Merge pull request #74 from bcipolli/fix_coverage

TST: fix coverage

.coveragerc

@@ -10,4 +10,5 @@ omit =
     nidata/*/*/tests.py
     nidata/core/_utils/niimg.py
     nidata/core/_utils/numpy_conversions.py
+    nidata/core/_utils/testing.py
     nidata/core/fetchers/http_fetcher.py

.travis.yml

@@ -15,7 +15,7 @@ notifications:
 
 before_install:
   # Setup anaconda
-  - pip install -U --upgrade pip
+  - pip install --upgrade pip
   - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
   - chmod +x miniconda.sh
   - ./miniconda.sh -b
@@ -27,7 +27,9 @@ install: # Install packages
   - echo $PATH
   - echo $PYTHONPATH
   - conda install --yes python=$TRAVIS_PYTHON_VERSION numpy h5py scipy virtualenv
-  - pip install nose setuptools pep8 pyflakes coverage python-coveralls nose-cov
+  - pip install --upgrade pip setuptools
+  - pip install nose pep8 pyflakes
+  - pip install coverage==3.7.1 python-coveralls nose-cov
   - pip install profilehooks
   - python setup.py install
 
@@ -38,3 +40,4 @@ script: # Run test
 
 after_success: # Calculate coverage
   - coveralls
+

nidata/anatomical/oasis_vbm/tests.py

@@ -2,14 +2,10 @@
 from unittest import TestCase
 
 from nidata.anatomical import OasisVbmDataset
-from nidata.core._utils.testing import DownloadTestMixin, InstallTestMixin
+from nidata.core._utils.testing import InstallThenDownloadTestMixin
 
 
-class OasisVbmDownloadTest(DownloadTestMixin, TestCase):
-    dataset_class = OasisVbmDataset
-
-
-class OasisVbmInstallTest(InstallTestMixin, TestCase):
+class OasisVbmTest(InstallThenDownloadTestMixin, TestCase):
     dataset_class = OasisVbmDataset
 
     def test_doc(self):

nidata/atlas/craddock_2012/tests.py

@@ -1,11 +1,8 @@
 from unittest import TestCase
-from nidata.atlas import Craddock2012Dataset
-from nidata.core._utils.testing import DownloadTestMixin, InstallTestMixin
-
 
-class Craddock2012DownloadTest(DownloadTestMixin, TestCase):
-    dataset_class = Craddock2012Dataset
+from nidata.atlas import Craddock2012Dataset
+from nidata.core._utils.testing import InstallThenDownloadTestMixin
 
 
-class Craddock2012InstallTest(InstallTestMixin, TestCase):
+class Craddock2012Test(InstallThenDownloadTestMixin, TestCase):
     dataset_class = Craddock2012Dataset

nidata/atlas/harvard_oxford/tests.py

@@ -1,15 +1,12 @@
 from unittest import TestCase
+
 from nidata.atlas import HarvardOxfordDataset
-from nidata.core._utils.testing import DownloadTestMixin, InstallTestMixin
+from nidata.core._utils.testing import InstallThenDownloadTestMixin
 
 
-class HarvardOxfordDownloadTest(DownloadTestMixin, TestCase):
+class HarvardOxfordTest(InstallThenDownloadTestMixin, TestCase):
     dataset_class = HarvardOxfordDataset
 
     def fetch(self, atlas_name='cort-maxprob-thr0-1mm', *args, **kwargs):
-        super(HarvardOxfordDownloadTest, self).fetch(
+        super(HarvardOxfordTest, self).fetch(
             atlas_name=atlas_name, *args, **kwargs)
-
-
-class HarvardOxfordInstallTest(InstallTestMixin, TestCase):
-    dataset_class = HarvardOxfordDataset

nidata/atlas/icbm152_2009/tests.py

@@ -1,11 +1,8 @@
 from unittest import TestCase
-from nidata.atlas import ICBM152Dataset
-from nidata.core._utils.testing import DownloadTestMixin, InstallTestMixin
-
 
