Merge pull request #1158 from jbarnoud/py3

Some fix for python 3

package/MDAnalysis/analysis/density.py

@@ -492,7 +492,7 @@ def current_coordinates():
     if tuple(angles) != (90., 90., 90.):
         msg = "Non-orthorhombic unit-cell --- make sure that it has been remapped properly!"
         warnings.warn(msg)
-        logger.warn(msg)
+        logger.warning(msg)
 
     # Make the box bigger to avoid as much as possible 'outlier'. This
     # is important if the sites are defined at a high density: in this

package/MDAnalysis/analysis/encore/utils.py

@@ -19,6 +19,7 @@
 # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
+from six.moves import range
 from multiprocessing.sharedctypes import SynchronizedArray
 from multiprocessing import Process, Manager
 import numpy as np
@@ -438,8 +439,8 @@ def trm_indices_nodiag(n):
         Matrix size
 """
 
-    for i in xrange(1, n):
-        for j in xrange(i):
+    for i in range(1, n):
+        for j in range(i):
             yield (i, j)
 
 
@@ -454,8 +455,8 @@ def trm_indices_diag(n):
         Matrix size
 """
 
-    for i in xrange(0, n):
-        for j in xrange(i+1):
+    for i in range(0, n):
+        for j in range(i + 1):
             yield (i, j)
 
 

package/MDAnalysis/core/topologyattrs.py

@@ -31,7 +31,7 @@
 These are usually read by the TopologyParser.
 """
 
-from six.moves import zip
+from six.moves import zip, range
 from collections import defaultdict
 import itertools
 import numpy as np
@@ -672,7 +672,7 @@ def shape_parameter(group, **kwargs):
             recenteredpos = atomgroup.positions - com
         tensor = np.zeros((3, 3))
 
-        for x in xrange(recenteredpos.shape[0]):
+        for x in range(recenteredpos.shape[0]):
             tensor += masses[x] * np.outer(recenteredpos[x, :],
                                            recenteredpos[x, :])
         tensor /= atomgroup.total_mass()
@@ -721,7 +721,7 @@ def asphericity(group, pbc=None):
                              atomgroup.center_of_mass(pbc=False))
 
         tensor = np.zeros((3, 3))
-        for x in xrange(recenteredpos.shape[0]):
+        for x in range(recenteredpos.shape[0]):
             tensor += masses[x] * np.outer(recenteredpos[x],
                                            recenteredpos[x])
 

package/MDAnalysis/core/topologyobjects.py

@@ -560,7 +560,7 @@ def __init__(self, bondidx, universe, btype=None, type=None, guessed=None,
 
             # Create vertical AtomGroups
             self._ags = [universe.atoms[self._bix[:, i]]
-                         for i in xrange(self._bix.shape[1])]
+                         for i in range(self._bix.shape[1])]
         else:
             # Empty TopologyGroup
             self._bix = np.array([])

package/MDAnalysis/lib/distances.py

@@ -118,7 +118,7 @@ def _run(funcname, args=None, kwargs=None, backend="serial"):
                           ortho_pbc,
                           triclinic_pbc)
 
-from c_distances_openmp import OPENMP_ENABLED as USED_OPENMP
+from .c_distances_openmp import OPENMP_ENABLED as USED_OPENMP
 
 
 def _box_check(box):

package/MDAnalysis/lib/util.py

@@ -1258,12 +1258,12 @@ def unique_rows(arr, return_index=False):
 
     if return_index:
         u, r_idx = np.unique(arr.view(dtype=np.dtype([(str(i), arr.dtype)
-                                                      for i in xrange(m)])),
+                                                      for i in range(m)])),
                              return_index=True)
         return u.view(arr.dtype).reshape(-1, m), r_idx
     else:
         u = np.unique(arr.view(
-            dtype=np.dtype([(str(i), arr.dtype) for i in xrange(m)])
+            dtype=np.dtype([(str(i), arr.dtype) for i in range(m)])
         ))
         return u.view(arr.dtype).reshape(-1, m)
 

