Comments attribute not documented?

[Yan Wong]

Hi - I see that I can set 'extract_comment_metadata=True' when reading newick/nexus files (and it is True by default), but I can't see much in the docs (e.g. by searching for the string 'comment' or 'comments') about what it does. Inspection of the tree objects shows that they contain a 'comments'  attribute - I guess this is the "approved" way to access them? Would it be possible to add this as an attribute listed in https://dendropy.org/library/treemodel.html#dendropy.datamodel.treemodel.Tree?

Yan

[Jeet Sukumaran]

The various Tree, Node, Edge, etc. classes already have a ``comment``
attribute, which is a list of comment strings. What would you like to
see added?

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[Yan Wong]

On Saturday, 26 January 2019 17:24:11 UTC, Jeet Sukumaran wrote:

The various Tree, Node, Edge, etc. classes already have a ``comment``
attribute, which is a list of comment strings. What would you like to
see added?

It's just that the "comment" attribute is not actually documented anywhere I can see (although perhaps I've missed it). I would sort-of expect it to be documented, or at least the attribute name mentioned somewhere. I had to list out the attributes of a Tree object to find the precise attribute name. Since it wasn't present in the documentation, I worried that this attribute was an unsupported addition to DendroPy. But as I said, perhaps I just missed the documentation?

Thanks!

Yan

[Jeet Sukumaran]

Ah, I see. I'm not sure, but I don't believe it is formally documented.
Should do so, I guess. In the mean time, you can rest assured that it is
not going anywhere or change in the way it works anytime soon. I.e., it
is "official".

-- jeet

[Yan Wong]

Thanks. That's just what I needed to know. I guess others might find it useful if it were mentioned somewhere in the docs, if only in passing (like the seed_node attribute is mentioned but not, I think, given an explicit place in the documentation). Perhaps within

https://dendropy.org/library/treemodel.html#dendropy.datamodel.treemodel.Tree.strip_comments

or 

https://dendropy.org/primer/working_with_metadata_annotations.html#metadata-annotation-creation

Thanks a lot

Yan