Remove py2 things from coordinates & topology (#2759)

* Removes py2 things from coordinates * Removes py2 things from coordinate tests * Removes py2 things from topology
MDAnalysis · Jun 16, 2020 · 0d951a2 · 0d951a2
1 parent 34288cc
commit 0d951a2
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Showing 104 changed files with 65 additions and 330 deletions.
diff --git a/package/MDAnalysis/coordinates/DLPoly.py b/package/MDAnalysis/coordinates/DLPoly.py
@@ -28,11 +28,6 @@
 
 .. _Poly: http://www.stfc.ac.uk/SCD/research/app/ccg/software/DL_POLY/44516.aspx
 """
-from __future__ import (absolute_import, division,
-                        print_function, unicode_literals)
-
-from six.moves import range
-
 import numpy as np
 
 from . import base

diff --git a/package/MDAnalysis/coordinates/DMS.py b/package/MDAnalysis/coordinates/DMS.py
@@ -32,8 +32,6 @@
 .. _Desmond: http://www.deshawresearch.com/resources_desmond.html
 .. _DMS: http://www.deshawresearch.com/Desmond_Users_Guide-0.7.pdf
 """
-from __future__ import absolute_import
-
 import numpy as np
 import sqlite3
 

diff --git a/package/MDAnalysis/coordinates/GMS.py b/package/MDAnalysis/coordinates/GMS.py
@@ -37,8 +37,6 @@
    :members:
 
 """
-from __future__ import absolute_import
-
 import os
 import errno
 import re

diff --git a/package/MDAnalysis/coordinates/GSD.py b/package/MDAnalysis/coordinates/GSD.py
@@ -45,9 +45,6 @@
    :inherited-members:
 
 """
-from __future__ import absolute_import, division
-from six import raise_from
-
 import numpy as np
 import os
 import gsd.hoomd
@@ -103,7 +100,7 @@ def _read_frame(self, frame):
         try :
             myframe = self._file[frame]
         except IndexError:
-            raise_from(IOError, None)
+            raise IOError from None
 
         # set frame number
         self._frame = frame

diff --git a/package/MDAnalysis/coordinates/INPCRD.py b/package/MDAnalysis/coordinates/INPCRD.py
@@ -37,9 +37,6 @@
    :members:
 
 """
-from __future__ import absolute_import, division, print_function, unicode_literals
-
-from six.moves import range
 
 from . import base
 

diff --git a/package/MDAnalysis/coordinates/LAMMPS.py b/package/MDAnalysis/coordinates/LAMMPS.py
@@ -121,10 +121,6 @@
    :inherited-members:
 
 """
-from __future__ import absolute_import
-
-from six.moves import zip, range, map
-from six import raise_from
 import os
 import numpy as np
 
@@ -161,9 +157,8 @@ def __init__(self, *args, **kwargs):
                 if units.unit_types[unit] != unit_type:
                     raise TypeError("LAMMPS DCDWriter: wrong unit {0!r} for unit type {1!r}".format(unit, unit_type))
             except KeyError:
-                raise_from(
-                    ValueError("LAMMPS DCDWriter: unknown unit {0!r}".format(unit)),
-                    None)
+                errmsg = f"LAMMPS DCDWriter: unknown unit {unit}"
+                raise ValueError(errmsg) from None
         super(DCDWriter, self).__init__(*args, **kwargs)
 
