phyloxml support for ete4

[alpae]

Hi,

it seems that with ete4 the support to load phyloxml trees has diminished. nothing mentioned in the docs anymore, but the phyloxml module is still available. However, loading a simple phyloxml tree results in an error:

In [13]: from ete4 import Phyloxml

In [14]: project = Phyloxml()
    ...: project.build_from_file("test.xml")
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[14], line 2
      1 project = Phyloxml()
----> 2 project.build_from_file("test.xml")

File ~/.pyenv/versions/3.12.2/envs/pyham-new/lib/python3.12/site-packages/ete4/phyloxml/__init__.py:22, in Phyloxml.build_from_file(self, fname)
     20     rootTag = 'phyloxml'
     21     rootClass = self.__class__
---> 22 self.build(rootNode)

File ~/.pyenv/versions/3.12.2/envs/pyham-new/lib/python3.12/site-packages/ete4/phyloxml/_phyloxml.py:421, in Phyloxml.build(self, node)
    419 for child in node:
    420     nodeName_ = Tag_pattern_.match(child.tag).groups()[-1]
--> 421     self.buildChildren(child, node, nodeName_)

File ~/.pyenv/versions/3.12.2/envs/pyham-new/lib/python3.12/site-packages/ete4/phyloxml/_phyloxml.py:426, in Phyloxml.buildChildren(self, child_, node, nodeName_, fromsubclass_)
    424 def buildChildren(self, child_, node, nodeName_, fromsubclass_=False):
    425     if nodeName_ == 'phylogeny':
--> 426         obj_ = Phylogeny.factory()
    427         obj_.build(child_)
    428         self.phylogeny.append(obj_)

File ~/.pyenv/versions/3.12.2/envs/pyham-new/lib/python3.12/site-packages/ete4/phyloxml/_phyloxml.py:474, in Phylogeny.factory(*args_, **kwargs_)
    472 def factory(*args_, **kwargs_):
    473     if Phylogeny.subclass:
--> 474         return Phylogeny.subclass(*args_, **kwargs_)
    475     else:
    476         return Phylogeny(*args_, **kwargs_)

File ~/.pyenv/versions/3.12.2/envs/pyham-new/lib/python3.12/site-packages/ete4/phyloxml/_phyloxml_tree.py:75, in PhyloxmlTree.__init__(self, phyloxml_clade, phyloxml_phylogeny, **kargs)
     71     #self.__support = Confidence(valueOf_=1.0, type_="branch_support")
     72     #self.phyloxml_clade.add_confidence(self.__support)
     73 else:
     74     self.phyloxml_clade = phyloxml_clade
---> 75 super(PhyloxmlTree, self).__init__(**kargs)

File ~/.pyenv/versions/3.12.2/envs/pyham-new/lib/python3.12/site-packages/ete4/phylo/phylotree.py:288, in PhyloTree.__init__(self, newick, children, alignment, alg_format, sp_naming_function, parser)
    272 def __init__(self, newick=None, children=None, alignment=None,
    273              alg_format="fasta", sp_naming_function=None,
    274              parser=None):
    275     """
    276     :param newick: If not None, initializes the tree from a newick,
    277         which can be a string or file object containing it.
   (...)    286         identifier.
    287     """
--> 288     super().__init__(data=newick, children=children, parser=parser)
    290     # This will be only executed after reading the whole tree,
    291     # because the argument 'alignment' is not passed to the
    292     # PhyloTree constructor during parsing.
    293     if alignment:

File ~/.pyenv/versions/3.12.2/envs/pyham-new/lib/python3.12/site-packages/ete4/core/tree.pyx:60, in ete4.core.tree.Tree.__init__()

AttributeError: property 'children' of 'PhyloxmlTree' object has no setter

any comments on your plans about phyloxml would be appreciated. thanks

Adrian