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AttributeError: module 'fa2.fa2util' has no attribute 'Node' for version 1.9.1 #2286

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wubaosheng opened this issue Jun 29, 2022 · 3 comments
Closed
2 of 3 tasks

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@wubaosheng
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wubaosheng commented Jun 29, 2022

  • I have checked that this issue has not already been reported.
  • I have confirmed this bug exists on the latest version of scanpy.
  • (optional) I have confirmed this bug exists on the master branch of scanpy.

AttributeError: module 'fa2.fa2util' has no attribute 'Node' for scanpy version 1.9.1

Note: Please read this guide detailing how to provide the necessary information for us to reproduce your bug.

Minimal code sample (that we can copy&paste without having any data)

adata = sc.datasets.paul15()
sc.pp.recipe_zheng17(adata)
sc.tl.pca(adata, svd_solver='arpack')
sc.pp.neighbors(adata, n_neighbors=4, n_pcs=20)
sc.tl.draw_graph(adata)
Traceback (most recent call last):
  File "C:\Users\wubaosheng\AppData\Local\Programs\Python\Python39\lib\site-packages\IPython\core\interactiveshell.py", line 3398, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-9-e2440b0eca68>", line 1, in <cell line: 1>
    sc.tl.draw_graph(adata)
  File "C:\Users\wubaosheng\AppData\Local\Programs\Python\Python39\lib\site-packages\scanpy\tools\_draw_graph.py", line 159, in draw_graph
    positions = forceatlas2.forceatlas2(
  File "C:\Users\wubaosheng\AppData\Local\Programs\Python\Python39\lib\site-packages\fa2-0.3.5-py3.9-win-amd64.egg\fa2\forceatlas2.py", line 162, in forceatlas2
    nodes, edges = self.init(G, pos)
  File "C:\Users\wubaosheng\AppData\Local\Programs\Python\Python39\lib\site-packages\fa2-0.3.5-py3.9-win-amd64.egg\fa2\forceatlas2.py", line 103, in init
    n = fa2util.Node()
AttributeError: module 'fa2.fa2util' has no attribute 'Node'

Versions

'1.9.1' for scanpy
3.9.7 for python

image

@tangguangjue
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hi,I wonder if this problem has been solved? This error also occurred recently when I used this code

@CZHanoi
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CZHanoi commented Mar 1, 2024

hi,I wonder if this problem has been solved? This error also occurred recently when I used this code, too.

@flying-sheep
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flying-sheep commented Mar 5, 2024

Please go here for help with your problem bhargavchippada/forceatlas2#32

We can‘t help you here, as we aren’t the forceatlas2 developers

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