Port analysis module to pytest

.travis.yml

@@ -23,9 +23,9 @@ env:
     - PYTHON_VERSION=2.7
     - COVERALLS=false
     - NOSE_FLAGS="--processes=2 --process-timeout=400 --no-open-files --with-timer --timer-top-n 50"
-    - NOSE_TEST_LIST="analysis"
+    - NOSE_TEST_LIST=""
     - PYTEST_FLAGS="--disable-pytest-warnings -n 2"
-    - PYTEST_LIST="testsuite/MDAnalysisTests/lib testsuite/MDAnalysisTests/formats testsuite/MDAnalysisTests/coordinates testsuite/MDAnalysisTests/utils testsuite/MDAnalysisTests/topology testsuite/MDAnalysisTests/auxiliary testsuite/MDAnalysisTests/core"
+    - PYTEST_LIST="testsuite/MDAnalysisTests/lib testsuite/MDAnalysisTests/formats testsuite/MDAnalysisTests/coordinates testsuite/MDAnalysisTests/utils testsuite/MDAnalysisTests/topology testsuite/MDAnalysisTests/auxiliary testsuite/MDAnalysisTests/core testsuite/MDAnalysisTests/analysis"
     - NOSE_COVERAGE_FILE="nose_coverage"
     - PYTEST_COVERAGE_FILE="pytest_coverage"
     - MAIN_CMD="pytest ${PYTEST_LIST} ${PYTEST_FLAGS}; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST} ${NOSE_FLAGS}"

testsuite/MDAnalysisTests/analysis/test_align.py

@@ -43,8 +43,8 @@
 warnings.simplefilter('always')
 
 
-class TestRotationMatrix(object):
-    def __init__(self):
+class TestRotationMatrix(TestCase):
+    def setUp(self):
         self.a = np.array([[0.1, 0.2, 0.3],
                            [1.1, 1.1, 1.1]])
         self.b = np.array([[0.1, 0.1, 0.1],
@@ -297,7 +297,7 @@ def test_alignto_partial_universe():
 
 
 
-class TestAlignmentProcessing(object):
+class TestAlignmentProcessing(TestCase):
     def setUp(self):
         self.seq = FASTA
         self.tempdir = tempdir.TempDir()

testsuite/MDAnalysisTests/analysis/test_base.py

@@ -21,6 +21,7 @@
 #
 from __future__ import division, absolute_import
 from six.moves import range
+from unittest import TestCase
 
 import numpy as np
 
@@ -60,7 +61,7 @@ def _single_frame(self):
         pass
 
 
-class TestAnalysisBase(object):
+class TestAnalysisBase(TestCase):
     @dec.skipif(parser_not_found('DCD'),
                 'DCD parser not available. Are you using python 3?')
     def setUp(self):

testsuite/MDAnalysisTests/analysis/test_contacts.py

@@ -21,6 +21,8 @@
 #
 from __future__ import print_function, division, absolute_import
 
+from unittest import TestCase
+
 import MDAnalysis as mda
 from MDAnalysis.analysis import contacts
 from MDAnalysis.analysis.distances import distance_array
@@ -151,11 +153,11 @@ def soft_cut(ref, u, selA, selB, radius=4.5, beta=5.0, lambda_constant=1.8):
     return np.asarray(results)
 
 
-class TestContacts(object):
+class TestContacts(TestCase):
     @dec.skipif(
         parser_not_found('DCD'),
         'DCD parser not available. Are you using python 3?')
-    def __init__(self):
+    def setUp(self):
         self.universe = mda.Universe(PSF, DCD)
         self.trajectory = self.universe.trajectory
 

testsuite/MDAnalysisTests/analysis/test_density.py

@@ -196,7 +196,7 @@ def test_presence_griddata(self):
                              an ImportError if gridData is available.''')
 
