Dendropy v4.6.0 causing SEPP to break

[berkelem]

A new version of Dendropy was released a week ago and it is causing the SEPP conda build to break. Could you look into this and either update SEPP to maintain compatibility or update the conda recipe to restrict it to older versions of Dendropy?

[ncolaian]

I think I am having the same problem. I keep getting this error -
ImportError: cannot import name '_convert_node_to_root_polytomy' from 'dendropy.datamodel.treemodel'

[lh3]

CC @mmore500

[mmore500]

Taking a look!

[mmore500]

Opened #126 with a patch for sepp and made note of the fact that this logic is currently only accessible via "private" (i.e., _*) interface in dendropy (jeetsukumaran/DendroPy#169). Will contribute another patch once we create and release a public interface for _convert_node_to_root_polytomy. :)

[nicolo-tellini]

Hello,

I am having the same issue :
ImportError: cannot import name '_convert_node_to_root_polytomy' from 'dendropy.datamodel.treemodel'

any solution for that ?

[mmore500]

Hi @nicolo-tellini

Pinning dendropy==4.5.2 within your runtime environment should fix this issue. You’l need to use your package manager (pip, poetry, conda, etc.) to accomplish this.

[nicolo-tellini]

Hi @mmore500 ,

thank you very much it works nicely

best

nic

[smirarab]

@mmore500 Thanks a ton for your PR and sorry I am so slow these days with these. I hope the merged PR fixes the issue?

[mmore500]

Yes! Thank you @smirarab :)

I don't have a button to close this issue, but if you do it should be able to be closed

[smirarab]

I also decided to make sepp backward compatible with dendropy <4.5.2. Fixed in 4.5.5. b3b3305