From 53b5fa5acd77f98a829a0cec98a7dddae9111604 Mon Sep 17 00:00:00 2001
From: Daniel McCloy <dan@mccloy.info>
Date: Fri, 5 May 2023 09:32:57 -0500
Subject: [PATCH 1/8] arg default deprecation

---
 mne/time_frequency/spectrum.py | 14 +++++++++++++-
 mne/utils/docs.py              |  4 ++--
 2 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/mne/time_frequency/spectrum.py b/mne/time_frequency/spectrum.py
index 06daec43495..16aeb31f97e 100644
--- a/mne/time_frequency/spectrum.py
+++ b/mne/time_frequency/spectrum.py
@@ -574,7 +574,7 @@ def plot(
         alpha=None,
         spatial_colors=True,
         sphere=None,
-        exclude="bads",
+        exclude=None,
         axes=None,
         show=True,
     ):
@@ -615,6 +615,10 @@ def plot(
         %(spatial_colors_psd)s
         %(sphere_topomap_auto)s
         %(exclude_spectrum_plot)s
+
+            .. versionchanged:: 1.5
+                In version 1.5, the default behavior will change from
+                ``exclude='bads'`` to ``exclude=()``.
         %(axes_spectrum_plot_topomap)s
         %(show)s
 
@@ -640,6 +644,14 @@ def plot(
         else:  # amplitude is boolean
             estimate = "amplitude" if amplitude else "power"
         # split picks by channel type
+        if exclude is None:
+            warn(
+                "in version 1.5, the default behavior of Spectrum.plot() will "
+                "change so that bad channels will be shown by default. To keep the "
+                "old default behavior (and silence this warning), explicitly pass "
+                "exclude='bads'."
+            )
+            exclude = "bads"
         picks = _picks_to_idx(self.info, picks, "data", with_ref_meg=False)
         (picks_list, units_list, scalings_list, titles_list) = _split_picks_by_type(
             self, picks, units, scalings, titles
diff --git a/mne/utils/docs.py b/mne/utils/docs.py
index cba3339b9ed..ed62d04a178 100644
--- a/mne/utils/docs.py
+++ b/mne/utils/docs.py
@@ -1311,9 +1311,9 @@ def _reflow_param_docstring(docstring, has_first_line=True, width=75):
 """
 
 _exclude_spectrum = """\
-exclude : list of str | 'bads'
+exclude : list of str | 'bads' | None
     Channel names to exclude{}. If ``'bads'``, channels
-    in ``spectrum.info['bads']`` are excluded; pass an empty list to
+    in ``spectrum.info['bads']`` are excluded; pass an empty list or tuple to
     plot all channels (including "bad" channels, if any).
 """
 

From 1d99bdfd39c7bd275f8fb3db9491b96da1cfe754 Mon Sep 17 00:00:00 2001
From: Daniel McCloy <dan@mccloy.info>
Date: Fri, 5 May 2023 09:33:20 -0500
Subject: [PATCH 2/8] FIX: actually *use* value of exclude

---
 mne/time_frequency/spectrum.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/mne/time_frequency/spectrum.py b/mne/time_frequency/spectrum.py
index 16aeb31f97e..157b48996a6 100644
--- a/mne/time_frequency/spectrum.py
+++ b/mne/time_frequency/spectrum.py
@@ -652,7 +652,9 @@ def plot(
                 "exclude='bads'."
             )
             exclude = "bads"
-        picks = _picks_to_idx(self.info, picks, "data", with_ref_meg=False)
+        picks = _picks_to_idx(
+            self.info, picks, "data", exclude=exclude, with_ref_meg=False
+        )
         (picks_list, units_list, scalings_list, titles_list) = _split_picks_by_type(
             self, picks, units, scalings, titles
         )

From 1140abe0e289534947cdda4cb7e4d5943f926b3e Mon Sep 17 00:00:00 2001
From: Daniel McCloy <dan@mccloy.info>
Date: Fri, 5 May 2023 09:40:39 -0500
Subject: [PATCH 3/8] change picks too

