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dereneaton / ipyrad

Interactive assembly and analysis of RAD-seq data sets
http://ipyrad.readthedocs.io
GNU General Public License v3.0
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numpy has no attribute 'int' #510

Closed isaacovercast closed 1 year ago

isaacovercast commented 1 year ago

Clean install inside binder with numpy 1.24.3

ipyrad -p params-wat.txt -s 1234567 -c 1

 -------------------------------------------------------------
  ipyrad [v.0.9.90]
  Interactive assembly and analysis of RAD-seq data
 ------------------------------------------------------------- 
  Parallel connection | jupyter-dereneaton-2dipyrad-2dway44tm8: 1 cores

  Step 1: Demultiplexing fastq data to Samples

  Encountered an Error.
  Message: 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
  Parallel connection closed.
isaacovercast commented 1 year ago

I replaced np.int with np.int64 in the few places it occurred and also np.bool with np.bool_ in write_outputs.py

dylanHco commented 1 year ago

Hey @isaacovercast I just got a similar error using ipyrad v. 0.9.90.. any thoughts? Thanks!

-------------------------------------------------------------
  ipyrad [v.0.9.90]
  Interactive assembly and analysis of RAD-seq data
 ------------------------------------------------------------- 
  Parallel connection | i51: 6 cores

  Step 7: Filtering and formatting output files 
  [####################] 100% 0:00:51 | applying filters       
/rhome/dcohen01/bigdata/.conda/ipyrad3/lib/python3.10/site-packages/ipyrad/assemble/write_outputs.py:321: FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar.
  mask = afilts[:, 0:2].sum(axis=1).astype(np.bool)

  Encountered an Error.
  Message: 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
  Parallel connection closed.
isaacovercast commented 1 year ago

Hello, yes this was fixed the other day and has gone out in v0.9.92, which I just pushed to bioconda and the new package should be up within 24 hours. Try to update to 0.9.92 tomorrow and it will work. Thanks for reporting!

dylanHco commented 1 year ago

Thanks @isaacovercast - I tried to conda/mamba install ipyrad the last two days but it keeps pulling v 9.90 and not the updated one - is there a way to conda/mamba install the latest version?

Thanks

dylanHco commented 1 year ago

@isaacovercast update - figured it out - used the git hub pull with the newest version, then just had to conda/mamba install some other things like samtools,bed, bwa, vsearch

isaacovercast commented 1 year ago

Cool, glad you figured it out. Thanks for letting me know. The bioconda process involves a human actually approving a merge and sometimes it can take an indeterminate amount of time. It should be up there in another couple days.