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Update for newer versions of Python, NumPy #106

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Update for newer versions of Python, NumPy #106

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74efb4a
Remove placeholder pypi package
WardLT Oct 10, 2023
ab008b0
MutableMapping has moved to .abc
WardLT Oct 10, 2023
11fe091
Quick fix: use == not is
WardLT Oct 10, 2023
2226851
Create a non-rectangular numpy array
WardLT Oct 10, 2023
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2 changes: 1 addition & 1 deletion catkit/gen/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
# (see accompanying license files for details).
"""Catalysis Generator."""

from collections import MutableMapping
from collections.abc import MutableMapping
import numpy as np
import ase

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6 changes: 3 additions & 3 deletions catkit/gen/adsorption.py
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Expand Up @@ -57,8 +57,8 @@ def __init__(self, slab, surface_atoms=None, tol=1e-5):

self.coordinates = np.array(self.coordinates)
self.connectivity = np.array(self.connectivity, dtype=int)
self.r1_topology = np.array(self.r1_topology)
self.r2_topology = np.array(self.r2_topology)
self.r1_topology = np.array(self.r1_topology, dtype=object)
self.r2_topology = np.array(self.r2_topology, dtype=object)
self.frac_coords = np.dot(self.coordinates, np.linalg.pinv(slab.cell))
self.slab = slab

Expand Down Expand Up @@ -514,7 +514,7 @@ def add_adsorbate(
raise ValueError('Specify the index of atom to bond.')

elif len(bonds) == 1:
if index is -1:
if index == -1:
slab = []
for i, _ in enumerate(self.get_symmetric_sites()):
slab += [self._single_adsorption(
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1 change: 0 additions & 1 deletion requirements.txt
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Expand Up @@ -3,7 +3,6 @@ numpy>=1.14
networkx>=2.1
spglib>=1.10
scipy>=0.1
sklearn
matplotlib>=2.2
future>=0.16
fireworks>=1.7
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