Enable Pylint warning unused-import

package/.pylintrc

@@ -185,6 +185,7 @@ enable=abstract-class-instantiated,
        unsubscriptable-object,
        unsupported-binary-operation,
        unsupported-membership-test,
+       unused-import,
        unused-format-string-argument,
        unused-format-string-key,
        useless-else-on-loop,
@@ -260,7 +261,6 @@ enable=abstract-class-instantiated,
        # unnecessary-semicolon,
        # unpacking-non-sequence,
        # unused-argument,
-       # unused-import,
        # unused-variable,
        # unused-wildcard-import,
        # used-before-assignment,
@@ -609,4 +609,4 @@ analyse-fallback-blocks=no
 
 # Exceptions that will emit a warning when being caught. Defaults to
 # "Exception"
-overgeneral-exceptions=Exception
+overgeneral-exceptions=builtins.Exception

package/AUTHORS

@@ -240,6 +240,7 @@ Chronological list of authors
   - Sampurna Mukherjee
   - Leon Wehrhan
   - Valerij Talagayev
+  - Daniil Vakhrameev
 
 
 

package/CHANGELOG

@@ -55,6 +55,7 @@ Enhancements
    DOI 10.1021/acs.jpcb.7b11988. (Issue #2039, PR #4524)
 
 Changes
+ * Enabled pylint warning 'unused-imports' (issue #1295, PR #4518)
  * As per SPEC0 the minimum supported Python version has been raised
    to 3.10 (PR #4502)
  * MDAnalysis.analysis.hole2 is now directly imported from the mdakit

package/MDAnalysis/analysis/bat.py

@@ -158,7 +158,6 @@ class to calculate dihedral angles for a given set of atoms or residues
 
 """
 import logging
-import warnings
 
 import numpy as np
 import copy

package/MDAnalysis/analysis/contacts.py

@@ -208,10 +208,7 @@ def is_any_closer(r, r0, dist=2.5):
 .. footbibliography::
 
 """
-import os
-import errno
 import warnings
-import bz2
 import functools
 
 import numpy as np
@@ -220,7 +217,6 @@ def is_any_closer(r, r0, dist=2.5):
 
 import MDAnalysis
 import MDAnalysis.lib.distances
-from MDAnalysis.lib.util import openany
 from MDAnalysis.analysis.distances import distance_array
 from MDAnalysis.core.groups import AtomGroup, UpdatingAtomGroup
 from .base import AnalysisBase

package/MDAnalysis/analysis/density.py

@@ -151,23 +151,12 @@
 
 """
 import numpy as np
-import sys
-import os
-import os.path
-import errno
 import warnings
 
 from gridData import Grid
 
-import MDAnalysis
-from MDAnalysis.core import groups
-from MDAnalysis.lib.util import (fixedwidth_bins, iterable, asiterable,
-                                 deprecate,)
-from MDAnalysis.lib import NeighborSearch as NS
-from MDAnalysis import NoDataError, MissingDataWarning
+from MDAnalysis.lib.util import fixedwidth_bins
 from .. import units
-from ..lib import distances
-from MDAnalysis.lib.log import ProgressBar
 
 from .base import AnalysisBase
 

package/MDAnalysis/analysis/distances.py

@@ -53,7 +53,6 @@
 from MDAnalysis.lib.distances import calc_bonds
 
 
-import warnings
 import logging
 logger = logging.getLogger("MDAnalysis.analysis.distances")
 

package/MDAnalysis/analysis/encore/confdistmatrix.py

@@ -40,11 +40,8 @@ class to compute an RMSD matrix in such a way is also available.
 from getpass import getuser
 from socket import gethostname
 from datetime import datetime
-from time import sleep
 import logging
-import warnings
 
-from ...core.universe import Universe
 
 from ..align import rotation_matrix
 

package/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py

@@ -33,7 +33,6 @@
 .. versionadded:: 0.16.0
 
 """
-import logging
 import warnings
 
 # Import native affinity propagation implementation

package/MDAnalysis/analysis/encore/similarity.py

@@ -165,7 +165,6 @@
 .. All functions are included via automodule :members:.
 
