FIX: Fix location of base.py

mne/epochs.py

@@ -29,7 +29,7 @@
 from .fiff.proj import setup_proj, ProjMixin
 from .fiff.channels import ContainsMixin, PickDropChannelsMixin
 from .fiff.evoked import aspect_rev
-from .raw import _BaseRaw, _time_as_index, _index_as_time
+from .fiff.base import _BaseRaw, _time_as_index, _index_as_time
 from .baseline import rescale
 from .utils import (check_random_state, _check_pandas_index_arguments,
                     _check_pandas_installed)

mne/fiff/__init__.py

@@ -9,19 +9,21 @@
 from .open import fiff_open, show_fiff
 from .evoked import Evoked, read_evoked, write_evoked
 from .meas_info import read_fiducials, write_fiducials, read_info, write_info
-from .raw import RawFIFF
 from .pick import (pick_types, pick_channels, pick_types_evoked,
                    pick_channels_regexp, pick_channels_forward,
                    pick_types_forward, pick_channels_cov,
                    pick_channels_evoked, pick_info, _has_kit_refs)
 
 from .proj import proj_equal, make_eeg_average_ref_proj
 from .cov import read_cov, write_cov
-from . import bti
-from . import kit
+from . import base
 from . import brainvision
+from . import bti
 from . import edf
+from . import egi
+from . import kit
+from . import fiff
 
 # for backward compatibility
-from .raw import RawFIFF as Raw
-from ..raw import concatenate_raws, get_chpi_positions, set_eeg_reference
+from .fiff import RawFIFF as Raw
+from .base import concatenate_raws, get_chpi_positions, set_eeg_reference

mne/raw.py → mne/fiff/base.py

@@ -16,25 +16,25 @@
 from scipy.signal import hilbert
 from scipy import linalg
 
-from .fiff.constants import FIFF
-from .fiff.meas_info import write_meas_info
-from .fiff.pick import pick_types, channel_type
-from .fiff.proj import (setup_proj, activate_proj, proj_equal, ProjMixin,
-                        _has_eeg_average_ref_proj, make_eeg_average_ref_proj)
-from .fiff.channels import ContainsMixin, PickDropChannelsMixin
-from .fiff.compensator import set_current_comp
-from .fiff.write import (start_file, end_file, start_block, end_block,
-                         write_dau_pack16, write_float, write_double,
-                         write_complex64, write_complex128, write_int,
-                         write_id)
-
-from .filter import (low_pass_filter, high_pass_filter, band_pass_filter,
-                     notch_filter, band_stop_filter, resample)
-from .parallel import parallel_func
-from .utils import (_check_fname, estimate_rank, _check_pandas_installed,
-                    logger, verbose)
-from .viz import plot_raw, plot_raw_psds, _mutable_defaults
-from .externals.six import string_types
+from .constants import FIFF
+from .meas_info import write_meas_info
+from .pick import pick_types, channel_type
+from .proj import (setup_proj, activate_proj, proj_equal, ProjMixin,
+                   _has_eeg_average_ref_proj, make_eeg_average_ref_proj)
+from .channels import ContainsMixin, PickDropChannelsMixin
+from .compensator import set_current_comp
+from .write import (start_file, end_file, start_block, end_block,
+                    write_dau_pack16, write_float, write_double,
+                    write_complex64, write_complex128, write_int,
+                    write_id)
+
+from ..filter import (low_pass_filter, high_pass_filter, band_pass_filter,
+                      notch_filter, band_stop_filter, resample)
+from ..parallel import parallel_func
+from ..utils import (_check_fname, estimate_rank, _check_pandas_installed,
+                     logger, verbose)
+from ..viz import plot_raw, plot_raw_psds, _mutable_defaults
+from ..externals.six import string_types
 
 
 class _BaseRaw(ProjMixin, ContainsMixin, PickDropChannelsMixin):

mne/fiff/brainvision/brainvision.py

@@ -19,7 +19,7 @@
 from ...utils import verbose, logger
 from ..constants import FIFF
 from ..meas_info import Info
-from ...raw import _BaseRaw
+from ..base import _BaseRaw
 
 
 class RawBrainVision(_BaseRaw):

mne/fiff/bti/raw.py

@@ -12,7 +12,7 @@
 import numpy as np
 
 from ...utils import logger, verbose, sum_squared
-from ...raw import _BaseRaw
+from ..base import _BaseRaw
 from .. import FIFF
 from .constants import BTI
 from .read import (read_int32, read_int16, read_str, read_float, read_double,

mne/fiff/channels.py

@@ -101,6 +101,7 @@ def _contains_ch_type(info, ch_type):
                                     valid=' or '.join(valid_channel_types)))
     return ch_type in [channel_type(info, ii) for ii in range(info['nchan'])]
 
