Replace which imports from monty to shutil

pymatgen/analysis/graphs.py

@@ -14,12 +14,12 @@
 from collections import defaultdict, namedtuple
 from itertools import combinations
 from operator import itemgetter
+from shutil import which
 
 import networkx as nx
 import networkx.algorithms.isomorphism as iso
 import numpy as np
 from monty.json import MSONable
-from monty.os.path import which
 from networkx.drawing.nx_agraph import write_dot
 from networkx.readwrite import json_graph
 from scipy.spatial import KDTree

pymatgen/analysis/magnetism/tests/test_analyzer.py

@@ -5,7 +5,7 @@
 import os
 import unittest
 
-from monty.os.path import which
+from shutil import which
 
 from pymatgen.analysis.magnetism import *
 from pymatgen.core import Element, Lattice, Species, Structure

pymatgen/analysis/tests/test_local_env.py

@@ -5,10 +5,10 @@
 import unittest
 import warnings
 from math import pi
+from shutil import which
 
 import numpy as np
 import pytest
-from monty.os.path import which
 
 from pymatgen.core.periodic_table import Element
 from pymatgen.core.lattice import Lattice

pymatgen/command_line/bader_caller.py

@@ -22,10 +22,11 @@
 import subprocess
 import warnings
 
+from shutil import which
+
 import numpy as np
 from monty.dev import requires
 from monty.io import zopen
-from monty.os.path import which
 from monty.tempfile import ScratchDir
 
 from pymatgen.io.cube import Cube

pymatgen/command_line/critic2_caller.py

@@ -42,11 +42,11 @@
 import subprocess
 import warnings
 from enum import Enum
+from shutil import which
 
 import numpy as np
 from monty.dev import requires
 from monty.json import MSONable
-from monty.os.path import which
 from monty.serialization import loadfn
 from monty.tempfile import ScratchDir
 from scipy.spatial import KDTree

pymatgen/command_line/enumlib_caller.py

@@ -36,11 +36,11 @@
 import re
 import subprocess
 from threading import Timer
+from shutil import which
 
 import numpy as np
 from monty.dev import requires
 from monty.fractions import lcm
-from monty.os.path import which
 from monty.tempfile import ScratchDir
 
 from pymatgen.core.periodic_table import DummySpecies

pymatgen/command_line/mcsqs_caller.py

@@ -6,13 +6,13 @@
 import os
 import tempfile
 import warnings
+from shutil import which
 from pathlib import Path
 from subprocess import Popen, TimeoutExpired
 from collections import namedtuple
 from typing import Dict, List, Optional, Union
 
 from monty.dev import requires
-from monty.os.path import which
 
 from pymatgen.core.structure import Structure
 

pymatgen/command_line/tests/test_critic2_caller.py

@@ -4,7 +4,7 @@
 
 import unittest
 
-from monty.os.path import which
+from shutil import which
 
 from pymatgen.command_line.critic2_caller import *
 from pymatgen.core.structure import Structure

pymatgen/command_line/tests/test_enumlib_caller.py

@@ -6,7 +6,7 @@
 import unittest
 import warnings
 
-from monty.os.path import which
+from shutil import which
 
 from pymatgen.core.periodic_table import Element
 from pymatgen.core.structure import Structure

pymatgen/command_line/tests/test_gulp_caller.py

@@ -12,7 +12,7 @@
 import sys
 import unittest
 
-from monty.os.path import which
+from shutil import which
 
 from pymatgen.analysis.bond_valence import BVAnalyzer
 from pymatgen.command_line.gulp_caller import (

pymatgen/command_line/tests/test_mcsqs_caller.py

@@ -1,7 +1,8 @@
 import os
 import unittest
 
-from monty.os.path import which
+from shutil import which
+
 from monty.serialization import loadfn
 
 from pymatgen.core.structure import Structure

pymatgen/command_line/tests/test_vampire_caller.py

@@ -6,8 +6,9 @@
 import unittest
 import warnings
 
+from shutil import which
+
 import pandas as pd
-from monty.os.path import which
 
 import pymatgen.command_line.vampire_caller as vampirecaller
 from pymatgen.core.structure import Structure

