FIX : avoid writing outside of build dir when running tests

FIX: Fixes for py2.6

MANIFEST.in

@@ -4,6 +4,7 @@ include mne/__init__.py
 recursive-include examples *.py
 recursive-include examples *.txt
 recursive-include mne *.py
+recursive-include mne/data *.dat
 recursive-include mne/data *.sel
 recursive-include mne/data *.fif.gz
 recursive-include mne/layouts *.lout

Makefile

@@ -34,7 +34,7 @@ $(CURDIR)/examples/MNE-sample-data/MEG/sample/sample_audvis_raw.fif:
 	wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/MNE-sample-data-processed.tar.gz
 	tar xvzf MNE-sample-data-processed.tar.gz
 	mv MNE-sample-data examples/
-	ln -s ${PWD}/examples/MNE-sample-data ${PWD}/MNE-sample-data -f
+	ln -sf ${PWD}/examples/MNE-sample-data ${PWD}/MNE-sample-data
 
 test: in sample_data
 	rm -f .coverage

bin/mne

@@ -33,4 +33,4 @@ elif sys.argv[1] not in valid_commands:
 else:
     cmd = sys.argv[1]
     cmd_path = op.join(mne_bin_dir, 'commands', 'mne_%s.py' % cmd)
-    sys.exit(subprocess.call([cmd_path] + sys.argv[2:]))
+    sys.exit(subprocess.call([sys.executable, cmd_path] + sys.argv[2:]))

doc/Makefile

@@ -15,7 +15,8 @@ ALLSPHINXOPTS   = -d build/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
 
 help:
 	@echo "Please use \`make <target>' where <target> is one of"
-	@echo "  html      to make standalone HTML files"
+	@echo "  html      to make standalone HTML files (stable version)"
+	@echo "  dev_html  to make standalone HTML files (dev version)"
 	@echo "  dirhtml   to make HTML files named index.html in directories"
 	@echo "  pickle    to make pickle files"
 	@echo "  json      to make JSON files"
@@ -39,11 +40,21 @@ html:
 	@echo
 	@echo "Build finished. The HTML pages are in build/html."
 
+html_dev:
+	BUILD_DEV_HTML=1 $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) build/html
+	@echo
+	@echo "Build finished. The HTML pages are in build/html."
+
 html-noplot:
 	$(SPHINXBUILD) -D plot_gallery=False -b html $(ALLSPHINXOPTS) build/html
 	@echo
 	@echo "Build finished. The HTML pages are in build/html/stable."
 
+html_dev-noplot:
+	BUILD_DEV_HTML=1 $(SPHINXBUILD) -D plot_gallery=False -b html $(ALLSPHINXOPTS) build/html
+	@echo
+	@echo "Build finished. The HTML pages are in build/html/stable."
+
 dirhtml:
 	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) build/dirhtml
 	@echo

doc/source/_templates/layout.html

@@ -45,16 +45,27 @@
         <!-- <li><a href="{{ pathto('search') }}">Search</a></li> -->
 {% endblock %}
 
-
 {% block relbar1 %}
-<div style="background-color: white; text-align: left; padding: 10px 10px 15px 15px">
+{% if build_dev_html|tobool %}
+<div style="background-color: red; color: white; font-weight:bold; text-align: center; padding: 10px; min-width: 910px">
+This documentation is for the development version ({{ release }}) - <a href="http://martinos.org/mne/stable">Stable version</a>
+</div>
+{% endif %}
+<div style="background-color: white; text-align: left; padding: 10px 7px 15px 15px; min-width: 910px">
+<div style="float: left">
 <a href="{{ pathto('index') }}"><img src="{{
-pathto("_static/logo.png", 1) }}" border="0" alt="py4sci"/></a>
+pathto("_static/mne_logo.png", 1) }}" border="0" alt="py4sci"/></a>
+</div>
+
+<div style="float: right">
+<a href="{{ pathto('index') }}"><img src="{{
+pathto("_static/institutions.png", 1) }}" border="0" alt="py4sci"/></a>
+</div>
+<br style="clear:both"/>
 </div>
 {{ super() }}
 {% endblock %}
 