+
 @verbose
 def equalize_channels(candidates, verbose=None):
     """Equalize channel picks for a collection of MNE-Python objects
@@ -139,6 +140,7 @@ def equalize_channels(candidates, verbose=None):
     else:
         logger.info('all channels are corresponding, nothing to do.')
 
+
 class ContainsMixin(object):
     """Mixin class for Raw, Evoked, Epochs
     """
@@ -195,7 +197,6 @@ def pick_channels(self, ch_names, copy=False):
 
         return inst
 
-
     #XXX : to be updated soon with BaseRaw
     def drop_channels(self, ch_names, copy=False):
         """Drop some channels
@@ -237,6 +238,7 @@ def drop_channels(self, ch_names, copy=False):
 
         return inst
 
+
 def rename_channels(info, mapping):
     """Rename channels and optionally change the sensor type.
 
@@ -266,15 +268,15 @@ def rename_channels(info, mapping):
     for ch_name, new_name in mapping.items():
         if ch_name not in ch_names:
             raise ValueError("This channel name (%s) doesn't exist in info."
-                              % ch_name)
+                             % ch_name)
 
         c_ind = ch_names.index(ch_name)
         if not isinstance(new_name, (string_types, tuple)):
             raise ValueError('Your mapping is not configured properly. '
                              'Please see the help: mne.rename_channels?')
 
         elif isinstance(new_name, tuple):  # name and type change
-            new_name, new_type =  new_name  # unpack
+            new_name, new_type = new_name  # unpack
             if new_type not in human2fiff:
                 raise ValueError('This function cannot change to this '
                                  'channel type: %s.' % new_type)
@@ -290,7 +292,7 @@ def rename_channels(info, mapping):
 
     # Reset ch_names and Check that all the channel names are unique.
     for key, collection in [('ch_name', new_names), ('kind', new_kinds)]:
-         for c_ind, new_name in collection:
+        for c_ind, new_name in collection:
             chs[c_ind][key] = new_name
     for c_ind, new_name in new_bads:
         bads[c_ind] = new_name

mne/fiff/edf/edf.py

@@ -17,7 +17,7 @@
 
 from ...transforms import als_ras_trans_mm, apply_trans
 from ...utils import verbose, logger
-from ...raw import _BaseRaw
+from ..base import _BaseRaw
 from ..meas_info import Info
 from ..constants import FIFF
 from ...coreg import get_ras_to_neuromag_trans

mne/fiff/egi/egi.py

@@ -7,7 +7,7 @@
 
 import numpy as np
 
-from .. import Raw
+from ..base import _BaseRaw
 from ..meas_info import Info
 from ..constants import FIFF
 from ...utils import verbose, logger
@@ -155,7 +155,7 @@ def read_raw_egi(input_fname, event_ids=None):
     return _RawEGI(input_fname, event_ids)
 
 
-class _RawEGI(Raw):
+class _RawEGI(_BaseRaw):
     """Raw object from EGI simple binary file
     """
     @verbose
@@ -169,9 +169,9 @@ def __init__(self, input_fname, event_ids=None, verbose=None):
             logger.info('    Reading data ...')
             # reads events as well
             data = _read_data(fid, egi_info).astype(np.float64)
-            if egi_info['value_range'] and  egi_info['bits']:
+            if egi_info['value_range'] and egi_info['bits']:
                 mv = egi_info['value_range'] / 2 ** egi_info['bits']
-            else: 
+            else:
                 mv = 1e-6
             data[:egi_info['n_channels']] = data[:egi_info['n_channels']] * mv
 

mne/fiff/egi/tests/test_egi.py

@@ -26,7 +26,7 @@ def test_io_egi():
     raw = read_raw_egi(egi_fname)
 
     _ = repr(raw)
-    _ = repr(raw.info)
+    _ = repr(raw.info)  # analysis:ignore, noqa
 
     assert_equal('eeg' in raw, True)
     out_fname = op.join(tempdir, 'test_egi_raw.fif')
@@ -45,7 +45,7 @@ def test_io_egi():
     assert_equal(len(picks), 256)
     assert_equal('STI 014' in raw.ch_names, True)
 
