Get rid of @attr

testsuite/MDAnalysisTests/analysis/test_align.py

@@ -33,7 +33,6 @@
                            assert_array_equal, assert_array_almost_equal,
                            assert_)
 import numpy as np
-from nose.plugins.attrib import attr
 
 from MDAnalysisTests.datafiles import PSF, DCD, FASTA, ALIGN_BOUND, ALIGN_UNBOUND
 from MDAnalysisTests import executable_not_found, parser_not_found, tempdir
@@ -262,7 +261,6 @@ def _assert_rmsd(self, fitted, frame, desired, weights=None):
                             err_msg="frame {0:d} of fit does not have "
                             "expected RMSD".format(frame))
 
-    @attr('issue')
     def test_alignto_checks_selections(self):
         """Testing that alignto() fails if selections do not
         match (Issue 143)"""
@@ -307,7 +305,6 @@ def setUp(self):
     def tearDown(self):
         del self.tempdir
 
-    @attr('issue')
     def test_fasta2select_aligned(self):
         """test align.fasta2select() on aligned FASTA (Issue 112)"""
         sel = align.fasta2select(self.seq, is_aligned=True)
@@ -317,7 +314,6 @@ def test_fasta2select_aligned(self):
         assert_equal(len(sel['mobile']), 30623,
                      err_msg="selection string has unexpected length")
 
-    @attr('issue')
     @dec.skipif(executable_not_found("clustalw2"),
                 msg="Test skipped because clustalw2 executable not found")
     def test_fasta2select_ClustalW(self):

testsuite/MDAnalysisTests/analysis/test_gnm.py

@@ -28,11 +28,11 @@
 from numpy.testing import (assert_equal, assert_almost_equal)
 import numpy as np
 
-from nose.plugins.attrib import attr
 
 from MDAnalysisTests.datafiles import GRO, XTC
 from MDAnalysisTests import tempdir
 
+
 class TestGNM(TestCase):
     def setUp(self):
         self.tmpdir = tempdir.TempDir()
@@ -82,7 +82,6 @@ def test_generate_kirchoff(self):
             0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
             0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
 
-    @attr('slow')
     def test_closeContactGNMAnalysis(self):
         gnm = MDAnalysis.analysis.gnm.closeContactGNMAnalysis(self.universe, weights="size")
         gnm.run()
@@ -113,7 +112,6 @@ def test_closeContactGNMAnalysis(self):
             0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
             0.0, 0.0, -2.263157894736841, -0.24333213169614382])
 
-    @attr('slow')
     def test_closeContactGNMAnalysis_weights_None(self):
         gnm = MDAnalysis.analysis.gnm.closeContactGNMAnalysis(self.universe, weights=None)
         gnm.run()

testsuite/MDAnalysisTests/analysis/test_hole.py

@@ -35,8 +35,6 @@
 import matplotlib
 import mpl_toolkits.mplot3d
 
-import nose
-from nose.plugins.attrib import attr
 
 import os
 import errno
@@ -74,7 +72,6 @@ def tearDown(self):
         del self.H
         del self.tempdir
 
-    @attr('slow')
     @dec.skipif(executable_not_found("hole"), msg="Test skipped because HOLE not found")
     def test_HOLE(self):
         profiles = self.H.profiles.values()
@@ -90,7 +87,6 @@ def test_HOLE(self):
         assert_almost_equal(p.radius.min(), 1.19707,
                             err_msg="wrong min HOLE radius")
 
-    @attr('slow')
     @dec.skipif(executable_not_found("hole"), msg="Test skipped because HOLE not found")
     def test_vmd_surface(self):
         with in_dir(self.tempdir.name):
@@ -127,7 +123,6 @@ def tearDownClass(cls):
         del cls.universe
 
     # This is VERY slow on 11 frames so we just take 2
-    @attr('slow')
     @dec.skipif(executable_not_found("hole"), msg="Test skipped because HOLE not found")
     def test_HOLEtraj(self):
         assert_array_equal(sorted(self.H.profiles.keys()), self.frames,
@@ -143,29 +138,25 @@ def test_HOLEtraj(self):
         assert_array_almost_equal(data[2], [1.19819, 1.29628],
                                   err_msg="wrong minimum radius")
 