 {# put the sidebar before the body #}
 {% block sidebar1 %}{{ sidebar() }}{% endblock %}
-{% block sidebar2 %}{% endblock %}
-
+{% block sidebar2 %}{% endblock %}

doc/source/_templates/sidebar.html

@@ -0,0 +1,5 @@
+<h3>Versions</h3>
+<ul class="current">
+    <li class="toctree-l1"><a href=http://martinos.org/mne/stable>Stable</a></li>
+    <li class="toctree-l1"><a href=http://martinos.org/mne/dev>Development</a></li>
+</ul>

doc/source/conf.py

@@ -160,7 +160,8 @@ html_last_updated_fmt = '%b %d, %Y'
 #html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
+html_sidebars = {'**': ['globaltoc.html', 'sourcelink.html', 'searchbox.html',
+                        'sidebar.html']}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
@@ -179,8 +180,10 @@ html_use_index = False
 html_show_sourcelink = False
 
 # variables to pass to HTML templating engine
+build_dev_html = bool(int(os.environ.get('BUILD_DEV_HTML', False)))
+
 html_context = {'use_google_analytics':True, 'use_twitter':True,
-                'use_media_buttons':True}
+                'use_media_buttons':True, 'build_dev_html':build_dev_html}
 
 # If true, an OpenSearch description file will be output, and all pages will
 # contain a <link> tag referring to it.  The value of this option must be the

doc/source/index.rst

@@ -29,9 +29,16 @@ component of MNE is presently evolving quickly and thanks to the
 adopted open development environment user contributions can be easily
 incorporated.
 
+The MNE development is supported by National Institute of Biomedical Imaging and Bioengineering 
+grants 5R01EB009048 and P41EB015896 (Center for Functional Neuroimaging Technologies) as well as 
+NSF awards 0958669 and 1042134.
+
 The Matlab and Python components of MNE are provided under the
 simplified BSD license.
 
+
+
+
   * `Download <http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/MNE_register/index.php>`_ MNE
   * Read the :ref:`manual`.
   * Get started with :ref:`mne_python`

doc/source/python_reference.rst

@@ -393,9 +393,9 @@ MRI Processing
 Step by step instructions for using :func:`gui.coregistration`:
 
  - `Coregistration for subjects with structural MRI 
-   <http://www.slideshare.net/slideshow/embed_code/28598463>`_ 
+   <http://www.slideshare.net/mne-python/mnepython-coregistration>`_ 
  - `Scaling a template MRI for subjects for which no MRI is available
-   <http://www.slideshare.net/slideshow/embed_code/28598561>`_
+   <http://www.slideshare.net/mne-python/mnepython-scale-mri>`_
 
 .. autosummary::
    :toctree: generated/

doc/sphinxext/gen_rst.py

@@ -61,16 +61,20 @@ class Tee(object):
 def get_data(url):
     """Helper function to get data over http or from a local file"""
     if url.startswith('http://'):
-        resp = urllib2.urlopen(url)
-        encoding = resp.headers.dict.get('content-encoding', 'plain')
-        data = resp.read()
-        if encoding == 'plain':
-            pass
-        elif encoding == 'gzip':
-            data = StringIO(data)
-            data = gzip.GzipFile(fileobj=data).read()
-        else:
-            raise RuntimeError('unknown encoding')
+        try:
+            resp = urllib2.urlopen(url)
+            encoding = resp.headers.dict.get('content-encoding', 'plain')
+            data = resp.read()
+            if encoding == 'plain':
+                pass
+            elif encoding == 'gzip':
+                data = StringIO(data)
+                data = gzip.GzipFile(fileobj=data).read()
+            else:
+                raise RuntimeError('unknown encoding')
+        except urllib2.HTTPError as err:
+            print 'Error downloading %s: %s' % (url, str(err))
+            return ''
     else:
         with open(url, 'r') as fid:
             data = fid.read()

doc/upload_html.sh

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
 
 #scp -r build/html/* martinos-data:/web/html/mne/
-rsync -rltvz --delete --perms --chmod=g+w build/html/ martinos-data:/web/html/mne/ -essh
-ssh martinos-data "chgrp -R megweb /web/html/mne"
+rsync -rltvz --delete --perms --chmod=g+w build/html/ martinos-data:/web/html/ext/mne/stable -essh
+ssh martinos-data "chgrp -R megweb /web/html/ext/mne/stable"

mne/__init__.py

@@ -1,7 +1,7 @@
 """MNE for MEG and EEG data analysis
 """
 
