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`np.bool` error in gr.head()

Open davidhbrann opened this issue 8 months ago • 0 comments

Right now gr.head() fails due to a reference to np.bool insteal of bool. I'm using numpy version '1.26.4'.

gr = pr.from_dict({'Chromosome': ['chr1', 'chr1'], 'Start': [3, 5], 'End': [9, 7],'Strand': ["+", "-"]})
gr.head()
np.bool` will be defined as the corresponding NumPy scalar.
  subsetter = np.zeros(len(self), dtype=np.bool)
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[52], line 1
----> 1 fragments.head()

File ~/micromamba/envs/scenicplus/lib/python3.11/site-packages/pyranges/pyranges.py:1708, in PyRanges.head(self, n)
   1650 def head(self, n=8):
   1652     """Return the n first rows.
   1653 
   1654     Parameters
   (...)
   1705     For printing, the PyRanges was sorted on Chromosome and Strand.
   1706     """
-> 1708     subsetter = np.zeros(len(self), dtype=np.bool)
   1709     subsetter[:n] = True
   1710     return self[subsetter]

File ~/micromamba/envs/scenicplus/lib/python3.11/site-packages/numpy/__init__.py:324, in __getattr__(attr)
    319     warnings.warn(
    320         f"In the future `np.{attr}` will be defined as the "
    321         "corresponding NumPy scalar.", FutureWarning, stacklevel=2)
    323 if attr in __former_attrs__:
--> 324     raise AttributeError(__former_attrs__[attr])
    326 if attr == 'testing':
    327     import numpy.testing as testing

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

davidhbrann avatar Jun 14 '24 22:06 davidhbrann