seantcaron
commented
7 months ago I was able to correct this in my environment by just modifying line 44 in jackknife.py to use np.bool_ instead of np.bool. This sed command should do the job:
sed -i -e 's/np.bool/np.bool_/' /usr/local/lib/python3.8/dist-packages/popcorn/jackknife.py
It looks like maybe the change didn't stick for you (see line 5 in the traceback - you still have np.bool and not np.bool_)? Perhaps you accidentally reinstalled the library from Github again over your modified version?
Best,
Sean
Sean Caron (she/they) OS Programmer Lead University of Michigan Center for Statistical Genetics Department of Biostatistics, School of Public Health *e: @. @.> p: 734-474-5962*
On Mon, Apr 22, 2024 at 9:46 AM francontiram @.***> wrote:
Hi @seantcaron https://github.com/seantcaron I am getting a very similar error message - see below. I have tried manually editing jackknife.py in my local environment, line 44 to np.bool_ as you have suggested but still getting the same error message - have you managed to fix this error? It is a while since I have used Python so grateful for any advice!
Performing jackknife estimation of the standard error using 200 blocks of size 17608 . /home/francesinez/.local/lib/python3.10/site-packages/popcorn/jackknife.py:44: FutureWarning: In the future np.bool will be defined as the corresponding NumPy scalar. k = np.ones((x.shape[0]),dtype=np.bool) Traceback (most recent call last): File "/home/francesinez/Popcorn/popcorn/main.py", line 246, in main() File "/home/francesinez/Popcorn/popcorn/main.py", line 218, in main res = fit.fit_pg(data.data,args,M=M) File "/home/francesinez/.local/lib/python3.10/site-packages/popcorn/fit.py", line 241, in init self.jackknife = jackknife.jackknife(close_call,data,res,args) File "/home/francesinez/.local/lib/python3.10/site-packages/popcorn/jackknife.py", line 19, in init self.psuedovalues, self.delete_values = self.jackknife(f,x,r) File "/home/francesinez/.local/lib/python3.10/site-packages/popcorn/jackknife.py", line 44, in jackknife k = np.ones((x.shape[0]),dtype=np.bool) File "/home/francesinez/.local/lib/python3.10/site-packages/numpy/init.py", line 324, in getattr raise AttributeError(former_attrs[attr]) AttributeError: module 'numpy' has no attribute 'bool'. np.bool was a deprecated alias for the builtin bool. To avoid this error in existing code, use bool by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.bool here. 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: 'bool'?
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francontiram
The following error is produced when running popcorn with NumPy >= 1.20.
Performing jackknife estimation of the standard error using 200 blocks of size 17925 . /usr/local/lib/python3.8/dist-packages/popcorn/jackknife.py:44: FutureWarning: In the future
sys.exit(main())
File "/usr/local/lib/python3.8/dist-packages/popcorn/main.py", line 218, in main
res = fit.fit_pg(data.data,args,M=M)
File "/usr/local/lib/python3.8/dist-packages/popcorn/fit.py", line 241, in init
self.jackknife = jackknife.jackknife(close_call,data,res,args)
File "/usr/local/lib/python3.8/dist-packages/popcorn/jackknife.py", line 19, in init
self.psuedovalues, self.delete_values = self.jackknife(f,x,r)
File "/usr/local/lib/python3.8/dist-packages/popcorn/jackknife.py", line 44, in jackknife
k = np.ones((x.shape[0]),dtype=np.bool)
File "/usr/local/lib/python3.8/dist-packages/numpy/init.py", line 305, in getattr
raise AttributeError(__former_attrs_[attr])
AttributeError: module 'numpy' has no attribute 'bool'.
np.boolwill be defined as the corresponding NumPy scalar. k = np.ones((x.shape[0]),dtype=np.bool) Traceback (most recent call last): File "/usr/local/bin/popcorn", line 8, innp.boolwas a deprecated alias for the builtinbool. To avoid this error in existing code, useboolby itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool` here. 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#deprecationsCould you please update line 44 in jackknife.py to replace np.bool with np.bool_ such that this will run properly with newer NumPy without modification?
Thank you!