From a85093cdd523726d62629724344fb941c3e03908 Mon Sep 17 00:00:00 2001
From: Ana Radanovic <radanovica@protonmail.com>
Date: Mon, 25 Sep 2023 14:44:04 -0400
Subject: [PATCH 01/38] adding unify channels to preproc

---
 mne/preprocessing/unify_bads.py | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 mne/preprocessing/unify_bads.py

diff --git a/mne/preprocessing/unify_bads.py b/mne/preprocessing/unify_bads.py
new file mode 100644
index 00000000000..6b24d2d078a
--- /dev/null
+++ b/mne/preprocessing/unify_bads.py
@@ -0,0 +1,32 @@
+
+#%%
+def unifying_bads(
+    list_instances,
+    
+):
+    
+    common_bad_channels = []
+    #first check that each object is mne object
+    
+    #then interate through the objects to get ch names as set
+    ch_set_1 = list_instances[0].info['bads']
+    common_bad_channels.extend(ch_set_1)
+    
+    for inst in list_instances[1:]:
+        ch_set_2 = set(inst.info['bads'])
+        set_of_bads = set(common_bad_channels)
+        new_bads = ch_set_2.difference(set_of_bads)
+        
+        if len(new_bads) >1 :
+            common_bad_channels.extend(list(new_bads))
+    
+    new_instances = []
+    
+    for inst in list_instances:
+        inst.info["bads"] = common_bad_channels
+        new_instances.append(inst)
+
+
+    return new_instances
+
+

From 02ecd49918c9fb320e18734881f7e679ac84325e Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 25 Sep 2023 18:46:50 +0000
Subject: [PATCH 02/38] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mne/preprocessing/unify_bads.py | 28 +++++++++++-----------------
 1 file changed, 11 insertions(+), 17 deletions(-)

diff --git a/mne/preprocessing/unify_bads.py b/mne/preprocessing/unify_bads.py
index 6b24d2d078a..1145192aa88 100644
--- a/mne/preprocessing/unify_bads.py
+++ b/mne/preprocessing/unify_bads.py
@@ -1,32 +1,26 @@
-
-#%%
+# %%
 def unifying_bads(
     list_instances,
-    
 ):
-    
     common_bad_channels = []
-    #first check that each object is mne object
-    
-    #then interate through the objects to get ch names as set
-    ch_set_1 = list_instances[0].info['bads']
+    # first check that each object is mne object
+
+    # then interate through the objects to get ch names as set
+    ch_set_1 = list_instances[0].info["bads"]
     common_bad_channels.extend(ch_set_1)
-    
+
     for inst in list_instances[1:]:
-        ch_set_2 = set(inst.info['bads'])
+        ch_set_2 = set(inst.info["bads"])
         set_of_bads = set(common_bad_channels)
         new_bads = ch_set_2.difference(set_of_bads)
-        
-        if len(new_bads) >1 :
+
+        if len(new_bads) > 1:
             common_bad_channels.extend(list(new_bads))
-    
+
     new_instances = []
-    
+
     for inst in list_instances:
         inst.info["bads"] = common_bad_channels
         new_instances.append(inst)
 
-
     return new_instances
-
-

From 0284caaab74d51026a49765f96f51df1c4f72d66 Mon Sep 17 00:00:00 2001
From: Ana Radanovic <79697247+anaradanovic@users.noreply.github.com>
Date: Mon, 25 Sep 2023 17:13:28 -0400
Subject: [PATCH 03/38] Update mne/preprocessing/unify_bads.py

Co-authored-by: Daniel McCloy <dan@mccloy.info>
---
 mne/preprocessing/unify_bads.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/mne/preprocessing/unify_bads.py b/mne/preprocessing/unify_bads.py
index 1145192aa88..1c0cf1b6793 100644
--- a/mne/preprocessing/unify_bads.py
+++ b/mne/preprocessing/unify_bads.py
@@ -4,7 +4,14 @@ def unifying_bads(
 ):
     common_bad_channels = []
     # first check that each object is mne object
-
+    inst_types = set(type(insts[0]))
+    valid_types = (Raw, Epochs, Evoked, Spectrum, EpochsSpectrum)
+    for inst in insts:
+        _validate_type(inst, valid_types, "instance type")
+        if type(inst) not in inst_types:
+            raise ValueError(
+                "all insts must be the same type"
+            )
     # then interate through the objects to get ch names as set
     ch_set_1 = list_instances[0].info["bads"]
     common_bad_channels.extend(ch_set_1)

From c3e979481ef2bd789969c576452ef5aa27524eae Mon Sep 17 00:00:00 2001
From: Ana Radanovic <79697247+anaradanovic@users.noreply.github.com>
Date: Mon, 25 Sep 2023 17:13:39 -0400
Subject: [PATCH 04/38] Update mne/preprocessing/unify_bads.py

Co-authored-by: Daniel McCloy <dan@mccloy.info>
---
 mne/preprocessing/unify_bads.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/mne/preprocessing/unify_bads.py b/mne/preprocessing/unify_bads.py
index 1c0cf1b6793..b5ea971f9b6 100644
--- a/mne/preprocessing/unify_bads.py
+++ b/mne/preprocessing/unify_bads.py
@@ -15,7 +15,10 @@ def unifying_bads(
     # then interate through the objects to get ch names as set
     ch_set_1 = list_instances[0].info["bads"]
     common_bad_channels.extend(ch_set_1)
-
+    all_bads = dict()
+    for inst in insts:
+        all_bads.update(dict.fromkeys(inst.info['bads']))
+    all_bads = list(all_bads)
     for inst in list_instances[1:]:
         ch_set_2 = set(inst.info["bads"])
         set_of_bads = set(common_bad_channels)

From aeb7a42495c8422d40d5d6810a15d00535ba754d Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 25 Sep 2023 21:14:20 +0000
Subject: [PATCH 05/38] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mne/preprocessing/unify_bads.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/mne/preprocessing/unify_bads.py b/mne/preprocessing/unify_bads.py
index b5ea971f9b6..a75034f390e 100644
--- a/mne/preprocessing/unify_bads.py
+++ b/mne/preprocessing/unify_bads.py
@@ -9,9 +9,7 @@ def unifying_bads(
     for inst in insts:
         _validate_type(inst, valid_types, "instance type")
         if type(inst) not in inst_types:
-            raise ValueError(
-                "all insts must be the same type"
-            )
+            raise ValueError("all insts must be the same type")
     # then interate through the objects to get ch names as set
     ch_set_1 = list_instances[0].info["bads"]
     common_bad_channels.extend(ch_set_1)

From 32f8b35e300f9a4c9031c0e952b8d8c76c310892 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 25 Sep 2023 21:15:16 +0000
Subject: [PATCH 06/38] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mne/preprocessing/unify_bads.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mne/preprocessing/unify_bads.py b/mne/preprocessing/unify_bads.py
index a75034f390e..be2ca2ac198 100644
--- a/mne/preprocessing/unify_bads.py
+++ b/mne/preprocessing/unify_bads.py
@@ -15,7 +15,7 @@ def unifying_bads(
     common_bad_channels.extend(ch_set_1)
     all_bads = dict()
     for inst in insts:
-        all_bads.update(dict.fromkeys(inst.info['bads']))
+        all_bads.update(dict.fromkeys(inst.info["bads"]))
     all_bads = list(all_bads)
     for inst in list_instances[1:]:
         ch_set_2 = set(inst.info["bads"])

From c22295658ae7ab474bc3ba4b826c23854b3df34a Mon Sep 17 00:00:00 2001
From: Ana Radanovic <radanovica@protonmail.com>
Date: Mon, 25 Sep 2023 18:46:06 -0400
Subject: [PATCH 07/38] updates to inprogress work unify bads

---
 mne/preprocessing/unify_bads.py | 38 +++++++++++++++++----------------
 1 file changed, 20 insertions(+), 18 deletions(-)

diff --git a/mne/preprocessing/unify_bads.py b/mne/preprocessing/unify_bads.py
index be2ca2ac198..aa32e403fa4 100644
--- a/mne/preprocessing/unify_bads.py
+++ b/mne/preprocessing/unify_bads.py
@@ -1,34 +1,36 @@
-# %%
-def unifying_bads(
-    list_instances,
+#%%
+
+from ..utils import _validate_type
+
+from ..io import BaseRaw
+from ..epochs import Epochs
+from ..evoked import Evoked
+from ..time_frequency.spectrum import BaseSpectrum
+
+#%%
+def unify_bad_channels(
+    insts,
 ):
-    common_bad_channels = []
     # first check that each object is mne object
-    inst_types = set(type(insts[0]))
-    valid_types = (Raw, Epochs, Evoked, Spectrum, EpochsSpectrum)
+    inst_type = type(insts[0])
+    valid_types = (BaseRaw, Epochs, Evoked, BaseSpectrum)
     for inst in insts:
-        _validate_type(inst, valid_types, "instance type")
-        if type(inst) not in inst_types:
+        _validate_type(inst, valid_types , "instance type")
+        if type(inst) != inst_type:
             raise ValueError("all insts must be the same type")
     # then interate through the objects to get ch names as set
-    ch_set_1 = list_instances[0].info["bads"]
-    common_bad_channels.extend(ch_set_1)
+
     all_bads = dict()
     for inst in insts:
         all_bads.update(dict.fromkeys(inst.info["bads"]))
     all_bads = list(all_bads)
-    for inst in list_instances[1:]:
-        ch_set_2 = set(inst.info["bads"])
-        set_of_bads = set(common_bad_channels)
-        new_bads = ch_set_2.difference(set_of_bads)
 
-        if len(new_bads) > 1:
-            common_bad_channels.extend(list(new_bads))
 
     new_instances = []
 
