Remove py2 things from aux, vis, transform, and others (#2762)

* Remove py2 things from aux

* rm py2 for selections, tests, transformations

* Remove py2 from visualization

* Remove misc py2 things

* errsmg typo

benchmarks/benchmarks/GRO.py

@@ -1,5 +1,3 @@
-from __future__ import division, absolute_import, print_function
-
 import numpy as np
 from MDAnalysis.coordinates.GRO import GROReader
 from MDAnalysis.topology.GROParser import GROParser

benchmarks/benchmarks/ag_methods.py

@@ -1,5 +1,3 @@
-from __future__ import division, absolute_import, print_function
-
 import MDAnalysis
 import numpy as np
 

benchmarks/benchmarks/analysis/distances.py

@@ -1,5 +1,3 @@
-from __future__ import division, absolute_import, print_function
-
 import MDAnalysis
 import numpy as np
 

benchmarks/benchmarks/analysis/leaflet.py

@@ -1,5 +1,3 @@
-from __future__ import division, absolute_import, print_function
-
 import MDAnalysis
 
 # use a lipid bilayer system for leaflet testing

benchmarks/benchmarks/analysis/psa.py

@@ -1,5 +1,3 @@
-from __future__ import division, absolute_import, print_function
-
 import MDAnalysis
 import numpy as np
 

benchmarks/benchmarks/analysis/rdf.py

@@ -1,5 +1,3 @@
-from __future__ import division, absolute_import, print_function
-
 import MDAnalysis
 
 try:

benchmarks/benchmarks/analysis/rms.py

@@ -1,5 +1,3 @@
-from __future__ import division, absolute_import, print_function
-
 import MDAnalysis
 
 try:

benchmarks/benchmarks/selections.py

@@ -1,5 +1,3 @@
-from __future__ import division, absolute_import, print_function
-
 import MDAnalysis
 
 try:

benchmarks/benchmarks/traj_reader.py

@@ -1,4 +1,3 @@
-from __future__ import division, absolute_import, print_function
 
 try:
     from MDAnalysis.coordinates.DCD import DCDReader

maintainer/adapt_sitemap.py

@@ -3,8 +3,6 @@
 #
 # Adjust path in sitemap.xml
 
-from __future__ import print_function
-
 from xml.etree import ElementTree
 import argparse
 

package/MDAnalysis/__init__.py

@@ -149,7 +149,6 @@
    doi:10.1016/j.jmb.2009.09.009
 
 """
-from __future__ import absolute_import
 
 __all__ = ['Universe', 'as_Universe', 'Writer', 'fetch_mmtf',
            'AtomGroup', 'ResidueGroup', 'SegmentGroup']

package/MDAnalysis/auxiliary/XVG.py

@@ -66,10 +66,6 @@
 .. autofunction:: uncomment
 
 """
-from __future__ import absolute_import
-
-from six import raise_from
-
 import numbers
 import os
 import numpy as np
@@ -150,13 +146,9 @@ def _select_data(self, key):
             try:
                 return self._data[key]
             except IndexError:
-                raise_from(
-                    ValueError(
-                        '{} not a valid index for data with {} '
-                        'columns'.format(key, len(self._data))
-                        ),
-                    None
-                    )
+                errmsg = (f'{key} not a valid index for data with '
+                          f'{len(self._data)} columns')
+                raise ValueError(errmsg) from None
         else:
             return np.array([self._select_data(i) for i in key])
 

package/MDAnalysis/auxiliary/__init__.py

@@ -517,8 +517,6 @@
 
 """
 
-from __future__ import absolute_import
-
 # registry of auxiliary readers
 _AUXREADERS = {}
 

package/MDAnalysis/auxiliary/base.py

@@ -39,10 +39,6 @@
 
 """
 
-from __future__ import division, absolute_import
-import six
-from six.moves import range
-
 import os
 import numbers
 import math
@@ -235,7 +231,7 @@ def _empty_data(self):
         return np.full_like(self.data, np.nan)
 
 
-class AuxReader(six.with_metaclass(_AuxReaderMeta)):
+class AuxReader(metaclass=_AuxReaderMeta):
     """ Base class for auxiliary readers.
 
