Adding a Tree class for constructing trees in Cytoscape

[xhluca]

About

Ok so this one is a more experimental PR, and the last one before 0.1.0 release (which will be a separate PR, but should be quick to review).

I've thought about this for a while and it seems to be pretty useful to have a Tree class that can be easily constructed as a nested object, then rendered into an element. For example,

>>> tree = Tree('a', [
...   Tree('b', [
...     Tree('c')
...   ]),
...   Tree('d')
... ])

running tree.get_elements() would result in:

[{'data': {'id': 'a'}},
 {'data': {'id': 'b'}},
 {'data': {'id': 'c'}},
 {'data': {'id': 'd'}},
 {'data': {'source': 'a', 'target': 'b'}},
 {'data': {'source': 'a', 'target': 'd'}},
 {'data': {'source': 'b', 'target': 'c'}}]

With a tree class, we can use useful methods to manipulate it, such as:

• get_nodes(), get_edges(): When we only want to access one type of elements from the tree
• find_by_id(): Using a tree traversal, retrieve a specific object in a subtree
• create_index(): Create a dictionary to easily retrieve a node in the subtree by its id

As well as more that I didn't think of.

My thought behind creating a prototype Tree class is to have a customized data structure for easily interacting with Cytoscape, which in the long term might be more appropriate than extending a tree library. For example, we can easily assign an ID to a node directly. However, there are excellent Tree libraries out there (treelib @ 357 stars seems pretty solid), writing a wrapper would indeed be possible if everyone thinks it's a good idea. In this case, there's no need to merge this class (will close this PR instead).

Please let me know your thoughts in whether we should create this class or not. Thanks!

Description of changes

• dash_cytoscape.utils.Tree: New Tree object
• demos/usage-dag-edges.py: Example using the tree

Pre-Merge checklist

• The project was correctly built with npm run build:all.
• If there was any conflict, it was solved correctly
• All changes were documented in CHANGELOG.md.
• All tests on CircleCI have passed.
• All Percy visual changes have been approved.
• Two people have 💃'd the pull request. You can be one of these people if you are a Dash Cytoscape core contributor.

Reference Issues

Closes #[issue number]

Other comments

[vivekvs1]

Wow great <3 . Quick question: how does it benefit having a tree structure when defining methods such as get_nodes(), get_edge() etc?
Right now I created callback functions to get node information, get parent node id info etc.

[xhluca]

@vivekvs1 The get_nodes() methods lets you directly get the nodes of the trees in the elements format, so you can perform adhoc manipulation before returning it. In the example above, you would get

[{'data': {'id': 'a'}},
 {'data': {'id': 'b'}},
 {'data': {'id': 'c'}},
 {'data': {'id': 'd'}}]

Which would be useful if you want to temporarily modify the data field (e.g. add a different label depending on the input of the callback), but don't want to affect the Tree structure.

Overall, a Tree class will be useful if you want to represent a graph that is inherently a tree, but don't want to directly manipulate an elements list. Once you built or modified a tree, e.g. inside a callback, you can simply convert it into an elements list and output it.

[vivekvs1]

Oh I see. Very nice! Thanks @xhlulu

[shammamah-zz]

Yay for using things we learn in our CS degrees! 🎉

[xhluca]

Thank you for the helpful review!

[mkcor]

You may want to assert len(children) > 1.
Is add_child a special case of add_children, which would still work when len(children) == 1?

[xhluca]

Yes. Add child is a special case of add_children. Sometimes the programmer might not know in advance how many children the tree might have (when it's decided programmatically). So they might just use add_children() with a list all the time.

[mkcor]

@xhlulu Then I would recommend removing method add_child and keep only method add_children (so there's one way to add children, however many they end up being).

[xhluca]

Thank you @mkcor for you reviews!

[shammamah-zz]

💃