Switch from ete3 to ete4

[dengzq1234]

PR Checklist

• [X] Referenced issue is linked
• [X] If you've fixed a bug or added code that should be tested, add tests!
• [ ] Documentation in docs is updated

Description of changes

This PR is the response to the issue https://github.com/etetoolkit/ete/issues/739, which aim to upgrade the usage of etetoolkit in pertpy from ete3 to ete4.

perpty implement ete for the following tasks: a) browsing trees, such as getting leaves, descendants, ancestors, etc. b) annotation of trees, such as adding information to nodes. c) drawing tree, including drawing tree with layouts of nodes' information.

This repo upgrade the syntax in regards to the first two tasks. The third task which include the drawing part will mostly maintain the usage of ete3 version expect for calling the module in new places

Technical details This PR mostly just correct the syntax of calling the methods or features from ete3 to ete4, straight forward and trivial. detailed differences can be found from

• migration noteos: https://github.com/etetoolkit/ete/wiki/3to4
• ete4 official tutorial https://etetoolkit.github.io/ete/tutorial/tutorial_trees.html#browsing-trees-traversing

I used two ways to conduct the test

1. Passed the unitest this folder /home/deng/Projects/metatree_drawer/test_pertpy/pertpy/tests/tools/_coda

2. Be able to recreate tree images from the step-by-step tutorial of tasccoda tree-aggregated analysis from https://pertpy.readthedocs.io/en/latest/tutorials/notebooks/tasccoda.html

Additional context ete4 installation, ete4 currently is released on githup repo as beta version therefore not yet available in pip nor conda. Users can install ete4 via githup pip install https://github.com/etetoolkit/ete/archive/ete4.zip

In regards to c) drawing tree, ete4 still contains the treeview inherited from ete3 which relies on novel PyQt6 module to render tree image. Users can install the depencies by pip install PyQt6 or install ete4 via pip install -e .[treeview] for a local editable installation.

Important information: In ete4 we will stop maintaining nor making new updates in the old treeview module which is used in pertpy, at this moment it is still functional.

Instead ete4 embrace the new smartview module which has abilities to visualize large tree dataset up to thousands of tips interactively and introduce with novel layouts. The new drawing engine has been implemented in some tools such as PhyloCloud https://phylocloud.cgmlab.org/ (https://doi.org/10.1093/nar/gkac324) TreeProfiler https://doi.org/10.1101/2023.09.21.558621

If pertpy has the demands to visualize trees with ete4 smartview, I'm more than welcome to provide a novel PR in regards to this feature.