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AttributeError Traceback (most recent call last)
Cell In[83], line 17
13 simulator = PhaseSimulation(
14 adata=adata_vel,
15 )
16 # set the velocity basis to use
---> 17 simulator.set_velocity_field(basis='pca')
18 # set starting locations for phase points
19 # using a categorical variable in `adata.obs`
20 simulator.set_starting_point(
21 method='metadata',
22 groupby='starting_points',
23 group='forward',
24 )
File ~/miniconda3/envs/remote_singlecellseq/lib/python3.9/site-packages/velodyn/velocity_dynsys.py:158, in PhaseSimulation.set_velocity_field(self, groupby, group, basis)
156 bidx = self.adata.obs[groupby] == group
157 else:
--> 158 bidx = np.ones(self.adata.shape[0]).astype(np.bool)
160 # get the relevant cells from the grouping
161 self.vadata = self.adata[bidx, :].copy()
File ~/miniconda3/envs/remote_singlecellseq/lib/python3.9/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
I believe for line 158 of velodyn/velocity_dynsys the np.bool needs to be changed to bool because of Numpy deprecation errors. Thank you!
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