     Allows iteration over a set of data from a trajectory, additional

package/MDAnalysis/auxiliary/core.py

@@ -28,13 +28,10 @@
 .. autofunction:: get_auxreader_for
 .. autofunction:: auxreader
 """
-from __future__ import absolute_import
-
-from six import raise_from, string_types
-
 from . import _AUXREADERS
 from ..lib import util
 
+
 def get_auxreader_for(auxdata=None, format=None):
     """Return the appropriate auxiliary reader class for *auxdata*/*format*.
 
@@ -65,7 +62,7 @@ def get_auxreader_for(auxdata=None, format=None):
         raise ValueError('Must provide either auxdata or format')
 
     if format is None:
-        if isinstance(auxdata, string_types):
+        if isinstance(auxdata, str):
             ## assume it's a filename?
             format = util.guess_format(auxdata)
         else:
@@ -75,19 +72,14 @@ def get_auxreader_for(auxdata=None, format=None):
         try:
             return _AUXREADERS[format]
         except KeyError:
-            raise_from(
-                ValueError(
-                    "Unknown auxiliary data format for auxdata: "
-                    "{0}".format(auxdata)),
-                None
-                )
+            errmsg = f"Unknown auxiliary data format for auxdata: {auxdata}"
+            raise ValueError(errmsg) from None
     else:
         try:
             return _AUXREADERS[format]
         except KeyError:
-            raise_from(
-                ValueError("Unknown auxiliary data format {0}".format(format)),
-                None)
+            errmsg = f"Unknown auxiliary data format {format}"
+            raise ValueError(errmsg) from None
 
 def auxreader(auxdata, format=None, **kwargs):
     """ Return an auxiliary reader instance for *auxdata*.

package/MDAnalysis/due.py

@@ -26,7 +26,6 @@
 
 """
 
-from __future__ import absolute_import
 __version__ = '0.0.5'
 
 

package/MDAnalysis/selections/__init__.py

@@ -44,9 +44,6 @@
 
 .. autofunction:: get_writer
 """
-from __future__ import absolute_import
-from six import raise_from
-
 import os.path
 
 from .. import _SELECTION_WRITERS
@@ -86,7 +83,6 @@ def get_writer(filename, defaultformat):
     try:
         return _SELECTION_WRITERS[format]
     except KeyError:
-        raise_from(NotImplementedError(
-            "Writing as {0!r} is not implemented;"
-            " only {1!r} will work.".format(format, _SELECTION_WRITERS.keys())),
-            None)
+        errmsg = (f"Writing as {format} is not implemented; only "
+                  f"{ _SELECTION_WRITERS.keys()} will work.")
+        raise NotImplementedError(errmsg) from None

package/MDAnalysis/selections/base.py

@@ -37,16 +37,12 @@
 .. autofunction:: join
 
 """
-from __future__ import absolute_import
-
-import six
-from six.moves import range
-
 import os.path
 
 from ..lib import util
 from . import _SELECTION_WRITERS
 
+
 def join(seq, string="", func=None):
     """Create a list from sequence.
 
@@ -75,7 +71,7 @@ def __init__(cls, name, bases, classdict):
                 _SELECTION_WRITERS[f] = cls
 
 
-class SelectionWriterBase(six.with_metaclass(_Selectionmeta)):
+class SelectionWriterBase(metaclass=_Selectionmeta):
     """Export a selection in MDAnalysis to a format usable in an external package.
 
     The :class:`SelectionWriterBase` writes a selection string to a file

package/MDAnalysis/selections/charmm.py

@@ -39,10 +39,9 @@
 .. _CHARMM: http://www.charmm.org
 .. _CHARMM selection: http://www.charmm.org/documentation/c34b1/select.html
 """
-from __future__ import absolute_import
-
 from . import base
 
+
 class SelectionWriter(base.SelectionWriterBase):
     format = ["CHARMM", "str"]
     ext = "str"

package/MDAnalysis/selections/gromacs.py

@@ -39,10 +39,9 @@
 .. autoclass:: SelectionWriter
    :inherited-members:
 """
-from __future__ import absolute_import
-
 from . import base
 
+
 class SelectionWriter(base.SelectionWriterBase):
     format = ["Gromacs", "ndx"]
     ext = "ndx"

package/MDAnalysis/selections/jmol.py

@@ -39,10 +39,9 @@
 .. _Jmol: http://wiki.jmol.org/index.php/Main_Page
 .. _Jmol selection: http://chemapps.stolaf.edu/jmol/docs/#define
 """
-from __future__ import absolute_import
-
 from . import base
 
