pySCENIC
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[BUG] Installation error
Describe the bug
pyscenic -h errors out after fresh installation via conda.
Seems numpy new version does not include np.object. Only object is there:
Following steps of installation on anaconda3 (2022.10):
(pyscenic) [root@gn-0012 site-packages]$ pyscenic -h
/gpfs/share/apps/anaconda3/gpu/2022.10/envs/pyscenic/lib/python3.10/site-packages/pyscenic/transform.py:42: FutureWarning: In the future np.object
will be defined as the corresponding NumPy scalar.
("Enrichment", COLUMN_NAME_ANNOTATION): np.object,
Traceback (most recent call last):
File "/gpfs/share/apps/anaconda3/gpu/2022.10/envs/pyscenic/bin/pyscenic", line 5, in np.object
was a deprecated alias for the builtin object
. To avoid this error in existing code, use object
by itself. Doing this will not modify any behavior and is safe.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations. Did you mean: 'object
Steps to reproduce the behavior
- Command run when the error occurred:
...
- Error encountered:
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Expected behavior A clear and concise description of what you expected to happen.
Please complete the following information:
- pySCENIC version: [e.g. 0.10.0, use
pyscenic -h
at the command line] - Installation method: [e.g. Conda, Pip, Docker, Singularity]
- Run environment: [e.g. Jupyter notebook, CLI, Nextflow, HPC script]
- OS: [e.g. Ubuntu]
- Package versions: [obtain using
pip freeze
,conda list
, or skip this if using Docker/Singularity]:
...