-    @attr('slow')
     @dec.skipif(executable_not_found("hole"), msg="Test skipped because HOLE not found")
     def test_min_radius(self):
         assert_array_almost_equal(self.H.min_radius(),
                                   np.array([[ 5.     ,  1.19819],
                                             [ 6.     ,  1.29628]]),
                                   err_msg="min_radius() array not correct")
 
-    @attr('slow')
     @dec.skipif(executable_not_found("hole"), msg="Test skipped because HOLE not found")
     def test_plot(self):
         ax = self.H.plot(label=True)
         assert_(isinstance(ax, matplotlib.axes.Axes),
                 msg="H.plot() did not produce an Axes instance")
 
-    @attr('slow')
     @dec.skipif(executable_not_found("hole"), msg="Test skipped because HOLE not found")
     def test_plot3D(self):
         ax = self.H.plot3D()
         assert_(isinstance(ax, mpl_toolkits.mplot3d.Axes3D),
                 msg="H.plot3D() did not produce an Axes3D instance")
 
-    @attr('slow')
     @dec.skipif(executable_not_found("hole"), msg="Test skipped because HOLE not found")
     def test_plot3D_rmax(self):
         ax = self.H.plot3D(rmax=2.5)
@@ -184,8 +175,6 @@ def setUp(self):
         except ImportError:
             pass
 
-    @attr('slow')
-    @attr('issue')
     @dec.skipif(rlimits_missing, msg="Test skipped because platform does not allow setting rlimits")
     @dec.skipif(executable_not_found("hole"), msg="Test skipped because HOLE not found")
     def test_hole_module_fd_closure(self):

testsuite/MDAnalysisTests/coordinates/base.py

@@ -24,7 +24,6 @@
 import numpy as np
 import pytest
 from six.moves import zip, range
-from nose.plugins.attrib import attr
 from unittest import TestCase
 from numpy.testing import (assert_equal, assert_raises, assert_almost_equal,
                            assert_array_almost_equal, raises, assert_allclose,
@@ -622,7 +621,6 @@ def test_set_triclinic_vectors(self, ts):
         assert_equal(ts.dimensions, self.newbox)
         assert_allclose(ts._unitcell, self.unitcell)
 
-    @attr('issue')
     def test_coordinate_getter_shortcuts(self, ts):
         """testing that reading _x, _y, and _z works as expected
         # (Issue 224) (TestTimestep)"""

testsuite/MDAnalysisTests/coordinates/test_chainreader.py

@@ -25,7 +25,6 @@
 import os
 from six.moves import zip
 
-from nose.plugins.attrib import attr
 from numpy.testing import (assert_equal, assert_array_equal,
                            assert_almost_equal, dec)
 from unittest import TestCase
@@ -156,22 +155,19 @@ class TestChainReaderFormats(TestCase):
     """Test of ChainReader with explicit formats (Issue 76)."""
 
     @staticmethod
-    @attr('issue')
     def test_set_all_format_tuples():
         universe = mda.Universe(GRO, [(PDB, 'pdb'), (XTC, 'xtc'),
                                       (TRR, 'trr')])
         assert_equal(universe.trajectory.n_frames, 21)
 
     @staticmethod
-    @attr('issue')
     @dec.skipif(parser_not_found('DCD'),
                 'DCD parset not available. Are you using python 3?')
     def test_set_one_format_tuple():
         universe = mda.Universe(PSF, [(PDB_small, 'pdb'), DCD])
         assert_equal(universe.trajectory.n_frames, 99)
 
     @staticmethod
-    @attr('issue')
     def test_set_all_formats():
         universe = mda.Universe(PSF, [PDB_small, PDB_closed], format='pdb')
         assert_equal(universe.trajectory.n_frames, 2)

testsuite/MDAnalysisTests/coordinates/test_gro.py

@@ -38,7 +38,6 @@
     GRO,
     GRO_large,
 )
-from nose.plugins.attrib import attr
 from numpy.testing import (
     assert_,
     assert_almost_equal,
@@ -252,7 +251,6 @@ def test_writer_no_atom_names(self, u_no_names, ref, tempdir):
         assert_equal(u.atoms.names, expected)
 