+
 class SelectionWriter(base.SelectionWriterBase):
     format = ["Jmol", "spt"]
     ext = "spt"

package/MDAnalysis/selections/pymol.py

@@ -40,10 +40,9 @@
 .. autoclass:: SelectionWriter
    :inherited-members:
 """
-from __future__ import absolute_import
-
 from . import base
 
+
 class SelectionWriter(base.SelectionWriterBase):
     format = ["PyMol", "pml"]
     ext = "pml"

package/MDAnalysis/selections/vmd.py

@@ -47,10 +47,9 @@
    :inherited-members:
 
 """
-from __future__ import absolute_import
-
 from . import base
 
+
 class SelectionWriter(base.SelectionWriterBase):
     format = "VMD"
     ext = "vmd"

package/MDAnalysis/tests/datafiles.py

@@ -36,8 +36,6 @@
    :mod:`MDAnalysisTests` package which must be downloaded from
    http://pypi.python.org/pypi/MDAnalysisTests and installed.
 """
-from __future__ import print_function, absolute_import
-from six import raise_from
 
 try:
     from MDAnalysisTests.datafiles import *
@@ -51,4 +49,4 @@
     print()
     print("and download and install the `MDAnalysisTests-x.y.z.tar.gz'")
     print("that matches your MDAnalysis release.")
-    raise_from(ImportError("MDAnalysisTests package not installed."), None)
+    raise ImportError("MDAnalysisTests package not installed.") from None

package/MDAnalysis/transformations/__init__.py

@@ -56,8 +56,6 @@ def wrapped(ts):
 
 """
 
-from __future__ import absolute_import
-
 from .translate import translate, center_in_box
 from .rotate import rotateby
 from .positionaveraging import PositionAverager

package/MDAnalysis/transformations/fit.py

@@ -32,9 +32,6 @@
 .. autofunction:: fit_rot_trans
 
 """
-from __future__ import absolute_import
-from six import raise_from
-
 import numpy as np
 from functools import partial
 
@@ -91,14 +88,14 @@ def fit_translation(ag, reference, plane=None, weights=None):
         try:
             plane = axes[plane]
         except (TypeError, KeyError):
-            raise_from(ValueError('{} is not a valid plane'.format(plane)), None)
+            raise ValueError(f'{plane} is not a valid plane') from None
     try:
         if ag.atoms.n_residues != reference.atoms.n_residues:
-            raise ValueError("{} and {} have mismatched number of residues".format(ag,reference))
+            errmsg = f"{ag} and {reference} have mismatched number of residues"
+            raise ValueError(errmsg)
     except AttributeError:
-        raise_from(
-            AttributeError("{} or {} is not valid Universe/AtomGroup".format(ag,reference)),
-            None)
+        errmsg = f"{ag} or {reference} is not valid Universe/AtomGroup"
+        raise AttributeError(errmsg) from None
     ref, mobile = align.get_matching_atoms(reference.atoms, ag.atoms)
     weights = align.get_weights(ref.atoms, weights=weights)
     ref_com = ref.center(weights)
@@ -168,12 +165,14 @@ def fit_rot_trans(ag, reference, plane=None, weights=None):
         try:
             plane = axes[plane]
         except (TypeError, KeyError):
-            raise_from(ValueError('{} is not a valid plane'.format(plane)), None)
+            raise ValueError(f'{plane} is not a valid plane') from None
     try:
         if ag.atoms.n_residues != reference.atoms.n_residues:
-            raise ValueError("{} and {} have mismatched number of residues".format(ag,reference))
+            errmsg = f"{ag} and {reference} have mismatched number of residues"
+            raise ValueError(errmsg)
     except AttributeError:
-        raise_from(AttributeError("{} or {} is not valid Universe/AtomGroup".format(ag,reference)), None)
+        errmsg = f"{ag} or {reference} is not valid Universe/AtomGroup"
+        raise AttributeError(errmsg) from None
     ref, mobile = align.get_matching_atoms(reference.atoms, ag.atoms)
     weights = align.get_weights(ref.atoms, weights=weights)
     ref_com = ref.center(weights)

package/MDAnalysis/transformations/positionaveraging.py

@@ -32,13 +32,10 @@
 .. autoclass:: PositionAverager
 
 """
-from __future__ import absolute_import
-
 import numpy as np
 import warnings
 
 
-
 class PositionAverager(object):  
     """