AttributeError: module 'numpy' has no attribute 'int'

[lubilok]

Hi,
I am learning the mdanalysis. I was trying to find out the true interface of the liquid/vapor interface in my system using Pytim modules, but I am getting an error like below

import MDAnalysis as mda
import pytim
from   pytim.datafil import *
u   = mda.Universe("md_0_1.gro")
interface = pytim.ITIM(u)
interface.writepdb('layers.pdb',centered='middle')
upper_layer = interface.layers[0,0]

AttributeError                            Traceback (most recent call last)
/tmp/ipykernel_80284/2357494757.py in <module>
      4 # initialize the interface, this has to be called only once
      5 # before iterating over the trajectory!
----> 6 interface = pytim.ITIM(u)
      7 
      8 # write a pdb with the information on the surface layers

~/anaconda3/lib/python3.9/site-packages/pytim/itim.py in __init__(self, universe, group, alpha, normal, molecular, max_layers, radii_dict, cluster_cut, cluster_threshold_density, extra_cluster_groups, info, centered, warnings, mesh, autoassign, **kargs)
    217                                      cluster_threshold_density, extra_cluster_groups)
    218         sanity.assign_normal(normal)
--> 219         sanity.assign_radii(radii_dict=radii_dict)
    220 
    221         self.grid = None

~/anaconda3/lib/python3.9/site-packages/pytim/sanity_check.py in assign_radii(self, radii_dict)
    146             self.patch_radii_dict()
    147 
--> 148         _missing_attributes(self.interface, self.interface.universe)
    149 
    150         try:

~/anaconda3/lib/python3.9/site-packages/pytim/properties.py in _missing_attributes(interface, universe)
     72     _check_missing_attribute(interface, 'elements', 'Elements', universe.atoms,
     73                              1)
---> 74     _extra_attributes(interface, universe)
     75 
     76 

~/anaconda3/lib/python3.9/site-packages/pytim/properties.py in _extra_attributes(interface, universe)
     81     for key in attr.keys():
     82         if key not in dir(universe.atoms):
---> 83             vals = np.zeros(len(universe.atoms), dtype=np.int) - 1
     84             universe.add_TopologyAttr(attr[key](vals))
     85 

~/anaconda3/lib/python3.9/site-packages/numpy/__init__.py in __getattr__(attr)
    282             return Tester
    283 
--> 284         raise AttributeError("module {!r} has no attribute "
    285                              "{!r}".format(__name__, attr))
    286 

AttributeError: module 'numpy' has no attribute 'int'

Please tell me how I can fix it.
Thank you.

[tylerjereddy]

As far as I can tell this error is coming from a package we don't maintain (PyTim). The solution is likely to use a version of NumPy compatible with that package and/or to ask the maintainer to modernize their code so they don't use deprecated NumPy type aliases.

>>> import numpy as np
>>> arr = np.array([0, 0], dtype=np.int)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/treddy/python_venvs/py_311_scipy_dev/lib/python3.11/site-packages/numpy/__init__.py", line 324, in __getattr__
    raise AttributeError(__former_attrs__[attr])
AttributeError: 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. Did you mean: 'inf'?

[orbeckst]

See Marcello-Sega/pytim#406 — this issue seems to have been fixed recently so I'd just update to a recent version of pytim.