 
-class TestNotWithin(object):
+class TestNotWithin(TestCase):
     # tests notwithin_coordinates_factory
     # only checks that KDTree and distance_array give same results
     def setUp(self):

testsuite/MDAnalysisTests/analysis/test_diffusionmap.py

@@ -20,6 +20,7 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 from __future__ import print_function, absolute_import
+from unittest import TestCase
 import numpy as np
 import MDAnalysis
 import MDAnalysis.analysis.diffusionmap as diffusionmap
@@ -30,7 +31,7 @@
 from MDAnalysisTests.datafiles import PDB, XTC
 
 
-class TestDiffusionmap(object):
+class TestDiffusionmap(TestCase):
     def setUp(self):
         self.u = MDAnalysis.Universe(PDB, XTC)
         self.dist = diffusionmap.DistanceMatrix(self.u, select='backbone')

testsuite/MDAnalysisTests/analysis/test_encore.py

@@ -30,6 +30,7 @@
 import sys
 import warnings
 
+import pytest
 from numpy.testing import (TestCase, dec, assert_equal, assert_almost_equal,
                            assert_warns)
 
@@ -826,20 +827,22 @@ def test_get_distance_matrix(self):
         dm = confdistmatrix.get_distance_matrix(u)
 
 class TestEncoreImportWarnings(object):
-    def setUp(self):
-        # clear cache of encore module
+    @block_import('sklearn')
+    def _check_sklearn_import_warns(self, package, recwarn):
         for mod in list(sys.modules):  # list as we're changing as we iterate
             if 'encore' in mod:
                 sys.modules.pop(mod, None)
-
-    @block_import('sklearn')
-    def _check_sklearn_import_warns(self, package):
         warnings.simplefilter('always')
-        assert_warns(ImportWarning, importlib.import_module, package)
+        # assert_warns(ImportWarning, importlib.import_module, package)
+        importlib.import_module(package)
+        assert recwarn.pop(ImportWarning)
 
-    def test_import_warnings(self):
+    def test_import_warnings(self, recwarn):
+        for mod in list(sys.modules):  # list as we're changing as we iterate
+            if 'encore' in mod:
+                sys.modules.pop(mod, None)
         for pkg in (
                 'MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod',
                 'MDAnalysis.analysis.encore.clustering.ClusteringMethod',
         ):
-            yield self._check_sklearn_import_warns, pkg
+            self._check_sklearn_import_warns(pkg, recwarn)

testsuite/MDAnalysisTests/analysis/test_gnm.py

@@ -24,6 +24,7 @@
 import MDAnalysis
 import MDAnalysis.analysis.gnm
 
+from unittest import TestCase
 from numpy.testing import (assert_equal, assert_almost_equal)
 import numpy as np
 
@@ -32,7 +33,7 @@
 from MDAnalysisTests.datafiles import GRO, XTC
 from MDAnalysisTests import tempdir
 
-class TestGNM(object):
+class TestGNM(TestCase):
     def setUp(self):
         self.tmpdir = tempdir.TempDir()
         self.universe = MDAnalysis.Universe(GRO, XTC)

testsuite/MDAnalysisTests/analysis/test_hbonds.py

@@ -21,6 +21,8 @@
 #
 from __future__ import print_function, absolute_import
 
+from unittest import TestCase
+
 import MDAnalysis
 import MDAnalysis.analysis.hbonds
 from MDAnalysis import SelectionError, SelectionWarning
@@ -46,7 +48,7 @@ def guess_types(names):
     return Atomtypes(np.array([guess_atom_type(name) for name in names], dtype=object))
 
 
-class TestHydrogenBondAnalysis(object):
+class TestHydrogenBondAnalysis(TestCase):
     def setUp(self):
         self.universe = u = MDAnalysis.Universe(PDB_helix)
         self.kwargs = {
@@ -239,7 +241,7 @@ def run_HBA_dynamic_selections(*args):
             self._tearDown()
 
 
-class TestHydrogenBondAnalysisTIP3P(object):
+class TestHydrogenBondAnalysisTIP3P(TestCase):
     @dec.skipif(parser_not_found('DCD'),
                 'DCD parser not available. Are you using python 3?')
     def setUp(self):

testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py

@@ -22,6 +22,8 @@
 from __future__ import division, absolute_import
 import six
 from six.moves import zip, range
+
+from unittest import TestCase
 from MDAnalysisTests.datafiles import TRZ, TRZ_psf, PRM, TRJ
 from MDAnalysisTests import module_not_found, tempdir
 from numpy.testing import assert_, assert_array_almost_equal, assert_raises, assert_, dec
@@ -32,7 +34,7 @@
 from MDAnalysis.analysis.hbonds import HydrogenBondAutoCorrel as HBAC
 
