[release]MNT: bump 0.20 + remove dead code (mne-tools#6821)

* Bump 0.20

* FIX: stim_channel in CNT

* fix

* FIX: remove _deprecate_stim_channel

* fix docstring

mne/__init__.py

@@ -16,7 +16,7 @@
 # Dev branch marker is: 'X.Y.devN' where N is an integer.
 #
 
-__version__ = '0.19.0'
+__version__ = '0.20.dev0'
 
 # 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/io/cnt/cnt.py

@@ -12,7 +12,6 @@
 from ...channels.layout import _topo_to_sphere
 from ..constants import FIFF
 from ..utils import (_mult_cal_one, _find_channels, _create_chs, read_str,
-                     _deprecate_stim_channel, _synthesize_stim_channel,
                      _deprecate_montage)
 from ..meas_info import _empty_info
 from ..base import BaseRaw
@@ -96,7 +95,7 @@ def _translating_function(offset, n_channels, event_type,
 @fill_doc
 def read_raw_cnt(input_fname, montage='deprecated', eog=(), misc=(), ecg=(),
                  emg=(), data_format='auto', date_format='mm/dd/yy',
-                 preload=False, stim_channel=False, verbose=None):
+                 preload=False, verbose=None):
     """Read CNT data as raw object.
 
     .. Note::
@@ -139,16 +138,6 @@ def read_raw_cnt(input_fname, montage='deprecated', eog=(), misc=(), ecg=(),
     date_format : 'mm/dd/yy' | 'dd/mm/yy'
         Format of date in the header. Defaults to 'mm/dd/yy'.
     %(preload)s
-    stim_channel : bool | None
-        Add a stim channel from the events. Defaults to None to trigger a
-        future warning.
-
-        .. warning:: This defaults to True in 0.18 but will change to False in
-                     0.19 (when no stim channel synthesis will be allowed)
-                     and be removed in 0.20; migrate code to use
-                     :func:`mne.events_from_annotations` instead.
-
-        .. versionadded:: 0.18
     %(verbose)s
 
     Returns
@@ -166,14 +155,12 @@ def read_raw_cnt(input_fname, montage='deprecated', eog=(), misc=(), ecg=(),
     """
     return RawCNT(input_fname, montage=montage, eog=eog, misc=misc, ecg=ecg,
                   emg=emg, data_format=data_format, date_format=date_format,
-                  preload=preload, stim_channel=stim_channel, verbose=verbose)
+                  preload=preload, verbose=verbose)
 
 
-def _get_cnt_info(input_fname, eog, ecg, emg, misc, data_format, date_format,
-                  stim_channel_toggle):
+def _get_cnt_info(input_fname, eog, ecg, emg, misc, data_format, date_format):
     """Read the cnt header."""
     # XXX stim_channel_toggle is used because stim_channel was in use already
-    _deprecate_stim_channel(stim_channel_toggle, removed_in='0.20')
 
     data_offset = 900  # Size of the 'SETUP' header.
     cnt_info = dict()
@@ -287,16 +274,6 @@ def _get_cnt_info(input_fname, eog, ecg, emg, misc, data_format, date_format,
             cal = np.fromfile(fid, dtype='f4', count=1)
             cals.append(cal * sensitivity * 1e-6 / 204.8)
 
-        if stim_channel_toggle:
-            data_format = 'int32' if n_bytes == 4 else 'int16'
-            annot = _read_annotations_cnt(input_fname, data_format=data_format)
-            events = (np.stack((annot.onset * sfreq,
-                                annot.duration * sfreq,
-                                annot.description.astype(int)))
-                      .astype(int)
-                      .transpose())
-            stim_channel = _synthesize_stim_channel(events, n_samples)
-
     info = _empty_info(sfreq)
     if lowpass_toggle == 1:
         info['lowpass'] = highcutoff
@@ -322,18 +299,6 @@ def _get_cnt_info(input_fname, eog, ecg, emg, misc, data_format, date_format,
     for ch, loc in zip(chs, locs):
         ch.update(loc=loc)
 