---
 mne/time_frequency/spectrum.py | 9 +++++++--
 mne/utils/spectrum.py          | 2 +-
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/mne/time_frequency/spectrum.py b/mne/time_frequency/spectrum.py
index 157b48996a6..9939e94a6b7 100644
--- a/mne/time_frequency/spectrum.py
+++ b/mne/time_frequency/spectrum.py
@@ -583,6 +583,11 @@ def plot(
         Parameters
         ----------
         %(picks_good_data_noref)s
+
+            .. versionchanged:: 1.5
+                In version 1.5, the default behavior will change so that all
+                :term:`data channels` (not just "good" data channels) are shown
+                by default.
         average : bool
             Whether to average across channels before plotting. If ``True``,
             interactive plotting of scalp topography is disabled, and
@@ -644,12 +649,12 @@ def plot(
         else:  # amplitude is boolean
             estimate = "amplitude" if amplitude else "power"
         # split picks by channel type
-        if exclude is None:
+        if picks is None or exclude is None:
             warn(
                 "in version 1.5, the default behavior of Spectrum.plot() will "
                 "change so that bad channels will be shown by default. To keep the "
                 "old default behavior (and silence this warning), explicitly pass "
-                "exclude='bads'."
+                "`picks='data', exclude='bads'`."
             )
             exclude = "bads"
         picks = _picks_to_idx(
diff --git a/mne/utils/spectrum.py b/mne/utils/spectrum.py
index d0f0d6c9c89..9857f333252 100644
--- a/mne/utils/spectrum.py
+++ b/mne/utils/spectrum.py
@@ -63,5 +63,5 @@ def _split_psd_kwargs(*, plot_fun=None, kwargs=None):
     # (otherwise integer picks could be wrong, `None` will be handled wrong
     # for `misc` data, etc)
     if plot_fun is Spectrum.plot:
-        plot_kwargs["picks"] = "all"  # TODO: this should be the default
+        plot_kwargs["picks"] = "all"  # TODO: this will be the default in v1.5
     return kwargs, plot_kwargs

From 7db5d0f18133fe723d87c26a4418f4072efeecda Mon Sep 17 00:00:00 2001
From: Daniel McCloy <dan@mccloy.info>
Date: Fri, 5 May 2023 10:01:41 -0500
Subject: [PATCH 4/8] fix tests

---
 mne/viz/tests/test_epochs.py | 10 ++++++----
 mne/viz/tests/test_raw.py    | 26 +++++++++++++++-----------
 2 files changed, 21 insertions(+), 15 deletions(-)

