Merge pull request #683 from jbarnoud/issue-260-more-fix

Issue #260 More python 3 compatibility fix

package/MDAnalysis/analysis/density.py

@@ -306,7 +306,7 @@ def make_density(self):
             warnings.warn(msg)
             return
 
-        dedges = map(np.diff, self.edges)
+        dedges = [np.diff(edge) for edge in self.edges]
         D = len(self.edges)
         for i in range(D):
             shape = np.ones(D, int)

package/MDAnalysis/analysis/hbonds/hbond_analysis.py

@@ -958,8 +958,8 @@ def generate_table(self):
         # build empty output table
         dtype = [
             ("time", float), ("donor_idx", int), ("acceptor_idx", int),
-            ("donor_resnm", "|S4"), ("donor_resid", int), ("donor_atom", "|S4"),
-            ("acceptor_resnm", "|S4"), ("acceptor_resid", int), ("acceptor_atom", "|S4"),
+            ("donor_resnm", "|U4"), ("donor_resid", int), ("donor_atom", "|U4"),
+            ("acceptor_resnm", "|U4"), ("acceptor_resid", int), ("acceptor_atom", "|U4"),
             ("distance", float), ("angle", float)]
         # according to Lukas' notes below, using a recarray at this stage is ineffective
         # and speedups of ~x10 can be achieved by filling a standard array, like this:
@@ -1040,8 +1040,8 @@ def count_by_type(self):
         # build empty output table
         dtype = [
             ('donor_idx', int), ('acceptor_idx', int),
-            ('donor_resnm', 'S4'), ('donor_resid', int), ('donor_heavy_atom', 'S4'), ('donor_atom', 'S4'),
-            ('acceptor_resnm', 'S4'), ('acceptor_resid', int), ('acceptor_atom', 'S4'),
+            ('donor_resnm', 'U4'), ('donor_resid', int), ('donor_heavy_atom', 'U4'), ('donor_atom', 'U4'),
+            ('acceptor_resnm', 'U4'), ('acceptor_resid', int), ('acceptor_atom', 'U4'),
             ('frequency', float)
         ]
         out = np.empty((len(hbonds),), dtype=dtype)
@@ -1101,8 +1101,8 @@ def timesteps_by_type(self):
         # build empty output table
         dtype = [
             ('donor_idx', int), ('acceptor_idx', int),
-            ('donor_resnm', 'S4'), ('donor_resid', int), ('donor_heavy_atom', 'S4'), ('donor_atom', 'S4'),
-            ('acceptor_resnm', 'S4'), ('acceptor_resid', int), ('acceptor_atom', 'S4'),
+            ('donor_resnm', 'U4'), ('donor_resid', int), ('donor_heavy_atom', 'U4'), ('donor_atom', 'U4'),
+            ('acceptor_resnm', 'U4'), ('acceptor_resid', int), ('acceptor_atom', 'U4'),
             ('time', float)]
         out = np.empty((out_nrows,), dtype=dtype)
 

package/MDAnalysis/analysis/leaflet.py

@@ -54,11 +54,12 @@
 
 from six.moves import range
 
+import warnings
+
 import numpy as np
-import MDAnalysis
 import networkx as NX
-import distances
-import warnings
+import MDAnalysis
+from . import distances
 
 
 class LeafletFinder(object):

package/MDAnalysis/coordinates/CRD.py

@@ -64,9 +64,9 @@ def _read_first_frame(self):
                 # process coordinates
                 try:
                     if extended:
-                        coords_list.append(np.array(map(float, line[45:100].split()[0:3])))
+                        coords_list.append(np.array(line[45:100].split()[0:3], dtype=float))
                     else:
-                        coords_list.append(np.array(map(float, line[20:50].split()[0:3])))
+                        coords_list.append(np.array(line[20:50].split()[0:3], dtype=float))
                 except:
                     raise ValueError("Check CRD format at line {0}: {1}"
                                      "".format(linenum, line.rstrip()))

package/MDAnalysis/coordinates/GMS.py

@@ -66,7 +66,7 @@ def __init__(self, outfilename, **kwargs):
         super(GMSReader, self).__init__(outfilename, **kwargs)
 
         # the filename has been parsed to be either b(g)zipped or not
-        self.outfile = util.anyopen(self.filename, 'r')
+        self.outfile = util.anyopen(self.filename, 'rt')
 
         # note that, like for xtc and trr files, _n_atoms and _n_frames are used quasi-private variables
         # to prevent the properties being recalculated
@@ -242,7 +242,7 @@ def open_trajectory(self):
             # must check; otherwise might segmentation fault
             raise IOError(errno.ENOENT, 'GMS file not found', self.filename)
 
-        self.outfile = util.anyopen(self.filename, 'r')
+        self.outfile = util.anyopen(self.filename, 'rt')
 