-    for inst in list_instances:
-        inst.info["bads"] = common_bad_channels
+    for inst in insts:
+        inst.info["bads"] = all_bads
         new_instances.append(inst)
 
     return new_instances
+

From 0fa5b18f0c1d327a9d11dca5866dfe81d6fd0bd1 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 25 Sep 2023 22:49:36 +0000
Subject: [PATCH 08/38] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mne/preprocessing/unify_bads.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/mne/preprocessing/unify_bads.py b/mne/preprocessing/unify_bads.py
index aa32e403fa4..c8b7d08e8e0 100644
--- a/mne/preprocessing/unify_bads.py
+++ b/mne/preprocessing/unify_bads.py
@@ -1,4 +1,4 @@
-#%%
+# %%
 
 from ..utils import _validate_type
 
@@ -7,7 +7,8 @@
 from ..evoked import Evoked
 from ..time_frequency.spectrum import BaseSpectrum
 
-#%%
+
+# %%
 def unify_bad_channels(
     insts,
 ):
@@ -15,7 +16,7 @@ def unify_bad_channels(
     inst_type = type(insts[0])
     valid_types = (BaseRaw, Epochs, Evoked, BaseSpectrum)
     for inst in insts:
-        _validate_type(inst, valid_types , "instance type")
+        _validate_type(inst, valid_types, "instance type")
         if type(inst) != inst_type:
             raise ValueError("all insts must be the same type")
     # then interate through the objects to get ch names as set
@@ -25,7 +26,6 @@ def unify_bad_channels(
         all_bads.update(dict.fromkeys(inst.info["bads"]))
     all_bads = list(all_bads)
 
-
     new_instances = []
 
     for inst in insts:
@@ -33,4 +33,3 @@ def unify_bad_channels(
         new_instances.append(inst)
 
     return new_instances
-

From 2c200a1dfc94a7667cc6e3c65425853e77b5e409 Mon Sep 17 00:00:00 2001
From: Ana Radanovic <radanovica@protonmail.com>
Date: Tue, 26 Sep 2023 15:53:01 -0400
Subject: [PATCH 09/38] Move unify_bad_channels function to
 preprocessing/bads.py

---
 mne/preprocessing/bads.py       | 66 +++++++++++++++++++++++++++++++++
 mne/preprocessing/unify_bads.py | 36 ------------------
 2 files changed, 66 insertions(+), 36 deletions(-)
 delete mode 100644 mne/preprocessing/unify_bads.py

diff --git a/mne/preprocessing/bads.py b/mne/preprocessing/bads.py
index 077145ff7c8..72a0a72c250 100644
--- a/mne/preprocessing/bads.py
+++ b/mne/preprocessing/bads.py
@@ -1,10 +1,19 @@
 # Authors: Denis Engemann <denis.engemann@gmail.com>
+#          Ana Radanovic <radanovica@protonmail.com>
+#          Erica Peterson <nordme@uw.edu>
 # License: BSD-3-Clause
 
 import numpy as np
 from scipy.stats import zscore
 
 
+from ..utils import _validate_type
+
+from ..io import BaseRaw
+from ..epochs import Epochs
+from ..evoked import Evoked
+from ..time_frequency.spectrum import BaseSpectrum
+
 def _find_outliers(X, threshold=3.0, max_iter=2, tail=0):
     """Find outliers based on iterated Z-scoring.
 
@@ -47,3 +56,60 @@ def _find_outliers(X, threshold=3.0, max_iter=2, tail=0):
 
     bad_idx = np.where(my_mask)[0]
     return bad_idx
+
+
+def unify_bad_channels(insts):
+    """Unify bad channels across list of instances.
+
+    This function looks across the list of instances to gather a list of 
+    "bad" channels. Every instance's info["bads"] is set with the same "bad" 
+    channels.
+
+    Parameters
+    ----------
+    insts : list
+        List of instances (:class:`~mne.io.Raw`, :class:`~mne.Epochs`, 
+        :class:`~mne.Evoked`, :class:`~mne.time_frequency.Spectrum`, 
+        :class:`~mne.time_frequency.EpochSpectrum`) to unify bad channels.
+
+    Returns
+    -------
+    new_insts : list
+        List of instances with bad channels unified across instances.
+        
+    Notes
+    -----
+    This function operates in-place.
+    
+    .. versionadded:: 1.6
+    """
+    # first check that each object is mne object
+    inst_type = type(insts[0])
+    valid_types = (BaseRaw, Epochs, Evoked, BaseSpectrum)
+    for inst in insts:
+        _validate_type(inst, valid_types , "instance type")
+        if type(inst) != inst_type:
+            raise ValueError("All insts must be the same type")
+        
+    #check that input is a list
+    if type(insts) != list :
+        raise ValueError(f"insts must be a *list* of mne objects, got {type(insts)}")
+    
+    if len(insts) == 0:
+        raise ValueError("Be sure insts is not empty list")
+        
+    # then interate through the insts to gather bads
+    all_bads = dict()
+    for inst in insts:
+        #using dictionary method to remove duplicates & preserve order
+        all_bads.update(dict.fromkeys(inst.info["bads"]))
+    all_bads = list(all_bads)
+
+    #apply bads set to all instances
+    new_insts = []
+
+    for inst in insts:
+        inst.info["bads"] = all_bads
+        new_insts.append(inst)
+
+    return new_insts
diff --git a/mne/preprocessing/unify_bads.py b/mne/preprocessing/unify_bads.py
deleted file mode 100644
index aa32e403fa4..00000000000
--- a/mne/preprocessing/unify_bads.py
+++ /dev/null
@@ -1,36 +0,0 @@
-#%%
-
-from ..utils import _validate_type
-
-from ..io import BaseRaw
-from ..epochs import Epochs
-from ..evoked import Evoked
-from ..time_frequency.spectrum import BaseSpectrum
-
-#%%
-def unify_bad_channels(
-    insts,
-):
-    # first check that each object is mne object
-    inst_type = type(insts[0])
-    valid_types = (BaseRaw, Epochs, Evoked, BaseSpectrum)
-    for inst in insts:
-        _validate_type(inst, valid_types , "instance type")
-        if type(inst) != inst_type:
-            raise ValueError("all insts must be the same type")
-    # then interate through the objects to get ch names as set
-
-    all_bads = dict()
-    for inst in insts:
-        all_bads.update(dict.fromkeys(inst.info["bads"]))
-    all_bads = list(all_bads)
-
-
-    new_instances = []
-
-    for inst in insts:
-        inst.info["bads"] = all_bads
-        new_instances.append(inst)
-
-    return new_instances
-

From 80c329d1dc5eede1c1345f18404130953e3eccd3 Mon Sep 17 00:00:00 2001
From: Ana Radanovic <radanovica@protonmail.com>
Date: Tue, 26 Sep 2023 16:05:26 -0400
Subject: [PATCH 10/38] add function to namespace

---
 mne/preprocessing/__init__.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/mne/preprocessing/__init__.py b/mne/preprocessing/__init__.py
index 8358f006e09..8aea05c369f 100644
--- a/mne/preprocessing/__init__.py
+++ b/mne/preprocessing/__init__.py
@@ -56,5 +56,6 @@
         "interpolate": ["equalize_bads", "interpolate_bridged_electrodes"],
         "_css": ["cortical_signal_suppression"],
         "hfc": ["compute_proj_hfc"],
+        "bads": ["unify_bad_channels"]
     },
 )

From fc917873cec6b10b99e33929dbe1103cdca1e796 Mon Sep 17 00:00:00 2001
From: Ana Radanovic <radanovica@protonmail.com>
Date: Tue, 26 Sep 2023 16:20:46 -0400
Subject: [PATCH 11/38] style fixes

---
 mne/preprocessing/__init__.py |  2 +-
 mne/preprocessing/bads.py     | 31 ++++++++++++++++---------------
 2 files changed, 17 insertions(+), 16 deletions(-)

diff --git a/mne/preprocessing/__init__.py b/mne/preprocessing/__init__.py
index 8aea05c369f..6d818ac60b0 100644
--- a/mne/preprocessing/__init__.py
+++ b/mne/preprocessing/__init__.py
@@ -56,6 +56,6 @@
         "interpolate": ["equalize_bads", "interpolate_bridged_electrodes"],
         "_css": ["cortical_signal_suppression"],
         "hfc": ["compute_proj_hfc"],
-        "bads": ["unify_bad_channels"]
+        "bads": ["unify_bad_channels"],
     },
 )
diff --git a/mne/preprocessing/bads.py b/mne/preprocessing/bads.py
index 72a0a72c250..453287dd311 100644
--- a/mne/preprocessing/bads.py
+++ b/mne/preprocessing/bads.py
@@ -14,6 +14,7 @@
 from ..evoked import Evoked
 from ..time_frequency.spectrum import BaseSpectrum
 
+
 def _find_outliers(X, threshold=3.0, max_iter=2, tail=0):
     """Find outliers based on iterated Z-scoring.
 
@@ -61,51 +62,51 @@ def _find_outliers(X, threshold=3.0, max_iter=2, tail=0):
 def unify_bad_channels(insts):
     """Unify bad channels across list of instances.
 
-    This function looks across the list of instances to gather a list of 
-    "bad" channels. Every instance's info["bads"] is set with the same "bad" 
+    This function looks across the list of instances to gather a list of
+    "bad" channels. Every instance's info["bads"] is set with the same "bad"
     channels.
 
     Parameters
     ----------
     insts : list
-        List of instances (:class:`~mne.io.Raw`, :class:`~mne.Epochs`, 
-        :class:`~mne.Evoked`, :class:`~mne.time_frequency.Spectrum`, 
+        List of instances (:class:`~mne.io.Raw`, :class:`~mne.Epochs`,
+        :class:`~mne.Evoked`, :class:`~mne.time_frequency.Spectrum`,
         :class:`~mne.time_frequency.EpochSpectrum`) to unify bad channels.
 