-class ICBM152DownloadTest(DownloadTestMixin, TestCase):
-    dataset_class = ICBM152Dataset
+from nidata.atlas import ICBM152Dataset
+from nidata.core._utils.testing import InstallThenDownloadTestMixin
 
 
-class ICBM152InstallTest(InstallTestMixin, TestCase):
+class ICBM152Test(InstallThenDownloadTestMixin, TestCase):
     dataset_class = ICBM152Dataset

nidata/atlas/mni152_template/tests.py

@@ -1,11 +1,8 @@
 from unittest import TestCase
-from nidata.atlas import MNI152Dataset
-from nidata.core._utils.testing import DownloadTestMixin, InstallTestMixin
-
 
-class MNI152DownloadTest(DownloadTestMixin, TestCase):
-    dataset_class = MNI152Dataset
+from nidata.atlas import MNI152Dataset
+from nidata.core._utils.testing import InstallThenDownloadTestMixin
 
 
-class MNI152InstallTest(InstallTestMixin, TestCase):
+class MNI152Test(InstallThenDownloadTestMixin, TestCase):
     dataset_class = MNI152Dataset

nidata/atlas/power_2011/tests.py

@@ -1,11 +1,8 @@
 from unittest import TestCase
-from nidata.atlas import Power2011Dataset
-from nidata.core._utils.testing import DownloadTestMixin, InstallTestMixin
-
 
-class Power2011DownloadTest(DownloadTestMixin, TestCase):
-    dataset_class = Power2011Dataset
+from nidata.atlas import Power2011Dataset
+from nidata.core._utils.testing import InstallThenDownloadTestMixin
 
 
-class Power2011InstallTest(InstallTestMixin, TestCase):
+class Power2011Test(InstallThenDownloadTestMixin, TestCase):
     dataset_class = Power2011Dataset

nidata/atlas/smith_2009/tests.py

@@ -1,11 +1,8 @@
 from unittest import TestCase
-from nidata.atlas import Smith2009Dataset
-from nidata.core._utils.testing import DownloadTestMixin, InstallTestMixin
-
 
-class Smith2009DownloadTest(DownloadTestMixin, TestCase):
-    dataset_class = Smith2009Dataset
+from nidata.atlas import Smith2009Dataset
+from nidata.core._utils.testing import InstallThenDownloadTestMixin
 
 
-class Smith2009InstallTest(InstallTestMixin, TestCase):
+class Smith2009Test(InstallThenDownloadTestMixin, TestCase):
     dataset_class = Smith2009Dataset

nidata/atlas/yeo_2011/tests.py

@@ -1,11 +1,8 @@
 from unittest import TestCase
-from nidata.atlas import Yeo2011Dataset
-from nidata.core._utils.testing import DownloadTestMixin, InstallTestMixin
-
 
-class Yeo2011DownloadTest(DownloadTestMixin, TestCase):
-    dataset_class = Yeo2011Dataset
+from nidata.atlas import Yeo2011Dataset
+from nidata.core._utils.testing import InstallThenDownloadTestMixin
 
 
-class Yeo2011InstallTest(InstallTestMixin, TestCase):
+class Yeo2011Test(InstallThenDownloadTestMixin, TestCase):
     dataset_class = Yeo2011Dataset

nidata/core/_utils/testing.py

@@ -87,16 +87,17 @@ def setUp(self):
         self.tmp_dir = tempfile.mkdtemp()
         self.data_dir = op.join(self.tmp_dir,
                                 op.basename(tempfile.mkstemp()[1]))
-        missing_dependencies = self.dataset_class.get_missing_dependencies()
-        if len(missing_dependencies) > 0:
-            raise SkipTest('Missing dependencies: %s' % (
-                ','.join(self.dataset_class.dependencies)))
 
     def tearDown(self):
         if op.exists(self.data_dir):
             shutil.rmtree(self.data_dir)
 
     def fetch(self, *args, **kwargs):
+        missing_dependencies = self.dataset_class.get_missing_dependencies()
+        if len(missing_dependencies) > 0:
+            raise SkipTest('Missing dependencies: %s' % (
+                ','.join(self.dataset_class.dependencies)))
+
         dset = self.dataset_class(data_dir=self.data_dir)
 
