numpy bool call throws exception for identification of hydration sites

[blakemertz]

I went to use the provided python script at the end of the example workflow and it threw an exception. Code:

#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
from gridData import Grid
from waterkit.analysis import HydrationSites
from waterkit.analysis import blur_map

gO = Grid("gist-gO.dx")
esw = Grid('gist-Esw-dens.dx')
eww = Grid('gist-Eww-dens.dx')
tst = Grid('gist-dTStrans-dens.dx')
tso = Grid('gist-dTSorient-dens.dx')
dg = (esw + 2 * eww) - (tst + tso)

# Identification of hydration site positions using gO
hs = HydrationSites(gridsize=0.5, water_radius=1.4, min_water_distance=2.5, min_density=2.0)
hydration_sites = hs.find(gO) # can pass "gist-gO.dx" directly also

# Get Gaussian smoothed energy for hydration sites only
dg_energy = hs.hydration_sites_energy(dg, water_radius=1.4)
hs.export_to_pdb("hydration_sites_dG_smoothed.pdb", hydration_sites, dg_energy)

# ... or get the whole Gaussian smoothed map
map_smooth = blur_map(dg, radius=1.4)
map_smooth.export("gist-dG-dens_smoothed.dx")

Error when trying to run:

python hydration.py 
Traceback (most recent call last):
  File "/media/bak11/modulus/MDH/waterkit/mdh-258-xtal/hydration.py", line 17, in <module>
    hydration_sites = hs.find(gO) # can pass "gist-gO.dx" directly also
                      ^^^^^^^^^^^
  File "/media/bak11/binaries/git/waterkit/waterkit/analysis/hydration_sites.py", line 117, in find
    hydration_sites, self._isocontour, self._cluster_ids = _hydration_sites(xyz, values, self._min_density,
                                                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/media/bak11/binaries/git/waterkit/waterkit/analysis/hydration_sites.py", line 26, in _hydration_sites
    mask = np.ones(tmp_values.shape, dtype=np.bool)
                                           ^^^^^^^
  File "/media/bak11/binaries/miniconda3/envs/waterkit/lib/python3.11/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_'?

I changed np.bool to bool in line 26 of hydration_sites.py and it completed successfully.

[jeeberhardt]

Thanks for your feedback @blakemertz, this is now fixed!