     Returns
     -------
     new_insts : list
         List of instances with bad channels unified across instances.
-        
+
     Notes
     -----
     This function operates in-place.
-    
+
     .. versionadded:: 1.6
     """
     # first check that each object is mne object
     inst_type = type(insts[0])
     valid_types = (BaseRaw, Epochs, Evoked, BaseSpectrum)
     for inst in insts:
-        _validate_type(inst, valid_types , "instance type")
+        _validate_type(inst, valid_types, "instance type")
         if type(inst) != inst_type:
             raise ValueError("All insts must be the same type")
-        
-    #check that input is a list
-    if type(insts) != list :
+
+    # check that input is a list
+    if not isinstance(insts, list):
         raise ValueError(f"insts must be a *list* of mne objects, got {type(insts)}")
-    
+
     if len(insts) == 0:
         raise ValueError("Be sure insts is not empty list")
-        
-    # then interate through the insts to gather bads
+
+    # then iterate through the insts to gather bads
     all_bads = dict()
     for inst in insts:
-        #using dictionary method to remove duplicates & preserve order
+        # using dictionary method to remove duplicates & preserve order
         all_bads.update(dict.fromkeys(inst.info["bads"]))
     all_bads = list(all_bads)
 
-    #apply bads set to all instances
+    # apply bads set to all instances
     new_insts = []
 
     for inst in insts:

From 58b96c3ce8106f1ff5b88d973dbfc32c59a090a6 Mon Sep 17 00:00:00 2001
From: nordme <nordme@uw.edu>
Date: Tue, 26 Sep 2023 08:45:40 -0700
Subject: [PATCH 12/38] test draft

---
 mne/preprocessing/tests/test_unify_bads.py | 58 ++++++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 mne/preprocessing/tests/test_unify_bads.py

diff --git a/mne/preprocessing/tests/test_unify_bads.py b/mne/preprocessing/tests/test_unify_bads.py
new file mode 100644
index 00000000000..8c696ba6e36
--- /dev/null
+++ b/mne/preprocessing/tests/test_unify_bads.py
@@ -0,0 +1,58 @@
+from pathlib import Path
+
+import numpy as np
+import pytest
+
+import mne
+from mne.preprocessing import unify_bad_channels
+from ..io import BaseRaw
+from ..epochs import Epochs
+from ..evoked import Evoked
+from ..time_frequency.spectrum import BaseSpectrum
+
+
+raw_fname = (
+    Path(__file__).parent.parent.parent / "io" / "tests" / "data" / "test_raw.fif"
+)
+@pytest.mark.parametrize('instance', ('raw', 'epochs', 'evoked', 'spectrum'))
+def test_instance_support(instance):
+    # test unify_bads function on instance (single input, no bads scenario)
+    unify_bad_channels(instance)
+
+
+def test_bads_order(raw):
+
+def test_unify_bads(raw, epochs):
+    ## test error raising
+    # err 1: no instance passed to function
+    with pytest.raises(UserWarning): # FIX RAISE TYPE
+        unify_bad_channels([])
+    # err 2: bad instance passed to function
+    bad_inst = 'bad_instance'
+    with pytest.raises(UserWarning):  # FIX RAISE TYPE
+        unify_bad_channels(bad_inst)
+    # err 3: mixed instance types passed to function
+    with pytest.raises(ValueError):
+        unify_bad_channels([raw, epochs])
+    ## check unification scenarios
+    # scnario 1: single instance with actual bads (already tested no bads)
+    raw.info['bads'] += raw.info['ch_names'][0]
+    s_unified = unify_bad_channels(raw)
+    assert len(s_unified) == 1
+    assert s_unified[0].info['bads'] == raw.info['ch_names'][0]
+    # scenario 2: multiple instances
+    # a) empty bads list, b) unique bads, c) overlapping out-of-order bads,
+    # d) channel name not included in raw channels
+    chns = raw.info['ch_names'][0:3]
+    raws = [raw, raw.copy(), raw.copy(), raw.copy(), raw.copy()]
+    assert raws[0].info['bads'] == [chns[0]]
+    raws[1].info['bads'] = []
+    raws[2].info['bads'] = [chns[2]]
+    raws[3].info['bads'] = [chns[2], chns[1]]
+    raws[4].info['bads'] = ['nonsense_ch_name']
+    # use unify_bads function
+    m_unified = unify_bad_channels(raws)
+    assert len(m_unified) == len(raws)
+    # check results
+    for i in np.arange(len(m_unified)):
+        assert m_unified[i].info['bads'] ==

From 7c28118dbf77ccc1f13e4443ad13aa35a40cb70b Mon Sep 17 00:00:00 2001
From: nordme <nordme@uw.edu>
Date: Tue, 26 Sep 2023 12:57:20 -0700
Subject: [PATCH 13/38] make functions work

---
 mne/preprocessing/tests/test_unify_bads.py | 67 +++++++++++-----------
 1 file changed, 32 insertions(+), 35 deletions(-)

diff --git a/mne/preprocessing/tests/test_unify_bads.py b/mne/preprocessing/tests/test_unify_bads.py
index 8c696ba6e36..f01a9d58809 100644
--- a/mne/preprocessing/tests/test_unify_bads.py
+++ b/mne/preprocessing/tests/test_unify_bads.py
@@ -1,49 +1,45 @@
-from pathlib import Path
-
 import numpy as np
 import pytest
 
-import mne
-from mne.preprocessing import unify_bad_channels
-from ..io import BaseRaw
-from ..epochs import Epochs
-from ..evoked import Evoked
-from ..time_frequency.spectrum import BaseSpectrum
-
+from mne.preprocessing.unify_bads import unify_bad_channels
+from mne.time_frequency.tests.test_spectrum import _get_inst()
 
-raw_fname = (
-    Path(__file__).parent.parent.parent / "io" / "tests" / "data" / "test_raw.fif"
-)
-@pytest.mark.parametrize('instance', ('raw', 'epochs', 'evoked', 'spectrum'))
-def test_instance_support(instance):
+@pytest.mark.parametrize('instance', ('raw', 'epochs', 'evoked', 'raw_spectrum', 'epochs_spectrum'))
+def test_instance_support(instance, request, evoked):
+    '''Tests support of different classes.'''
     # test unify_bads function on instance (single input, no bads scenario)
-    unify_bad_channels(instance)
+    inst = _get_inst(instance, request, evoked)
+    inst_out = unify_bad_channels([inst])
+    assert inst_out == [inst]
+
 
+@pytest.mark.parametrize('instance', ([], ['bad_instance'], 'mixed'))
+def test_error_raising(instance, request, evoked):
+    '''Tests input checking.'''
+    if instance == 'mixed':
+        instance = [_get_inst('raw', request, evoked),
+                    _get_inst('epochs', request, evoked)]
+    with pytest.raises(TypeError):
+        unify_bad_channels(instance)
 
-def test_bads_order(raw):
 
-def test_unify_bads(raw, epochs):
-    ## test error raising
-    # err 1: no instance passed to function
-    with pytest.raises(UserWarning): # FIX RAISE TYPE
-        unify_bad_channels([])
-    # err 2: bad instance passed to function
-    bad_inst = 'bad_instance'
-    with pytest.raises(UserWarning):  # FIX RAISE TYPE
-        unify_bad_channels(bad_inst)
-    # err 3: mixed instance types passed to function
-    with pytest.raises(ValueError):
-        unify_bad_channels([raw, epochs])
+def test_bads_compilation(raw):
+    '''Tests that bads are compiled properly in two cases: a) single instance
+    passed to function with an existing bad, and b) multiple instances passed
+    to function with varying compilation scenarios including empty bads,
+    unique bads, partially duplicated bads listed out-of-order, and
+    nonsense channel names.'''
     ## check unification scenarios
-    # scnario 1: single instance with actual bads (already tested no bads)
-    raw.info['bads'] += raw.info['ch_names'][0]
-    s_unified = unify_bad_channels(raw)
+    chns = raw.info['ch_names'][0:3]
+    # scnario 1: single instance passed with actual bads (already tested no bads)
+    assert raw.info['bads'] == []
+    raw.info['bads'] += [chns[0]]
+    s_unified = unify_bad_channels([raw])
     assert len(s_unified) == 1
-    assert s_unified[0].info['bads'] == raw.info['ch_names'][0]
-    # scenario 2: multiple instances
+    assert s_unified[0].info['bads'] == [chns[0]], (s_unified[0].info['bads'], chns[0])
+    # scenario 2: multiple instances passed, bads types as follows:
     # a) empty bads list, b) unique bads, c) overlapping out-of-order bads,
     # d) channel name not included in raw channels
-    chns = raw.info['ch_names'][0:3]
     raws = [raw, raw.copy(), raw.copy(), raw.copy(), raw.copy()]
     assert raws[0].info['bads'] == [chns[0]]
     raws[1].info['bads'] = []
@@ -54,5 +50,6 @@ def test_unify_bads(raw, epochs):
     m_unified = unify_bad_channels(raws)
     assert len(m_unified) == len(raws)
     # check results
+    correct_bads = [chns[0], chns[2], chns[1], 'nonsense_ch_name']
     for i in np.arange(len(m_unified)):
-        assert m_unified[i].info['bads'] ==
+        assert m_unified[i].info['bads'] == correct_bads

From d89431e313e0595f16184be9f3cb7a94c93c8397 Mon Sep 17 00:00:00 2001
From: nordme <nordme@uw.edu>
Date: Tue, 26 Sep 2023 13:55:16 -0700
Subject: [PATCH 14/38] style fixes

---
 mne/preprocessing/tests/test_unify_bads.py | 59 ++++++++++++----------
 1 file changed, 33 insertions(+), 26 deletions(-)

diff --git a/mne/preprocessing/tests/test_unify_bads.py b/mne/preprocessing/tests/test_unify_bads.py
index f01a9d58809..96edf86c1ae 100644
--- a/mne/preprocessing/tests/test_unify_bads.py
+++ b/mne/preprocessing/tests/test_unify_bads.py
@@ -1,55 +1,62 @@
 import numpy as np
 import pytest
 