pymatgen/command_line/vampire_caller.py

@@ -20,10 +20,11 @@
 import logging
 import subprocess
 
+from shutil import which
+
 import pandas as pd
 from monty.dev import requires
 from monty.json import MSONable
-from monty.os.path import which
 
 from pymatgen.analysis.magnetism.heisenberg import HeisenbergMapper
 

pymatgen/core/tests/test_structure.py

@@ -7,10 +7,10 @@
 import unittest
 import warnings
 from pathlib import Path
+from shutil import which
 
 import pytest  # type: ignore
 import numpy as np
-from monty.os.path import which
 
 from pymatgen.core.composition import Composition
 from pymatgen.core.lattice import Lattice

pymatgen/electronic_structure/boltztrap.py

@@ -26,11 +26,12 @@
 import tempfile
 import time
 
+from shutil import which
+
 import numpy as np
 from monty.dev import requires
 from monty.json import MSONable, jsanitize
 from monty.os import cd
-from monty.os.path import which
 from scipy import constants
 from scipy.spatial import distance
 

pymatgen/electronic_structure/tests/test_boltztrap.py

@@ -8,7 +8,8 @@
 import unittest
 import warnings
 
-from monty.os.path import which
+from shutil import which
+
 from monty.serialization import loadfn
 
 from pymatgen.electronic_structure.bandstructure import BandStructure

pymatgen/electronic_structure/tests/test_plotter.py

@@ -7,9 +7,9 @@
 import unittest
 import warnings
 from io import open
+from shutil import which
 
 import scipy
-from monty.os.path import which
 
 from pymatgen.core.structure import Structure
 from pymatgen.electronic_structure.bandstructure import BandStructureSymmLine

pymatgen/ext/cod.py

@@ -33,9 +33,10 @@
 import re
 import subprocess
 
+from shutil import which
+
 import requests
 from monty.dev import requires
-from monty.os.path import which
 
 from pymatgen.core.composition import Composition
 from pymatgen.core.structure import Structure

pymatgen/ext/tests/test_cod.py

@@ -8,7 +8,7 @@
 
 import requests
 
-from monty.os.path import which
+from shutil import which
 
 from pymatgen.ext.cod import COD
 

pymatgen/io/ambertools.py

@@ -12,10 +12,10 @@ class does not work properly.
 import tempfile
 import numpy as np
 import parmed as pmd
+from shutil import which
 from collections import namedtuple, OrderedDict
 
 from monty.dev import requires
-from monty.os.path import which
 from monty.tempfile import ScratchDir
 
 from pymatgen.core.structure import Molecule

pymatgen/io/lammps/utils.py

@@ -11,6 +11,7 @@
 import tempfile
 from io import open
 from subprocess import PIPE, Popen
+from shutil import which
 
 import numpy as np
 
@@ -19,7 +20,6 @@
 except ImportError:
     pb = None
 
-from monty.os.path import which
 from monty.tempfile import ScratchDir
 
 from pymatgen.core.structure import Molecule

pymatgen/io/qchem/tests/test_outputs.py

@@ -6,7 +6,8 @@
 import os
 import unittest
 
-from monty.os.path import which
+from shutil import which
+
 from monty.serialization import dumpfn, loadfn
 
 from pymatgen.core.structure import Molecule

pymatgen/transformations/tests/test_advanced_transformations.py

@@ -7,8 +7,9 @@
 import unittest
 import warnings
 
+from shutil import which
+
 import numpy as np
-from monty.os.path import which
 from monty.serialization import loadfn
 
 from pymatgen.core.lattice import Lattice

pymatgen/transformations/tests/test_site_transformations.py

@@ -5,8 +5,9 @@
 
 import unittest
 
+from shutil import which
+
 import numpy as np
-from monty.os.path import which
 
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Structure, Molecule

pymatgen/transformations/tests/test_standard_transformations.py

@@ -9,8 +9,9 @@
 import unittest
 import warnings
 
+from shutil import which
+
 from monty.json import MontyDecoder
-from monty.os.path import which
 
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.periodic_table import Element