-__version__ = '0.7'
+__version__ = '0.7.1'
 
 # have to import verbose first since it's needed by many things
 from .utils import (set_log_level, set_log_file, verbose, set_config,

mne/coreg.py

@@ -715,13 +715,13 @@ def _is_mri_subject(subject, subjects_dir=None):
         Whether ``subject`` is an mri subject.
     """
     subjects_dir = get_subjects_dir(subjects_dir, raise_error=True)
-    sdir = os.path.join(subjects_dir, subject)
 
-    fname = os.path.join(sdir, 'bem', '%s-head.fif' % subject)
+    fname = head_bem_fname.format(subjects_dir=subjects_dir, subject=subject)
     if not os.path.exists(fname):
         return False
 
-    fname = os.path.join(sdir, 'bem', '%s-*-bem.fif' % subject)
+    fname = bem_fname.format(subjects_dir=subjects_dir, subject=subject,
+                             name='*')
     if len(glob(fname)) == 0:
         return False
 

mne/fiff/brainvision/brainvision.py

@@ -205,16 +205,27 @@ def _read_vmrk(vmrk_fname):
     stim_channel : array
         An array containing the whole recording's event marking
     """
+    # read vmrk file
+    with open(vmrk_fname) as fid:
+        txt = fid.read()
 
-    with open(vmrk_fname) as f:
-    # setup config reader
-        assert (f.readline().strip() ==
-                'Brain Vision Data Exchange Marker File, Version 1.0')
+    start_tag = 'Brain Vision Data Exchange Marker File, Version 1.0'
+    if not txt.startswith(start_tag):
+        raise ValueError("vmrk file should start with %r" % start_tag)
 
-        cfg = SafeConfigParser()
-        cfg.readfp(f)
+    # extract Marker Infos block
+    m = re.search("\[Marker Infos\]", txt)
+    if not m:
+        return np.zeros(0)
+    mk_txt = txt[m.end():]
+    m = re.search("\[.*\]", mk_txt)
+    if m:
+        mk_txt = mk_txt[:m.start()]
+
+    # extract event information
+    items = re.findall("^Mk\d+=(.*)", mk_txt, re.MULTILINE)
     events = []
-    for _, info in cfg.items('Marker Infos'):
+    for info in items:
         mtype, mdesc, offset, duration = info.split(',')[:4]
         if mtype == 'Stimulus':
             trigger = int(re.findall('S\s?(\d+)', mdesc)[0])

mne/fiff/edf/edf.py

@@ -417,11 +417,12 @@ def _get_edf_info(fname, n_eeg, stim_channel, annot, annotmap, hpts, preload):
     if hpts and os.path.lexists(hpts):
         fid = open(hpts, 'rb').read()
         locs = {}
-        temp = re.findall('eeg\s(\w+)\s(-?\d+)\s(-?\d+)\s(-?\d+)', fid)
-        temp = temp + re.findall('cardinal\s(\d+)\s(-?\d+)\s(-?\d+)\s(-?\d+)',
-                                 fid)
+        temp = re.findall('eeg\s(\w+)\s(-?[\d,.]+)\s(-?[\d,.]+)\s(-?[\d,.]+)',
+                          fid)
+        temp += re.findall('cardinal\s([\d,.]+)\s(-?[\d,.]+)\s(-?[\d,.]+)\s(-?'
+                           '[\d,.]+)', fid)
         for loc in temp:
-            coord = np.array(map(int, loc[1:]))
+            coord = np.array(map(float, loc[1:]))
             coord = apply_trans(als_ras_trans_mm, coord)
             locs[loc[0].lower()] = coord
         trans = get_ras_to_neuromag_trans(nasion=locs['2'], lpa=locs['1'],

mne/fiff/edf/tests/data/biosemi.hpts

@@ -7,7 +7,7 @@
 #
 # 64 eeg channels
 # ---------------
-eeg Fp1 -95 -31 -3
+eeg Fp1 -95.0 -31.0 -3.0
 eeg AF7 -81 -59 -3
 eeg AF3 -87 -41 28
 eeg F1 -71 -29 64

mne/fiff/edf/tests/test_edf.py

@@ -7,7 +7,7 @@
 import os.path as op
 import inspect
 
-from nose.tools import assert_equal
+from nose.tools import assert_equal, assert_true
 from numpy.testing import assert_array_almost_equal, assert_array_equal
 from scipy import io
 