         # Replace the fetcher (or fetch function itself)
@@ -108,7 +109,7 @@ def fetch(self, *args, **kwargs):
                 dset.fetch = instancemethod(func, dset)
             else:
                 func = func.__func__
-                dset.fetch = instancemethod(func, dset, dset.__class)
+                dset.fetch = instancemethod(func, dset, dset.__class__)
         else:
             instancemethod = dset.fetcher.fetch.__class__
             func = _DummyFetcher.fetch
@@ -219,6 +220,25 @@ def test_install(self):
                      ','.join(self.dataset_class.get_missing_dependencies()))
 
 
+class InstallThenDownloadTestMixin(InstallTestMixin, DownloadTestMixin):
+    def setUp(self):
+        InstallTestMixin.setUp(self)
+
+        # Instantiate the object to trigger the install.
+        self.dataset_class()
+
+        DownloadTestMixin.setUp(self)
+
+    def tearDown(self):
+        DownloadTestMixin.tearDown(self)
+        InstallTestMixin.tearDown(self)
+
+    def test_install(self):
+        # check dependencies now!
+        assert_equal(0, len(self.dataset_class.get_missing_dependencies()),
+                     ','.join(self.dataset_class.get_missing_dependencies()))
+
+
 @contextlib.contextmanager
 def write_tmp_imgs(*imgs, **kwargs):
     """Context manager for writing Nifti images.

nidata/core/datasets/__init__.py

@@ -5,7 +5,6 @@
 import inspect
 import os
 import os.path as op
-import warnings
 
 from six import with_metaclass
 
@@ -127,7 +126,6 @@ def get_dataset_descr(cls):
             with open(rst_path) as fp:
                 return fp.read()
         except IOError:
-            warnings.warn("Could not find dataset description: %s" % rst_path)
             return ''
 
     def __init__(self, data_dir=None):
@@ -210,11 +208,16 @@ class NilearnDataset(FetcherFunctionDataset):
 
     @classmethod
     def get_dataset_descr_path(cls):
+        # Grab it from nilearn.
         import nilearn.datasets.description as descr
         class_path = op.dirname(inspect.getfile(cls))
         name = getattr(cls, 'nilearn_name', op.basename(class_path))
         descr_path = op.dirname(descr.__file__)
         cls.rst_path = op.join(descr_path, '%s.rst' % name)
+
+        # ...or locally.
+        if not op.exists(cls.rst_path):
+            cls.rst_path = FetcherFunctionDataset.get_dataset_descr_path()
         return cls.rst_path
 
 

nidata/core/objdep.py

@@ -19,7 +19,7 @@ def install_dependency(module_name, install_info=None, verify=False):
     # Install it.
     try:
         print("Installing %s from %s..." % (module_name, install_info))
-        rv = pip.main(['install', install_info])
+        rv = pip.main(['install', '-q', install_info])
         if rv != 0:
             warnings.warn('Pip returned %d' % rv)
     except Exception as ex:

nidata/localizer/brainomics/tests.py

@@ -1,15 +1,12 @@
 from unittest import TestCase
+
 from nidata.localizer import BrainomicsDataset
-from nidata.core._utils.testing import DownloadTestMixin, InstallTestMixin
+from nidata.core._utils.testing import InstallThenDownloadTestMixin
 
 
-class BrainomicsDownloadTest(DownloadTestMixin, TestCase):
+class BrainomicsTest(InstallThenDownloadTestMixin, TestCase):
     dataset_class = BrainomicsDataset
 
     def fetch(self, contrasts=('checkerboard',), *args, **kwargs):
-        super(BrainomicsDownloadTest, self).fetch(
+        super(BrainomicsTest, self).fetch(
             contrasts=contrasts, *args, **kwargs)
-
-
-class BrainomicsTest(InstallTestMixin, TestCase):
-    dataset_class = BrainomicsDataset

nidata/multimodal/hcp/tests.py

@@ -5,7 +5,7 @@
 from unittest import TestCase
 
 from nidata.multimodal import HcpDataset
-from nidata.core._utils.testing import DownloadTestMixin, InstallTestMixin
+from nidata.core._utils.testing import (DownloadTestMixin, InstallTestMixin)
 
