diff --git a/jdaviz/configs/cubeviz/plugins/parsers.py b/jdaviz/configs/cubeviz/plugins/parsers.py
index 017cde1264..9cce81d361 100644
--- a/jdaviz/configs/cubeviz/plugins/parsers.py
+++ b/jdaviz/configs/cubeviz/plugins/parsers.py
@@ -1,4 +1,3 @@
-import logging
 import os
 import warnings
 
@@ -282,12 +281,12 @@ def _parse_hdulist(app, hdulist, file_name=None,
             try:
                 flux_unit = u.Unit(hdu.header['BUNIT'])
             except Exception:
-                logging.warning("Invalid BUNIT, using count as data unit")
+                warnings.warn("Invalid BUNIT, using count as data unit", UserWarning)
                 flux_unit = u.count
         elif data_type == 'mask':  # DQ flags have no unit
             flux_unit = u.dimensionless_unscaled
         else:
-            logging.warning("Invalid BUNIT, using count as data unit")
+            warnings.warn("Invalid BUNIT, using count as data unit", UserWarning)
             flux_unit = u.count
 
         flux = hdu.data << flux_unit
diff --git a/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py b/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py
index 2cc950a742..65f09f9e57 100644
--- a/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py
+++ b/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_helper.py
@@ -1,3 +1,4 @@
+import pytest
 from specutils import SpectralRegion
 
 from jdaviz import Cubeviz
@@ -17,6 +18,8 @@ def test_nested_helper(cubeviz_helper):
     assert spec_viewer.jdaviz_helper == cubeviz_helper
 
 
+# Some API might be going through deprecation, so ignore the warning.
+@pytest.mark.filterwarnings("ignore::DeprecationWarning")
 def test_plugin_user_apis(cubeviz_helper):
     for plugin_name, plugin_api in cubeviz_helper.plugins.items():
         plugin = plugin_api._obj
diff --git a/jdaviz/configs/default/plugins/plot_options/plot_options.py b/jdaviz/configs/default/plugins/plot_options/plot_options.py
index 526ad276e2..a1a011ebf4 100644
--- a/jdaviz/configs/default/plugins/plot_options/plot_options.py
+++ b/jdaviz/configs/default/plugins/plot_options/plot_options.py
@@ -1,14 +1,11 @@
-import logging
 import math
 import os
+import warnings
+
 import matplotlib
 import numpy as np
-
-from astropy.visualization import ManualInterval, ContrastBiasStretch
-
 from echo import delay_callback
-from traitlets import Any, Dict, Float, Bool, Int, List, Unicode, observe
-
+from astropy.visualization import ManualInterval, ContrastBiasStretch
 from glue.core.subset_group import GroupedSubset
 from glue.config import stretches as glue_stretches
 from glue.viewers.scatter.state import ScatterViewerState
@@ -18,6 +15,8 @@
 from glue.viewers.image.composite_array import COLOR_CONVERTER
 from glue_jupyter.bqplot.image.state import BqplotImageLayerState
 from glue_jupyter.common.toolbar_vuetify import read_icon
+from scipy.interpolate import PchipInterpolator
+from traitlets import Any, Dict, Float, Bool, Int, List, Unicode, observe
 
 from jdaviz.core.registries import tray_registry
 from jdaviz.core.template_mixin import (PluginTemplateMixin, ViewerSelectMixin, LayerSelect,
@@ -30,9 +29,6 @@
 # by importing from utils, glue_colormaps will include the custom Random colormap
 from jdaviz.utils import is_not_wcs_only, cmap_samples, glue_colormaps
 
-
-from scipy.interpolate import PchipInterpolator
-
 __all__ = ['PlotOptions']
 
 RANDOM_SUBSET_SIZE = 10_000
@@ -663,12 +659,18 @@ def user_api(self):
 
     @property
     def multiselect(self):
-        logging.warning(f"DeprecationWarning: multiselect has been replaced by separate viewer_multiselect and layer_multiselect and will be removed in the future.  This currently evaluates viewer_multiselect or layer_multiselect")  # noqa
+        warnings.warn(
+            "multiselect has been replaced by separate viewer_multiselect and "
+            "layer_multiselect and will be removed in the future. "
+            "This currently evaluates viewer_multiselect or layer_multiselect", DeprecationWarning)
         return self.viewer_multiselect or self.layer_multiselect
 
     @multiselect.setter
     def multiselect(self, value):
-        logging.warning(f"DeprecationWarning: multiselect has been replaced by separate viewer_multiselect and layer_multiselect and will be removed in the future.  This currently sets viewer_multiselect and layer_multiselect")  # noqa
+        warnings.warn(
+            "multiselect has been replaced by separate viewer_multiselect and "
+            "layer_multiselect and will be removed in the future. "
+            "This currently sets viewer_multiselect and layer_multiselect", DeprecationWarning)
         self.viewer_multiselect = value
         self.layer_multiselect = value
 
diff --git a/jdaviz/configs/default/plugins/plot_options/tests/test_plot_options.py b/jdaviz/configs/default/plugins/plot_options/tests/test_plot_options.py
index db18a7e16b..6631cf5337 100644
--- a/jdaviz/configs/default/plugins/plot_options/tests/test_plot_options.py
+++ b/jdaviz/configs/default/plugins/plot_options/tests/test_plot_options.py
@@ -346,7 +346,8 @@ def test_track_mixed_states(imviz_helper):
         po.image_color.value = rgb_colors[i]
 