     @dec.slow
-    @attr('issue')
     def test_check_coordinate_limits_min(self, ref, tempdir):
         """Test that illegal GRO coordinates (x <= -999.9995 nm) are caught
         with ValueError (Issue 57)"""
@@ -264,7 +262,6 @@ def test_check_coordinate_limits_min(self, ref, tempdir):
         assert_raises(ValueError, u.atoms.write, outfile)
 
     @dec.slow
-    @attr('issue')
     def test_check_coordinate_limits_max(self, ref, tempdir):
         """Test that illegal GRO coordinates (x > 9999.9995 nm) are caught
         with ValueError (Issue 57)"""
@@ -394,7 +391,6 @@ def ref():
         return GROLargeReference()
 
     @dec.slow
-    @attr('issue')
     def test_writer_large(self, ref, tempdir):
         """
         Test that atom numbers are truncated for large
@@ -414,7 +410,6 @@ def test_writer_large(self, ref, tempdir):
                                      "coords does not truncate properly.")
 
     @dec.slow
-    @attr('issue')
     def test_writer_large_residue_count(self, ref, tempdir):
         """
         Ensure large residue number truncation for

testsuite/MDAnalysisTests/coordinates/test_netcdf.py

@@ -30,7 +30,6 @@
 from scipy.io import netcdf
 
 import pytest
-from nose.plugins.attrib import attr
 from numpy.testing import (assert_, assert_equal, assert_array_almost_equal,
                            assert_array_equal,
                            assert_almost_equal, assert_raises, dec)
@@ -286,7 +285,6 @@ def _check_new_traj(self):
                                               err_msg="Variable {0} not written "
                                     "correctly".format(k))
 
-    @attr('slow')
     def test_TRR2NCDF(self):
         trr = mda.Universe(GRO, TRR)
         with mda.Writer(self.outfile, trr.trajectory.n_atoms,
@@ -318,7 +316,6 @@ def test_TRR2NCDF(self):
                                       err_msg="unitcells are not identical")
         del trr
 
-    @attr('issue')
     def test_write_AtomGroup(self):
         """test to write NCDF from AtomGroup (Issue 116)"""
         p = self.universe.select_atoms("not resname WAT")

testsuite/MDAnalysisTests/coordinates/test_pdb.py

@@ -36,7 +36,6 @@
                                        INC_PDB, PDB_xlserial, ALIGN, ENT,
                                        PDB_cm, PDB_cm_gz, PDB_cm_bz2,
                                        PDB_mc, PDB_mc_gz, PDB_mc_bz2)
-from nose.plugins.attrib import attr
 from numpy.testing import (assert_equal, dec,
                            assert_array_almost_equal,
                            assert_almost_equal, assert_raises, assert_)
@@ -243,7 +242,6 @@ def test_writer_no_tempfactors(self):
         expected = np.zeros(self.u_no_names.atoms.n_atoms)
         assert_equal(u.atoms.tempfactors, expected)
 
-    @attr('issue')
     def test_write_single_frame_Writer(self):
         """Test writing a single frame from a DCD trajectory to a PDB using
         MDAnalysis.Writer (Issue 105)"""
@@ -257,7 +255,6 @@ def test_write_single_frame_Writer(self):
                      1,
                      err_msg="The number of frames should be 1.")
 
-    @attr('issue')
     def test_write_single_frame_AtomGroup(self):
         """Test writing a single frame from a DCD trajectory to a PDB using
         AtomGroup.write() (Issue 105)"""
@@ -273,7 +270,6 @@ def test_write_single_frame_AtomGroup(self):
                                                "agree with original coordinates from frame %d" %
                                                u.trajectory.frame)
 
-    @attr('issue')
     def test_check_coordinate_limits_min(self):
         """Test that illegal PDB coordinates (x <= -999.9995 A) are caught
         with ValueError (Issue 57)"""
@@ -283,7 +279,6 @@ def test_check_coordinate_limits_min(self):
         u.atoms[2000].position = [0, -999.9995, 22.8]
         assert_raises(ValueError, u.atoms.write, self.outfile)
 