 
 @unittest.skipIf(os.environ.get('NIDATA_HCP_USERNAME') is None,

nidata/multimodal/my_connectome_2015/tests.py

@@ -1,11 +1,8 @@
 from unittest import TestCase
-from nidata.multimodal import MyConnectome2015Dataset
-from nidata.core._utils.testing import DownloadTestMixin, InstallTestMixin
-
 
-class MyConnectomeDownloadTest(DownloadTestMixin, TestCase):
-    dataset_class = MyConnectome2015Dataset
+from nidata.multimodal import MyConnectome2015Dataset
+from nidata.core._utils.testing import InstallThenDownloadTestMixin
 
 
-class MyConnectomeInstallTest(InstallTestMixin, TestCase):
+class MyConnectome2015Test(InstallThenDownloadTestMixin, TestCase):
     dataset_class = MyConnectome2015Dataset

nidata/resting_state/ABIDE_pcp/tests.py

@@ -1,11 +1,8 @@
 from unittest import TestCase
-from nidata.resting_state import AbidePcpDataset
-from nidata.core._utils.testing import DownloadTestMixin, InstallTestMixin
-
 
-class AbidePcpDownloadTest(DownloadTestMixin, TestCase):
-    dataset_class = AbidePcpDataset
+from nidata.resting_state import AbidePcpDataset
+from nidata.core._utils.testing import InstallThenDownloadTestMixin
 
 
-class AbidePcpInstallTest(InstallTestMixin, TestCase):
+class AbidePcpTest(InstallThenDownloadTestMixin, TestCase):
     dataset_class = AbidePcpDataset

nidata/resting_state/adhd/tests.py

@@ -1,11 +1,8 @@
-from nidata.resting_state import AdhdRestDataset
 from unittest import TestCase
-from nidata.core._utils.testing import DownloadTestMixin, InstallTestMixin
-
 
-class AdhdRestDownloadTest(DownloadTestMixin, TestCase):
-    dataset_class = AdhdRestDataset
+from nidata.resting_state import AdhdRestDataset
+from nidata.core._utils.testing import InstallThenDownloadTestMixin
 
 
-class AdhdRestInstallTest(InstallTestMixin, TestCase):
+class AdhdRestTest(InstallThenDownloadTestMixin, TestCase):
     dataset_class = AdhdRestDataset

nidata/resting_state/nyu/tests.py

@@ -1,11 +1,8 @@
 from unittest import TestCase
-from nidata.resting_state import NyuRestDataset
-from nidata.core._utils.testing import DownloadTestMixin, InstallTestMixin
-
 
-class NyuRestDownloadTest(DownloadTestMixin, TestCase):
-    dataset_class = NyuRestDataset
+from nidata.resting_state import NyuRestDataset
+from nidata.core._utils.testing import InstallThenDownloadTestMixin
 
 
-class NyuRestInstallTest(InstallTestMixin, TestCase):
+class NyuRestTest(InstallThenDownloadTestMixin, TestCase):
     dataset_class = NyuRestDataset

nidata/task/haxby_etal_2001/tests.py

@@ -1,11 +1,8 @@
 from unittest import TestCase
-from nidata.task import Haxby2001Dataset
-from nidata.core._utils.testing import DownloadTestMixin, InstallTestMixin
-
 
-class Haxby2001DownloadTest(DownloadTestMixin, TestCase):
-    dataset_class = Haxby2001Dataset
+from nidata.task import Haxby2001Dataset
+from nidata.core._utils.testing import InstallThenDownloadTestMixin
 
 
-class Haxby2001InstallTest(InstallTestMixin, TestCase):
+class Haxby2001Test(InstallThenDownloadTestMixin, TestCase):
     dataset_class = Haxby2001Dataset