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pachterlab / GSP_2019

Code for reproducing results from the paper "RNA velocity and protein acceleration from single-cell multiomics experiments."
BSD 2-Clause "Simplified" License
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AttributeError: module 'louvain' has no attribute 'set_rng_seed' #2

Open 1cm-cyber opened 2 years ago

1cm-cyber commented 2 years ago

Hello， I am trying to analysis the CITE-seq data using protaccel totally following the 'CITE-seq protein acceleration analysis' in the github.

I got the following error when I ran "[cluster_ID, num_clusters] = pa.identify_clusters(vlm,vlm.connectivity,correct_tags=True,tag_correction_list=t_cl,method_name='ModularityVertexPartition')": Traceback (most recent call last): File "", line 1, in File "~/.conda/envs/protaccel/lib/python3.9/site-packages/protaccel/protaccel.py", line 175, in identify_clusters partition_kwargs["seed"] = random_state AttributeError: module 'louvain' has no attribute 'set_rng_seed'

Python 3.9.12

Versions: bezier 2021.2.12，louvain 0.7.1， matplotlib 3.5.1，numpy 1.21.5， pandas 1.4.3， protaccel 0.301，pysam 0.19.1，velocyto 0.17.17

gennadygorin commented 1 year ago

I apologize for the late response, and thank you for bringing this to my attention. For some context, protaccel is not one of the current strategic priorities. At this time, I am working on wrapping up my dissertation. In addition, as outlined in a later article, I see limited long-term prospects for velocity-inspired and more generally graph-based analysis methods in this field.

Nevertheless, I do hope to go back through and fix this issue for the sake of reproducibility in the coming months. This is a tough problem. Louvain needs to be at 0.6.1. For reasons which are obscure to me, pip installing this version or its igraph prerequisites fails at the wheel level. I will need to try other versions, or possibly remove the seeding call altogether. If you succeed in solving this issue, please submit a pull request.