Remove py2 things from lib

package/MDAnalysis/lib/NeighborSearch.py

@@ -28,8 +28,6 @@
 This module contains classes that allow neighbor searches directly with
 `AtomGroup` objects from `MDAnalysis`.
 """
-from __future__ import absolute_import
-
 import numpy as np
 from MDAnalysis.lib.distances import capped_distance
 from MDAnalysis.lib.util import unique_int_1d

package/MDAnalysis/lib/__init__.py

@@ -27,8 +27,6 @@
 ================================================================
 """
 
-from __future__ import absolute_import
-
 __all__ = ['log', 'transformations', 'util', 'mdamath', 'distances',
            'NeighborSearch', 'formats', 'pkdtree', 'nsgrid']
 

package/MDAnalysis/lib/correlations.py

@@ -68,7 +68,6 @@
 
 """
 
-from __future__ import absolute_import, division
 import numpy as np
 from copy import deepcopy
 

package/MDAnalysis/lib/distances.py

@@ -66,10 +66,6 @@
 .. autofunction:: augment_coordinates(coordinates, box, r)
 .. autofunction:: undo_augment(results, translation, nreal)
 """
-from __future__ import division, absolute_import
-from six.moves import range
-from six import raise_from
-
 import numpy as np
 from numpy.lib.utils import deprecate
 
@@ -99,12 +95,10 @@ def _run(funcname, args=None, kwargs=None, backend="serial"):
     backend = backend.lower()
     try:
         func = getattr(_distances[backend], funcname)
-    except KeyError:
-        raise_from(
-            ValueError(
-                "Function {0} not available with backend {1}; try one "
-                "of: {2}".format(funcname, backend, _distances.keys())),
-            None)
+    except KeyError as exc:
+        errmsg = (f"Function {funcname} not available with backend {backend} "
+                  f"try one of: {_distances.keys()}")
+        raise ValueError(errmsg) from exc
     return func(*args, **kwargs)
 
 # serial versions are always available (and are typically used within

package/MDAnalysis/lib/formats/__init__.py

@@ -20,7 +20,6 @@
 # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
-from __future__ import absolute_import
 from . import libmdaxdr
 from . import libdcd
 

package/MDAnalysis/lib/formats/libdcd.pyx

@@ -62,13 +62,9 @@ from VMD's `molfile`_ plugin and `catdcd`_.
 .. _catdcd: http://www.ks.uiuc.edu/Development/MDTools/catdcd/
 
 """
-from six.moves import range
-
-
 from os import path
 import numpy as np
 from collections import namedtuple
-import six
 import string
 import sys
 
@@ -497,7 +493,7 @@ cdef class DCDFile:
             self.charmm = DCD_HAS_EXTRA_BLOCK | DCD_IS_CHARMM
         self.natoms = natoms
 
-        if isinstance(remarks, six.string_types):
+        if isinstance(remarks, str):
             try:
                 remarks = bytearray(remarks, 'ascii')
             except UnicodeDecodeError:

package/MDAnalysis/lib/log.py

@@ -84,8 +84,6 @@
 .. autogenerated, see Online Docs
 
 """
-from __future__ import absolute_import
-
 import sys
 import logging
 import re

package/MDAnalysis/lib/mdamath.py

@@ -43,8 +43,6 @@
 .. versionchanged: 1.0.0
    Unused function :func:`_angle()` has now been removed.
 """
-from __future__ import division, absolute_import
-from six.moves import zip
 import numpy as np
 
 from ..exceptions import NoDataError

package/MDAnalysis/lib/pkdtree.py

@@ -28,8 +28,6 @@
 boundary conditions.
 """
 
-from __future__ import absolute_import
-
 import itertools
 import numpy as np
 from scipy.spatial import cKDTree

package/MDAnalysis/lib/transformations.py

@@ -188,10 +188,6 @@
    MDAnalysis.lib.transformations
 """
 
-from __future__ import division, absolute_import
-
-from six.moves import range
-
 import sys
 import os
 import warnings

package/MDAnalysis/lib/util.py

@@ -179,9 +179,6 @@
    underlying stream and ``NamedStream.close(force=True)`` will also
    close it.
 """
-from __future__ import division, absolute_import
-import six
-from six.moves import range, map
 import sys
 