 
@@ -343,10 +338,9 @@ def _write_bonds(self, bonds):
                 self.f.write('{:d} {:d} '.format(i, int(bond.type))+\
                         ' '.join((bond.atoms.indices + 1).astype(str))+'\n')
             except TypeError:
-                raise_from(TypeError('LAMMPS DATAWriter: Trying to write bond, '
-                                'but bond type {} is not '
-                                'numerical.'.format(bond.type)),
-                            None)
+                errmsg = (f"LAMMPS DATAWriter: Trying to write bond, but bond "
+                          f"type {bond.type} is not numerical.")
+                raise TypeError(errmsg) from None
 
     def _write_dimensions(self, dimensions):
         """Convert dimensions to triclinic vectors, convert lengths to native
@@ -405,11 +399,9 @@ def write(self, selection, frame=None):
         try:
             atoms.types.astype(np.int32)
         except ValueError:
-            raise_from(
-                ValueError(
-                    'LAMMPS.DATAWriter: atom types must be '
-                    'convertible to integers'),
-                    None)
+            errmsg = ("LAMMPS.DATAWriter: atom types must be convertible to "
+                      "integers")
+            raise ValueError(errmsg) from None
 
         try:
             velocities = atoms.velocities

diff --git a/package/MDAnalysis/coordinates/MMTF.py b/package/MDAnalysis/coordinates/MMTF.py
@@ -41,8 +41,6 @@
 .. _MMTF: https://mmtf.rcsb.org/
 
 """
-from __future__ import absolute_import
-
 import mmtf
 
 from . import base

diff --git a/package/MDAnalysis/coordinates/MOL2.py b/package/MDAnalysis/coordinates/MOL2.py
@@ -111,9 +111,6 @@
     1   BENZENE 1   PERM    0   ****    ****    0   ROOT
 
 """
-from __future__ import absolute_import
-from six import raise_from
-
 import numpy as np
 
 from . import base
@@ -219,9 +216,9 @@ def _read_frame(self, frame):
         try:
             block = self.frames[frame]
         except IndexError:
-            raise_from(IOError("Invalid frame {0} for trajectory with length {1}"
-                          "".format(frame, len(self))),
-                       None)
+            errmsg = (f"Invalid frame {frame} for trajectory with length "
+                      f"{len(self)}")
+            raise IOError(errmsg) from None
 
         sections, coords = self.parse_block(block)
 
@@ -319,9 +316,8 @@ def encode_block(self, obj):
         try:
             molecule = ts.data['molecule']
         except KeyError:
-            raise_from(NotImplementedError(
-                "MOL2Writer cannot currently write non MOL2 data"),
-                None)
+            errmsg = "MOL2Writer cannot currently write non MOL2 data"
+            raise NotImplementedError(errmsg) from None
 
         # Need to remap atom indices to 1 based in this selection
         mapping = {a: i for i, a in enumerate(obj.atoms, start=1)}

diff --git a/package/MDAnalysis/coordinates/PDB.py b/package/MDAnalysis/coordinates/PDB.py
@@ -140,11 +140,7 @@
     http://www.wwpdb.org/documentation/file-format-content/format32/v3.2.html
 
 """
-from __future__ import absolute_import
-
-from six.moves import range, zip
-from six import raise_from, StringIO, BytesIO
-
+from io import StringIO, BytesIO
 import os
 import errno
 import itertools
@@ -394,7 +390,7 @@ def _read_frame(self, frame):
             start = self._start_offsets[frame]
             stop = self._stop_offsets[frame]
         except IndexError:  # out of range of known frames
-            raise_from(IOError, None)
+            raise IOError from None
 
         pos = 0
         occupancy = np.ones(self.n_atoms)
@@ -940,12 +936,9 @@ def _write_next_frame(self, ts=None, **kwargs):
             try:
                 ts = self.ts
             except AttributeError:
-                raise_from(
-                    NoDataError(
-                        "PBDWriter: no coordinate data to write to "
-                        "trajectory file"
-                        ),
-                    None)
+                errmsg = ("PBDWriter: no coordinate data to write to "
+                          "trajectory file")
+                raise NoDataError(errmsg) from None
         self._check_pdb_coordinates()
         self._write_timestep(ts, **kwargs)
 

diff --git a/package/MDAnalysis/coordinates/PDBQT.py b/package/MDAnalysis/coordinates/PDBQT.py
@@ -38,7 +38,6 @@
    http://autodock.scripps.edu/
 """
 