         # reset ts
         ts = self.ts

package/MDAnalysis/coordinates/GRO.py

@@ -122,7 +122,7 @@ class GROReader(base.SingleFrameReader):
     _Timestep = Timestep
 
     def _read_first_frame(self):
-        with util.openany(self.filename, 'r') as grofile:
+        with util.openany(self.filename, 'rt') as grofile:
             # Read first two lines to get number of atoms
             grofile.readline()
             self.n_atoms = n_atoms = int(grofile.readline())
@@ -281,7 +281,7 @@ def write(self, selection, frame=None):
                              "".format(self.gro_coor_limits["min"],
                                        self.gro_coor_limits["max"]))
 
-        with util.openany(self.filename, 'w') as output_gro:
+        with util.openany(self.filename, 'wt') as output_gro:
             # Header
             output_gro.write('Written by MDAnalysis\n')
             output_gro.write(self.fmt['n_atoms'].format(len(atoms)))

package/MDAnalysis/coordinates/PDB.py

@@ -475,7 +475,7 @@ def __init__(self, filename, **kwargs):
 
         pos = 0  # atom position for filling coordinates array
         occupancy = np.ones(self._n_atoms)
-        with util.openany(filename, 'r') as pdbfile:
+        with util.openany(filename, 'rt') as pdbfile:
             for i, line in enumerate(pdbfile):
                 line = line.strip()  # Remove extra spaces
                 if len(line) == 0:  # Skip line if empty
@@ -594,7 +594,7 @@ def _read_frame(self, frame):
         #       forth; should improve performance substantially
         pos = 0
         occupancy = np.ones(self._n_atoms)
-        with util.openany(self.filename, 'r') as f:
+        with util.openany(self.filename, 'rt') as f:
             for i in range(line):
                 next(f)  # forward to frame
             for line in f:
@@ -776,7 +776,7 @@ def __init__(self, filename, bonds="conect", n_atoms=None, start=0, step=1,
         self.step = step
         self.remarks = remarks
 
-        self.pdbfile = util.anyopen(self.filename, 'w')  # open file on init
+        self.pdbfile = util.anyopen(self.filename, 'wt')  # open file on init
         self.has_END = False
 
     def close(self):

package/MDAnalysis/coordinates/XDR.py

@@ -93,7 +93,7 @@ def _load_offsets(self):
             self._read_offsets(store=True)
             return
 
-        with open(fname) as f:
+        with open(fname, 'rb') as f:
             data = {k: v for k, v in six.iteritems(np.load(f))}
 
         ctime_ok = getctime(self.filename) == data['ctime']
@@ -116,8 +116,12 @@ def _read_offsets(self, store=False):
                 np.savez(offsets_filename(self.filename),
                          offsets=offsets, size=size, ctime=ctime)
             except Exception as e:
-                warnings.warn("Couldn't save offsets because: {}".format(
-                    e.message))
+                try:
+                    warnings.warn("Couldn't save offsets because: {}".format(
+                        e.message))
+                except AttributeError:
+                    warnings.warn("Couldn't save offsets because: {}".format(e))
+
 
     def rewind(self):
         """Read the first frame again"""
@@ -133,7 +137,7 @@ def _reopen(self):
         self.ts.frame = 0
         self._frame = -1
         self._xdr.close()
-        self._xdr.open(self.filename, 'r')
+        self._xdr.open(self.filename.encode('utf-8'), 'r')
 
     def _read_frame(self, i):
         """read frame i"""

package/MDAnalysis/coordinates/XYZ.py

@@ -139,7 +139,7 @@ def __init__(self, filename, n_atoms=None, atoms='X', convert_units=None,
             self.__class__.__name__, __version__)
         self.remark = default_remark if remark == 'default' else remark
         # can also be gz, bz2
-        self._xyz = util.anyopen(self.filename, 'w')
+        self._xyz = util.anyopen(self.filename, 'wt')
 
     def _get_atomnames(self, atoms):
         """Return a list of atom names"""

package/MDAnalysis/coordinates/base.py

@@ -1165,7 +1165,7 @@ def apply_limits(frame):
         elif isinstance(frame, (list, np.ndarray)):
             def listiter(frames):
                 for f in frames:
-                    if not isinstance(f, int):
+                    if not isinstance(f, (int, np.integer)):
                         raise TypeError("Frames indices must be integers")
                     yield self._read_frame(apply_limits(f))
             return listiter(frame)

package/MDAnalysis/core/Selection.py

@@ -29,15 +29,17 @@
 
 This is all invisible to the user through ag.select_atoms
 """
+import six
+from six.moves import zip
 
 import collections
 import re
+import functools
+import warnings
+
 import numpy as np
 from numpy.lib.utils import deprecate
 from Bio.KDTree import KDTree
-import warnings
-import six
-from six.moves import zip
 
 from MDAnalysis.core import flags
 from ..lib import distances
@@ -909,7 +911,7 @@ def apply(self, group):
         if self.prop == 'fragment':
             # Combine all fragments together, then check where group
             # indices are same as fragment(s) indices
-            allfrags = reduce(lambda x, y: x + y, res.fragments)
+            allfrags = functools.reduce(lambda x, y: x + y, res.fragments)
 
             mask = np.in1d(group.indices, allfrags.indices)
             return unique(group[mask])