More work on making indexing arrays use intp (#1362)

- Added tests for 32 bit index support
- added @rathann to AUTHORS

package/AUTHORS

@@ -90,6 +90,8 @@ Chronological list of authors
   - Sang Young Noh
   - Andrew William King
   - Kathleen Clark
+  - Dominik 'Rathann' Mierzejewski
+
 
 External code
 -------------

package/CHANGELOG

@@ -15,12 +15,13 @@ The rules for this file:
 ------------------------------------------------------------------------------
 mm/dd/17
 
-  * 0.16.2 richardjgowers
+  * 0.16.2 richardjgowers, rathann
 
 Enhancements
 
 Fixes
   * fixed GROWriter truncating long resids from the wrong end (Issue #1395)
+  * Fixed dtype of numpy arrays to accomodate 32 bit architectures (Issue #1362)
 
 Changes
 

package/MDAnalysis/core/groups.py

@@ -2464,7 +2464,7 @@ def ix_array(self):
         --------
         ix
         """
-        return np.array([self.ix])
+        return np.array([self.ix], dtype=np.intp)
 
 
 class Atom(ComponentBase):
@@ -2736,7 +2736,7 @@ def update_selection(self):
             ix = sum([sel.apply(bg) for sel in sels[1:]],
                      sels[0].apply(bg)).ix
         else:
-            ix = np.array([], dtype=np.int)
+            ix = np.array([], dtype=np.intp)
         # Run back through AtomGroup init with this information to remake ourselves
         super(UpdatingAtomGroup, self).__init__(ix, self.universe)
         self.is_uptodate = True

package/MDAnalysis/core/topology.py

@@ -125,12 +125,12 @@ def make_downshift_arrays(upshift, nparents):
         counter += 1
         # If parent is skipped, eg (0, 0, 2, 2, etc)
         while counter != upshift[order[x:y][0]]:
-            downshift.append(np.array([], dtype=np.int64))
+            downshift.append(np.array([], dtype=np.intp))
             counter += 1
-        downshift.append(np.sort(np.array(order[x:y], copy=True, dtype=np.int64)))
+        downshift.append(np.sort(np.array(order[x:y], copy=True, dtype=np.intp)))
     # Add entries for childless parents at end of range
     while counter < (nparents - 1):
-        downshift.append(np.array([], dtype=np.int64))
+        downshift.append(np.array([], dtype=np.intp))
         counter += 1
     # Add None to end of array to force it to be of type Object
     # Without this, a rectangular array gets squashed into a single array
@@ -210,18 +210,18 @@ def __init__(self,
 
         # built atom-to-residue mapping, and vice-versa
         if atom_resindex is None:
-            self._AR = np.zeros(n_atoms, dtype=np.int64)
+            self._AR = np.zeros(n_atoms, dtype=np.intp)
         else:
-            self._AR = atom_resindex.copy()
+            self._AR = np.asarray(atom_resindex, dtype=np.intp).copy()
             if not len(self._AR) == n_atoms:
                 raise ValueError("atom_resindex must be len n_atoms")
         self._RA = make_downshift_arrays(self._AR, n_residues)
 
         # built residue-to-segment mapping, and vice-versa
         if residue_segindex is None:
-            self._RS = np.zeros(n_residues, dtype=np.int64)
+            self._RS = np.zeros(n_residues, dtype=np.intp)
         else:
-            self._RS = residue_segindex.copy()
+            self._RS = np.asarray(residue_segindex, dtype=np.intp).copy()
             if not len(self._RS) == n_residues:
                 raise ValueError("residue_segindex must be len n_residues")
         self._SR = make_downshift_arrays(self._RS, n_segments)

testsuite/MDAnalysisTests/core/test_index_dtype.py

@@ -0,0 +1,92 @@
+# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
+#
+# MDAnalysis --- http://www.mdanalysis.org
+# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
+# (see the file AUTHORS for the full list of names)
+#
+# Released under the GNU Public Licence, v2 or any higher version
+#
+# Please cite your use of MDAnalysis in published work:
+#
+# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
+# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
+# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
+# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
+# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
+#
+# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
+# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
+# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
+#
+
+"""32 bit compat tests
+
+Tests for making sure that integer arrays used for indexing use `np.intp`.
+This dtype is important for platform independent indexing of other arrays.
+
+"""
+from __future__ import absolute_import
+
+import numpy as np
+from numpy.testing import (
+    assert_,
+)
+from MDAnalysisTests import make_Universe
+
+
+class TestIndexDtype(object):
+    def setUp(self):
+        self.u = make_Universe()
+
+    def tearDown(self):
+        del self.u
+
+    def test_ag_ix(self):
+        assert_(self.u.atoms.ix.dtype == np.intp)
+
+    def test_rg_ix(self):
+        assert_(self.u.residues.ix.dtype == np.intp)
+
+    def test_sg_ix(self):
+        assert_(self.u.segments.ix.dtype == np.intp)
+
+    def test_atom_ix_array(self):
+        assert_(self.u.atoms[0].ix_array.dtype == np.intp)
+
+    def test_residue_ix_array(self):
+        assert_(self.u.residues[0].ix_array.dtype == np.intp)
+
+    def test_segment_ix_array(self):
+        assert_(self.u.segments[0].ix_array.dtype == np.intp)
+
+    def test_atomgroup_indices(self):
+        assert_(self.u.atoms.indices.dtype == np.intp)
+
+    def test_atomgroup_residue_upshift(self):
+        assert_(self.u.atoms.resindices.dtype == np.intp)
+
+    def test_atomgroup_segment_upshift(self):
+        assert_(self.u.atoms.segindices.dtype == np.intp)
+
+    def test_residuegroup_atom_downshift(self):
+        # downshift arrays are a list (one for each residue)
+        assert_(all((arr.dtype == np.intp)
+                    for arr in self.u.residues.indices))
+
+    def test_residuegroup_resindices(self):
+        assert_(self.u.residues.resindices.dtype == np.intp)
+
+    def test_residuegroup_segment_upshift(self):
+        assert_(self.u.residues.segindices.dtype == np.intp)
+
+    def test_segmentgroup_atom_downshift(self):
+        assert_(all((arr.dtype == np.intp)
+                    for arr in self.u.segments.indices))
+
+    def test_segmentgroup_residue_downshift(self):
+        assert_(all((arr.dtype == np.intp)
+                    for arr in self.u.segments.resindices))
+
+    def test_segmentgroup_segindices(self):
+        assert_(self.u.segments.segindices.dtype == np.intp)