-from mne.preprocessing.unify_bads import unify_bad_channels
-from mne.time_frequency.tests.test_spectrum import _get_inst()
+from mne.preprocessing import unify_bad_channels
+from mne.time_frequency.tests.test_spectrum import _get_inst
 
-@pytest.mark.parametrize('instance', ('raw', 'epochs', 'evoked', 'raw_spectrum', 'epochs_spectrum'))
+
+@pytest.mark.parametrize(
+    "instance", ("raw", "epochs", "evoked", "raw_spectrum", "epochs_spectrum")
+)
 def test_instance_support(instance, request, evoked):
-    '''Tests support of different classes.'''
+    """Tests support of different classes."""
     # test unify_bads function on instance (single input, no bads scenario)
     inst = _get_inst(instance, request, evoked)
     inst_out = unify_bad_channels([inst])
     assert inst_out == [inst]
 
 
-@pytest.mark.parametrize('instance', ([], ['bad_instance'], 'mixed'))
+@pytest.mark.parametrize("instance", ([], ["bad_instance"], "mixed"))
 def test_error_raising(instance, request, evoked):
-    '''Tests input checking.'''
-    if instance == 'mixed':
-        instance = [_get_inst('raw', request, evoked),
-                    _get_inst('epochs', request, evoked)]
+    """Tests input checking."""
+    if instance == "mixed":
+        instance = [
+            _get_inst("raw", request, evoked),
+            _get_inst("epochs", request, evoked),
+        ]
     with pytest.raises(TypeError):
         unify_bad_channels(instance)
 
 
 def test_bads_compilation(raw):
-    '''Tests that bads are compiled properly in two cases: a) single instance
-    passed to function with an existing bad, and b) multiple instances passed
-    to function with varying compilation scenarios including empty bads,
-    unique bads, partially duplicated bads listed out-of-order, and
-    nonsense channel names.'''
+    """Tests that bads are compiled properly.
+
+    Tests two cases: a) single instance passed to function with an existing
+    bad, and b) multiple instances passed to function with varying compilation
+    scenarios including empty bads, unique bads, partially duplicated bads
+    listed out-of-order, and nonsense channel names.
+    """
     ## check unification scenarios
-    chns = raw.info['ch_names'][0:3]
-    # scnario 1: single instance passed with actual bads (already tested no bads)
-    assert raw.info['bads'] == []
-    raw.info['bads'] += [chns[0]]
+    chns = raw.info["ch_names"][0:3]
+    # scenario 1: single instance passed with actual bads (already tested no bads)
+    assert raw.info["bads"] == []
+    raw.info["bads"] += [chns[0]]
     s_unified = unify_bad_channels([raw])
     assert len(s_unified) == 1
-    assert s_unified[0].info['bads'] == [chns[0]], (s_unified[0].info['bads'], chns[0])
+    assert s_unified[0].info["bads"] == [chns[0]], (s_unified[0].info["bads"], chns[0])
     # scenario 2: multiple instances passed, bads types as follows:
     # a) empty bads list, b) unique bads, c) overlapping out-of-order bads,
     # d) channel name not included in raw channels
     raws = [raw, raw.copy(), raw.copy(), raw.copy(), raw.copy()]
-    assert raws[0].info['bads'] == [chns[0]]
-    raws[1].info['bads'] = []
-    raws[2].info['bads'] = [chns[2]]
-    raws[3].info['bads'] = [chns[2], chns[1]]
-    raws[4].info['bads'] = ['nonsense_ch_name']
+    assert raws[0].info["bads"] == [chns[0]]
+    raws[1].info["bads"] = []
+    raws[2].info["bads"] = [chns[2]]
+    raws[3].info["bads"] = [chns[2], chns[1]]
+    raws[4].info["bads"] = ["nonsense_ch_name"]
     # use unify_bads function
     m_unified = unify_bad_channels(raws)
     assert len(m_unified) == len(raws)
     # check results
-    correct_bads = [chns[0], chns[2], chns[1], 'nonsense_ch_name']
+    correct_bads = [chns[0], chns[2], chns[1], "nonsense_ch_name"]
     for i in np.arange(len(m_unified)):
-        assert m_unified[i].info['bads'] == correct_bads
+        assert m_unified[i].info["bads"] == correct_bads

From 9b745cb6ece743d857fc5692f6223a645b23dd39 Mon Sep 17 00:00:00 2001
From: nordme <nordme@uw.edu>
Date: Wed, 27 Sep 2023 09:54:21 -0700
Subject: [PATCH 15/38] style fix

---
 mne/preprocessing/tests/test_unify_bads.py | 63 ++++++++++------------
 1 file changed, 29 insertions(+), 34 deletions(-)

diff --git a/mne/preprocessing/tests/test_unify_bads.py b/mne/preprocessing/tests/test_unify_bads.py
index 96edf86c1ae..da4d01716de 100644
--- a/mne/preprocessing/tests/test_unify_bads.py
+++ b/mne/preprocessing/tests/test_unify_bads.py
@@ -16,16 +16,18 @@ def test_instance_support(instance, request, evoked):
     assert inst_out == [inst]
 
 
-@pytest.mark.parametrize("instance", ([], ["bad_instance"], "mixed"))
-def test_error_raising(instance, request, evoked):
+def test_error_raising(raw, epochs):
     """Tests input checking."""
-    if instance == "mixed":
-        instance = [
-            _get_inst("raw", request, evoked),
-            _get_inst("epochs", request, evoked),
-        ]
-    with pytest.raises(TypeError):
-        unify_bad_channels(instance)
+    with pytest.raises(IndexError, match=r"empty list"):
+        unify_bad_channels([])
+    with pytest.raises(TypeError, match=r"must be an instance of"):
+        unify_bad_channels(["bad_instance"])
+    with pytest.raises(ValueError, match=r"same type"):
+        unify_bad_channels([raw, epochs])
+    with pytest.raises(AssertionError):
+        raw_alt = raw.copy()
+        raw_alt.info["ch_names"] = raw.info["ch_names"][0]
+        unify_bad_channels([raw, raw_alt])
 
 
 def test_bads_compilation(raw):
@@ -33,30 +35,23 @@ def test_bads_compilation(raw):
 
     Tests two cases: a) single instance passed to function with an existing
     bad, and b) multiple instances passed to function with varying compilation
-    scenarios including empty bads, unique bads, partially duplicated bads
-    listed out-of-order, and nonsense channel names.
+    scenarios including empty bads, unique bads, and partially duplicated bads
+    listed out-of-order.
     """
-    ## check unification scenarios
-    chns = raw.info["ch_names"][0:3]
-    # scenario 1: single instance passed with actual bads (already tested no bads)
     assert raw.info["bads"] == []
-    raw.info["bads"] += [chns[0]]
-    s_unified = unify_bad_channels([raw])
-    assert len(s_unified) == 1
-    assert s_unified[0].info["bads"] == [chns[0]], (s_unified[0].info["bads"], chns[0])
-    # scenario 2: multiple instances passed, bads types as follows:
-    # a) empty bads list, b) unique bads, c) overlapping out-of-order bads,
-    # d) channel name not included in raw channels
-    raws = [raw, raw.copy(), raw.copy(), raw.copy(), raw.copy()]
-    assert raws[0].info["bads"] == [chns[0]]
-    raws[1].info["bads"] = []
-    raws[2].info["bads"] = [chns[2]]
-    raws[3].info["bads"] = [chns[2], chns[1]]
-    raws[4].info["bads"] = ["nonsense_ch_name"]
-    # use unify_bads function
-    m_unified = unify_bad_channels(raws)
-    assert len(m_unified) == len(raws)
-    # check results
-    correct_bads = [chns[0], chns[2], chns[1], "nonsense_ch_name"]
-    for i in np.arange(len(m_unified)):
-        assert m_unified[i].info["bads"] == correct_bads
+    chns = raw.info["ch_names"][0:3]
+    no_bad = raw.copy()
+    one_bad = raw.copy()
+    one_bad.info["bads"] = chns[1]
+    three_bad = raw.copy()
+    three_bad.info["bads"] = chns
+    # scenario 1: single instance passed with actual bads
+    s_out = unify_bad_channels([one_bad])
+    assert len(s_out) == 1
+    assert s_out[0].info["bads"] == [chns[1]], (s_out[0].info["bads"], chns[1])
+    # scenario 2: multiple instances passed
+    m_out = unify_bad_channels([one_bad, no_bad, three_bad])
+    assert len(m_out) == 3
+    correct_bads = [chns[1], chns[0], chns[2]]
+    for i in np.arange(len(m_out)):
+        assert m_out[i].info["bads"] == correct_bads

From b32f318d83548e47c18bb9c6be0fd629a3eac5f8 Mon Sep 17 00:00:00 2001
From: nordme <nordme@uw.edu>
Date: Wed, 27 Sep 2023 10:12:16 -0700
Subject: [PATCH 16/38] fixes

---
 mne/preprocessing/tests/test_unify_bads.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/mne/preprocessing/tests/test_unify_bads.py b/mne/preprocessing/tests/test_unify_bads.py
index da4d01716de..6ca9d60fa72 100644
--- a/mne/preprocessing/tests/test_unify_bads.py
+++ b/mne/preprocessing/tests/test_unify_bads.py
@@ -18,7 +18,7 @@ def test_instance_support(instance, request, evoked):
 
 def test_error_raising(raw, epochs):
     """Tests input checking."""
-    with pytest.raises(IndexError, match=r"empty list"):
+    with pytest.raises(IndexError, match=r"list index"):
         unify_bad_channels([])
     with pytest.raises(TypeError, match=r"must be an instance of"):
         unify_bad_channels(["bad_instance"])
@@ -42,7 +42,7 @@ def test_bads_compilation(raw):
     chns = raw.info["ch_names"][0:3]
     no_bad = raw.copy()
     one_bad = raw.copy()
-    one_bad.info["bads"] = chns[1]
+    one_bad.info["bads"] = [chns[1]]
     three_bad = raw.copy()
     three_bad.info["bads"] = chns
     # scenario 1: single instance passed with actual bads

