MRG, MAINT: 0.22 deprecations (mne-tools#8301)

* MAINT: 0.22 deprecations

* FIX: Missed

* FIX: Refs

doc/changes/0.15.inc

@@ -244,11 +244,11 @@ API
 
 - Deprecate ``plot_trans`` in favor of :func:`mne.viz.plot_alignment` and add ``bem`` parameter for plotting conductor model by `Jaakko Leppakangas`_
 
-- :func:`mne.beamformer.tf_lcmv` now has a ``raw`` parameter to accommodate epochs objects that already have data loaded with ``preload=True``, with :meth:`mne.Epochs.load_data`, or that are read from disk, by `Eric Larson`_
+- ``mne.beamformer.tf_lcmv`` now has a ``raw`` parameter to accommodate epochs objects that already have data loaded with ``preload=True``, with :meth:`mne.Epochs.load_data`, or that are read from disk, by `Eric Larson`_
 
 - :func:`mne.time_frequency.psd_welch` and :func:`mne.time_frequency.psd_array_welch` now use a Hamming window (instead of a Hann window) by `Clemens Brunner`_
 
-- ``picks`` parameter in ``mne.beamformer.lcmv``, ``mne.beamformer.lcmv_epochs``, ``mne.beamformer.lcmv_raw``, :func:`mne.beamformer.tf_lcmv` and :func:`mne.beamformer.rap_music` is now deprecated and will be removed in 0.16, by `Britta Westner`_, `Alex Gramfort`_, and `Denis Engemann`_.
+- ``picks`` parameter in ``mne.beamformer.lcmv``, ``mne.beamformer.lcmv_epochs``, ``mne.beamformer.lcmv_raw``, ``mne.beamformer.tf_lcmv`` and :func:`mne.beamformer.rap_music` is now deprecated and will be removed in 0.16, by `Britta Westner`_, `Alex Gramfort`_, and `Denis Engemann`_.
 
 - The keyword argument ``frequencies`` has been deprecated in favor of ``freqs`` in various time-frequency functions, e.g. :func:`mne.time_frequency.tfr_array_morlet`, by `Eric Larson`_
 

doc/changes/0.19.inc

@@ -121,7 +121,7 @@ Bug
 
 - Fix bug in :meth:`mne.SourceMorph.apply` where the default was errantly ``mri_space=False`` instead of ``mri_space=None`` (as documented), by `Eric Larson`_
 
-- Fix :meth:`mne.VolVectorSourceEstimate.normal` and :func:`mne.minimum_norm.apply_inverse` to only allow normal extraction/orientation for surface and discrete source spaces by `Eric Larson`_
+- Fix ``mne.VolVectorSourceEstimate.normal`` and :func:`mne.minimum_norm.apply_inverse` to only allow normal extraction/orientation for surface and discrete source spaces by `Eric Larson`_
 
 - Fix :meth:`mne.io.Raw.set_annotations` for ``meas_date`` previous to 1970 by `Joan Massich`_
 

doc/changes/0.20.inc

@@ -154,7 +154,7 @@ Bug
 
 - Allow :func:`mne.channels.read_dig_hpts` to accept point categories (eg. EEG) to be specified in upper case by `Alex Gramfort`_.
 
-- Fix a bug in :meth:`mne.MixedSourceEstimate.plot_surface` that prevented plotting in latest PySurfer by `Christian O'Reilly`_.
+- Fix a bug in ``mne.MixedSourceEstimate.plot_surface`` that prevented plotting in latest PySurfer by `Christian O'Reilly`_.
 
 - Fix ``method='eLORETA'`` in :func:`mne.minimum_norm.apply_inverse`, by `Eric Larson`_:
 
@@ -171,7 +171,7 @@ Bug
 
 - Fix bug in :func:`mne.compute_covariance` and :func:`mne.compute_raw_covariance` where biased normalization (based on degrees of freedom) was used and ``cov.nfree`` was not set properly by `Eric Larson`_
 
-- Fix :func:`mne.VectorSourceEstimate.normal` to account for cortical patch statistics using ``use_cps=True`` by `Eric Larson`_
+- Fix ``mne.VectorSourceEstimate.normal`` to account for cortical patch statistics using ``use_cps=True`` by `Eric Larson`_
 
 - Fix ``pick_ori='normal'`` for :func:`mne.minimum_norm.apply_inverse` when the inverse was computed with ``loose=1.`` and the forward solution was not in surface orientation, by `Eric Larson`_
 

doc/python_reference.rst

@@ -742,7 +742,6 @@ Inverse Solutions
    apply_dics_epochs
    rap_music
    tf_dics
-   tf_lcmv
    make_lcmv_resolution_matrix
 
