module 'networkx' has no attribute 'to_scipy_sparse_matrix'

[Roaringman]

Hello,

Thank you for creating this great tool!

Issue:

When running litstudy.plot_cocitation_network() I get the error - module 'networkx' has no attribute 'to_scipy_sparse_matrix'.

To reproduce:

Edition Windows 10 Enterprise
Version 22H2
Installed on ‎23-‎05-‎2023
OS build 19045.3693
Experience Windows Feature Experience Pack 1000.19053.1000.0

On both:
Microsoft Edge for Business
Learn more about Microsoft Edge for Business
Version 120.0.2210.61 (Official build) (64-bit)

and

Google chrome Version 119.0.6045.160 (Official Build) (64-bit)

Here is the full error message:

Warning: When cdn_resources is 'local' jupyter notebook has issues displaying graphics on chrome/safari. Use cdn_resources='in_line' or cdn_resources='remote' if you have issues viewing graphics in a notebook.

AttributeError Traceback (most recent call last)
Cell In[49], line 1
----> 1 litstudy.plot_cocitation_network(docs, max_edges=500)

File ~\AppData\Local\anaconda3\envs\LitStudy\lib\site-packages\litstudy\network.py:305, in plot_cocitation_network(docs, max_edges, node_size, **kwargs)
301 """Plot a citation network.
302
303 This is a shorthand for plot_network(build_cocitation_network(docs))."""
304 b, p = split_kwargs(**kwargs)
--> 305 return plot_network(
306 build_cocitation_network(docs, max_edges=max_edges, **b),
307 # min_node_size=node_size,
308 # max_node_size=node_size,
309 **p
310 )

File ~\AppData\Local\anaconda3\envs\LitStudy\lib\site-packages\litstudy\network.py:88, in plot_network(g, height, smooth_edges, max_node_size, min_node_size, largest_component, interactive, controls, scale, iterations, gravity)
85 else:
86 sizes = [g for (_, g) in g.degree]
---> 88 layout = calculate_layout(g, gravity=gravity, iterations=iterations)
89 sizes = np.array(sizes, dtype=np.float32)
90 ratio = (max_node_size - min_node_size) / np.amax(sizes)

File ~\AppData\Local\anaconda3\envs\LitStudy\lib\site-packages\litstudy\network.py:22, in calculate_layout(g, iterations, gravity)
14 from fa2 import ForceAtlas2
16 model = ForceAtlas2(
17 verbose=True,
18 scalingRatio=1,
19 gravity=gravity,
20 )
---> 22 matrix = nx.to_scipy_sparse_matrix(g, dtype="f", format="lil", weight="weight")
23 pos = model.forceatlas2(matrix, iterations=iterations)
25 return dict(zip(g.nodes(), pos))

AttributeError: module 'networkx' has no attribute 'to_scipy_sparse_matrix'

[stijnh]

It seems that ForceAtlas is no longer maintained is no compatible with newer versions of networkx.

Relevant issue: bhargavchippada/forceatlas2#41

[stijnh]

And another relevant issue: bhargavchippada/forceatlas2#45