remove annoying node dots on branches

[arlin]

Trees are once again appearing with dots or squares for internal nodes with 1 child. Users do not expect this and do not know what it means. Therefore, it is confusing. Please remove it.

[bomeara]

Generally, having an option to return a tree without singleton nodes would be great -- it would fix the problem here, as well as for some of @jwiggi18's current work intended for displaying trees on EOL

[abusalehmdtayeen]

I have added the singleton node removal feature by default as @bomeara suggested. I think it is fixed now. @arlin can you please test your example again?

[arlin]

Thanks!

[arlin]

I'm seeing this problem again. I think that the problem was never fixed. I don't see a problem with the original tree, only with the scaled trees.

To reproduce the bug, here is what to do. Begin with this list

• Equus caballus
• Cervus canadensis
• Sus scrofa
• Balaenoptera acutorostrata
• Balaena mysticetus
• Orcinus orca
• Platanista gangetica
• Hippopotamus amphibius
• Mirounga leonina
• Hydrurga leptonyx
• Phoca vitulina
• Otaria byronia
• Elephas maximus
• Dugong dugon
• Trichechus manatus
• Ursus maritimus
• Procyon lotor

Get the tree. Get the OT scaled tree. Add the 3 yellow boxes.

Now do the same thing, but use the Median scaled tree. the images below show both of them.

[abusalehmdtayeen]

@ducvan0212, I think the problem is happening because ete preserves the node actions between different calls. Since the tree is changed after scaling, sometimes the boxes remain in their old places. Can you please change the treeid every time scaling method is called. That would reset the actions and probably solve the problem.

[ducvan0212]

@abusalehmdtayeen can you check if the issue still exists?

[abusalehmdtayeen]

I think the problem is fixed now. We clear the node actions when any scaling method is applied. So the user needs to reapply his actions for the new version of the tree.

[abusalehmdtayeen]

@arlin , if you are referring to the little misplaced dots, then we can't fix it. It is an internal issue of ETE.

[arlin]

is the fix on production yet? I tried it tonight and I still see the problem.

[abusalehmdtayeen]

@arlin , I think I have finally fixed the problem. Can you please check? I want to close this issue as soon as possible.