Comments attribute not documented?

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Yan Wong

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Jan 25, 2019, 5:52:12 AM1/25/19
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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

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Jan 26, 2019, 12:24:11 PM1/26/19
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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

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Jan 27, 2019, 5:31:40 PM1/27/19
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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

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Jan 28, 2019, 2:16:17 PM1/28/19
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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

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Jan 29, 2019, 12:08:58 PM1/29/19
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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



Yan
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