package/MDAnalysis/topology/PSFParser.py

@@ -43,8 +43,8 @@
 
 """
 from __future__ import absolute_import
-
 from six.moves import range
+
 import logging
 import functools
 from math import ceil
@@ -103,7 +103,7 @@ def parse(self):
         """
         # Open and check psf validity
         with openany(self.filename, 'r') as psffile:
-            header = psffile.next()
+            header = next(psffile)
             if not header.startswith("PSF"):
                 err = ("{0} is not valid PSF file (header = {1})"
                        "".format(self.filename, header))
@@ -146,7 +146,7 @@ def parse(self):
 
             try:
                 for attr, info in sections:
-                    psffile.next()
+                    next(psffile)
                     top.add_TopologyAttr(
                         attr(self._parse_sec(psffile, info)))
             except StopIteration:
@@ -272,7 +272,7 @@ def _parseatoms(self, lines, atoms_per, numlines):
         charges = np.zeros(numlines, dtype=np.float32)
         masses = np.zeros(numlines, dtype=np.float64)
 
-        for i in xrange(numlines):
+        for i in range(numlines):
             try:
                 line = lines()
             except StopIteration:

package/MDAnalysis/topology/TOPParser.py

@@ -167,7 +167,7 @@ def parse(self):
                 header = self.topfile.next()
             self.topfile.next()
 
-            topremarks = [self.topfile.next().strip() for i in xrange(4)]
+            topremarks = [self.topfile.next().strip() for i in range(4)]
             sys_info = [int(k) for i in topremarks for k in i.split()]
 
             header = self.topfile.next()
@@ -284,7 +284,7 @@ def parse_residx(self, atoms_per, numlines):
     def parsebond(self, atoms_per, numlines):
         y = self.topfile.next().strip("%FORMAT(")
         section = []
-        for i in xrange(numlines):
+        for i in range(numlines):
             l = self.topfile.next()
             # Subtract 1 from each number to ensure zero-indexing for the atoms
             fields = map(lambda x: int(x) - 1, l.split())
@@ -297,9 +297,9 @@ def parsesection_mapper(self, atoms_per, numlines, mapper):
         y = self.topfile.next().strip("%FORMAT(")
         y.strip(")")
         x = FORTRANReader(y)
-        for i in xrange(numlines):
+        for i in range(numlines):
             l = self.topfile.next()
-            for j in xrange(len(x.entries)):
+            for j in range(len(x.entries)):
                 val = l[x.entries[j].start:x.entries[j].stop].strip()
                 if val:
                     section.append(mapper(val))

package/MDAnalysis/topology/base.py

@@ -37,6 +37,8 @@
 """
 import six
 from six.moves import zip
+# While reduce is a built-in in python 2, it is not in python 3
+from functools import reduce
 
 import itertools
 import numpy as np

package/MDAnalysis/topology/guessers.py

@@ -27,6 +27,8 @@
 while `guess_Xs` will work on an array of many atoms.
 
 """
+from six.moves import map
+
 import numpy as np
 import warnings
 
@@ -46,7 +48,7 @@ def guess_masses(atom_types):
     -------
     atom_masses : np.ndarray dtype float64
     """
-    masses = np.array(map(get_atom_mass, atom_types), dtype=np.float64)
+    masses = np.array(list(map(get_atom_mass, atom_types)), dtype=np.float64)
     if np.any(masses == 0.0):
         # figure out where the misses were and report
         misses = np.unique(np.asarray(atom_types)[np.where(masses == 0.0)])
@@ -67,7 +69,7 @@ def guess_types(atom_names):
     -------
     atom_types : np.ndarray dtype object
     """
-    return np.array(map(guess_atom_element, atom_names),
+    return np.array(list(map(guess_atom_element, atom_names)),
                     dtype=object)
 
 

testsuite/MDAnalysisTests/analysis/test_base.py

@@ -131,6 +131,8 @@ def simple_function(mobile):
     return mobile.center_of_geometry()
 
 
+@dec.skipif(parser_not_found('DCD'),
+            'DCD parser not available. Are you using python 3?')
 def test_AnalysisFromFunction():
     u = mda.Universe(PSF, DCD)
     step = 2
@@ -150,6 +152,8 @@ def test_AnalysisFromFunction():
         assert_array_equal(results, ana.results)
 
