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bacpop / PopPUNK

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
https://www.bacpop.org/poppunk
Apache License 2.0
91 stars 18 forks source link

issue with recent joblib update #238

Closed jts1044 closed 1 year ago

jts1044 commented 1 year ago

Hi, I just installed the new version of poppunk (2.5.0) and got this error when using --create-db: 

Traceback (most recent call last):
  File "/home/joshua.smith4/software/miniconda3/envs/poppunk/bin/poppunk", line 11, in <module>
    sys.exit(main())
  File "/home/joshua.smith4/software/miniconda3/envs/poppunk/lib/python3.9/site-packages/PopPUNK/__main__.py", line 213, in main
    from .models import loadClusterFit, BGMMFit, DBSCANFit, RefineFit, LineageFit
  File "/home/joshua.smith4/software/miniconda3/envs/poppunk/lib/python3.9/site-packages/PopPUNK/models.py", line 19, in <module>
    import hdbscan
  File "/home/joshua.smith4/software/miniconda3/envs/poppunk/lib/python3.9/site-packages/hdbscan/__init__.py", line 1, in <module>
    from .hdbscan_ import HDBSCAN, hdbscan
  File "/home/joshua.smith4/software/miniconda3/envs/poppunk/lib/python3.9/site-packages/hdbscan/hdbscan_.py", line 509, in <module>
    memory=Memory(cachedir=None, verbose=0),
TypeError: __init__() got an unexpected keyword argument 'cachedir'

Upon checking the hdbscan github issues page, it appears that a recent joblib update from 1.1.0 to 1.2.0 causes this error. https://github.com/scikit-learn-contrib/hdbscan/issues/565

Downgrading this package to 1.1.0 seems to have fixed the problem. Just thought it would be worth giving a heads up in case others are running into this issue.

jts1044 commented 1 year ago

Sorry, I missed the previous issue that already mentions this.