From 023db18096be813d7470041667847261a171809d Mon Sep 17 00:00:00 2001
From: Ana Radanovic <radanovica@protonmail.com>
Date: Wed, 27 Sep 2023 13:17:06 -0400
Subject: [PATCH 17/38] adding ch_name check to function

---
 mne/preprocessing/bads.py | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/mne/preprocessing/bads.py b/mne/preprocessing/bads.py
index 453287dd311..b566495a79d 100644
--- a/mne/preprocessing/bads.py
+++ b/mne/preprocessing/bads.py
@@ -95,9 +95,22 @@ def unify_bad_channels(insts):
     # check that input is a list
     if not isinstance(insts, list):
         raise ValueError(f"insts must be a *list* of mne objects, got {type(insts)}")
-
+    # check input is not an empty list
     if len(insts) == 0:
         raise ValueError("Be sure insts is not empty list")
+    # check that all channels have the same name and same number
+    ch_names = insts[0].info.ch_names
+    diff_chns = []
+    for inst in insts[1:]:
+        if inst.info.ch_names != ch_names:
+            dif = set(inst.info.ch_names).difference(set(ch_names))
+            diff_chns.extend(list(dif))
+
+    if len(diff_chns) > 0:
+        raise ValueError(
+            "Channel names are not consistent across instances."
+            f" Mismatch channels are {diff_chns}"
+        )
 
     # then iterate through the insts to gather bads
     all_bads = dict()

From ce03592f0085a2e1d28047992f709696d5d1687c Mon Sep 17 00:00:00 2001
From: Ana Radanovic <radanovica@protonmail.com>
Date: Wed, 27 Sep 2023 13:22:06 -0400
Subject: [PATCH 18/38] moving len check to first check

---
 mne/preprocessing/bads.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/mne/preprocessing/bads.py b/mne/preprocessing/bads.py
index b566495a79d..0e3bc46fd55 100644
--- a/mne/preprocessing/bads.py
+++ b/mne/preprocessing/bads.py
@@ -84,6 +84,10 @@ def unify_bad_channels(insts):
 
     .. versionadded:: 1.6
     """
+    # check input is not an empty list
+    if len(insts) == 0:
+        raise ValueError("Be sure insts is not empty list")
+
     # first check that each object is mne object
     inst_type = type(insts[0])
     valid_types = (BaseRaw, Epochs, Evoked, BaseSpectrum)
@@ -95,9 +99,7 @@ def unify_bad_channels(insts):
     # check that input is a list
     if not isinstance(insts, list):
         raise ValueError(f"insts must be a *list* of mne objects, got {type(insts)}")
-    # check input is not an empty list
-    if len(insts) == 0:
-        raise ValueError("Be sure insts is not empty list")
+
     # check that all channels have the same name and same number
     ch_names = insts[0].info.ch_names
     diff_chns = []

From dc8a71a174e91c55c9d591f3d4c4f2af3b8abedb Mon Sep 17 00:00:00 2001
From: nordme <nordme@uw.edu>
Date: Wed, 27 Sep 2023 10:23:19 -0700
Subject: [PATCH 19/38] reconcile with Ana

---
 mne/preprocessing/tests/test_unify_bads.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/mne/preprocessing/tests/test_unify_bads.py b/mne/preprocessing/tests/test_unify_bads.py
index 6ca9d60fa72..d5fe4f2b849 100644
--- a/mne/preprocessing/tests/test_unify_bads.py
+++ b/mne/preprocessing/tests/test_unify_bads.py
@@ -18,15 +18,15 @@ def test_instance_support(instance, request, evoked):
 
 def test_error_raising(raw, epochs):
     """Tests input checking."""
-    with pytest.raises(IndexError, match=r"list index"):
+    with pytest.raises(ValueError, match=r"empty list"):
         unify_bad_channels([])
     with pytest.raises(TypeError, match=r"must be an instance of"):
         unify_bad_channels(["bad_instance"])
     with pytest.raises(ValueError, match=r"same type"):
         unify_bad_channels([raw, epochs])
-    with pytest.raises(AssertionError):
+    with pytest.raises(ValueError):
         raw_alt = raw.copy()
-        raw_alt.info["ch_names"] = raw.info["ch_names"][0]
+        raw_alt.drop_channels(raw.info["ch_names"][0])
         unify_bad_channels([raw, raw_alt])
 
 

From 7e38dd59b452c24aaf2c6b0a279f1e204900d438 Mon Sep 17 00:00:00 2001
From: Ana Radanovic <radanovica@protonmail.com>
Date: Wed, 27 Sep 2023 13:50:11 -0400
Subject: [PATCH 20/38] changing ch_name check

---
 mne/preprocessing/bads.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mne/preprocessing/bads.py b/mne/preprocessing/bads.py
index 0e3bc46fd55..27b0679f82c 100644
--- a/mne/preprocessing/bads.py
+++ b/mne/preprocessing/bads.py
@@ -105,7 +105,7 @@ def unify_bad_channels(insts):
     diff_chns = []
     for inst in insts[1:]:
         if inst.info.ch_names != ch_names:
-            dif = set(inst.info.ch_names).difference(set(ch_names))
+            dif = set(inst.info.ch_names) ^ (set(ch_names))
             diff_chns.extend(list(dif))
 
     if len(diff_chns) > 0:

From 2d4528ed87d52ae984c4e5249ef7840981c55eb3 Mon Sep 17 00:00:00 2001
From: Ana Radanovic <79697247+anaradanovic@users.noreply.github.com>
Date: Wed, 27 Sep 2023 15:35:22 -0400
Subject: [PATCH 21/38] Update mne/preprocessing/bads.py

Co-authored-by: Daniel McCloy <dan@mccloy.info>
---
 mne/preprocessing/bads.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mne/preprocessing/bads.py b/mne/preprocessing/bads.py
index 27b0679f82c..4a71b4019a1 100644
--- a/mne/preprocessing/bads.py
+++ b/mne/preprocessing/bads.py
@@ -60,7 +60,7 @@ def _find_outliers(X, threshold=3.0, max_iter=2, tail=0):
 
 
 def unify_bad_channels(insts):
-    """Unify bad channels across list of instances.
+    """Unify bad channels across a list of instances, using the union.
 
     This function looks across the list of instances to gather a list of
     "bad" channels. Every instance's info["bads"] is set with the same "bad"

From a525f33ec943a3946c12214db392b7f33e29b774 Mon Sep 17 00:00:00 2001
From: Ana Radanovic <79697247+anaradanovic@users.noreply.github.com>
Date: Wed, 27 Sep 2023 15:35:49 -0400
Subject: [PATCH 22/38] Update mne/preprocessing/bads.py

Co-authored-by: Daniel McCloy <dan@mccloy.info>
---
 mne/preprocessing/bads.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/mne/preprocessing/bads.py b/mne/preprocessing/bads.py
index 4a71b4019a1..8f7d42655ab 100644
--- a/mne/preprocessing/bads.py
+++ b/mne/preprocessing/bads.py
@@ -62,10 +62,6 @@ def _find_outliers(X, threshold=3.0, max_iter=2, tail=0):
 def unify_bad_channels(insts):
     """Unify bad channels across a list of instances, using the union.
 
-    This function looks across the list of instances to gather a list of
-    "bad" channels. Every instance's info["bads"] is set with the same "bad"
-    channels.
-
     Parameters
     ----------
     insts : list

From ccba9359494d762f96445ff977d7a1fc2880c61e Mon Sep 17 00:00:00 2001
From: Ana Radanovic <79697247+anaradanovic@users.noreply.github.com>
Date: Wed, 27 Sep 2023 15:36:00 -0400
Subject: [PATCH 23/38] Update mne/preprocessing/bads.py

Co-authored-by: Daniel McCloy <dan@mccloy.info>
---
 mne/preprocessing/bads.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mne/preprocessing/bads.py b/mne/preprocessing/bads.py
index 8f7d42655ab..20a5b7f9625 100644
--- a/mne/preprocessing/bads.py
+++ b/mne/preprocessing/bads.py
@@ -67,7 +67,7 @@ def unify_bad_channels(insts):
     insts : list
         List of instances (:class:`~mne.io.Raw`, :class:`~mne.Epochs`,
         :class:`~mne.Evoked`, :class:`~mne.time_frequency.Spectrum`,
-        :class:`~mne.time_frequency.EpochSpectrum`) to unify bad channels.
+        :class:`~mne.time_frequency.EpochSpectrum`) across which to unify bad channels.
 
     Returns
     -------

From e0050141deaa8a7293c4312992606f05b0d5d8cf Mon Sep 17 00:00:00 2001
From: Ana Radanovic <79697247+anaradanovic@users.noreply.github.com>
Date: Wed, 27 Sep 2023 15:36:15 -0400
Subject: [PATCH 24/38] Update mne/preprocessing/bads.py

Co-authored-by: Daniel McCloy <dan@mccloy.info>
---
 mne/preprocessing/bads.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mne/preprocessing/bads.py b/mne/preprocessing/bads.py
index 20a5b7f9625..7ecd52fe04d 100644
--- a/mne/preprocessing/bads.py
+++ b/mne/preprocessing/bads.py
@@ -71,7 +71,7 @@ def unify_bad_channels(insts):
 
     Returns
     -------
-    new_insts : list
+    insts : list
         List of instances with bad channels unified across instances.
 
