UnboundLocalError: local variable 'chr_results' referenced before assignment

[yuanlizhanshi]

Error on the dev branch (0.3.5) version:

--> 269 adata.varp[key] = sliding_graphical_lasso(
270 adata=adata,
271 window_size=window_size,
272 unit_distance=unit_distance,
273 distance_constraint=distance_constraint,
274 s=s,
275 organism=organism,
276 max_alpha_iteration=max_alpha_iteration,
277 distance_parameter_convergence=distance_parameter_convergence,
278 max_elements=max_elements,
279 n_samples=n_samples,
280 n_samples_maxtry=n_samples_maxtry,
281 seed=seed,
282 njobs=njobs,
283 verbose=verbose
284 )

File ~/miniconda3/envs/omicverse/lib/python3.10/site-packages/circe/circe.py:1036, in sliding_graphical_lasso(adata, window_size, unit_distance, distance_constraint, s, organism, max_alpha_iteration, distance_parameter_convergence, max_elements, n_samples, n_samples_maxtry, init_method, verbose, seed, njobs, threads_per_worker)
1033 except Exception as e:
1034 logger.warning("Exception occurred: %s", e)
-> 1036 full_results = sp.sparse.block_diag(chr_results)
1038 # Display collected log messages at the end of the script
1039 if verbose:

UnboundLocalError: local variable 'chr_results' referenced before assignment

[r-trimbour]

Hi !

I wasn't able to reproduce your issue on the data you send, the code ran through for me. I just updated the verbose in the dev branch to make debugging easier when re-downloading.

It's thus more likely a package compatibility version issue that a data compatibility issue.

1. If you're working with conda, maybe you can try to create a new empty environment and run it there ?
2. Can you try running there: ci.compute_atac_network(atac, verbose=True) if you still have the issue ? It should now displays more details.
3. If you have still the issue then, could send me the package version of your environment to try to reproduce the error ?
   You can have it with pip list and conda list

[r-trimbour]

Hi @yuanlizhanshi,
Could you solve your problem ?
I'll close the issue by the end of the week :)