 
-class TestHydrogenBondAutocorrel(object):
+class TestHydrogenBondAutocorrel(TestCase):
     def setUp(self):
         u = self.u = mda.Universe(TRZ_psf, TRZ)
         self.H = u.atoms.select_atoms('name Hn')

testsuite/MDAnalysisTests/analysis/test_nuclinfo.py

@@ -21,6 +21,8 @@
 #
 from __future__ import absolute_import
 
+from unittest import TestCase
+
 from numpy.testing import (
     assert_,
     assert_almost_equal,
@@ -33,7 +35,7 @@
 from MDAnalysisTests.datafiles import NUCL
 
 
-class TestNuclinfo(object):
+class TestNuclinfo(TestCase):
     def setUp(self):
         self.u = mda.Universe(NUCL)
 

testsuite/MDAnalysisTests/analysis/test_pca.py

@@ -20,6 +20,9 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 from __future__ import print_function, absolute_import
+
+from unittest import TestCase
+
 import numpy as np
 import MDAnalysis
 import MDAnalysis.analysis.pca as pca
@@ -32,7 +35,7 @@
 from MDAnalysisTests import module_not_found
 
 
-class TestPCA(object):
+class TestPCA(TestCase):
     """ Test the PCA class """
     def setUp(self):
         self.u = MDAnalysis.Universe(PSF, DCD)

testsuite/MDAnalysisTests/analysis/test_persistencelength.py

@@ -21,6 +21,8 @@
 #
 from __future__ import print_function, division, absolute_import
 
+from unittest import TestCase
+
 import MDAnalysis
 from MDAnalysis.analysis import polymer
 from MDAnalysis.exceptions import NoDataError
@@ -39,7 +41,7 @@
 from MDAnalysisTests import module_not_found
 
 
-class TestPersistenceLength(object):
+class TestPersistenceLength(TestCase):
     def setUp(self):
         self.u = MDAnalysis.Universe(Plength)
 
@@ -89,7 +91,7 @@ def test_raise_NoDataError(self):
         p = self._make_p()
         assert_raises(NoDataError, p.perform_fit)
 
-class TestFitExponential(object):
+class TestFitExponential(TestCase):
     def setUp(self):
         self.x = np.linspace(0, 250, 251)
         self.a_ref = 20.0

testsuite/MDAnalysisTests/analysis/test_psa.py

@@ -185,6 +185,8 @@ class _BaseHausdorffDistance(TestCase):
     for various Hausdorff distance
     calculation properties.'''
 
+    __test__ = False
+
     def setUp(self):
         self.random_angles = np.random.random((100,)) * np.pi * 2
         self.random_columns = np.column_stack((self.random_angles,
@@ -233,6 +235,8 @@ class TestHausdorffSymmetric(_BaseHausdorffDistance):
     '''Tests for conventional and symmetric (undirected)
     Hausdorff distance between point sets in 3D.'''
 
+    __test__ = True
+
     def setUp(self):
         super(TestHausdorffSymmetric, self).setUp()
         self.h = PSA.hausdorff
@@ -243,6 +247,8 @@ class TestWeightedAvgHausdorffSymmetric(_BaseHausdorffDistance):
     '''Tests for weighted average and symmetric (undirected)
     Hausdorff distance between point sets in 3D.'''
 
+    __test__ = True
+
     def setUp(self):
         super(TestWeightedAvgHausdorffSymmetric, self).setUp()
         self.h = PSA.hausdorff_wavg
@@ -265,6 +271,8 @@ class TestAvgHausdorffSymmetric(_BaseHausdorffDistance):
     '''Tests for unweighted average and symmetric (undirected)
     Hausdorff distance between point sets in 3D.'''
 
+    __test__ = True
+
     def setUp(self):
         super(TestAvgHausdorffSymmetric, self).setUp()
         self.h = PSA.hausdorff_avg

testsuite/MDAnalysisTests/analysis/test_rdf.py

@@ -22,6 +22,8 @@
 from __future__ import absolute_import
 from six.moves import zip
 
+from unittest import TestCase
+
 from numpy.testing import assert_
 
 import MDAnalysis as mda
@@ -30,7 +32,7 @@
 from MDAnalysisTests.datafiles import two_water_gro
 
 
-class TestInterRDF(object):
+class TestInterRDF(TestCase):
     def setUp(self):
         self.u = mda.Universe(two_water_gro)