     Notes

From adfb46b84649c786ae2f20074ac53235856091c4 Mon Sep 17 00:00:00 2001
From: Ana Radanovic <79697247+anaradanovic@users.noreply.github.com>
Date: Wed, 27 Sep 2023 15:36:29 -0400
Subject: [PATCH 25/38] Update mne/preprocessing/bads.py

Co-authored-by: Daniel McCloy <dan@mccloy.info>
---
 mne/preprocessing/bads.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mne/preprocessing/bads.py b/mne/preprocessing/bads.py
index 7ecd52fe04d..85aa455dd63 100644
--- a/mne/preprocessing/bads.py
+++ b/mne/preprocessing/bads.py
@@ -97,7 +97,7 @@ def unify_bad_channels(insts):
         raise ValueError(f"insts must be a *list* of mne objects, got {type(insts)}")
 
     # check that all channels have the same name and same number
-    ch_names = insts[0].info.ch_names
+    ch_names = insts[0].ch_names
     diff_chns = []
     for inst in insts[1:]:
         if inst.info.ch_names != ch_names:

From cfa1c740f258395845b731630d58ebb615d655af Mon Sep 17 00:00:00 2001
From: Ana Radanovic <79697247+anaradanovic@users.noreply.github.com>
Date: Wed, 27 Sep 2023 15:36:37 -0400
Subject: [PATCH 26/38] Update mne/preprocessing/bads.py

Co-authored-by: Daniel McCloy <dan@mccloy.info>
---
 mne/preprocessing/bads.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mne/preprocessing/bads.py b/mne/preprocessing/bads.py
index 85aa455dd63..e7f24086bd6 100644
--- a/mne/preprocessing/bads.py
+++ b/mne/preprocessing/bads.py
@@ -100,7 +100,7 @@ def unify_bad_channels(insts):
     ch_names = insts[0].ch_names
     diff_chns = []
     for inst in insts[1:]:
-        if inst.info.ch_names != ch_names:
+        if inst.ch_names != ch_names:
             dif = set(inst.info.ch_names) ^ (set(ch_names))
             diff_chns.extend(list(dif))
 

From 3085fa0576bdd55ddab795ad81927edfedf736cb Mon Sep 17 00:00:00 2001
From: Ana Radanovic <79697247+anaradanovic@users.noreply.github.com>
Date: Wed, 27 Sep 2023 15:36:59 -0400
Subject: [PATCH 27/38] Update mne/preprocessing/bads.py

Co-authored-by: Daniel McCloy <dan@mccloy.info>
---
 mne/preprocessing/bads.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/mne/preprocessing/bads.py b/mne/preprocessing/bads.py
index e7f24086bd6..00df9ba2988 100644
--- a/mne/preprocessing/bads.py
+++ b/mne/preprocessing/bads.py
@@ -113,7 +113,6 @@ def unify_bad_channels(insts):
     # then iterate through the insts to gather bads
     all_bads = dict()
     for inst in insts:
-        # using dictionary method to remove duplicates & preserve order
         all_bads.update(dict.fromkeys(inst.info["bads"]))
     all_bads = list(all_bads)
 

From 12b8e8480319a6a5bf8064f19371bfdaa6503eba Mon Sep 17 00:00:00 2001
From: Ana Radanovic <79697247+anaradanovic@users.noreply.github.com>
Date: Wed, 27 Sep 2023 15:37:09 -0400
Subject: [PATCH 28/38] Update mne/preprocessing/bads.py

Co-authored-by: Daniel McCloy <dan@mccloy.info>
---
 mne/preprocessing/bads.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/mne/preprocessing/bads.py b/mne/preprocessing/bads.py
index 00df9ba2988..ea6ba1fc9a7 100644
--- a/mne/preprocessing/bads.py
+++ b/mne/preprocessing/bads.py
@@ -110,7 +110,8 @@ def unify_bad_channels(insts):
             f" Mismatch channels are {diff_chns}"
         )
 
-    # then iterate through the insts to gather bads
+    # collect bads as dict keys so that insertion order is preserved
+    # then later cast to list.
     all_bads = dict()
     for inst in insts:
         all_bads.update(dict.fromkeys(inst.info["bads"]))

From 9cb0cf3a5215b1e087c3e365ca41f4674c2f6496 Mon Sep 17 00:00:00 2001
From: Ana Radanovic <radanovica@protonmail.com>
Date: Wed, 27 Sep 2023 16:30:05 -0400
Subject: [PATCH 29/38] further changes on unify_bad_channels

---
 doc/preprocessing.rst         |  1 +
 mne/channels/__init__.py      |  1 +
 mne/channels/channels.py      | 86 +++++++++++++++++++++++++++++++++++
 mne/preprocessing/__init__.py |  1 -
 mne/preprocessing/bads.py     | 79 +-------------------------------
 5 files changed, 89 insertions(+), 79 deletions(-)

diff --git a/doc/preprocessing.rst b/doc/preprocessing.rst
index 7c4e430780f..cbfda1ac49b 100644
--- a/doc/preprocessing.rst
+++ b/doc/preprocessing.rst
@@ -57,6 +57,7 @@ Projections:
    get_builtin_ch_adjacencies
    read_ch_adjacency
    equalize_channels
+   unify_bad_channels
    rename_channels
    generate_2d_layout
    make_1020_channel_selections
diff --git a/mne/channels/__init__.py b/mne/channels/__init__.py
index 13b002e5a59..3591d7aeeb4 100644
--- a/mne/channels/__init__.py
+++ b/mne/channels/__init__.py
@@ -22,6 +22,7 @@
             "_EEG_SELECTIONS",
             "_divide_to_regions",
             "get_builtin_ch_adjacencies",
+            "unify_bad_channels",
         ],
         "layout": [
             "Layout",
diff --git a/mne/channels/channels.py b/mne/channels/channels.py
index 0b022569ef5..7967b7633c7 100644
--- a/mne/channels/channels.py
+++ b/mne/channels/channels.py
@@ -5,6 +5,8 @@
 #          Andrew Dykstra <andrew.r.dykstra@gmail.com>
 #          Teon Brooks <teon.brooks@gmail.com>
 #          Daniel McCloy <dan.mccloy@gmail.com>
+#          Ana Radanovic <radanovica@protonmail.com>
+#          Erica Peterson <nordme@uw.edu>
 #
 # License: BSD-3-Clause
 
@@ -206,6 +208,90 @@ def equalize_channels(instances, copy=True, verbose=None):
     return equalized_instances
 
 
+def unify_bad_channels(insts):
+    """Unify bad channels across a list of instances, using the union.
+
+    Parameters
+    ----------
+    insts : list
+        List of instances (:class:`~mne.io.Raw`, :class:`~mne.Epochs`,
+        :class:`~mne.Evoked`, :class:`~mne.time_frequency.Spectrum`,
+        :class:`~mne.time_frequency.EpochSpectrum`) across which to unify bad channels.
+
+    Returns
+    -------
+    insts : list
+        List of instances with bad channels unified across instances.
+
+    See Also
+    --------
+    mne.channels.equalize_channels
+    mne.channels.rename_channels
+    mne.channels.combine_channels
+
+    Notes
+    -----
+    This function modifies the instances in-place.
+
+    .. versionadded:: 1.6
+    """
+    from ..utils import _validate_type
+
+    from ..io import BaseRaw
+    from ..epochs import Epochs
+    from ..evoked import Evoked
+    from ..time_frequency.spectrum import BaseSpectrum
+
+    # check that input is a list
+    _validate_type(insts, (list, tuple), "instance type")
+
+    # check input is not an empty list
+    if len(insts) == 0:
+        raise ValueError("Be sure insts is not empty list")
+
+    # first check that each object is mne object
+    inst_type = type(insts[0])
+    valid_types = (BaseRaw, Epochs, Evoked, BaseSpectrum)
+    for inst in insts:
+        _validate_type(inst, valid_types, "instance type")
+        if type(inst) != inst_type:
+            raise ValueError("All insts must be the same type")
+
+    # check that all channels have the same name and same number
+    ch_names = insts[0].ch_names
+    diff_chns = []
+    for inst in insts[1:]:
+        if inst.ch_names != ch_names:
+            dif = set(inst.ch_names) ^ (set(ch_names))
+            diff_chns.extend(list(dif))
+            if ch_names.sort() == inst.ch_names.sort():
+                raise ValueError(
+                    "Channel names are sorted differently across"
+                    "instances. Please use"
+                    "mne.channels.equalize_channels."
+                )
+
+    if len(diff_chns) > 0:
+        raise ValueError(
+            "Channel names are not consistent across instances. Be sure"
+            "consistent naming is used across channels. Mismatched channels"
+            f"are {diff_chns}"
+        )
+
+    # collect bads as dict keys so that insertion order is preserved
+    # then later cast to list.
+    all_bads = dict()
+    for inst in insts:
+        all_bads.update(dict.fromkeys(inst.info["bads"]))
+    all_bads = list(all_bads)
+
+    # apply bads set to all instances
+    for inst in insts:
+        inst.info["bads"] = all_bads
+
+    return insts
+
+
 class ReferenceMixin(MontageMixin):
     """Mixin class for Raw, Evoked, Epochs."""
 
diff --git a/mne/preprocessing/__init__.py b/mne/preprocessing/__init__.py
index 6d818ac60b0..8358f006e09 100644
--- a/mne/preprocessing/__init__.py
+++ b/mne/preprocessing/__init__.py
@@ -56,6 +56,5 @@
         "interpolate": ["equalize_bads", "interpolate_bridged_electrodes"],
         "_css": ["cortical_signal_suppression"],
         "hfc": ["compute_proj_hfc"],
-        "bads": ["unify_bad_channels"],
     },
 )
diff --git a/mne/preprocessing/bads.py b/mne/preprocessing/bads.py
index ea6ba1fc9a7..8b7e23a3484 100644
--- a/mne/preprocessing/bads.py
+++ b/mne/preprocessing/bads.py
@@ -1,20 +1,11 @@
 # Authors: Denis Engemann <denis.engemann@gmail.com>
-#          Ana Radanovic <radanovica@protonmail.com>
-#          Erica Peterson <nordme@uw.edu>
+#
 # License: BSD-3-Clause
 
 import numpy as np
 from scipy.stats import zscore
 
 
-from ..utils import _validate_type
-
-from ..io import BaseRaw
-from ..epochs import Epochs
-from ..evoked import Evoked
-from ..time_frequency.spectrum import BaseSpectrum
-
-
 def _find_outliers(X, threshold=3.0, max_iter=2, tail=0):
     """Find outliers based on iterated Z-scoring.
 