diff --git a/mne/viz/tests/test_epochs.py b/mne/viz/tests/test_epochs.py
index 5dabfa7fafa..c87755e37b7 100644
--- a/mne/viz/tests/test_epochs.py
+++ b/mne/viz/tests/test_epochs.py
@@ -361,9 +361,10 @@ def test_plot_drop_log(epochs_unloaded):
 def test_plot_psd_epochs(epochs):
     """Test plotting epochs psd (+topomap)."""
     spectrum = epochs.compute_psd()
-    spectrum.plot(average=True, spatial_colors=False)
-    spectrum.plot(average=False, spatial_colors=True)
-    spectrum.plot(average=False, spatial_colors=False)
+    old_defaults = dict(picks="data", exclude="bads")
+    spectrum.plot(average=True, spatial_colors=False, **old_defaults)
+    spectrum.plot(average=False, spatial_colors=True, **old_defaults)
+    spectrum.plot(average=False, spatial_colors=False, **old_defaults)
     # test plot_psd_topomap errors
     with pytest.raises(RuntimeError, match="No frequencies in band"):
         spectrum.plot_topomap(bands=dict(foo=(0, 0.01)))
@@ -457,13 +458,14 @@ def test_plot_psd_epochs_ctf(raw_ctf):
     """Test plotting CTF epochs psd (+topomap)."""
     evts = make_fixed_length_events(raw_ctf)
     epochs = Epochs(raw_ctf, evts, preload=True)
+    old_defaults = dict(picks="data", exclude="bads")
     # EEG060 is flat in this dataset
     with pytest.warns(UserWarning, match="for channel EEG060"):
         spectrum = epochs.compute_psd()
         for dB in [True, False]:
             spectrum.plot(dB=dB)
     spectrum.drop_channels(["EEG060"])
-    spectrum.plot(spatial_colors=False, average=False)
+    spectrum.plot(spatial_colors=False, average=False, **old_defaults)
     with pytest.raises(RuntimeError, match="No frequencies in band"):
         spectrum.plot_topomap(bands=[(0, 0.01, "foo")])
     spectrum.plot_topomap()
diff --git a/mne/viz/tests/test_raw.py b/mne/viz/tests/test_raw.py
index 1bc13505a7e..5533b5870c1 100644
--- a/mne/viz/tests/test_raw.py
+++ b/mne/viz/tests/test_raw.py
@@ -791,29 +791,33 @@ def test_plot_raw_filtered(filtorder, raw, browser_backend):
 def test_plot_raw_psd(raw, raw_orig):
     """Test plotting of raw psds."""
     raw_unchanged = raw.copy()
-    # normal mode
     spectrum = raw.compute_psd()
-    fig = spectrum.plot(average=False)
+    # deprecation change handler
+    old_defaults = dict(picks="data", exclude="bads")
+    with pytest.warns(RuntimeWarning, match="bad channels will be shown"):
+        fig = spectrum.plot(average=False)
+    # normal mode
+    fig = spectrum.plot(average=False, **old_defaults)
     fig.canvas.callbacks.process(
         "resize_event", backend_bases.ResizeEvent("resize_event", fig.canvas)
     )
     # specific mode
     picks = pick_types(spectrum.info, meg="mag", eeg=False)[:4]
-    spectrum.plot(picks=picks, ci="range", spatial_colors=True)
-    raw.compute_psd(tmax=20.0).plot(color="yellow", dB=False, alpha=0.4)
+    spectrum.plot(picks=picks, ci="range", spatial_colors=True, exclude="bads")
+    raw.compute_psd(tmax=20.0).plot(color="yellow", dB=False, alpha=0.4, **old_defaults)
     plt.close("all")
     # one axes supplied
     ax = plt.axes()
-    spectrum.plot(picks=picks, axes=ax, average=True)
+    spectrum.plot(picks=picks, axes=ax, average=True, exclude="bads")
     plt.close("all")
     # two axes supplied
     _, axs = plt.subplots(2)
-    spectrum.plot(axes=axs, average=True)
+    spectrum.plot(axes=axs, average=True, **old_defaults)
     plt.close("all")
     # need 2, got 1
     ax = plt.axes()
     with pytest.raises(ValueError, match="of length 2.*the length is 1"):
-        spectrum.plot(axes=ax, average=True)
+        spectrum.plot(axes=ax, average=True, **old_defaults)
     plt.close("all")
     # topo psd
     ax = plt.subplot()
@@ -859,8 +863,8 @@ def test_plot_raw_psd(raw, raw_orig):
     raw = raw_orig.crop(0, 1)
     picks = pick_types(raw.info, meg=True)
     spectrum = raw.compute_psd(picks=picks)
-    spectrum.plot(average=False)
-    spectrum.plot(average=True)
+    spectrum.plot(average=False, **old_defaults)
+    spectrum.plot(average=True, **old_defaults)
     plt.close("all")
     raw.set_channel_types(
         {
@@ -871,7 +875,7 @@ def test_plot_raw_psd(raw, raw_orig):
         },
         verbose="error",
     )
-    fig = raw.compute_psd().plot()
+    fig = raw.compute_psd().plot(**old_defaults)
     assert len(fig.axes) == 10
     plt.close("all")
 
@@ -882,7 +886,7 @@ def test_plot_raw_psd(raw, raw_orig):
     raw = RawArray(data, info)
     picks = pick_types(raw.info, misc=True)
     spectrum = raw.compute_psd(picks=picks, n_fft=n_fft)
-    spectrum.plot(spatial_colors=False, picks=picks)
+    spectrum.plot(spatial_colors=False, picks=picks, exclude="bads")
     plt.close("all")
 
 