 """
-import warnings
 import logging
 
 import numpy as np

package/MDAnalysis/analysis/encore/utils.py

@@ -25,7 +25,6 @@
 from multiprocessing import Process, Manager
 from joblib import cpu_count
 import numpy as np
-import sys
 
 import MDAnalysis as mda
 from ...coordinates.memory import MemoryReader

package/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py

@@ -714,7 +714,7 @@ def analysis(current, output, u, **kwargs):
 from ..base import AnalysisBase
 from MDAnalysis.lib.NeighborSearch import AtomNeighborSearch
 from MDAnalysis.lib.distances import capped_distance, calc_angles
-from MDAnalysis import NoDataError, MissingDataWarning, SelectionError
+from MDAnalysis import NoDataError, MissingDataWarning
 
 logger = logging.getLogger('MDAnalysis.analysis.WaterBridgeAnalysis')
 

package/MDAnalysis/analysis/legacy/x3dna.py

@@ -117,7 +117,6 @@
 .. autoexception:: ApplicationError
 
 """
-import glob
 import os
 import errno
 import shutil
@@ -131,8 +130,8 @@
 import numpy as np
 import matplotlib.pyplot as plt
 
-from MDAnalysis import ApplicationError
-from MDAnalysis.lib.util import which, realpath, asiterable, deprecate
+from MDAnalysis import ApplicationError # pylint: disable=unused-import # module will be removed in 3.0.0
+from MDAnalysis.lib.util import which, realpath, asiterable, deprecate # pylint: disable=unused-import
 
 import logging
 

package/MDAnalysis/analysis/lineardensity.py

@@ -28,8 +28,6 @@
 cartesian axes [xyz] of the simulation cell. Works only for orthorombic,
 fixed volume cells (thus for simulations in canonical NVT ensemble).
 """
-import os.path as path
-
 import numpy as np
 import warnings
 

package/MDAnalysis/analysis/nucleicacids.py

@@ -70,7 +70,7 @@
 
 import MDAnalysis as mda
 from .distances import calc_bonds
-from .base import AnalysisBase, Results
+from .base import AnalysisBase
 from MDAnalysis.core.groups import Residue, ResidueGroup
 
 

package/MDAnalysis/analysis/psa.py

@@ -46,7 +46,7 @@
 
 import warnings
 
-from pathsimanalysis import (
+from pathsimanalysis import ( # pylint: disable=unused-import # will be removed completely in version 3.0.0
     get_path_metric_func,
     sqnorm,
     get_msd_matrix,

package/MDAnalysis/analysis/rms.py

@@ -168,7 +168,7 @@
 
 import MDAnalysis.lib.qcprot as qcp
 from MDAnalysis.analysis.base import AnalysisBase
-from MDAnalysis.exceptions import SelectionError, NoDataError
+from MDAnalysis.exceptions import SelectionError
 from MDAnalysis.lib.util import asiterable, iterable, get_weights
 
 

package/MDAnalysis/analysis/waterdynamics.py

@@ -41,7 +41,7 @@
 """
 import warnings
 
-from waterdynamics.waterdynamics import (
+from waterdynamics.waterdynamics import ( # pylint: disable=unused-import #will be removed in version 3.0.0
     WaterOrientationalRelaxation,
     AngularDistribution,
     MeanSquareDisplacement,

package/MDAnalysis/auxiliary/base.py

@@ -50,7 +50,6 @@
 import numpy as np
 
 from ..lib.util import asiterable, anyopen
-from .. import units
 
 from . import _AUXREADERS
 from .core import auxreader

package/MDAnalysis/converters/ParmEd.py

@@ -84,7 +84,6 @@
 from . import base
 from ..coordinates.base import SingleFrameReaderBase
 from ..topology.tables import SYMB2Z
-from ..core.universe import Universe
 from ..exceptions import NoDataError
 
 

package/MDAnalysis/coordinates/DCD.py

@@ -56,15 +56,11 @@
    :inherited-members:
 
 """
-import os
-import errno
 import numpy as np
-import struct
-import types
 import warnings
 
 from .. import units as mdaunits  # use mdaunits instead of units to avoid a clash
-from . import base, core
+from . import base
 from ..lib.formats.libdcd import DCDFile
 from ..lib.mdamath import triclinic_box
 from ..lib.util import store_init_arguments

package/MDAnalysis/coordinates/DLPoly.py

@@ -31,7 +31,7 @@
 import numpy as np
 
 from . import base
-from . import core
+from ..lib.mdamath import triclinic_box
 from ..lib import util
 from ..lib.util import cached, store_init_arguments
 
@@ -123,7 +123,7 @@ def _read_first_frame(self):
         if has_forces:
             ts._forces = forces
         if not imcon == 0:
-            ts.dimensions = core.triclinic_box(*unitcell)
+            ts.dimensions = triclinic_box(*unitcell)
 
         ts.frame = 0
 
@@ -176,7 +176,7 @@ def _read_next_timestep(self, ts=None):
             unitcell[0] = self._file.readline().split()
             unitcell[1] = self._file.readline().split()
             unitcell[2] = self._file.readline().split()
-            ts.dimensions = core.triclinic_box(*unitcell)            
+            ts.dimensions = triclinic_box(*unitcell)            
 
