Remove explicit calls to nose from library code (nilearn#2277)

* Fixed existing test for view_connectome's parameter deprecation

* Fixed existing tests for replace_parameters

* Removed final nose based fixture from code

 -  Renamed a fixture for clarity & non-ambiguity

* Simplified code for checking when pytest is running

* Placate flake8

* Removed remaining letover instances of assert_raises, assert_warns

* Removed nose from requirements & config

* Added docstrings for the mocker fixture

* Typo corrected

continuous_integration/install.sh

@@ -22,18 +22,18 @@ create_new_venv() {
     deactivate
     virtualenv --system-site-packages testvenv
     source testvenv/bin/activate
-    pip install nose pytest
+    pip install pytest
 }
 
 echo_requirements_string() {
     # Echo a requirement string for example
-    # "pip nose python='2.7.3 scikit-learn=*". It has a hardcoded
+    # "pip pytest python='2.7.3 scikit-learn=*". It has a hardcoded
     # list of possible packages to install and looks at _VERSION
     # environment variables to know whether to install a given package and
     # if yes which version to install. For example:
     #   - for numpy, NUMPY_VERSION is used
     #   - for scikit-learn, SCIKIT_LEARN_VERSION is used
-    TO_INSTALL_ALWAYS="pip nose pytest"
+    TO_INSTALL_ALWAYS="pip pytest"
     REQUIREMENTS="$TO_INSTALL_ALWAYS"
     TO_INSTALL_MAYBE="numpy scipy matplotlib scikit-learn pandas flake8 lxml joblib"
     for PACKAGE in $TO_INSTALL_MAYBE; do
@@ -68,13 +68,11 @@ create_new_travisci_env() {
 
 if [[ "$DISTRIB" == "neurodebian" ]]; then
     create_new_venv
-    pip install nose-timer
     bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
-    sudo apt-get install -qq python-scipy python-nose python-nibabel python-sklearn python-joblib
+    sudo apt-get install -qq python-scipy python-pytest python-nibabel python-sklearn python-joblib
 
 elif [[ "$DISTRIB" == "travisci" ]]; then
     create_new_travisci_env
-    pip install nose-timer
     # Note: nibabel is in setup.py install_requires so nibabel will
     # always be installed eventually. Defining NIBABEL_VERSION is only
     # useful if you happen to want a specific nibabel version rather

continuous_integration/test_script.sh

@@ -9,7 +9,7 @@ fi
 if [[ "$SKIP_TESTS" != "true" ]]; then
     python continuous_integration/show-python-packages-versions.py
     # Copy setup.cfg to TEST_RUN_FOLDER where we are going to run the tests from
-    # Mainly for nose config settings
+    # Mainly for test config settings
     cp setup.cfg "$TEST_RUN_FOLDER"
     cp .coveragerc "$TEST_RUN_FOLDER"
     # We want to back out of the current working directory to make

nilearn/_utils/testing.py

@@ -244,23 +244,9 @@ def __call__(self, *args, **kwargs):
 
 
 def are_tests_running():
-    """Returns whether we are running the nose test loader
+    """Returns whether we are running the pytest test loader
     """
-    if 'nose' not in sys.modules:
-        return
-    try:
-        import nose
-    except ImportError:
-        return False
-    # Now check that we have the loader in the call stask
-    stack = inspect.stack()
-    loader_file_name = nose.loader.__file__
-    if loader_file_name.endswith('.pyc'):
-        loader_file_name = loader_file_name[:-1]
-    for _, file_name, _, _, _, _ in stack:
-        if file_name == loader_file_name:
-            return True
-    return False
+    return 'PYTEST_CURRENT_TEST' in os.environ
 
 
 def skip_if_running_tests(msg=''):

nilearn/datasets/tests/test_atlas.py

@@ -13,7 +13,6 @@
 import nibabel
 import pytest
 
-from nose import with_setup
 from numpy.testing import assert_array_equal
 
 from . import test_utils as tst
@@ -25,7 +24,10 @@
 
 
 @pytest.fixture()
-def request_mock():
+def request_mocker():
+    """ Mocks URL calls for atlas fetchers during testing.
+    Tests the fetcher code without actually downloading the files.
+    """
     tst.setup_mock(utils, atlas)
     yield
     tst.teardown_mock(utils, atlas)
@@ -248,7 +250,7 @@ def test_fail_fetch_atlas_harvard_oxford(tmp_path):
     assert ho.labels[6] == "Right R3"
 