-from __future__ import absolute_import
 import os
 import errno
 import itertools

diff --git a/package/MDAnalysis/coordinates/ParmEd.py b/package/MDAnalysis/coordinates/ParmEd.py
@@ -72,7 +72,6 @@
 
 
 """
-from __future__ import absolute_import
 import functools
 
 from . import base

diff --git a/package/MDAnalysis/coordinates/TXYZ.py b/package/MDAnalysis/coordinates/TXYZ.py
@@ -45,10 +45,6 @@
    :inherited-members:
 
 """
-from __future__ import absolute_import, division
-from six.moves import range
-from six import raise_from
-
 import numpy as np
 import os
 import errno
@@ -155,7 +151,7 @@ def _read_next_timestep(self, ts=None):
             ts.frame += 1
             return ts
         except (ValueError, IndexError) as err:
-            raise_from(EOFError(err), None)
+            raise EOFError(err) from None
 
     def _reopen(self):
         self.close()

diff --git a/package/MDAnalysis/coordinates/XDR.py b/package/MDAnalysis/coordinates/XDR.py
@@ -33,8 +33,6 @@
 MDAnalysis.coordinates.TRR: Read and write GROMACS TRR trajectory files.
 MDAnalysis.lib.formats.libmdaxdr: Low level xdr format reader
 """
-from __future__ import absolute_import
-import six
 
 import errno
 import numpy as np
@@ -83,7 +81,7 @@ def read_numpy_offsets(filename):
 
     """
     try:
-        return {k: v for k, v in six.iteritems(np.load(filename))}
+        return {k: v for k, v in np.load(filename).items()}
     except IOError:
         warnings.warn("Failed to load offsets file {}\n".format(filename))
         return False

diff --git a/package/MDAnalysis/coordinates/__init__.py b/package/MDAnalysis/coordinates/__init__.py
@@ -707,11 +707,8 @@ class can choose an appropriate reader automatically.
    raw :class:`~MDAnalysis.coordinates.base.Timestep` objects.
 
 """
-from __future__ import absolute_import
 __all__ = ['reader', 'writer']
 
-import six
-
 from . import base
 from .core import reader, writer
 from . import chain

diff --git a/package/MDAnalysis/coordinates/chain.py b/package/MDAnalysis/coordinates/chain.py
@@ -41,8 +41,6 @@
    .. automethod:: _chained_iterator
 
 """
-from __future__ import absolute_import
-
 import warnings
 
 import os.path

diff --git a/package/MDAnalysis/coordinates/core.py b/package/MDAnalysis/coordinates/core.py
@@ -37,9 +37,6 @@
 .. autofunction:: get_writer_for
 
 """
-from __future__ import absolute_import
-
-import six
 
 from ..lib import util
 from ..lib.mdamath import triclinic_box, triclinic_vectors, box_volume
@@ -84,14 +81,8 @@ def reader(filename, format=None, **kwargs):
     try:
         return Reader(filename, **kwargs)
     except ValueError:
-        six.raise_from(
-            TypeError(
-                'Unable to read {fn} with {r}.'.format(
-                    fn=filename,
-                    r=Reader
-                    )
-                ),
-            None)
+        errmsg = f'Unable to read {filename} with {Reader}.'
+        raise TypeError(errmsg) from None
 
 
 def writer(filename, n_atoms=None, **kwargs):

diff --git a/package/MDAnalysis/coordinates/memory.py b/package/MDAnalysis/coordinates/memory.py
@@ -184,8 +184,6 @@
    :inherited-members:
 