         # If ids are given, put them in here
         # and later sort by them

package/MDAnalysis/coordinates/DMS.py

@@ -36,7 +36,7 @@
 import sqlite3
 
 from . import base
-from .core import triclinic_box
+from ..lib.mdamath import triclinic_box
 
 
 class DMSReader(base.SingleFrameReaderBase):

package/MDAnalysis/coordinates/FHIAIMS.py

@@ -102,18 +102,15 @@
 .. _FHI-AIMS format: https://doi.org/10.6084/m9.figshare.12413477.v1
 
 """
-import re
-
 import itertools
 import warnings
 
 import numpy as np
 
 from . import base
-from .core import triclinic_box, triclinic_vectors
+from ..lib.mdamath import triclinic_box
 from ..exceptions import NoDataError
 from ..lib import util
-from ..lib import mdamath
 
 
 class FHIAIMSReader(base.SingleFrameReaderBase):

package/MDAnalysis/coordinates/GRO.py

@@ -108,7 +108,7 @@
 import numpy as np
 
 from . import base
-from .core import triclinic_box, triclinic_vectors
+from ..lib.mdamath import triclinic_box
 from ..exceptions import NoDataError
 from ..lib import util
 from .timestep import Timestep

package/MDAnalysis/coordinates/H5MD.py

@@ -210,10 +210,11 @@
 
 import numpy as np
 import MDAnalysis as mda
-from . import base, core
+from . import base
 from ..exceptions import NoDataError
 from ..due import due, Doi
 from MDAnalysis.lib.util import store_init_arguments
+from MDAnalysis.lib.mdamath import triclinic_box
 try:
     import h5py
 except ImportError:
@@ -652,7 +653,7 @@ def _read_frame(self, frame):
             if edges.shape == (3,):
                 ts.dimensions = [*edges, 90, 90, 90]
             else:
-                ts.dimensions = core.triclinic_box(*edges)
+                ts.dimensions = triclinic_box(*edges)
         else:
             ts.dimensions = None
 

package/MDAnalysis/coordinates/PDB.py

@@ -155,7 +155,6 @@
 from ..lib.util import store_init_arguments
 from . import base
 from .timestep import Timestep
-from ..topology.core import guess_atom_element
 from ..exceptions import NoDataError
 
 

package/MDAnalysis/coordinates/PQR.py

@@ -106,7 +106,6 @@
 .. _PDB:     http://www.wwpdb.org/documentation/file-format
 """
 import itertools
-import numpy as np
 import warnings
 
 from ..lib import util

package/MDAnalysis/coordinates/ParmEd.py

@@ -21,8 +21,6 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 import warnings
-from ..converters.ParmEd import (ParmEdConverter, ParmEdReader,
-                                 get_indices_from_subset, MDA2PMD,)
 
 
 warnings.warn(

package/MDAnalysis/coordinates/TRR.py

@@ -32,7 +32,6 @@
 MDAnalysis.coordinates.XDR: BaseReader/Writer for XDR based formats
 """
 import errno
-from . import base
 from .XDR import XDRBaseReader, XDRBaseWriter
 from ..lib.formats.libmdaxdr import TRRFile
 from ..lib.mdamath import triclinic_vectors, triclinic_box

package/MDAnalysis/coordinates/TRZ.py

@@ -55,7 +55,7 @@
 from .timestep import Timestep
 from ..lib import util
 from ..lib.util import cached, store_init_arguments
-from .core import triclinic_box, triclinic_vectors
+from ..lib.mdamath import triclinic_box, triclinic_vectors
 
 
 class TRZReader(base.ReaderBase):

package/MDAnalysis/coordinates/TXYZ.py

@@ -45,13 +45,12 @@
    :inherited-members:
 
 """
-import numpy as np
 import os
 import errno
 
 from ..lib import util
 from . import base
-from ..lib.util import openany, cached, store_init_arguments
+from ..lib.util import cached, store_init_arguments
 from .timestep import Timestep
 
 class TXYZReader(base.ReaderBase):

package/MDAnalysis/coordinates/XTC.py

@@ -33,7 +33,6 @@
 """
 
 import errno
-from . import base
 from .XDR import XDRBaseReader, XDRBaseWriter
 from ..lib.formats.libmdaxdr import XTCFile
 from ..lib.mdamath import triclinic_vectors, triclinic_box