From 8557b599f7266973bacd6ff15fa3bf0ede2c7242 Mon Sep 17 00:00:00 2001
From: Daniel McCloy <dan@mccloy.info>
Date: Fri, 5 May 2023 14:11:08 -0500
Subject: [PATCH 5/8] fix report and IO array tests

---
 mne/io/array/tests/test_array.py |  8 +++++++-
 mne/report/tests/test_report.py  | 32 +++++++++++++++++++-------------
 2 files changed, 26 insertions(+), 14 deletions(-)

diff --git a/mne/io/array/tests/test_array.py b/mne/io/array/tests/test_array.py
index 1a96b9e4488..63160ba639b 100644
--- a/mne/io/array/tests/test_array.py
+++ b/mne/io/array/tests/test_array.py
@@ -150,7 +150,13 @@ def test_array_raw():
 
     # plotting
     raw2.plot()
-    (raw2.compute_psd(tmax=2.0, n_fft=1024).plot(average=True, spatial_colors=False))
+    # TODO remove context handler after 1.4 release.
+    with pytest.warns(RuntimeWarning, match="bad channels will be shown"):
+        (
+            raw2.compute_psd(tmax=2.0, n_fft=1024).plot(
+                average=True, spatial_colors=False
+            )
+        )
     plt.close("all")
 
     # epoching
diff --git a/mne/report/tests/test_report.py b/mne/report/tests/test_report.py
index c7357b53c41..24b0d4bbe9a 100644
--- a/mne/report/tests/test_report.py
+++ b/mne/report/tests/test_report.py
@@ -347,12 +347,14 @@ def test_report_raw_psd_and_date(tmp_path):
     raw_fname_new = tmp_path / "temp_raw.fif"
     raw.save(raw_fname_new)
     report = Report(raw_psd=True)
-    report.parse_folder(
-        data_path=tmp_path,
-        render_bem=False,
-        on_error="raise",
-        raw_butterfly=False,
-    )
+    # TODO: remove context handler after 1.4 release.
+    with pytest.warns(RuntimeWarning, match="bad channels will be shown"):
+        report.parse_folder(
+            data_path=tmp_path,
+            render_bem=False,
+            on_error="raise",
+            raw_butterfly=False,
+        )
     assert isinstance(report.html, list)
     assert "PSD" in "".join(report.html)
     assert "Unknown" not in "".join(report.html)
@@ -851,7 +853,8 @@ def test_manual_report_2d(tmp_path, invisible_fig):
     ica_ecg_scores = ica_eog_scores = np.array([3, 0])
     ica_ecg_evoked = ica_eog_evoked = epochs_without_metadata.average()
 
-    r.add_raw(raw=raw, title="my raw data", tags=("raw",), psd=True, projs=False)
+    with pytest.warns(RuntimeWarning, match="bad channels will be shown"):
+        r.add_raw(raw=raw, title="my raw data", tags=("raw",), psd=True, projs=False)
     r.add_raw(raw=raw, title="my raw data 2", psd=False, projs=False, butterfly=1)
     r.add_events(events=events_fname, title="my events", sfreq=raw.info["sfreq"])
     r.add_epochs(
@@ -861,12 +864,15 @@ def test_manual_report_2d(tmp_path, invisible_fig):
         psd=False,
         projs=False,
     )
-    r.add_epochs(
-        epochs=epochs_without_metadata, title="my epochs 2", psd=1, projs=False
-    )
-    r.add_epochs(
-        epochs=epochs_without_metadata, title="my epochs 2", psd=True, projs=False
-    )
+    # TODO: remove next two context handlers after 1.4 release.
+    with pytest.warns(RuntimeWarning, match="bad channels will be shown"):
+        r.add_epochs(
+            epochs=epochs_without_metadata, title="my epochs 2", psd=1, projs=False
+        )
+    with pytest.warns(RuntimeWarning, match="bad channels will be shown"):
+        r.add_epochs(
+            epochs=epochs_without_metadata, title="my epochs 2", psd=True, projs=False
+        )
     assert "Metadata" not in r.html[-1]
 