 """
-from __future__ import absolute_import
-from six import raise_from
 import logging
 import errno
 import numpy as np
@@ -319,10 +317,9 @@ def __init__(self, coordinate_array, order='fac',
             if coordinate_array.ndim == 2 and coordinate_array.shape[1] == 3:
                 coordinate_array = coordinate_array[np.newaxis, :, :]
         except AttributeError:
-            raise_from(TypeError("The input has to be a numpy.ndarray that "
-                            "corresponds to the layout specified by the "
-                            "'order' keyword."),
-                        None)
+            errmsg = ("The input has to be a numpy.ndarray that corresponds "
+                      "to the layout specified by the 'order' keyword.")
+            raise TypeError(errmsg) from None
 
         self.set_array(coordinate_array, order)
         self.n_frames = \
@@ -334,10 +331,9 @@ def __init__(self, coordinate_array, order='fac',
             try:
                 velocities = np.asarray(velocities, dtype=np.float32)
             except ValueError:
-                raise_from(
-                    TypeError("'velocities' must be array-like got {}"
-                              "".format(type(velocities))),
-                    None)
+                errmsg = (f"'velocities' must be array-like got "
+                          f"{type(velocities)}")
+                raise TypeError(errmsg) from None
             # if single frame, make into array of 1 frame
             if velocities.ndim == 2:
                 velocities = velocities[np.newaxis, :, :]
@@ -354,9 +350,8 @@ def __init__(self, coordinate_array, order='fac',
             try:
                 forces = np.asarray(forces, dtype=np.float32)
             except ValueError:
-                raise_from(TypeError("'forces' must be array like got {}"
-                                     "".format(type(forces))),
-                           None)
+                errmsg = f"'forces' must be array like got {type(forces)}"
+                raise TypeError(errmsg) from None
             if forces.ndim == 2:
                 forces = forces[np.newaxis, :, :]
             if not forces.shape == self.coordinate_array.shape:
@@ -386,9 +381,9 @@ def __init__(self, coordinate_array, order='fac',
             try:
                 dimensions = np.asarray(dimensions, dtype=np.float32)
             except ValueError:
-                raise_from(TypeError("'dimensions' must be array-like got {}"
-                                     "".format(type(dimensions))),
-                           None)
+                errmsg = (f"'dimensions' must be array-like got "
+                          f"{type(dimensions)}")
+                raise TypeError(errmsg) from None
             if dimensions.shape == (6,):
                 # single box, tile this to trajectory length
                 # allows modifying the box of some frames

diff --git a/package/MDAnalysis/coordinates/null.py b/package/MDAnalysis/coordinates/null.py
@@ -37,8 +37,6 @@
    :members:
 
 """
-from __future__ import absolute_import
-
 from . import base
 
 

diff --git a/package/MDAnalysis/topology/CRDParser.py b/package/MDAnalysis/topology/CRDParser.py
@@ -45,9 +45,6 @@
    :inherited-members:
 
 """
-from __future__ import absolute_import
-from six import raise_from
-
 import numpy as np
 
 from ..lib.util import openany, FORTRANReader
@@ -123,9 +120,9 @@ def parse(self, **kwargs):
                     (serial, resnum, resName, name,
                      x, y, z, segid, resid, tempFactor) = r.read(line)
                 except Exception:
-                    raise_from(ValueError("Check CRD format at line {0}: {1}"
-                                     "".format(linenum + 1, line.rstrip())),
-                               None)
+                    errmsg = (f"Check CRD format at line {linenum + 1}: "
+                              f"{line.rstrip()}")
+                    raise ValueError(errmsg) from None
 
                 atomids.append(serial)
                 atomnames.append(name)

diff --git a/package/MDAnalysis/topology/DLPolyParser.py b/package/MDAnalysis/topology/DLPolyParser.py
@@ -35,9 +35,6 @@
 
 .. _Poly: http://www.stfc.ac.uk/SCD/research/app/ccg/software/DL_POLY/44516.aspx
 """
-from __future__ import (absolute_import, division,
-                        print_function, unicode_literals)
-
 import numpy as np
 
 from . import guessers
-Original file line number
+Diff line change
@@ Expand Up / @@ -72,7 +72,6 @@ @@
     """
-    from __future__ import absolute_import
     import functools
     from . import base
@@ Expand Down @@