 
+@dec.skipif(parser_not_found('DCD'),
+            'DCD parser not available. Are you using python 3?')
 def test_analysis_class():
     ana_class = base.analysis_class(simple_function)
     assert_(issubclass(ana_class, base.AnalysisBase))

testsuite/MDAnalysisTests/analysis/test_contacts.py

@@ -112,6 +112,8 @@ def test_contact_matrix():
     assert_array_equal(out, [True, True, True, False, False])
 
 
+@dec.skipif(parser_not_found('DCD'),
+            'DCD parser not available. Are you using python 3?')
 def test_new_selection():
     u = mda.Universe(PSF, DCD)
     selections = ('all', )
@@ -293,6 +295,8 @@ def test_save(self):
             assert_array_almost_equal(ca.timeseries, saved)
 
 
+@dec.skipif(parser_not_found('DCD'),
+            'DCD parser not available. Are you using python 3?')
 def test_q1q2():
     u = mda.Universe(PSF, DCD)
     q1q2 = contacts.q1q2(u, 'name CA', radius=8)

testsuite/MDAnalysisTests/analysis/test_hbonds.py

@@ -20,6 +20,7 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 from __future__ import print_function
+from six.moves import map
 
 import MDAnalysis
 import MDAnalysis.analysis.hbonds
@@ -39,7 +40,7 @@
 
 def guess_types(names):
     """GRO doesn't supply types, this returns an Attr"""
-    return Atomtypes(np.array(map(guess_atom_type, names), dtype=object))
+    return Atomtypes(np.array(list(map(guess_atom_type, names)), dtype=object))
 
 class TestHydrogenBondAnalysis(object):
     def setUp(self):

testsuite/MDAnalysisTests/analysis/test_rms.py

@@ -42,6 +42,8 @@
 
 
 class Testrmsd(object):
+    @dec.skipif(parser_not_found('DCD'),
+                'DCD parser not available. Are you using python 3?')
     def __init__(self):
         shape = (5, 3)
         # vectors with length one

testsuite/MDAnalysisTests/coordinates/test_memory.py

@@ -5,10 +5,13 @@
 from MDAnalysisTests.coordinates.base import (BaseReference,
                                               BaseReaderTest)
 from MDAnalysis.coordinates.memory import Timestep
-from numpy.testing import assert_equal
+from numpy.testing import assert_equal, dec
+from MDAnalysisTests import parser_not_found
 
 
 class MemoryReference(BaseReference):
+    @dec.skipif(parser_not_found('DCD'),
+                'DCD parser not available. Are you using python 3?')
     def __init__(self):
         super(MemoryReference, self).__init__()
 

testsuite/MDAnalysisTests/test_atomgroup.py

@@ -1440,6 +1440,8 @@ def setUp(self):
         self.sB = self.universe.segments[1]
 
     # VALID but temporary
+    @dec.skipif(parser_not_found('DCD'),
+                'DCD parser not available. Are you using python 3?')
     def setUp(self):
         self.universe = MDAnalysis.Universe(PSF, DCD)
 
@@ -2385,6 +2387,8 @@ def test_adding_empty_ags(self):
 
 
 class TestDihedralSelections(object):
+    @dec.skipif(parser_not_found('DCD'),
+                'DCD parser not available. Are you using python 3?')
     def setUp(self):
         self.universe = MDAnalysis.Universe(PSF, DCD)
         self.dih_prec = 2

testsuite/MDAnalysisTests/util.py

@@ -24,7 +24,15 @@
 
 """
 
-import __builtin__
+try:
+    import __builtin__
+    builtins_name = '__builtin__'
+    importer = __builtin__.__import__
+except ImportError:
+    import builtins
+    builtins_name = 'builtins'
+    importer = builtins.__import__
+
 from functools import wraps
 import mock
 
@@ -44,8 +52,8 @@ def try_and_do_something():
     def blocker_wrapper(func):
         @wraps(func)
         def func_wrapper(*args, **kwargs):
-            with mock.patch('__builtin__.__import__',
-                            wraps=__builtin__.__import__) as mbi:
+            with mock.patch('{}.__import__'.format(builtins_name),
+                            wraps=importer) as mbi:
                 def blocker(*args, **kwargs):
                     if package in args:
                         raise ImportError("Blocked by block_import")