Avoid isinstance(something, int)

Testing that arguments where integer by using `isinstance(arg, int)` has
proven itself detrimental on several occasions. Indeed, the test refuses
other types that would be legitimate such as numpy integers. This commit
replaces the remaining occurences of the too narrow test by the solution
that has already been used on multiple places of the code: testing
against `numbers.Integral`. This new way matches everything that looks
enough like an integer, and behave the same on python 2 and python 3 on
the contrary to testing against `int`.

package/MDAnalysis/analysis/encore/utils.py

@@ -20,6 +20,7 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 from six.moves import range
+import numbers
 from multiprocessing.sharedctypes import SynchronizedArray
 from multiprocessing import Process, Manager
 from joblib import cpu_count
@@ -67,7 +68,7 @@ def __init__(self, size, metadata=None, loadfile=None):
         self.size = size
         if loadfile:
             self.loadz(loadfile)
-        elif isinstance(size, int):
+        elif isinstance(size, numbers.Integral):
             self.size = size
             self._elements = np.zeros((size + 1) * size / 2, dtype=np.float64)
         elif isinstance(size, SynchronizedArray):

package/MDAnalysis/auxiliary/XVG.py

@@ -68,6 +68,7 @@
 
 from six.moves import range
 
+import numbers
 import os
 import numpy as np
 from . import base
@@ -132,7 +133,7 @@ def _select_time(self, key):
         if key is None:
             # here so that None is a valid value; just return
             return
-        if isinstance(key, int):
+        if isinstance(key, numbers.Integral):
             return self._select_data(key)
         else:
              raise ValueError('Time selector must be single index')
@@ -141,7 +142,7 @@ def _select_data(self, key):
         if key is None:
             # here so that None is a valid value; just return
             return
-        if isinstance(key, int):
+        if isinstance(key, numbers.Integral):
             try:
                 return self._data[key]
             except IndexError:

package/MDAnalysis/auxiliary/base.py

@@ -42,10 +42,12 @@
 from six.moves import range
 
 import os
-import numpy as np
+import numbers
 import math
 import warnings
 
+import numpy as np
+
 from ..lib.util import asiterable
 
 from . import _AUXREADERS
@@ -561,7 +563,7 @@ def __getitem__(self, i):
              for auxstep in aux_reader[::10]       # analyse every 10th step        
                  run_analysis(auxstep)
         """
-        if isinstance(i, int):
+        if isinstance(i, numbers.Integral):
             i = self._check_index(i)
             return self._go_to_step(i)
 
@@ -578,7 +580,7 @@ def __getitem__(self, i):
                     else self._check_index(i.stop) if i.stop is not None 
                     else self.n_steps)
             step = i.step or 1
-            if not isinstance(step, int) or step < 1:
+            if not isinstance(step, numbers.Integral) or step < 1:
                 raise ValueError("Step must be positive integer") # allow -ve?
             if start > stop:
                 raise IndexError("Stop frame is lower than start frame")
@@ -587,7 +589,7 @@ def __getitem__(self, i):
             raise TypeError("Index must be integer, list of integers or slice")
 
     def _check_index(self, i):
-        if not isinstance(i, (int, np.integer)):
+        if not isinstance(i, numbers.Integral):
                 raise TypeError("Step indices must be integers")
         if i < 0:
             i = i + self.n_steps

package/MDAnalysis/coordinates/base.py

@@ -363,7 +363,7 @@ def __getitem__(self, atoms):
            correspond to atom indices,
            :attr:`MDAnalysis.core.groups.Atom.index` (0-based)
         """
-        if isinstance(atoms, int):
+        if isinstance(atoms, numbers.Integral):
             return self._pos[atoms]
         elif isinstance(atoms, (slice, np.ndarray)):
             return self._pos[atoms]
@@ -1199,7 +1199,7 @@ def apply_limits(frame):
                                  "".format(frame, len(self)))
             return frame
 
-        if isinstance(frame, int):
+        if isinstance(frame, numbers.Integral):
             frame = apply_limits(frame)
             return self._read_frame_with_aux(frame)
         elif isinstance(frame, (list, np.ndarray)):
@@ -1211,7 +1211,7 @@ def apply_limits(frame):
 
             def listiter(frames):
                 for f in frames:
-                    if not isinstance(f, (int, np.integer)):
+                    if not isinstance(f, numbers.Integral):
                         raise TypeError("Frames indices must be integers")
                     yield self._read_frame_with_aux(apply_limits(f))
 

package/MDAnalysis/core/groups.py

@@ -96,6 +96,7 @@
 import numpy as np
 import functools
 import itertools
+import numbers
 import os
 import warnings
 
@@ -432,7 +433,7 @@ def __getitem__(self, item):
         # because our _ix attribute is a numpy array
         # it can be sliced by all of these already,
         # so just return ourselves sliced by the item
-        if isinstance(item, (int, np.int_)):
+        if isinstance(item, numbers.Integral):
             return self.level.singular(self.ix[item], self.universe)
         else:
             if isinstance(item, list) and item:  # check for empty list

package/MDAnalysis/core/topologyattrs.py

@@ -39,6 +39,7 @@
 from collections import defaultdict
 import functools
 import itertools
+import numbers
 import numpy as np
 
 from . import flags
@@ -607,7 +608,7 @@ def __init__(self, values, guessed=False):
     def get_residues(self, rg):
         resatoms = self.top.tt.residues2atoms_2d(rg._ix)
 
-        if isinstance(rg._ix, int):
+        if isinstance(rg._ix, numbers.Integral):
             # for a single residue
             masses = self.values[resatoms].sum()
         else:
@@ -621,7 +622,7 @@ def get_residues(self, rg):
     def get_segments(self, sg):
         segatoms = self.top.tt.segments2atoms_2d(sg._ix)
 
-        if isinstance(sg._ix, int):
+        if isinstance(sg._ix, numbers.Integral):
             # for a single segment
             masses = self.values[segatoms].sum()
         else:
@@ -933,7 +934,7 @@ class Charges(AtomAttr):
     def get_residues(self, rg):
         resatoms = self.top.tt.residues2atoms_2d(rg._ix)
 
-        if isinstance(rg._ix, int):
+        if isinstance(rg._ix, numbers.Integral):
             charges = self.values[resatoms].sum()
         else:
             charges = np.empty(len(rg))
@@ -945,7 +946,7 @@ def get_residues(self, rg):
     def get_segments(self, sg):
         segatoms = self.top.tt.segments2atoms_2d(sg._ix)
 
-        if isinstance(sg._ix, int):
+        if isinstance(sg._ix, numbers.Integral):
             # for a single segment
             charges = self.values[segatoms].sum()
         else:

package/MDAnalysis/core/topologyobjects.py

@@ -30,6 +30,7 @@
 from __future__ import print_function, absolute_import
 
 from six.moves import zip
+import numbers
 import numpy as np
 import functools
 
@@ -751,7 +752,7 @@ def __getitem__(self, item):
            Allows indexing via boolean numpy array
         """
         # Grab a single Item, similar to Atom/AtomGroup relationship
-        if isinstance(item, int):
+        if isinstance(item, numbers.Integral):
             outclass = {'bond': Bond,
                         'angle': Angle,
                         'dihedral': Dihedral,