@@ -43,6 +43,11 @@ def test_bdf_data():
 
     assert_array_almost_equal(data_py, data_eeglab)
 
+    # Manually checking that float coordinates are imported
+    assert_true((raw_py.info['chs'][0]['eeg_loc']).any())
+    assert_true((raw_py.info['chs'][25]['eeg_loc']).any())
+    assert_true((raw_py.info['chs'][63]['eeg_loc']).any())
+
 
 def test_edf_data():
     """Test reading raw edf files

mne/fiff/tag.py

@@ -94,11 +94,14 @@ def read_big(fid, size=None):
         >>> with open(fname, 'wb') as fid: x.tofile(fid)
         >>> with open(fname, 'rb') as fid: y = np.fromstring(read_big(fid))
         >>> assert np.all(x == y)
-        >>> with gzip.open(fname_gz, 'wb') as fid: fid.write(x.tostring())
-        24000000
-        >>> with gzip.open(fname_gz, 'rb') as fid: y = np.fromstring(read_big(fid))
+        >>> fid_gz = gzip.open(fname_gz, 'wb')
+        >>> _ = fid_gz.write(x.tostring())
+        >>> fid_gz.close()
+        >>> fid_gz = gzip.open(fname_gz, 'rb')
+        >>> y = np.fromstring(read_big(fid_gz))
         >>> assert np.all(x == y)
         >>> shutil.rmtree(os.path.dirname(fname))
+        >>> fid_gz.close()
 
     """
     # buf_size is chosen as a largest working power of 2 (16 MB):

mne/forward/forward.py

@@ -1500,8 +1500,8 @@ def do_forward_solution(subject, meas, fname=None, src=None, spacing=None,
         logger.info('Running forward solution generation command with '
                     'subjects_dir %s' % subjects_dir)
         run_subprocess(cmd, env=env)
-    except Exception as exception:
-        raise exception
+    except:
+        raise
     else:
         fwd = read_forward_solution(op.join(path, fname), verbose=False)
     finally:

mne/gui/__init__.py

@@ -45,9 +45,9 @@ def coregistration(tabbed=False, split=True, scene_width=01, raw=None,
     All parameters are optional, since they can be set through the GUI.
     Step by step instructions for the coregistrations can be accessed as
     slides, `for subjects with structural MRI
-    <http://www.slideshare.net/slideshow/embed_code/28598463>`_ and `for
+    <http://www.slideshare.net/mne-python/mnepython-coregistration>`_ and `for
     subjects for which no MRI is available
-    <http://www.slideshare.net/slideshow/embed_code/28598561>`_.
+    <http://www.slideshare.net/mne-python/mnepython-scale-mri>`_.
     """
     from ._coreg_gui import CoregFrame, _make_view
     view = _make_view(tabbed, split, scene_width)

mne/gui/_coreg_gui.py

@@ -73,8 +73,7 @@ from ..utils import get_subjects_dir, logger
 from ._fiducials_gui import MRIHeadWithFiducialsModel, FiducialsPanel
 from ._file_traits import (assert_env_set, trans_wildcard, RawSource,
                            SubjectSelectorPanel)
-from ._viewer import (defaults, HeadViewController, PointObject, SurfaceObject,
-                      headview_borders)
+from ._viewer import defaults, HeadViewController, PointObject, SurfaceObject
 
 
 laggy_float_editor = TextEditor(auto_set=False, enter_set=True, evaluate=float)
@@ -523,6 +522,12 @@ class CoregModel(HasPrivateTraits):
         head_mri_trans = info['trans']
         self.set_trans(head_mri_trans)
 
