Merge pull request #1480 from utkbansal/f-u-nose

Dropping nose as a dependency

.gitignore

@@ -20,7 +20,7 @@ examples/output.txt
 .eggs
 # ignore Vagrant virtual machines
 .vagrant
-# ignore nosetest/coverage files
+# ignore coverage files
 .coverage
 .noseids
 # ignore trajectory offset caches

maintainer/conda/MDAnalysis/meta.yaml

@@ -24,7 +24,6 @@ requirements:
   run:
     - python
     - biopython
-    - nose ==1.3.7
     - joblib
     - scipy
     - griddataformats

package/MDAnalysis/tests/__init__.py

@@ -39,33 +39,6 @@
    >>> import MDAnalysis.tests
    >>> MDAnalysis.tests.test()
 
-Some tests can take a few seconds; in order to skip the slow tests run
-
-   >>> MDAnalysis.tests.test(label='fast')
-
-Additional information is displayed at a higher verbosity level (the default is
-1):
-
-   >>> MDAnalysis.tests.test(label='fast', argv=['--verbosity=3'])
-
-Note that if no tests are being run then one might have to run the
-tests with the ``--exe`` flag
-
-   >>> MDAnalysis.tests.test(label='fast', argv=['--exe'])
-
-(This happens when python files are installed with the executable bit set. By
-default the nose_ testing framework refuses to use those files and must be
-encouraged to do so with the ``--exe`` switch.)
-
-See `nose commandline options`_ for additional options that can be used.
-
-For the particular case of code coverage MDAnalysis mustn't be imported prior
-to testing, and testing must be invoked directly from `:meth:MDAnalysisTests.run`:
-
-  >>> import MDAnalysisTests
-  >>> MDAnalysisTests.run(argv=['--exe', '--with-coverage', '--cover-package=MDAnalysis'])
-
-
 Data
 ====
 
@@ -92,16 +65,14 @@
 Writing test cases
 ==================
 
-The unittests use the :mod:`unittest` module together with nose_. See the
+The unittests use the :mod:`pytest_` module. See the
 examples provided alongside the ``MDAnalysisTests`` module.
 
 The `SciPy testing guidelines`_ are also a good howto for writing test cases.
 
 
-.. _nose:
-   http://somethingaboutorange.com/mrl/projects/nose/0.11.3/index.html
-.. _nose commandline options:
-   http://somethingaboutorange.com/mrl/projects/nose/0.11.3/usage.html#extended-usage
+.. _pytest:
+   https://docs.pytest.org/en/latest/
 .. _SciPy testing guidelines:
    http://projects.scipy.org/numpy/wiki/TestingGuidelines#id11
 .. _Charmm: http://www.charmm.org

testsuite/CHANGELOG

@@ -15,7 +15,8 @@ and https://github.com/MDAnalysis/mdanalysis/wiki/UnitTests
 ------------------------------------------------------------------------------
 mm/dd/yy
 
-  * 0.16.2
+  * 0.16.2 utkbansal
+    - Port to pytest - removed nose as a dependency (Issue #884)
 
 06/03/17 xiki_tempula
 

testsuite/INSTALL

@@ -84,16 +84,17 @@ From sources
 
 From the top directory of the checked out sources:
 
-  ./testsuite/MDAnalysisTests/mda_nosetests --exe -v --processes=4 --process-timeout=120 
+  pytest /testsuite/MDAnalysisTests/ --numprocesses 4
 
-(use --processes=4 if you have 4 cores available to run in parallel or
+(use --numprocesses 4 if you have 4 cores available to run in parallel or
 adapt to available cores.)
 
+To run tests in parallel you will need pytest-xdist>=1.18.1 installed.
 
 From installed package
 ----------------------
 
 The test runner can be launched as
 
-  python -c 'from MDAnalysis.tests import test; test(argv=["--exe", "-v", "--processes=4", "--process-timeout=120"])'
+  python -c 'from MDAnalysis.tests import test; test()'
 

testsuite/MANIFEST.in

@@ -1,7 +1,6 @@
 graft scripts
 include README INSTALL CHANGELOG LICENSE AUTHORS TODO SUMMARY.txt
 include setup.py
-include MDAnalysisTests/mda_nosetests
 include MDAnalysisTests/data/*/*
 global-exclude *~
 global-exclude *.pkl