@@ -57,71 +48,3 @@ def _find_outliers(X, threshold=3.0, max_iter=2, tail=0):
 
     bad_idx = np.where(my_mask)[0]
     return bad_idx
-
-
-def unify_bad_channels(insts):
-    """Unify bad channels across a list of instances, using the union.
-
-    Parameters
-    ----------
-    insts : list
-        List of instances (:class:`~mne.io.Raw`, :class:`~mne.Epochs`,
-        :class:`~mne.Evoked`, :class:`~mne.time_frequency.Spectrum`,
-        :class:`~mne.time_frequency.EpochSpectrum`) across which to unify bad channels.
-
-    Returns
-    -------
-    insts : list
-        List of instances with bad channels unified across instances.
-
-    Notes
-    -----
-    This function operates in-place.
-
-    .. versionadded:: 1.6
-    """
-    # check input is not an empty list
-    if len(insts) == 0:
-        raise ValueError("Be sure insts is not empty list")
-
-    # first check that each object is mne object
-    inst_type = type(insts[0])
-    valid_types = (BaseRaw, Epochs, Evoked, BaseSpectrum)
-    for inst in insts:
-        _validate_type(inst, valid_types, "instance type")
-        if type(inst) != inst_type:
-            raise ValueError("All insts must be the same type")
-
-    # check that input is a list
-    if not isinstance(insts, list):
-        raise ValueError(f"insts must be a *list* of mne objects, got {type(insts)}")
-
-    # check that all channels have the same name and same number
-    ch_names = insts[0].ch_names
-    diff_chns = []
-    for inst in insts[1:]:
-        if inst.ch_names != ch_names:
-            dif = set(inst.info.ch_names) ^ (set(ch_names))
-            diff_chns.extend(list(dif))
-
-    if len(diff_chns) > 0:
-        raise ValueError(
-            "Channel names are not consistent across instances."
-            f" Mismatch channels are {diff_chns}"
-        )
-
-    # collect bads as dict keys so that insertion order is preserved
-    # then later cast to list.
-    all_bads = dict()
-    for inst in insts:
-        all_bads.update(dict.fromkeys(inst.info["bads"]))
-    all_bads = list(all_bads)
-
-    # apply bads set to all instances
-    new_insts = []
-
-    for inst in insts:
-        inst.info["bads"] = all_bads
-        new_insts.append(inst)
-
-    return new_insts

From 52c4d21d93b1bb4df41f2c247bd9e6183a7b65e3 Mon Sep 17 00:00:00 2001
From: Daniel McCloy <dan@mccloy.info>
Date: Wed, 27 Sep 2023 16:15:47 -0500
Subject: [PATCH 30/38] Apply suggestions from code review

---
 mne/channels/channels.py  | 48 ++++++++++++++++-----------------------
 mne/preprocessing/bads.py |  1 -
 2 files changed, 19 insertions(+), 30 deletions(-)

diff --git a/mne/channels/channels.py b/mne/channels/channels.py
index 7967b7633c7..18291cdece4 100644
--- a/mne/channels/channels.py
+++ b/mne/channels/channels.py
@@ -209,8 +209,11 @@ def equalize_channels(instances, copy=True, verbose=None):
 
 
 def unify_bad_channels(insts):
-    """Unify bad channels across a list of instances, using the union.
+    """Unify bad channels across a list of instances.
 
+    All instances must be of the same type and have matching channel names and channel
+    order. The ``.info["bads"]`` of each instance will be set to the union of
+    ``.info["bads"]`` across all instances.
     Parameters
     ----------
     insts : list
@@ -235,21 +238,17 @@ def unify_bad_channels(insts):
 
     .. versionadded:: 1.6
     """
-    from ..utils import _validate_type
-
     from ..io import BaseRaw
     from ..epochs import Epochs
     from ..evoked import Evoked
     from ..time_frequency.spectrum import BaseSpectrum
 
-    # check that input is a list
+    # ensure input is list-like
     _validate_type(insts, (list, tuple), "instance type")
-
-    # check input is not an empty list
+    # ensure non-empty
     if len(insts) == 0:
         raise ValueError("Be sure insts is not empty list")
-
-    # first check that each object is mne object
+    # ensure all insts are MNE objects, and all the same type
     inst_type = type(insts[0])
     valid_types = (BaseRaw, Epochs, Evoked, BaseSpectrum)
     for inst in insts:
@@ -257,35 +256,26 @@ def unify_bad_channels(insts):
         if type(inst) != inst_type:
             raise ValueError("All insts must be the same type")
 
-    # check that all channels have the same name and same number
+    # ensure all insts have the same channels and channel order
     ch_names = insts[0].ch_names
-    diff_chns = []
     for inst in insts[1:]:
-        if inst.ch_names != ch_names:
-            dif = set(inst.ch_names) ^ (set(ch_names))
-            diff_chns.extend(list(dif))
-            if ch_names.sort() == inst.ch_names.sort():
-                raise ValueError(
-                    "Channel names are sorted differently across"
-                    "instances. Please use"
-                    "mne.channels.equalize_channels."
-                )
-
-    if len(diff_chns) > 0:
-        raise ValueError(
-            "Channel names are not consistent across instances. Be sure"
-            "consistent naming is used across channels. Mismatched channels"
-            f"are {diff_chns}"
-        )
+        dif = set(inst.ch_names) ^ set(ch_names)
+        if len(dif):
+            # TODO raise error, we know some chs need to be dropped
+            raise ValueError("")
+        elif inst.ch_names != ch_names:
+            raise ValueError(
+                "Channel names are sorted differently across instances. Please use "
+                "mne.channels.equalize_channels."
+            )
 
-    # collect bads as dict keys so that insertion order is preserved
-    # then later cast to list.
+    # collect bads as dict keys so that insertion order is preserved, then cast to list
     all_bads = dict()
     for inst in insts:
         all_bads.update(dict.fromkeys(inst.info["bads"]))
     all_bads = list(all_bads)
 
-    # apply bads set to all instances
+    # update bads on all instances
     for inst in insts:
         inst.info["bads"] = all_bads
 
diff --git a/mne/preprocessing/bads.py b/mne/preprocessing/bads.py
index 8b7e23a3484..077145ff7c8 100644
--- a/mne/preprocessing/bads.py
+++ b/mne/preprocessing/bads.py
@@ -1,5 +1,4 @@
 # Authors: Denis Engemann <denis.engemann@gmail.com>
-#
 # License: BSD-3-Clause
 
 import numpy as np

From 83407f6c918cb6e651760be062730e503681bda9 Mon Sep 17 00:00:00 2001
From: nordme <nordme@uw.edu>
Date: Wed, 27 Sep 2023 14:19:05 -0700
Subject: [PATCH 31/38] fixes for Ana fixes

---
 mne/preprocessing/tests/test_unify_bads.py | 40 ++++++++++------------
 1 file changed, 18 insertions(+), 22 deletions(-)

diff --git a/mne/preprocessing/tests/test_unify_bads.py b/mne/preprocessing/tests/test_unify_bads.py
index d5fe4f2b849..1788d863849 100644
--- a/mne/preprocessing/tests/test_unify_bads.py
+++ b/mne/preprocessing/tests/test_unify_bads.py
@@ -1,33 +1,26 @@
-import numpy as np
 import pytest
-
-from mne.preprocessing import unify_bad_channels
-from mne.time_frequency.tests.test_spectrum import _get_inst
-
-
-@pytest.mark.parametrize(
-    "instance", ("raw", "epochs", "evoked", "raw_spectrum", "epochs_spectrum")
-)
-def test_instance_support(instance, request, evoked):
-    """Tests support of different classes."""
-    # test unify_bads function on instance (single input, no bads scenario)
-    inst = _get_inst(instance, request, evoked)
-    inst_out = unify_bad_channels([inst])
-    assert inst_out == [inst]
+from mne.channels import unify_bad_channels
 
 
 def test_error_raising(raw, epochs):
     """Tests input checking."""
+    with pytest.raises(TypeError, match=r"must be an instance of list"):
+        unify_bad_channels("bad input")
     with pytest.raises(ValueError, match=r"empty list"):
         unify_bad_channels([])
     with pytest.raises(TypeError, match=r"must be an instance of"):
         unify_bad_channels(["bad_instance"])
     with pytest.raises(ValueError, match=r"same type"):
         unify_bad_channels([raw, epochs])
-    with pytest.raises(ValueError):
-        raw_alt = raw.copy()
-        raw_alt.drop_channels(raw.info["ch_names"][0])
-        unify_bad_channels([raw, raw_alt])
+    with pytest.raises(ValueError, match=r"sorted differently"):
+        raw_alt1 = raw.copy()
+        raw_alt1.drop_channels(raw.info["ch_names"][-1])
+        unify_bad_channels([raw, raw_alt1])  # ch diff preserving order
+    with pytest.raises(ValueError, match=r"not consistent"):
+        raw_alt2 = raw.copy()
+        new_order = [raw.info["ch_names"][-1]] + raw.info["ch_names"][:-1]
+        raw_alt2.reorder_channels(new_order)
+        unify_bad_channels([raw, raw_alt2])
 
 
 def test_bads_compilation(raw):
@@ -37,6 +30,9 @@ def test_bads_compilation(raw):
     bad, and b) multiple instances passed to function with varying compilation
     scenarios including empty bads, unique bads, and partially duplicated bads
     listed out-of-order.
+
+    Only the Raw instance type is tested, since bad channel implementation is
+    controlled across instance types with a MixIn class.
     """
     assert raw.info["bads"] == []
     chns = raw.info["ch_names"][0:3]
@@ -47,11 +43,11 @@ def test_bads_compilation(raw):
     three_bad.info["bads"] = chns
     # scenario 1: single instance passed with actual bads
     s_out = unify_bad_channels([one_bad])
-    assert len(s_out) == 1
+    assert len(s_out) == 1, len(s_out)
     assert s_out[0].info["bads"] == [chns[1]], (s_out[0].info["bads"], chns[1])
     # scenario 2: multiple instances passed
     m_out = unify_bad_channels([one_bad, no_bad, three_bad])
-    assert len(m_out) == 3
+    assert len(m_out) == 3, len(m_out)
     correct_bads = [chns[1], chns[0], chns[2]]
-    for i in np.arange(len(m_out)):
+    for i in range(len(m_out)):
         assert m_out[i].info["bads"] == correct_bads