-    @attr('issue')
     def test_check_coordinate_limits_max(self):
         """Test that illegal PDB coordinates (x > 9999.9995 A) are caught
         with ValueError (Issue 57)"""
@@ -295,7 +290,6 @@ def test_check_coordinate_limits_max(self):
         assert_raises(ValueError, u.atoms.write, self.outfile)
         del u
 
-    @attr('issue')
     def test_check_header_title_multiframe(self):
         """Check whether HEADER and TITLE are written just once in a multi-
         frame PDB file (Issue 741)"""
@@ -328,12 +322,10 @@ def tearDown(self):
         del self.multiverse
         del self.conect
 
-    @attr('slow')
     def test_n_frames(self):
         assert_equal(self.multiverse.trajectory.n_frames, 24,
                      "Wrong number of frames read from PDB muliple model file")
 
-    @attr('slow')
     def test_n_atoms_frame(self):
         u = self.multiverse
         desired = 392
@@ -343,7 +335,6 @@ def test_n_atoms_frame(self):
                                                         "of atoms in the test case (%d) at frame %d" % (
                                                             len(u.atoms), desired, u.trajectory.frame))
 
-    @attr('slow')
     def test_rewind(self):
         u = self.multiverse
         u.trajectory[11]
@@ -353,7 +344,6 @@ def test_rewind(self):
         assert_equal(u.trajectory.ts.frame, 0,
                      "Failed to rewind to 0th frame (frame index 0)")
 
-    @attr('slow')
     def test_iteration(self):
         u = self.multiverse
         frames = []
@@ -369,7 +359,6 @@ def test_iteration(self):
             "trajectory iterator fails to rewind" %
             (len(frames), u.trajectory.n_frames))
 
-    @attr('slow')
     def test_slice_iteration(self):
         u = self.multiverse
         frames = []
@@ -379,7 +368,6 @@ def test_slice_iteration(self):
                      np.arange(u.trajectory.n_frames)[4:-2:4],
                      err_msg="slicing did not produce the expected frames")
 
-    @attr('slow')
     def test_conect_bonds_conect(self):
         conect = self.conect
         assert_equal(len(conect.atoms), 1890)
@@ -395,7 +383,6 @@ def test_conect_bonds_conect(self):
             assert_equal(len(u1.atoms), 1890)
             assert_equal(len(u1.bonds), 1922)
 
-    @attr('slow')
     def test_conect_bonds_all(self):
         conect = self.conect
         assert_equal(len(conect.atoms), 1890)
@@ -413,7 +400,6 @@ def test_conect_bonds_all(self):
 
             # assert_equal(len([b for b in conect.bonds if not b.is_guessed]), 1922)
 
-    @attr('slow')
     def test_numconnections(self):
         u = self.multiverse
 
@@ -501,7 +487,6 @@ def tearDown(self):
         del self.universe, self.multiverse, self.universe2
         del self.tmpdir
 
-    @attr('slow')
     def test_write_atomselection(self):
         """Test if multiframe writer can write selected frames for an
         atomselection."""
@@ -524,7 +509,6 @@ def test_write_atomselection(self):
                              "AtomGroup contains %d frames, it should have %d" % (
                                  len(u.trajectory), desired_frames))
 
-    @attr('slow')
     def test_write_all_timesteps(self):
         """
         Test write_all_timesteps() of the  multiframe writer (selected frames
@@ -548,7 +532,6 @@ def test_write_all_timesteps(self):
                              "AtomGroup contains %d frames, it should have %d" % (
                                  len(u.trajectory), desired_frames))
 
-    @attr('slow')
     def test_write_atoms(self):
         u = self.universe2
         W = mda.Writer(self.outfile, multiframe=True)
@@ -632,7 +615,6 @@ def test_selection(self):
                      "Atom selection of last atoms in file")
 
     @dec.slow
-    @attr('issue')
     def test_unitcell(self):
         assert_array_almost_equal(
             self.universe.coord.dimensions,