[med-svn] [mne-python] 01/03: Imported Upstream version 0.7~rc4
Andreas Tille
tille at debian.org
Sat Nov 23 23:06:43 UTC 2013
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tille pushed a commit to branch master
in repository mne-python.
commit 3943434cbe9061efe5cc08b072d978d16ff104bb
Author: Andreas Tille <tille at debian.org>
Date: Sat Nov 23 23:10:13 2013 +0100
Imported Upstream version 0.7~rc4
---
mne/datasets/sample/sample.py | 9 +++------
mne/datasets/utils.py | 19 ++++++++++---------
mne/tests/test_utils.py | 4 ++--
mne/time_frequency/tests/test_ar.py | 19 +++++++++----------
mne/utils.py | 21 +++++++++++++++++++++
mne/viz.py | 2 +-
6 files changed, 46 insertions(+), 28 deletions(-)
diff --git a/mne/datasets/sample/sample.py b/mne/datasets/sample/sample.py
index 8a2eb30..560dad0 100644
--- a/mne/datasets/sample/sample.py
+++ b/mne/datasets/sample/sample.py
@@ -6,11 +6,8 @@
import numpy as np
from ...utils import get_config, verbose
-from ...fixes import partial
from ..utils import has_dataset, _data_path, _doc
-has_sample_data = partial(has_dataset, name='sample')
-
@verbose
def data_path(path=None, force_update=False, update_path=True,
download=True, verbose=None):
@@ -26,6 +23,6 @@ data_path.__doc__ = _doc.format(name='sample',
# `make test-no-sample`
has_sample_data = has_dataset('sample')
skip_sample = get_config('MNE_SKIP_SAMPLE_DATASET_TESTS', 'false') == 'true'
-requires_sample_data = np.testing.dec.skipif(not has_sample_data
- or skip_sample,
- 'Requires sample dataset')
+requires_sample_data = np.testing.dec.skipif(not has_dataset('sample')
+ or skip_sample,
+ 'Requires sample dataset')
diff --git a/mne/datasets/utils.py b/mne/datasets/utils.py
index 6b24081..1fd8c2b 100644
--- a/mne/datasets/utils.py
+++ b/mne/datasets/utils.py
@@ -55,8 +55,8 @@ def _dataset_version(path, name):
fid.close()
else:
# Sample dataset versioning was introduced after 0.3
- # SPM dataset was introduced after 0.6
- version = '0.3' if name == 'sample' else '0.6'
+ # SPM dataset was introduced with 0.7
+ version = '0.3' if name == 'sample' else '0.7'
return version
@@ -161,16 +161,17 @@ def _data_path(path=None, force_update=False, update_path=True,
# compare the version of the Sample dataset and mne
data_version = _dataset_version(path, name)
try:
- from distutils.version import LooseVersion
+ from distutils.version import LooseVersion as LV
except:
warn('Could not determine sample dataset version; dataset could\n'
'be out of date. Please install the "distutils" package.')
- else:
- if LooseVersion(data_version) < LooseVersion(mne_version):
- warn('Sample dataset (version %s) is older than mne-python '
- '(version %s). If the examples fail, you may need to update '
- 'the sample dataset by using force_update=True'
- % (data_version, mne_version))
+ else: # 0.7 < 0.7.git shoud be False, therefore strip
+ if LV(data_version) < LV(mne_version.strip('.git')):
+ warn('The {name} dataset (version {current}) is older than '
+ 'the mne-python (version {newest}). If the examples fail, '
+ 'you may need to update the {name} dataset by using'
+ 'force_update=True'.format(name=name, current=data_version,
+ newest=mne_version))
return path
diff --git a/mne/tests/test_utils.py b/mne/tests/test_utils.py
index cad5074..201a6a0 100644
--- a/mne/tests/test_utils.py
+++ b/mne/tests/test_utils.py
@@ -204,7 +204,7 @@ def test_fetch_file():
"""
# Skipping test if no internet connection available
try:
- urllib2.urlopen("http://github.com", timeout=1)
+ urllib2.urlopen("http://github.com", timeout=2)
except urllib2.URLError:
from nose.plugins.skip import SkipTest
raise SkipTest('No internet connection, skipping download test.')