From df45b8640d21c0978740bcf67e823e4392b039dc Mon Sep 17 00:00:00 2001
From: nordme <nordme@uw.edu>
Date: Wed, 27 Sep 2023 14:24:23 -0700
Subject: [PATCH 32/38] move tests file

---
 mne/{preprocessing => channels}/tests/test_unify_bads.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename mne/{preprocessing => channels}/tests/test_unify_bads.py (100%)

diff --git a/mne/preprocessing/tests/test_unify_bads.py b/mne/channels/tests/test_unify_bads.py
similarity index 100%
rename from mne/preprocessing/tests/test_unify_bads.py
rename to mne/channels/tests/test_unify_bads.py

From 8b37d1eea4f0c89129c85d46ff91bfd8e1f75043 Mon Sep 17 00:00:00 2001
From: Daniel McCloy <dan@mccloy.info>
Date: Wed, 27 Sep 2023 16:26:35 -0500
Subject: [PATCH 33/38] Update mne/channels/channels.py

---
 mne/channels/channels.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/mne/channels/channels.py b/mne/channels/channels.py
index 18291cdece4..5cb3d22c3e1 100644
--- a/mne/channels/channels.py
+++ b/mne/channels/channels.py
@@ -214,6 +214,7 @@ def unify_bad_channels(insts):
     All instances must be of the same type and have matching channel names and channel
     order. The ``.info["bads"]`` of each instance will be set to the union of
     ``.info["bads"]`` across all instances.
+
     Parameters
     ----------
     insts : list

From b7834d5fb8aadb20a124bfc7f77fcc87300f2b55 Mon Sep 17 00:00:00 2001
From: Daniel McCloy <dan@mccloy.info>
Date: Wed, 27 Sep 2023 16:43:15 -0500
Subject: [PATCH 34/38] Apply more suggestions from code review

---
 mne/channels/channels.py | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/mne/channels/channels.py b/mne/channels/channels.py
index 5cb3d22c3e1..194d3fa08a8 100644
--- a/mne/channels/channels.py
+++ b/mne/channels/channels.py
@@ -245,15 +245,15 @@ def unify_bad_channels(insts):
     from ..time_frequency.spectrum import BaseSpectrum
 
     # ensure input is list-like
-    _validate_type(insts, (list, tuple), "instance type")
+    _validate_type(insts, (list, tuple), "insts")
     # ensure non-empty
     if len(insts) == 0:
-        raise ValueError("Be sure insts is not empty list")
+        raise ValueError("insts must not be empty")
     # ensure all insts are MNE objects, and all the same type
     inst_type = type(insts[0])
     valid_types = (BaseRaw, Epochs, Evoked, BaseSpectrum)
     for inst in insts:
-        _validate_type(inst, valid_types, "instance type")
+        _validate_type(inst, valid_types, "each object in insts")
         if type(inst) != inst_type:
             raise ValueError("All insts must be the same type")
 
@@ -262,8 +262,10 @@ def unify_bad_channels(insts):
     for inst in insts[1:]:
         dif = set(inst.ch_names) ^ set(ch_names)
         if len(dif):
-            # TODO raise error, we know some chs need to be dropped
-            raise ValueError("")
+            raise ValueError(
+                "Channels do not match across the objects in insts. Consider calling "
+                "equalize_channels before calling this function."
+            )
         elif inst.ch_names != ch_names:
             raise ValueError(
                 "Channel names are sorted differently across instances. Please use "

From 0309925780066f87edc055596e689b34cec26452 Mon Sep 17 00:00:00 2001
From: nordme <38704848+nordme@users.noreply.github.com>
Date: Wed, 27 Sep 2023 14:58:06 -0700
Subject: [PATCH 35/38] Apply suggestions from code review

Co-authored-by: Daniel McCloy <dan@mccloy.info>
---
 mne/channels/tests/test_unify_bads.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/mne/channels/tests/test_unify_bads.py b/mne/channels/tests/test_unify_bads.py
index 1788d863849..771a52af51c 100644
--- a/mne/channels/tests/test_unify_bads.py
+++ b/mne/channels/tests/test_unify_bads.py
@@ -8,17 +8,17 @@ def test_error_raising(raw, epochs):
         unify_bad_channels("bad input")
     with pytest.raises(ValueError, match=r"empty list"):
         unify_bad_channels([])
-    with pytest.raises(TypeError, match=r"must be an instance of"):
+    with pytest.raises(TypeError, match=r"each object in insts must be an instance of"):
         unify_bad_channels(["bad_instance"])
     with pytest.raises(ValueError, match=r"same type"):
         unify_bad_channels([raw, epochs])
-    with pytest.raises(ValueError, match=r"sorted differently"):
+    with pytest.raises(ValueError, match=r"Channels do not match across"):
         raw_alt1 = raw.copy()
         raw_alt1.drop_channels(raw.info["ch_names"][-1])
         unify_bad_channels([raw, raw_alt1])  # ch diff preserving order
-    with pytest.raises(ValueError, match=r"not consistent"):
+    with pytest.raises(ValueError, match=r"sorted differently"):
         raw_alt2 = raw.copy()
-        new_order = [raw.info["ch_names"][-1]] + raw.info["ch_names"][:-1]
+        new_order = [raw.ch_names[-1]] + raw.ch_names[:-1]
         raw_alt2.reorder_channels(new_order)
         unify_bad_channels([raw, raw_alt2])
 
@@ -35,7 +35,7 @@ def test_bads_compilation(raw):
     controlled across instance types with a MixIn class.
     """
     assert raw.info["bads"] == []
-    chns = raw.info["ch_names"][0:3]
+    chns = raw.ch_names[:3]
     no_bad = raw.copy()
     one_bad = raw.copy()
     one_bad.info["bads"] = [chns[1]]
@@ -48,6 +48,6 @@ def test_bads_compilation(raw):
     # scenario 2: multiple instances passed
     m_out = unify_bad_channels([one_bad, no_bad, three_bad])
     assert len(m_out) == 3, len(m_out)
-    correct_bads = [chns[1], chns[0], chns[2]]
-    for i in range(len(m_out)):
-        assert m_out[i].info["bads"] == correct_bads
+    expected_order = [chns[1], chns[0], chns[2]]
+    for inst in m_out:
+        assert inst.info["bads"] == expected_order

From 6c610d1b341abd0ba89b24b3ab46d3503e85c2ea Mon Sep 17 00:00:00 2001
From: nordme <nordme@uw.edu>
Date: Wed, 27 Sep 2023 15:01:58 -0700
Subject: [PATCH 36/38] pytest fix

---
 mne/channels/tests/test_unify_bads.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mne/channels/tests/test_unify_bads.py b/mne/channels/tests/test_unify_bads.py
index 771a52af51c..ac04983802b 100644
--- a/mne/channels/tests/test_unify_bads.py
+++ b/mne/channels/tests/test_unify_bads.py
@@ -6,7 +6,7 @@ def test_error_raising(raw, epochs):
     """Tests input checking."""
     with pytest.raises(TypeError, match=r"must be an instance of list"):
         unify_bad_channels("bad input")
-    with pytest.raises(ValueError, match=r"empty list"):
+    with pytest.raises(ValueError, match=r"insts must not be empty"):
         unify_bad_channels([])
     with pytest.raises(TypeError, match=r"each object in insts must be an instance of"):
         unify_bad_channels(["bad_instance"])

From 292c3e400a6af8b20b62ee8fa971e68443144314 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Thu, 28 Sep 2023 09:46:45 -0400
Subject: [PATCH 37/38] Update mne/channels/channels.py

---
 mne/channels/channels.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mne/channels/channels.py b/mne/channels/channels.py
index 194d3fa08a8..7c3de44fdd8 100644
--- a/mne/channels/channels.py
+++ b/mne/channels/channels.py
@@ -220,7 +220,7 @@ def unify_bad_channels(insts):
     insts : list
         List of instances (:class:`~mne.io.Raw`, :class:`~mne.Epochs`,
         :class:`~mne.Evoked`, :class:`~mne.time_frequency.Spectrum`,
-        :class:`~mne.time_frequency.EpochSpectrum`) across which to unify bad channels.
+        :class:`~mne.time_frequency.EpochsSpectrum`) across which to unify bad channels.
 
     Returns
     -------

From 7f80011f6b94e1e2e2a2ca25f41a425ae84c5e61 Mon Sep 17 00:00:00 2001
From: Ana Radanovic <radanovica@protonmail.com>
Date: Thu, 28 Sep 2023 12:20:19 -0400
Subject: [PATCH 38/38] tst:ping CIs