     # Try with metadata

From d5acbf4d0927c2116ed9933eb24696b444d4723d Mon Sep 17 00:00:00 2001
From: Daniel McCloy <dan@mccloy.info>
Date: Fri, 5 May 2023 14:28:40 -0500
Subject: [PATCH 6/8] missed one

---
 mne/io/array/tests/test_array.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/mne/io/array/tests/test_array.py b/mne/io/array/tests/test_array.py
index 63160ba639b..dffba1da152 100644
--- a/mne/io/array/tests/test_array.py
+++ b/mne/io/array/tests/test_array.py
@@ -189,5 +189,7 @@ def test_array_raw():
     raw = RawArray(data, info)
     raw.set_montage(montage)
     spectrum = raw.compute_psd()
-    spectrum.plot(average=False)  # looking for nonexistent layout
+    # TODO remove context handler after 1.4 release.
+    with pytest.warns(RuntimeWarning, match="bad channels will be shown"):
+        spectrum.plot(average=False)  # looking for nonexistent layout
     spectrum.plot_topo()

From d01d4a65461d3937b40b0539fa15d487098a295d Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Fri, 5 May 2023 15:31:43 -0400
Subject: [PATCH 7/8] FIX: Conditional

---
 mne/decoding/tests/test_base.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/mne/decoding/tests/test_base.py b/mne/decoding/tests/test_base.py
index c7773a217d4..e372bd194f9 100644
--- a/mne/decoding/tests/test_base.py
+++ b/mne/decoding/tests/test_base.py
@@ -15,7 +15,7 @@
 
 from mne import create_info, EpochsArray
 from mne.fixes import is_regressor, is_classifier
-from mne.utils import requires_sklearn
+from mne.utils import requires_sklearn, check_version
 from mne.decoding.base import (
     _get_inverse_funcs,
     LinearModel,
@@ -285,6 +285,10 @@ def test_get_coef_multiclass(n_features, n_targets):
 
 
 @requires_sklearn
+@pytest.mark.xfail(
+    when=check_version("sklearn", "1.3"),
+    reason="https://github.com/scikit-learn/scikit-learn/issues/26336",
+)
 @pytest.mark.parametrize(
     "n_classes, n_channels, n_times",
     [

From fabe1e711a69c88436c1c3cec89d5c541e8bd385 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Fri, 5 May 2023 15:43:12 -0400
Subject: [PATCH 8/8] FIX: Correct fix

---
 mne/decoding/base.py            | 6 ++++++
 mne/decoding/tests/test_base.py | 6 +-----
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/mne/decoding/base.py b/mne/decoding/base.py
index 348ee2ee0f7..247c6f89f2d 100644
--- a/mne/decoding/base.py
+++ b/mne/decoding/base.py
@@ -214,6 +214,12 @@ def score(self, X, y):
         """
         return self.model.score(X, y)
 
+    # Needed for sklearn 1.3+
+    @property
+    def classes_(self):
+        """The classes (pass-through to model)."""
+        return self.model.classes_
+
 
 def _set_cv(cv, estimator=None, X=None, y=None):
     """Set the default CV depending on whether clf is classifier/regressor."""
diff --git a/mne/decoding/tests/test_base.py b/mne/decoding/tests/test_base.py
index e372bd194f9..c7773a217d4 100644
--- a/mne/decoding/tests/test_base.py
+++ b/mne/decoding/tests/test_base.py
@@ -15,7 +15,7 @@
 
 from mne import create_info, EpochsArray
 from mne.fixes import is_regressor, is_classifier
-from mne.utils import requires_sklearn, check_version
+from mne.utils import requires_sklearn
 from mne.decoding.base import (
     _get_inverse_funcs,
     LinearModel,
@@ -285,10 +285,6 @@ def test_get_coef_multiclass(n_features, n_targets):
 
 
 @requires_sklearn
-@pytest.mark.xfail(
-    when=check_version("sklearn", "1.3"),
-    reason="https://github.com/scikit-learn/scikit-learn/issues/26336",
-)
 @pytest.mark.parametrize(
     "n_classes, n_channels, n_times",
     [