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aertslab / pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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[BUG]pyscenic error with numpy has no attribute 'object' #579

Open anyang-kevin opened 3 days ago

anyang-kevin commented 3 days ago

pyscenic grn /public/home/anyang/tool/conda/miniconda3/envs/scanpy/lib/python3.11/site-packages/pyscenic/transform.py:42: FutureWarning: In the futurenp.objectwill be defined as the corresponding NumPy scalar. ("Enrichment", COLUMN_NAME_ANNOTATION): np.object, Traceback (most recent call last): File "/public/home/anyang/tool/conda/miniconda3/envs/scanpy/bin/pyscenic", line 5, in <module> from pyscenic.cli.pyscenic import main File "/public/home/anyang/tool/conda/miniconda3/envs/scanpy/lib/python3.11/site-packages/pyscenic/cli/pyscenic.py", line 26, in <module> from pyscenic.prune import _prepare_client, find_features, prune2df File "/public/home/anyang/tool/conda/miniconda3/envs/scanpy/lib/python3.11/site-packages/pyscenic/prune.py", line 27, in <module> from .transform import ( File "/public/home/anyang/tool/conda/miniconda3/envs/scanpy/lib/python3.11/site-packages/pyscenic/transform.py", line 42, in <module> ("Enrichment", COLUMN_NAME_ANNOTATION): np.object, ^^^^^^^^^ File "/public/home/anyang/tool/conda/miniconda3/envs/scanpy/lib/python3.11/site-packages/numpy/__init__.py", line 305, in __getattr__ raise AttributeError(__former_attrs__[attr]) AttributeError: module 'numpy' has no attribute 'object'. np.objectwas a deprecated alias for the builtinobject. To avoid this error in existing code, useobjectby 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_'? Here is my error when i use pyscenic. My numpy version is 1.24.3. How do I fix it?

anyang-kevin commented 2 days ago

Numpy deleted np.object in 1.20. The only way right now is change the code in pyscenic/transform.py. Change all np.object to object can call out the help page.