testsuite/MDAnalysisTests/__init__.py

@@ -37,31 +37,8 @@
 
 Run all the tests with
 
-   >>> import MDAnalysisTests.tests
-   >>> MDAnalysisTests.tests.test(label='full')
-
-Some tests can take a few seconds; in order to skip the slow tests run
-
-   >>> MDAnalysisTests.tests.test(label='fast')
-
-Additional information is displayed at a higher verbosity level (the default is
-1):
-
-   >>> MDAnalysisTests.tests.test(label='fast', verbose=3)
-
-Note that if no tests are being run then one might have to run the
-tests with the ``--exe`` flag
-
-   >>> MDAnalysisTests.tests.test(label='fast', extra_argv=['--exe'])
-
-(This happens when python files are installed with the executable bit set. By
-default the nose_ testing framework refuses to use those files and must be
-encouraged to do so with the ``--exe`` switch.)
-
-See `nose commandline options`_ for additional options that can be used; for
-instance, code coverage can also be checked:
-
-  >>> MDAnalysisTests.tests.test(label='full', extra_argv=['--exe', '--with-coverage'])
+   >>> from MDAnalysisTests import run
+   >>> run()
 
 
 Data
@@ -90,22 +67,13 @@
 Writing test cases
 ==================
 
-The unittests use the :mod:`unittest` module together with nose_. See the
+The unittests use the :mod:`pytest <https://docs.pytest.org/en/latest/>`_ module. See the
 examples in the ``MDAnalysisTests`` directory.
 
 The `SciPy testing guidelines`_ are a good howto for writing test cases,
 especially as we are directly using this framework (imported from numpy).
 
-A number of plugins external to nose are automatically loaded. The `knownfailure`
-plugin provides the `@knownfailure()` decorator, which can be used to mark tests
-that are expected to fail. If used with default arguments the parentheses can be
-excluded.
-
 .. _NumPy: http://www.numpy.org/
-.. _nose:
-   http://nose.readthedocs.org/en/latest/
-.. _nose commandline options:
-  http://nose.readthedocs.org/en/latest/man.html?highlight=command%20line
 .. _SciPy testing guidelines:
    http://projects.scipy.org/numpy/wiki/TestingGuidelines#id11
 .. _Charmm: http://www.charmm.org
@@ -114,6 +82,9 @@
 """
 from __future__ import absolute_import
 import logging
+
+import pytest
+
 logger = logging.getLogger("MDAnalysisTests.__init__")
 
 __version__ = "0.17.0-dev"  # keep in sync with RELEASE in setup.py
@@ -131,9 +102,6 @@
 import os
 import sys
 
-# We get our nose from the plugins so that version-checking needs only be done there.
-from MDAnalysisTests.plugins import nose, loaded_plugins
-
 # Any tests that plot with matplotlib need to run with the simple agg backend because
 # on Travis there is no DISPLAY set
 try:
@@ -152,26 +120,6 @@
 )
 from MDAnalysisTests.core.util import make_Universe
 
-def run(*args, **kwargs):
-    """Test-running function that loads plugins, sets up arguments, and calls `nose.run_exit()`"""
-    try:
-        kwargs['argv'] = sys.argv + kwargs['argv'] #sys.argv takes precedence
-    except KeyError:
-        kwargs['argv'] = sys.argv
-    # We emulate numpy's treament of the 'fast' label.
-    if 'label' in kwargs:
-        label = kwargs.pop('label')
-        if label == 'fast':
-            kwargs['argv'].extend(['-A','not slow'])
-    # We keep accepting numpy's 'extra_argv'
-    if 'extra_argv' in kwargs:
-        kwargs['argv'].extend(kwargs.pop('extra_argv'))
-    try:
-        kwargs['addplugins'].extend(loaded_plugins.values())
-    except KeyError:
-        kwargs['addplugins'] = loaded_plugins.values()
-    # By default, test our testsuite
-    kwargs['defaultTest'] = os.path.dirname(__file__)
-    return nose.run_exit(*args, **kwargs)
-
 
+def run(*args, **kwargs):
+    pytest.main()

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

@@ -32,6 +32,7 @@
 
 from MDAnalysisTests.datafiles import GRO, XTC
 
+
 class TestGNM(object):
     @staticmethod
     @pytest.fixture()
@@ -81,6 +82,7 @@ def test_generate_kirchoff(self, universe):
 
     def test_closeContactGNMAnalysis(self, universe):
         gnm = MDAnalysis.analysis.gnm.closeContactGNMAnalysis(universe, weights="size")
+
         gnm.run()
 
         result = gnm.results
@@ -111,6 +113,7 @@ def test_closeContactGNMAnalysis(self, universe):
 
     def test_closeContactGNMAnalysis_weights_None(self, universe):
         gnm = MDAnalysis.analysis.gnm.closeContactGNMAnalysis(universe, weights=None)
+
         gnm.run()
 
         result = gnm.results