+    def reset(self):
+        """Reset all the parameters affecting the coregistration"""
+        self.reset_traits(('n_scaling_params', 'scale_x', 'scale_y', 'scale_z',
+                           'rot_x', 'rot_y', 'rot_z', 'trans_x', 'trans_y',
+                           'trans_z'))
+
     def set_trans(self, head_mri_trans):
         """Set rotation and translation parameters from a transformation matrix
 
@@ -885,9 +890,7 @@ class CoregPanel(HasPrivateTraits):
             warning(None, err, "MNE_ROOT Not Set")
 
     def _reset_params_fired(self):
-        self.reset_traits(('n_scaling_params', 'scale_x', 'scale_y', 'scale_z',
-                           'rot_x', 'rot_y', 'rot_z', 'trans_x', 'trans_y',
-                           'trans_z'))
+        self.model.reset()
 
     def _rot_x_dec_fired(self):
         self.rot_x -= self.rot_step

mne/gui/_file_traits.py

@@ -297,7 +297,7 @@ class RawSource(HasPrivateTraits):
     def _get_fid_points(self):
         if not self.raw:
             return {}
-        digs = {d['ident']: d for d in self.fid_dig}
+        digs = dict((d['ident'], d) for d in self.fid_dig)
         return digs
 
     @cached_property
@@ -321,6 +321,9 @@ class RawSource(HasPrivateTraits):
         else:
             return np.zeros((1, 3))
 
+    def _file_changed(self):
+        self.reset_traits(('points_filter',))
+
 
 class MRISubjectSource(HasPrivateTraits):
     """Find subjects in SUBJECTS_DIR and select one

mne/gui/tests/test_coreg_gui.py

@@ -4,24 +4,25 @@
 
 import os
 
-import numpy as np
+import numpy as np
 from numpy.testing import assert_allclose
 from nose.tools import (assert_equal, assert_almost_equal, assert_false,
-                        assert_is_instance, assert_less, assert_raises,
-                        assert_true)
+                        assert_raises, assert_true)
 
 import mne
 from mne.datasets import sample
+from mne.fiff.kit.tests import data_dir as kit_data_dir
 from mne.utils import _TempDir, requires_traits, requires_mne_fs_in_env
 
 
 data_path = sample.data_path(download=False)
 raw_path = os.path.join(data_path, 'MEG', 'sample', 'sample_audvis_raw.fif')
+kit_raw_path = os.path.join(kit_data_dir, 'test_bin.fif')
 subjects_dir = os.path.join(data_path, 'subjects')
 
 tempdir = _TempDir()
-
-trans_dst = os.path.join(tempdir, 'test-trans.fif')
+
+trans_dst = os.path.join(tempdir, 'test-trans.fif')
 
 
 @sample.requires_sample_data
@@ -35,40 +36,40 @@ def test_coreg_model():
 
     model.mri.subjects_dir = subjects_dir
     model.mri.subject = 'sample'
-
-    assert_false(model.mri.fid_ok)
-    model.mri.lpa = [[-0.06, 0, 0]]
-    model.mri.nasion = [[0, 0.05, 0]]
-    model.mri.rpa = [[0.08, 0, 0]]
-    assert_true(model.mri.fid_ok)
-
-    model.hsp.file = raw_path
-    assert_allclose(model.hsp.lpa, [[-7.137e-2, 0, 5.122e-9]], 1e-4)
-    assert_allclose(model.hsp.rpa, [[ 7.527e-2, 0, 5.588e-9]], 1e-4)
-    assert_allclose(model.hsp.nasion, [[ 3.725e-9, 1.026e-1, 4.191e-9]], 1e-4)
-    assert_true(model.has_fid_data)
+
+    assert_false(model.mri.fid_ok)
+    model.mri.lpa = [[-0.06, 0, 0]]
+    model.mri.nasion = [[0, 0.05, 0]]
+    model.mri.rpa = [[0.08, 0, 0]]
+    assert_true(model.mri.fid_ok)
+
+    model.hsp.file = raw_path
+    assert_allclose(model.hsp.lpa, [[-7.137e-2, 0, 5.122e-9]], 1e-4)
+    assert_allclose(model.hsp.rpa, [[+7.527e-2, 0, 5.588e-9]], 1e-4)
+    assert_allclose(model.hsp.nasion, [[+3.725e-9, 1.026e-1, 4.191e-9]], 1e-4)
+    assert_true(model.has_fid_data)
 
     lpa_distance = model.lpa_distance
     nasion_distance = model.nasion_distance
     rpa_distance = model.rpa_distance
     avg_point_distance = np.mean(model.point_distance)
 