 
-def test_fetch_atlas_craddock_2012(tmp_path, request_mock):
+def test_fetch_atlas_craddock_2012(tmp_path, request_mocker):
     bunch = atlas.fetch_atlas_craddock_2012(data_dir=str(tmp_path),
                                             verbose=0)
 
@@ -268,7 +270,7 @@ def test_fetch_atlas_craddock_2012(tmp_path, request_mock):
     assert bunch.description != ''
 
 
-def test_fetch_atlas_smith_2009(tmp_path, request_mock):
+def test_fetch_atlas_smith_2009(tmp_path, request_mocker):
     bunch = atlas.fetch_atlas_smith_2009(data_dir=str(tmp_path), verbose=0)
 
     keys = ("rsn20", "rsn10", "rsn70",
@@ -311,7 +313,7 @@ def test_fetch_coords_seitzman_2018():
     assert np.any(bunch.networks != np.sort(bunch.networks))
 
 
-def test_fetch_atlas_destrieux_2009(tmp_path, request_mock):
+def test_fetch_atlas_destrieux_2009(tmp_path, request_mocker):
     datadir = str(tmp_path / 'destrieux_2009')
     os.mkdir(datadir)
     dummy = open(os.path.join(
@@ -337,7 +339,7 @@ def test_fetch_atlas_destrieux_2009(tmp_path, request_mock):
         datadir, 'destrieux2009_rois.nii.gz')
 
 
-def test_fetch_atlas_msdl(tmp_path, request_mock):
+def test_fetch_atlas_msdl(tmp_path, request_mocker):
     datadir = str(tmp_path / 'msdl_atlas')
     os.mkdir(datadir)
     os.mkdir(os.path.join(datadir, 'MSDL_rois'))
@@ -361,7 +363,7 @@ def test_fetch_atlas_msdl(tmp_path, request_mock):
     assert dataset.description != ''
 
 
-def test_fetch_atlas_yeo_2011(tmp_path, request_mock):
+def test_fetch_atlas_yeo_2011(tmp_path, request_mocker):
     dataset = atlas.fetch_atlas_yeo_2011(data_dir=str(tmp_path), verbose=0)
     assert isinstance(dataset.anat, _basestring)
     assert isinstance(dataset.colors_17, _basestring)
@@ -374,7 +376,7 @@ def test_fetch_atlas_yeo_2011(tmp_path, request_mock):
     assert dataset.description != ''
 
 
-def test_fetch_atlas_aal(tmp_path, request_mock):
+def test_fetch_atlas_aal(tmp_path, request_mocker):
     ho_dir = str(tmp_path / 'aal_SPM12' / 'aal' / 'atlas')
     os.makedirs(ho_dir)
     with open(os.path.join(ho_dir, 'AAL.xml'), 'w') as xml_file:
@@ -397,7 +399,7 @@ def test_fetch_atlas_aal(tmp_path, request_mock):
     assert dataset.description != ''
 
 
-def test_fetch_atlas_basc_multiscale_2015(tmp_path, request_mock):
+def test_fetch_atlas_basc_multiscale_2015(tmp_path, request_mocker):
     # default version='sym',
     data_sym = atlas.fetch_atlas_basc_multiscale_2015(data_dir=str(tmp_path),
                                                       verbose=0)
@@ -449,7 +451,7 @@ def test_fetch_coords_dosenbach_2010():
     assert np.any(bunch.networks != np.sort(bunch.networks))
 
 
-def test_fetch_atlas_allen_2011(tmp_path, request_mock):
+def test_fetch_atlas_allen_2011(tmp_path, request_mocker):
     bunch = atlas.fetch_atlas_allen_2011(data_dir=str(tmp_path), verbose=0)
     keys = ("maps",
             "rsn28",
@@ -467,7 +469,7 @@ def test_fetch_atlas_allen_2011(tmp_path, request_mock):
     assert bunch.description != ''
 
 
-def test_fetch_atlas_surf_destrieux(tmp_path, request_mock, verbose=0):
+def test_fetch_atlas_surf_destrieux(tmp_path, request_mocker, verbose=0):
     data_dir = str(tmp_path / 'destrieux_surface')
     os.mkdir(data_dir)
     # Create mock annots
@@ -507,7 +509,7 @@ def _mock_talairach_fetch_files(data_dir, *args, **kwargs):
     return [file_name]
 
 
-def test_fetch_atlas_talairach(tmp_path, request_mock):
+def test_fetch_atlas_talairach(tmp_path, request_mocker):
     atlas._fetch_files = _mock_talairach_fetch_files
     level_values = np.ones((81, 3)) * [0, 1, 2]
     talairach = atlas.fetch_atlas_talairach('hemisphere',