@@ -214,7 +214,7 @@ def test_fetch_file():
for url in urls:
archive_name = op.join(tempdir, "download_test")
_fetch_file(url, archive_name, print_destination=False)
- assert_raises(Exception, _fetch_file, 'http://0.0',
+ assert_raises(Exception, _fetch_file, 'NOT_AN_ADDRESS',
op.join(tempdir, 'test'))
resume_name = op.join(tempdir, "download_resume")
# touch file
diff --git a/mne/time_frequency/tests/test_ar.py b/mne/time_frequency/tests/test_ar.py
index b8003fe..a8dcf2a 100644
--- a/mne/time_frequency/tests/test_ar.py
+++ b/mne/time_frequency/tests/test_ar.py
@@ -2,27 +2,26 @@ import os.path as op
import numpy as np
from numpy.testing import assert_array_almost_equal
from nose.tools import assert_true
-import nose
from mne import fiff
from mne.time_frequency import yule_walker, ar_raw
+from mne.utils import requires_statsmodels
+
raw_fname = op.join(op.dirname(__file__), '..', '..', 'fiff', 'tests', 'data',
'test_raw.fif')
+ at requires_statsmodels
def test_yule_walker():
"""Test Yule-Walker against statsmodels
"""
- try:
- from statsmodels.regression.linear_model import yule_walker as sm_yw
- d = np.random.randn(100)
- sm_rho, sm_sigma = sm_yw(d, order=2)
- rho, sigma = yule_walker(d, order=2)
- assert_array_almost_equal(sm_sigma, sigma)
- assert_array_almost_equal(sm_rho, rho)
- except ImportError:
- raise nose.SkipTest("XFailed Test")
+ from statsmodels.regression.linear_model import yule_walker as sm_yw
+ d = np.random.randn(100)
+ sm_rho, sm_sigma = sm_yw(d, order=2)
+ rho, sigma = yule_walker(d, order=2)
+ assert_array_almost_equal(sm_sigma, sigma)
+ assert_array_almost_equal(sm_rho, rho)
def test_ar_raw():
diff --git a/mne/utils.py b/mne/utils.py
index 04e053c..003421d 100644
--- a/mne/utils.py
+++ b/mne/utils.py
@@ -507,6 +507,27 @@ def requires_tvtk(function):
return dec
+def requires_statsmodels(function):
+ """Decorator to skip test if statsmodels is not available"""
+ @wraps(function)
+ def dec(*args, **kwargs):
+ skip = False
+ try:
+ from tvtk.api import tvtk # analysis:ignore
+ except ImportError:
+ skip = True
+
+ if skip is True:
+ from nose.plugins.skip import SkipTest
+ raise SkipTest('Test %s skipped, requires statsmodels'
+ % function.__name__)
+ ret = function(*args, **kwargs)
+
+ return ret
+
+ return dec
+
+
def make_skipper_dec(module, skip_str):
"""Helper to make skipping decorators"""
skip = False
diff --git a/mne/viz.py b/mne/viz.py
index b290ff4..9d41570 100644
--- a/mne/viz.py
+++ b/mne/viz.py
@@ -3485,7 +3485,7 @@ def plot_source_spectrogram(stcs, freq_bins, source_index=None, colorbar=False,
# Covering frequency gaps with horizontal bars
for lower_bound, upper_bound in gap_bounds:
plt.barh(lower_bound, time_bounds[-1] - time_bounds[0], upper_bound -
- lower_bound, time_bounds[0], color='lightgray')
+ lower_bound, time_bounds[0], color='#666666')
if show:
plt.show()
--
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