-    model.fit_auricular_points()
-    old_x = lpa_distance ** 2 + rpa_distance ** 2
+    model.fit_auricular_points()
+    old_x = lpa_distance ** 2 + rpa_distance ** 2
     new_x = model.lpa_distance ** 2 + model.rpa_distance ** 2
-    assert_less(new_x, old_x)
-
-    model.fit_fiducials()
-    old_x = lpa_distance ** 2 + rpa_distance ** 2 + nasion_distance ** 2
+    assert_true(new_x < old_x)
+
+    model.fit_fiducials()
+    old_x = lpa_distance ** 2 + rpa_distance ** 2 + nasion_distance ** 2
     new_x = (model.lpa_distance ** 2 + model.rpa_distance ** 2
-             + model.nasion_distance ** 2)
-    assert_less(new_x, old_x)
-
-    model.fit_hsp_points()
-    assert_less(np.mean(model.point_distance), avg_point_distance)
-
-    model.save_trans(trans_dst)
-    trans = mne.read_trans(trans_dst)
+             + model.nasion_distance ** 2)
+    assert_true(new_x < old_x)
+
+    model.fit_hsp_points()
+    assert_true(np.mean(model.point_distance) < avg_point_distance)
+
+    model.save_trans(trans_dst)
+    trans = mne.read_trans(trans_dst)
     assert_allclose(trans['trans'], model.head_mri_trans)
 
     # test restoring trans
@@ -92,9 +93,9 @@ def test_coreg_model():
     assert_almost_equal(model.rot_z, rot_z)
 
     # info
-    assert_is_instance(model.fid_eval_str, basestring)
-    assert_is_instance(model.points_eval_str, basestring)
-
+    assert_true(isinstance(model.fid_eval_str, basestring))
+    assert_true(isinstance(model.points_eval_str, basestring))
+
 
 @sample.requires_sample_data
 @requires_traits
@@ -127,22 +128,22 @@ def test_coreg_model_with_fsaverage():
     assert_equal(model.hsp.n_omitted, 1)
 
     # scale with 1 parameter
-    model.n_scale_params = 1
-
-    model.fit_scale_auricular_points()
+    model.n_scale_params = 1
+
+    model.fit_scale_auricular_points()
     old_x = lpa_distance ** 2 + rpa_distance ** 2
     new_x = model.lpa_distance ** 2 + model.rpa_distance ** 2
-    assert_less(new_x, old_x)
+    assert_true(new_x < old_x)
 
     model.fit_scale_fiducials()
     old_x = lpa_distance ** 2 + rpa_distance ** 2 + nasion_distance ** 2
     new_x = (model.lpa_distance ** 2 + model.rpa_distance ** 2
              + model.nasion_distance ** 2)
-    assert_less(new_x, old_x)
+    assert_true(new_x < old_x)
 
     model.fit_scale_hsp_points()
     avg_point_distance_1param = np.mean(model.point_distance)
-    assert_less(avg_point_distance_1param, avg_point_distance)
+    assert_true(avg_point_distance_1param < avg_point_distance)
 
     desc, func, args, kwargs = model.get_scaling_job('test')
     assert_true(isinstance(desc, basestring))
@@ -154,4 +155,9 @@ def test_coreg_model_with_fsaverage():
     # scale with 3 parameters
     model.n_scale_params = 3
     model.fit_scale_hsp_points()
-    assert_less(np.mean(model.point_distance), avg_point_distance_1param)
+    assert_true(np.mean(model.point_distance) < avg_point_distance_1param)
+
+    # test switching raw disables point omission
+    assert_equal(model.hsp.n_omitted, 1)
+    model.hsp.file = kit_raw_path
+    assert_equal(model.hsp.n_omitted, 0)