-    events = find_events(raw)
+    events = find_events(raw, stim_channel='STI 014')
     assert_equal(len(events), 2)  # ground truth
     assert_equal(np.unique(events[:, 1])[0], 0)
     assert_true(np.unique(events[:, 0])[0] != 0)

mne/fiff/fiff/__init__.py

@@ -0,0 +1 @@
+from .raw import RawFIFF

mne/fiff/raw.py → mne/fiff/fiff/raw.py

@@ -12,17 +12,17 @@
 
 import numpy as np
 
-from .constants import FIFF
-from .open import fiff_open
-from .meas_info import read_meas_info
-from .tree import dir_tree_find
-from .tag import read_tag
-from .proj import proj_equal
-from .compensator import get_current_comp, set_current_comp, make_compensator
-
-from ..raw import _BaseRaw
-from ..utils import logger, verbose
-from ..externals.six import string_types
+from ..constants import FIFF
+from ..open import fiff_open
+from ..meas_info import read_meas_info
+from ..tree import dir_tree_find
+from ..tag import read_tag
+from ..proj import proj_equal
+from ..compensator import get_current_comp, set_current_comp, make_compensator
+from ..base import _BaseRaw
+
+from ...utils import logger, verbose
+from ...externals.six import string_types
 
 
 class RawFIFF(_BaseRaw):

mne/fiff/tests/test_raw.py → mne/fiff/fiff/tests/test_raw.py

@@ -15,16 +15,16 @@
                            assert_allclose)
 from nose.tools import assert_true, assert_raises, assert_equal
 
-from mne.fiff import Raw, pick_types, pick_channels, FIFF
-from mne.raw import concatenate_raws, get_chpi_positions, set_eeg_reference
+from mne.fiff import (Raw, pick_types, pick_channels, FIFF,
+                      concatenate_raws, get_chpi_positions, set_eeg_reference)
 from mne import concatenate_events, find_events, equalize_channels
 from mne.utils import (_TempDir, requires_nitime, requires_pandas,
                        requires_mne, run_subprocess)
 from mne.externals.six.moves import zip
 
 warnings.simplefilter('always')  # enable b/c these tests throw warnings
 
-base_dir = op.join(op.dirname(__file__), 'data')
+base_dir = op.join(op.dirname(__file__), '..', '..', 'tests', 'data')
 fif_fname = op.join(base_dir, 'test_raw.fif')
 fif_gz_fname = op.join(base_dir, 'test_raw.fif.gz')
 ctf_fname = op.join(base_dir, 'test_ctf_raw.fif')

mne/fiff/kit/kit.py

@@ -21,7 +21,7 @@
                       get_ras_to_neuromag_trans)
 from ...utils import verbose, logger
 from ...transforms import apply_trans, als_ras_trans, als_ras_trans_mm
-from ...raw import _BaseRaw
+from ..base import _BaseRaw
 from ..constants import FIFF
 from ..meas_info import Info
 from ..tag import _loc_to_trans

mne/forward/forward.py

@@ -30,7 +30,7 @@
 from ..fiff.write import (write_int, start_block, end_block,
                           write_coord_trans, write_ch_info, write_name_list,
                           write_string, start_file, end_file, write_id)
-from ..raw import _BaseRaw
+from ..fiff.base import _BaseRaw
 from ..fiff.evoked import Evoked, write_evoked
 from ..epochs import Epochs
 from ..source_space import (read_source_spaces_from_tree,

setup.py

@@ -5,7 +5,7 @@
 import os
 from os import path as op
 
-import setuptools  # we are using a setuptools namespace
+import setuptools  # noqa; analysis:ignore; we are using a setuptools namespace
 from numpy.distutils.core import setup
 
 # get the version (don't import mne here, so dependencies are not needed)
@@ -67,6 +67,7 @@
                     'mne.datasets.spm_face',
                     'mne.externals',
                     'mne.fiff', 'mne.fiff.tests',
+                    'mne.fiff.fiff', 'mne.fiff.fiff.tests',
                     'mne.fiff.bti', 'mne.fiff.bti.tests',
                     'mne.fiff.kit', 'mne.fiff.kit.tests',
                     'mne.fiff.edf', 'mne.fiff.edf.tests',