-    if stim_channel_toggle:
-        chan_info = {'cal': 1.0, 'logno': len(chs) + 1, 'scanno': len(chs) + 1,
-                     'range': 1.0, 'unit_mul': 0., 'ch_name': 'STI 014',
-                     'unit': FIFF.FIFF_UNIT_NONE,
-                     'coord_frame': FIFF.FIFFV_COORD_UNKNOWN,
-                     'loc': np.zeros(12),
-                     'coil_type': FIFF.FIFFV_COIL_NONE,
-                     'kind': FIFF.FIFFV_STIM_CH}
-        chs.append(chan_info)
-        baselines.append(0)  # For stim channel
-        cnt_info.update(stim_channel=stim_channel)
-
     cnt_info.update(baselines=np.array(baselines), n_samples=n_samples,
                     n_bytes=n_bytes)
 
@@ -411,8 +376,7 @@ class RawCNT(BaseRaw):
 
     def __init__(self, input_fname, montage='deprecated', eog=(), misc=(),
                  ecg=(), emg=(), data_format='auto', date_format='mm/dd/yy',
-                 preload=False, stim_channel=False,
-                 verbose=None):  # noqa: D102
+                 preload=False, verbose=None):  # noqa: D102
 
         _check_option('date_format', date_format, ['mm/dd/yy', 'dd/mm/yy'])
         if date_format == 'dd/mm/yy':
@@ -422,7 +386,7 @@ def __init__(self, input_fname, montage='deprecated', eog=(), misc=(),
 
         input_fname = path.abspath(input_fname)
         info, cnt_info = _get_cnt_info(input_fname, eog, ecg, emg, misc,
-                                       data_format, _date_format, stim_channel)
+                                       data_format, _date_format)
         last_samps = [cnt_info['n_samples'] - 1]
         super(RawCNT, self).__init__(
             info, preload, filenames=[input_fname], raw_extras=[cnt_info],

mne/io/fieldtrip/tests/helpers.py

@@ -26,8 +26,7 @@
 info_long_fields = ('hpi_meas', )
 
 system_to_reader_fn_dict = {'neuromag306': mne.io.read_raw_fif,
-                            'CNT': partial(mne.io.read_raw_cnt,
-                                           stim_channel=False),
+                            'CNT': partial(mne.io.read_raw_cnt),
                             'CTF': partial(mne.io.read_raw_ctf,
                                            clean_names=True),
                             'BTI': partial(mne.io.read_raw_bti,

mne/io/utils.py

@@ -15,7 +15,6 @@
 
 from .constants import FIFF
 from .meas_info import _get_valid_units
-from .. import __version__
 from ..utils import warn
 
 
@@ -33,33 +32,6 @@ def _deprecate_montage(raw, raw_type, montage, **kwargs):
         warn(_MSG, DeprecationWarning)
 
 
-def _deprecate_stim_channel(stim_channel, removed_in='0.19'):
-    minor_current = int(__version__.split('.')[1])
-    minor_removed_in = int(removed_in.split('.')[1])
-    if minor_current == minor_removed_in - 2:
-        if stim_channel is None:
-            _MSG = (
-                'The parameter `stim_channel` controlling the stim channel'
-                ' synthesis has not been specified. In 0.%s it defaults to'
-                ' True but will change to False in 0.%s (when no stim channel'
-                ' synthesis will be allowed) and be removed in %s; migrate'
-                ' code to use `stim_channel=False` and'
-                ' :func:`mne.events_from_annotations` or set'
-                ' `stim_channel=True` to avoid this warning.'
-                % (minor_removed_in - 2, minor_removed_in - 1, removed_in))
-            warn(_MSG, FutureWarning)
-
-    elif minor_current == minor_removed_in - 1:
-        if stim_channel is not False:
-            _MSG = ('stim_channel must be False or omitted; it will be '
-                    'removed in %s' % removed_in)
-            raise ValueError(_MSG, DeprecationWarning)
-    else:
-        raise RuntimeError('stim_channel was supposed to be removed in version'
-                           ' %s, and it is still present in %s' %
-                           (removed_in, __version__))
-
-
 def _check_orig_units(orig_units):
     """Check original units from a raw file.