mne/tests/test_epochs.py

@@ -664,7 +664,7 @@ def test_epoch_eq():
             epochs[key]
         except KeyError:
             caught += 1
-    assert_raises(caught == 2)
+    assert_raises(Exception, caught == 2)
     assert_true(not np.any(epochs.events[:, 2] == 1))
     assert_true(not np.any(epochs.events[:, 2] == 2))
     epochs = combine_event_ids(epochs, ['c', 'd'], {'cd': 34})

mne/tests/test_utils.py

@@ -122,14 +122,14 @@ def test_config():
     del os.environ[key]
     # catch the warning about it being a non-standard config key
     with warnings.catch_warnings(True) as w:
-        set_config(key, None)
+        set_config(key, None, home_dir=tempdir)
         assert_true(len(w) == 1)
-    assert_true(get_config(key) is None)
+    assert_true(get_config(key, home_dir=tempdir) is None)
     assert_raises(KeyError, get_config, key, raise_error=True)
     with warnings.catch_warnings(True):
-        set_config(key, value)
-        assert_true(get_config(key) == value)
-        set_config(key, None)
+        set_config(key, value, home_dir=tempdir)
+        assert_true(get_config(key, home_dir=tempdir) == value)
+        set_config(key, None, home_dir=tempdir)
     if old_val is not None:
         os.environ[key] = old_val
 

mne/time_frequency/tests/test_csd.py

@@ -1,5 +1,6 @@
 import numpy as np
-from nose.tools import assert_raises, assert_equal, assert_almost_equal
+from nose.tools import (assert_raises, assert_equal, assert_almost_equal,
+                        assert_true)
 from numpy.testing import assert_array_equal
 from os import path as op
 
@@ -124,8 +125,8 @@ def test_compute_epochs_csd_on_artificial_data():
     data_csd_mt = compute_epochs_csd(epochs_sin, mode='multitaper')
     fourier_power = np.abs(data_csd_fourier.data[0, 0]) * sfreq
     mt_power = np.abs(data_csd_mt.data[0, 0]) * sfreq
-    assert_almost_equal(fourier_power, signal_power, delta=0.5)
-    assert_almost_equal(mt_power, signal_power, delta=1)
+    assert_true(abs(fourier_power - signal_power) <= 0.5)
+    assert_true(abs(mt_power - signal_power) <= 1)
 
     # Power per sample should not depend on time window length
     for tmax in [0.2, 0.4, 0.6, 0.8]:
@@ -139,9 +140,8 @@ def test_compute_epochs_csd_on_artificial_data():
                                                   fmax=np.inf, n_fft=n_fft)
             fourier_power_per_sample = np.abs(data_csd_fourier.data[0, 0]) *\
                 sfreq / data_csd_fourier.n_fft
-            assert_almost_equal(signal_power_per_sample,
-                                fourier_power_per_sample, delta=0.003)
-
+            assert_true(abs(signal_power_per_sample -
+                            fourier_power_per_sample) < 0.003)
         # Power per sample should not depend on number of tapers
         for n_tapers in [1, 2, 3, 5]:
             for add_n_fft in [30, 0, 30]:
@@ -159,5 +159,5 @@ def test_compute_epochs_csd_on_artificial_data():
                     delta = 0.05
                 else:
                     delta = 0.004
-                assert_almost_equal(signal_power_per_sample,
-                                    mt_power_per_sample, delta=delta)
+                assert_true(abs(signal_power_per_sample - mt_power_per_sample)
+                            < delta)

mne/utils.py

@@ -215,8 +215,12 @@ def run_subprocess(command, *args, **kwargs):
 
     output = (stdout_, stderr)
     if p.returncode:
-        print output
-        raise subprocess.CalledProcessError(p.returncode, command, output)
+        print(output)
+        err_fun = subprocess.CalledProcessError.__init__
+        if 'output' in inspect.getargspec(err_fun).args:
+            raise subprocess.CalledProcessError(p.returncode, command, output)
+        else:
+            raise subprocess.CalledProcessError(p.returncode, command)
 
     return output
 
@@ -704,9 +708,15 @@ def get_subjects_dir(subjects_dir=None, raise_error=False):
     return subjects_dir
 