 __docformat__ = "restructuredtext en"
@@ -438,7 +435,7 @@ def _get_stream(filename, openfunction=open, mode='r'):
         # case we have to ignore the error and return None. Second is when openfunction can't open the file because
         # either the file isn't there or the permissions don't allow access.
         if errno.errorcode[err.errno] in ['ENOENT', 'EACCES']:
-            six.reraise(*sys.exc_info())
+            raise sys.exc_info()[0](sys.exc_info()[1]) from err
         return None
     if mode.startswith('r'):
         # additional check for reading (eg can we uncompress) --- is this needed?
@@ -853,11 +850,10 @@ def fileno(self):
         """
         try:
             return self.stream.fileno()
-        except AttributeError:
+        except AttributeError as exc:
             # IOBase.fileno does not raise IOError as advertised so we do this here
-            six.raise_from(
-                IOError("This NamedStream does not use a file descriptor."),
-                None)
+            errmsg = "This NamedStream does not use a file descriptor."
+            raise IOError(errmsg) from exc
 
     def readline(self):
         try:
@@ -962,11 +958,9 @@ def check_compressed_format(root, ext):
     if ext.lower() in ("bz2", "gz"):
         try:
             root, ext = get_ext(root)
-        except Exception:
-            six.raise_from(
-                TypeError("Cannot determine coordinate format for '{0}.{1}'"
-                          "".format(root, ext)),
-                None)
+        except Exception as exc:
+            errmsg = f"Cannot determine coordinate format for '{root}.{ext}'"
+            raise TypeError(errmsg) from exc
 
     return ext.upper()
 
@@ -989,12 +983,11 @@ def format_from_filename_extension(filename):
     """
     try:
         root, ext = get_ext(filename)
-    except Exception:
-        six.raise_from(TypeError(
-            "Cannot determine file format for file '{0}'.\n"
-            "           You can set the format explicitly with "
-            "'Universe(..., format=FORMAT)'.".format(filename)),
-            None)
+    except Exception as exc:
+        errmsg = (f"Cannot determine file format for file '{filename}'.\n"
+                  f"           You can set the format explicitly with "
+                  f"'Universe(..., format=FORMAT)'.")
+        raise TypeError(errmsg) from exc
     format = check_compressed_format(root, ext)
     return format
 
@@ -1030,12 +1023,11 @@ def guess_format(filename):
         # perhaps StringIO or open stream
         try:
             format = format_from_filename_extension(filename.name)
-        except AttributeError:
+        except AttributeError as exc:
             # format is None so we need to complain:
-            six.raise_from(
-                ValueError("guess_format requires an explicit format specifier "
-                           "for stream {0}".format(filename)),
-                None)
+            errmsg = (f"guess_format requires an explicit format specifier "
+                      f"for stream {filename}")
+            raise ValueError(errmsg) from exc
     else:
         # iterator, list, filename: simple extension checking... something more
         # complicated is left for the ambitious.
@@ -1050,7 +1042,7 @@ def guess_format(filename):
 def iterable(obj):
     """Returns ``True`` if `obj` can be iterated over and is *not* a  string
     nor a :class:`NamedStream`"""
-    if isinstance(obj, (six.string_types, NamedStream)):
+    if isinstance(obj, (str, NamedStream)):
         return False  # avoid iterating over characters of a string
 
     if hasattr(obj, 'next'):
@@ -1121,12 +1113,10 @@ def read(self, line):
         """Read the entry from `line` and convert to appropriate type."""
         try:
             return self.convertor(line[self.start:self.stop])
-        except ValueError:
-            six.raise_from(
-                ValueError(
-                    "{0!r}: Failed to read&convert {1!r}".format(
-                        self, line[self.start:self.stop])),
-                None)
+        except ValueError as exc:
+            errmsg = (f"{self}: Failed to read&convert "
+                      f"{line[self.start:self.stop]}")
+            raise ValueError(errmsg) from exc
 
     def __len__(self):
         """Length of the field in columns (stop - start)"""
@@ -1359,10 +1349,9 @@ def get_weights(atoms, weights):
     if not iterable(weights) and weights == "mass":
         try:
             weights = atoms.masses
-        except AttributeError:
-            six.raise_from(
-                TypeError("weights='mass' selected but atoms.masses is missing"),
-                None)
+        except AttributeError as exc:
+            errmsg = "weights='mass' selected but atoms.masses is missing"
+            raise TypeError(errmsg) from exc
 
