^^^^

  File "/opt/homebrew/Caskroom/miniforge/base/lib/python3.12/site-packages/ete4/tools/ete.py", line 64, in main

    _main(sys.argv)

  File "/opt/homebrew/Caskroom/miniforge/base/lib/python3.12/site-packages/ete4/tools/ete.py", line 256, in _main

    args.func(args)

  File "/opt/homebrew/Caskroom/miniforge/base/lib/python3.12/site-packages/ete4/tools/ete_ncbiquery.py", line 129, in run

    n.add_properties(taxid=n.name)

    ^^^^^^^^^^^^^^^^

AttributeError: 'PhyloTree' object has no attribute 'add_properties'

The same set of taxa with --info instead of tree returns the expected information.

[Jordi Burguet Castell]

Hi Mark,

Thank you for reporting this. The tools really need a thorough review, they have not been tested like other areas in the transition from ete3 to ete4. But at least the problem you were having seemed easy enough to fix. It should work now if you want to try with the latest revision from the repository (pip install --force-reinstall https://github.com/etetoolkit/ete/archive/ete4.zip).

Cheers,

Jordi

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[Mark Blaxter]

Thanks Jordi; installed and passeed tests just finee; your help much apppreciated, and on christmas eve too. ete continues to be a core toolkit in our work!

> On 23 Dec 2025, at 22:47, Jordi Burguet Castell <jordi.burg...@gmail.com> wrote:
>
> This Message Is From an Untrusted Sender
> You have not previously corresponded with this sender.
> Report Suspicious
> Hi Mark,
>
> Thank you for reporting this. The tools really need a thorough review, they have not been tested like other areas in the transition from ete3 to ete4. But at least the problem you were having seemed easy enough to fix. It should work now if you want to try with the latest revision from the repository (pip install --force-reinstall https://github.com/etetoolkit/ete/archive/ete4.zip [github.com]).

>
> Cheers,
> Jordi
>
> On Tue, Dec 23, 2025 at 8:31 PM Mark Blaxter <mb...@sanger.ac.uk> wrote:
> I have just installed ete4 [I know, very late to the party] using pip and am getting the following error when trying to run a toy ncbi query which I always used to test ete3 install with:
>
> ete4 ncbiquery --tree --search 9606 9598 10090 7707 8782
>
> this yields:
> Traceback (most recent call last):
> File "/opt/homebrew/Caskroom/miniforge/base/bin/ete4", line 8, in <module>
> sys.exit(main())
> ^^^^^^
> File "/opt/homebrew/Caskroom/miniforge/base/lib/python3.12/site-packages/ete4/tools/ete.py", line 64, in main
> _main(sys.argv)
> File "/opt/homebrew/Caskroom/miniforge/base/lib/python3.12/site-packages/ete4/tools/ete.py", line 256, in _main
> args.func(args)
> File "/opt/homebrew/Caskroom/miniforge/base/lib/python3.12/site-packages/ete4/tools/ete_ncbiquery.py", line 129, in run

> n.add_properties(taxid=n.name [n.name])

> ^^^^^^^^^^^^^^^^
> AttributeError: 'PhyloTree' object has no attribute 'add_properties'
> The same set of taxa with --info instead of tree returns the expected information.
>
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