 .. currentmodule:: mne

mne/__init__.py

@@ -122,23 +122,6 @@
 from . import viz
 from . import decoding
 
-from .utils import deprecated_alias
-deprecated_alias(
-    'spatial_src_connectivity', spatial_src_adjacency)
-deprecated_alias(
-    'spatial_tris_connectivity', spatial_tris_adjacency)
-deprecated_alias(
-    'spatial_dist_connectivity', spatial_dist_adjacency)
-deprecated_alias(
-    'spatial_inter_hemi_connectivity', spatial_inter_hemi_adjacency)
-deprecated_alias(
-    'spatio_temporal_src_connectivity', spatio_temporal_src_adjacency)
-deprecated_alias(
-    'spatio_temporal_tris_connectivity', spatio_temporal_tris_adjacency)
-deprecated_alias(
-    'spatio_temporal_dist_connectivity', spatio_temporal_dist_adjacency)
-del deprecated_alias
-
 # initialize logging
 set_log_level(None, False)
 set_log_file()

mne/beamformer/__init__.py

@@ -1,7 +1,7 @@
 """Beamformers for source localization."""
 
 from ._lcmv import (make_lcmv, apply_lcmv, apply_lcmv_epochs, apply_lcmv_raw,
-                    tf_lcmv, apply_lcmv_cov)
+                    apply_lcmv_cov)
 from ._dics import (make_dics, apply_dics, apply_dics_epochs, apply_dics_csd,
                     tf_dics)
 from ._rap_music import rap_music

mne/beamformer/_dics.py

@@ -25,7 +25,7 @@
 def make_dics(info, forward, csd, reg=0.05, noise_csd=None, label=None,
               pick_ori=None, rank=None, weight_norm=None,
               reduce_rank=False, depth=1., real_filter=False,
-              inversion='matrix', normalize_fwd=None, verbose=None):
+              inversion='matrix', verbose=None):
     """Compute a Dynamic Imaging of Coherent Sources (DICS) spatial filter.
 
     This is a beamformer filter that can be used to estimate the source power
@@ -76,8 +76,6 @@ def make_dics(info, forward, csd, reg=0.05, noise_csd=None, label=None,
 
         .. versionchanged:: 0.21
            Default changed to ``'matrix'``.
-    normalize_fwd : bool
-        Deprecated, use ``depth`` instead.
     %(verbose)s
 
     Returns
@@ -158,10 +156,6 @@ def make_dics(info, forward, csd, reg=0.05, noise_csd=None, label=None,
     ----------
     .. footbibliography::
     """  # noqa: E501
-    if normalize_fwd is not None:
-        warn('normalize_fwd is deprecated and will be removed in 0.22, use '
-             'depth instead', DeprecationWarning)
-        depth = 1. if normalize_fwd else 0.
     rank = _check_rank(rank)
     _check_option('pick_ori', pick_ori, [None, 'normal', 'max-power'])
     _check_option('inversion', inversion, ['single', 'matrix'])
@@ -484,7 +478,7 @@ def tf_dics(epochs, forward, noise_csds, tmin, tmax, tstep, win_lengths,
             mt_adaptive=False, mt_low_bias=True, cwt_n_cycles=7, decim=1,
             reg=0.05, label=None, pick_ori=None, rank=None, inversion='single',
             weight_norm=None, depth=1., real_filter=False,
-            reduce_rank=False, normalize_fwd=None, verbose=None):
+            reduce_rank=False, verbose=None):
     """5D time-frequency beamforming based on DICS.
 
     Calculate source power in time-frequency windows using a spatial filter
@@ -605,8 +599,6 @@ def tf_dics(epochs, forward, noise_csds, tmin, tmax, tstep, win_lengths,
         If ``True``, take only the real part of the cross-spectral-density
         matrices to compute real filters. Defaults to ``False``.
     %(reduce_rank)s
-    normalize_fwd : bool
-        Deprecated, use ``depth`` instead.
     %(verbose)s
 
     Returns
@@ -622,7 +614,7 @@ def tf_dics(epochs, forward, noise_csds, tmin, tmax, tstep, win_lengths,
     DICS.
 
     An alternative to using noise CSDs is to normalize the forward solution
-    (``normalize_fwd``) or the beamformer weights (``weight_norm``). In
+    (``depth``) or the beamformer weights (``weight_norm``). In
     this case, ``noise_csds`` may be set to ``None``.
 
     References
@@ -752,7 +744,6 @@ def tf_dics(epochs, forward, noise_csds, tmin, tmax, tstep, win_lengths,
                                     label=label, pick_ori=pick_ori,
                                     rank=rank, inversion=inversion,
                                     weight_norm=weight_norm, depth=depth,
-                                    normalize_fwd=normalize_fwd,
                                     reduce_rank=reduce_rank,
                                     real_filter=real_filter, verbose=False)
                 stc, _ = apply_dics_csd(csd, filters, verbose=False)