     if iterable(weights):
         if len(np.asarray(weights).shape) != 1:
@@ -1441,12 +1430,10 @@ def convert_aa_code(x):
 
     try:
         return d[x.upper()]
-    except KeyError:
-        six.raise_from(
-            ValueError(
-                "No conversion for {0} found (1 letter -> 3 letter or 3/4 letter -> 1 letter)".format(x)
-                ),
-            None)
+    except KeyError as exc:
+        errmsg = (f"No conversion for {x} found (1 letter -> 3 letter or 3/4 "
+                  f"letter -> 1 letter)")
+        raise ValueError(errmsg) from exc
 
 
 #: Regular expression to match and parse a residue-atom selection; will match
@@ -1695,21 +1682,19 @@ def __getattr__(self, key):
         # a.this causes a __getattr__ call for key = 'this'
         try:
             return dict.__getitem__(self, key)
-        except KeyError:
-            six.raise_from(AttributeError('"{}" is not known in the namespace.'
-                                 .format(key)), None)
+        except KeyError as exc:
+            errmsg = f'"{key}" is not known in the namespace.'
+            raise AttributeError(errmsg) from exc
 
     def __setattr__(self, key, value):
         dict.__setitem__(self, key, value)
 
     def __delattr__(self, key):
         try:
             dict.__delitem__(self, key)
-        except KeyError:
-            six.raise_from(
-                AttributeError('"{}" is not known in the namespace.'
-                                 .format(key)),
-                None)
+        except KeyError as exc:
+            errmsg = f'"{key}" is not known in the namespace.'
+            raise AttributeError(errmsg) from exc
 
     def __eq__(self, other):
         try:
@@ -2014,12 +1999,10 @@ def _check_coords(coords, argname):
                                      "".format(fname, argname, coords.shape))
             try:
                 coords = coords.astype(np.float32, order='C', copy=enforce_copy)
-            except ValueError:
-                six.raise_from(
-                    TypeError(
-                        "{}(): {}.dtype must be convertible to float32,"
-                        " got {}.".format(fname, argname, coords.dtype)),
-                    None)
+            except ValueError as exc:
+                errmsg = (f"{fname}(): {argname}.dtype must be convertible to "
+                          f"float32, got {coords.dtype}.")
+                raise TypeError(errmsg) from exc
             return coords, is_single
 
         @wraps(func)

testsuite/MDAnalysisTests/lib/test_augment.py

@@ -20,7 +20,6 @@
 # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 
-from __future__ import absolute_import
 import pytest
 import numpy as np
 from numpy.testing import assert_almost_equal, assert_equal

testsuite/MDAnalysisTests/lib/test_cutil.py

@@ -20,8 +20,6 @@
 # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
-from __future__ import absolute_import
-
 import pytest
 import numpy as np
 from numpy.testing import assert_equal

testsuite/MDAnalysisTests/lib/test_distances.py

@@ -20,8 +20,6 @@
 # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
-
-from __future__ import division, absolute_import
 import pytest
 import numpy as np
 from numpy.testing import assert_equal, assert_almost_equal

testsuite/MDAnalysisTests/lib/test_log.py

@@ -20,8 +20,6 @@
 # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
-
-from __future__ import absolute_import
 import warnings
 import pytest
 

testsuite/MDAnalysisTests/lib/test_neighborsearch.py

@@ -21,8 +21,6 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 
-from __future__ import print_function, absolute_import
-
 import pytest
 from numpy.testing import assert_equal
 

testsuite/MDAnalysisTests/lib/test_nsgrid.py

@@ -21,8 +21,6 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 
-from __future__ import print_function, absolute_import
-
 import pytest
 
 from numpy.testing import assert_equal, assert_allclose

testsuite/MDAnalysisTests/lib/test_pkdtree.py

@@ -21,8 +21,6 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 
-from __future__ import print_function, absolute_import
-
 import pytest
 import numpy as np
 from numpy.testing import assert_equal

testsuite/MDAnalysisTests/lib/test_util.py

@@ -20,10 +20,7 @@
 # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
-from __future__ import absolute_import, division
-
-
-from six.moves import range, StringIO
+from io import StringIO
 import pytest
 import os
 import warnings