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lilab-bcb / cirrocumulus

Bring your single-cell data to life
https://cirrocumulus.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
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ImportError: cannot import name 'Index1D' from 'anndata.compat' #208

Closed anishchakka closed 10 months ago

anishchakka commented 10 months ago

Describe the bug Error while deploying cirro to server after updating to v1.1.57

To Reproduce I had previously installed v1.1.54 cirro and updated the version to 1.1.57. This update does not deploy the app on server.

Command I had used to deploy:

cirro serve -b server:8443 &

Expected behavior The same steps worked with v54. It failed with v57.

Screenshots

Below is the error I received.

ImportError: cannot import name 'Index1D' from 'anndata.compat' (/home/svc_bicore/miniconda3/envs/cirro_8443_clone/lib/python3.9/site-packages/anndata/compat/__init__.py)
[2023-12-18 12:52:57 -0800] [9330] [INFO] Worker exiting (pid: 9330)
Traceback (most recent call last):
  File "/home/miniconda3/envs/cirro_8443_clone/bin/cirro", line 8, in <module>
    sys.exit(main())
  File "/home/miniconda3/envs/cirro_8443_clone/lib/python3.9/site-packages/cirrocumulus/__main__.py", line 20, in main
    cmd.main(command_args)
  File "/home/miniconda3/envs/cirro_8443_clone/lib/python3.9/site-packages/cirrocumulus/serve.py", line 146, in main
    subprocess.check_call(run_args)
  File "/home/miniconda3/envs/cirro_8443_clone/lib/python3.9/subprocess.py", line 373, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['gunicorn', '-b', 'server:8443', '-w', '16', '-t', '30', '-n', 'cirrocumulus-webserver', 'cirrocumulus.serve:cached_app()']' returned non-zero exit status 1.
^C

Desktop (please complete the following information):

joshua-gould commented 10 months ago

Please upgrade anndata (pip install --upgrade anndata). Thanks.