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Magdoll / cDNA_Cupcake

Miscellaneous collection of Python and R scripts for processing Iso-Seq data
BSD 3-Clause Clear License
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AttributeError: module 'numpy' has no attribute 'int'. #245

Closed Journeyant closed 6 months ago

Journeyant commented 9 months ago

Hi, Magdoll, After I installed the cDNA_cupcake, I ran the "collapse_isoforms_by_sam.py", but I'm getting the following error:

Traceback (most recent call last): File ".../SQANTI3_v5.2/cDNA_Cupcake/cDNA_Cupcake/cupcake/tofu/./collapse_isoforms_by_sam.py", line 31, in from cupcake.tofu.branch import branch_simple2 File ".../anaconda3/envs/SQANTI3-5.2/lib/python3.10/site-packages/cupcake/tofu/branch/branch_simple2.py", line 6, in import cupcake.tofu.branch.c_branch as c_branch File "cupcake/tofu/branch/c_branch.pyx", line 6, in init cupcake.tofu.branch.c_branch File ".../anaconda3/envs/SQANTI3-5.2/lib/python3.10/site-packages/numpy/init.py", line 324, in getattr raise AttributeError(__former_attrs__[attr]) AttributeError: module 'numpy' has no attribute 'int'. np.int was a deprecated alias for the builtin int. To avoid this error in existing code, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information. 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

What should I do? It would be very helpful if you could help me with this problem. Thank you. @Magdoll Journeyant

tky199996 commented 6 months ago

I encountered the same problem as you，Have you solved this problem?

Magdoll commented 6 months ago

Hi @tky199996 - Cupcake is no longer supported. See my other comments.