 
-def get_config_path():
+def get_config_path(home_dir=None):
     """Get path to standard mne-python config file
 
+    Parameters
+    ----------
+    home_dir : str | None
+        The folder that contains the .mne config folder.
+        If None, it is found automatically.
+
     Returns
     -------
     config_path : str
@@ -714,16 +724,17 @@ def get_config_path():
         will be '%APPDATA%\.mne\mne-python.json'. On every other
         system, this will be $HOME/.mne/mne-python.json.
     """
+    if home_dir is None:
+        # this has been checked on OSX64, Linux64, and Win32
+        home_dir = os.getenv('APPDATA' if 'nt' == os.name.lower() else 'HOME',
+                             None)
 
-    # this has been checked on OSX64, Linux64, and Win32
-    val = os.getenv('APPDATA' if 'nt' == os.name.lower() else 'HOME', None)
-    if val is None:
+    if home_dir is None:
         raise ValueError('mne-python config file path could '
                          'not be determined, please report this '
                          'error to mne-python developers')
 
-    val = op.join(val, '.mne', 'mne-python.json')
-    return val
+    return op.join(home_dir, '.mne', 'mne-python.json')
 
 
 def set_cache_dir(cache_dir):
@@ -787,7 +798,7 @@ known_config_wildcards = [
     ]
 
 
-def get_config(key, default=None, raise_error=False):
+def get_config(key, default=None, raise_error=False, home_dir=None):
     """Read mne(-python) preference from env, then mne-python config
 
     Parameters
@@ -800,6 +811,9 @@ def get_config(key, default=None, raise_error=False):
     raise_error : bool
         If True, raise an error if the key is not found (instead of returning
         default).
+    home_dir : str | None
+        The folder that contains the .mne config folder.
+        If None, it is found automatically.
 
     Returns
     -------
@@ -815,7 +829,7 @@ def get_config(key, default=None, raise_error=False):
         return os.environ[key]
 
     # second, look for it in mne-python config file
-    config_path = get_config_path()
+    config_path = get_config_path(home_dir=home_dir)
     if not op.isfile(config_path):
         key_found = False
         val = default
@@ -838,7 +852,7 @@ def get_config(key, default=None, raise_error=False):
     return val
 
 
-def set_config(key, value):
+def set_config(key, value, home_dir=None):
     """Set mne-python preference in config
 
     Parameters
@@ -848,8 +862,10 @@ def set_config(key, value):
     value : str |  None
         The value to assign to the preference key. If None, the key is
         deleted.
+    home_dir : str | None
+        The folder that contains the .mne config folder.
+        If None, it is found automatically.
     """
-
     if not isinstance(key, basestring):
         raise ValueError('key must be a string')
     # While JSON allow non-string types, we allow users to override config
@@ -861,7 +877,7 @@ def set_config(key, value):
         warnings.warn('Setting non-standard config type: "%s"' % key)
 
     # Read all previous values
-    config_path = get_config_path()
+    config_path = get_config_path(home_dir=home_dir)
     if op.isfile(config_path):
         with open(config_path, 'r') as fid:
             config = json.load(fid)
@@ -921,7 +937,7 @@ class ProgressBar(object):
     """
 
     spinner_symbols = ['|', '/', '-', '\\']
-    template = '\r[{}{}] {:.05f} {} {}   '
+    template = '\r[{0}{1}] {2:.05f} {3} {4}   '
 
     def __init__(self, max_value, initial_value=0, mesg='', max_chars=40,
                  progress_character='.', spinner=False):
@@ -1162,7 +1178,7 @@ def sizeof_fmt(num):
         exponent = min(int(log(num, 1024)), len(unit_list) - 1)
         quotient = float(num) / 1024 ** exponent
         unit, num_decimals = unit_list[exponent]
-        format_string = '{:.%sf} {}' % (num_decimals)
+        format_string = '{0:.%sf} {1}' % (num_decimals)
         return format_string.format(quotient, unit)
     if num == 0:
         return '0 bytes'