dynamo-release: UnboundLocalError in dyn.ext.ddhodge

Hi, there is a error when I run ddhodge as below:

dyn.ext.ddhodge(adata, basis='pca')
~/.local/lib/python3.8/site-packages/anndata/_core/anndata.py:1095: FutureWarning: The `inplace` parameter in pandas.Categorical.remove_unused_categories is deprecated and will be removed in a future version.
  df_sub[k].cat.remove_unused_categories(inplace=True)
|-----------> not all cells are used, set diag to 1...
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "~/.local/lib/python3.8/site-packages/dynamo/external/hodge.py", line 214, in ddhodge
    k = nbrs_idx.shape[1]
UnboundLocalError: local variable 'nbrs_idx' referenced before assignment

I don’t know how to solve it.

About this issue

Original URL
State: closed
Created 2 years ago
Comments: 16 (8 by maintainers)

Commits related to this issue

fix issue #289 and add docs — committed to dummyindex/dynamo-release by dummyindex 2 years ago
Merge pull request #290 from dummyindex/update-docs Update sphinx docs (readthedocs) and fix issue #289 (graphize_velocity return value type change) — committed to aristoteleo/dynamo-release by Xiaojieqiu 2 years ago
Merge pull request #291 from dummyindex/fix-issue-289 fix query_W matrix construction issue mentioned in #289 — committed to aristoteleo/dynamo-release by Xiaojieqiu 2 years ago

Most upvoted comments

Hi @lh12565 ,

Yes the issue was confirmed. We fixed it and it should work now. Please try
source activate dynamonew
pip uninstall dynamo
pip install git+https://github.com/dummyindex/dynamo-release.git@fix-issue-289
Or you can wait the #291 to be merged soon. Sorry for the glitches and thanks for your report. Please let us know if this fixes the problem.

Thanks! It works! You are the most efficient person I have ever met.

lh12565 on Mar 1, 2022