     # Switch to multiselect to test mixing and unmixing of states
-    po.multiselect = True
+    po.viewer_multiselect = True
+    po.layer_multiselect = True
     po.viewer_selected = ["imviz-0", "imviz-1"]
     assert po.layer.items[-1]["label"] == "array_2"
     # The corresponding layer in each viewer is the same color,
diff --git a/jdaviz/configs/imviz/tests/test_helper.py b/jdaviz/configs/imviz/tests/test_helper.py
index f2e4410cb7..73a762f13f 100644
--- a/jdaviz/configs/imviz/tests/test_helper.py
+++ b/jdaviz/configs/imviz/tests/test_helper.py
@@ -1,6 +1,9 @@
 import numpy as np
+import pytest
 
 
+# Some API might be going through deprecation, so ignore the warning.
+@pytest.mark.filterwarnings("ignore::DeprecationWarning")
 def test_plugin_user_apis(imviz_helper):
     for plugin_name, plugin_api in imviz_helper.plugins.items():
         plugin = plugin_api._obj
diff --git a/jdaviz/configs/imviz/tests/test_viewers.py b/jdaviz/configs/imviz/tests/test_viewers.py
index c948a96e2c..da226fb165 100644
--- a/jdaviz/configs/imviz/tests/test_viewers.py
+++ b/jdaviz/configs/imviz/tests/test_viewers.py
@@ -27,7 +27,8 @@ def test_create_destroy_viewer(imviz_helper, desired_name, actual_name):
     assert sorted(imviz_helper.plugins['Compass'].viewer.labels) == viewer_names
 
     po = imviz_helper.plugins['Plot Options']
-    po.multiselect = True
+    po.viewer_multiselect = True
+    po.layer_multiselect = True
     po.viewer = viewer_names
 
     imviz_helper.destroy_viewer(actual_name)
diff --git a/jdaviz/configs/mosviz/tests/test_helper.py b/jdaviz/configs/mosviz/tests/test_helper.py
index a55031b741..918df5de3a 100644
--- a/jdaviz/configs/mosviz/tests/test_helper.py
+++ b/jdaviz/configs/mosviz/tests/test_helper.py
@@ -115,6 +115,8 @@ def test_redshift_column(mosviz_helper, mos_image, spectrum1d, mos_spectrum2d):
     assert_allclose(mosviz_helper.get_spectrum_1d(apply_slider_redshift=True, row=1).redshift.value, 0.0)  # noqa: E501
 
 
+# Some API might be going through deprecation, so ignore the warning.
+@pytest.mark.filterwarnings("ignore::DeprecationWarning")
 def test_plugin_user_apis(mosviz_helper):
     for plugin_name, plugin_api in mosviz_helper.plugins.items():
         plugin = plugin_api._obj
diff --git a/jdaviz/configs/rampviz/plugins/parsers.py b/jdaviz/configs/rampviz/plugins/parsers.py
index 4d30c8c90a..d1a43f8b6f 100644
--- a/jdaviz/configs/rampviz/plugins/parsers.py
+++ b/jdaviz/configs/rampviz/plugins/parsers.py
@@ -1,5 +1,6 @@
-import logging
 import os
+import warnings
+
 import numpy as np
 import astropy.units as u
 from astropy.io import fits
@@ -277,10 +278,10 @@ def _parse_hdulist(
         try:
             flux_unit = u.Unit(hdu.header['BUNIT'])
         except Exception:
-            logging.warning("Invalid BUNIT, using DN as data unit")
+            warnings.warn("Invalid BUNIT, using DN as data unit", UserWarning)
             flux_unit = u.DN
     else:
-        logging.warning("Invalid BUNIT, using DN as data unit")
+        warnings.warn("Invalid BUNIT, using DN as data unit", UserWarning)
         flux_unit = u.DN
 
     # index the ramp array by the integration to load. returns all groups and pixels.
diff --git a/jdaviz/configs/specviz/tests/test_helper.py b/jdaviz/configs/specviz/tests/test_helper.py
index 3c0f7f5223..1163bd7fde 100644
--- a/jdaviz/configs/specviz/tests/test_helper.py
+++ b/jdaviz/configs/specviz/tests/test_helper.py
@@ -454,6 +454,8 @@ def test_plot_uncertainties(specviz_helper, spectrum1d):
     assert len([m for m in specviz_viewer.figure.marks if isinstance(m, LineUncertainties)]) == 0
 
 
+# Some API might be going through deprecation, so ignore the warning.
+@pytest.mark.filterwarnings("ignore::DeprecationWarning")
 def test_plugin_user_apis(specviz_helper):
     for plugin_name, plugin_api in specviz_helper.plugins.items():
         plugin = plugin_api._obj
diff --git a/jdaviz/configs/specviz2d/tests/test_helper.py b/jdaviz/configs/specviz2d/tests/test_helper.py
index a6eb3a203b..2090d720b8 100644
--- a/jdaviz/configs/specviz2d/tests/test_helper.py
+++ b/jdaviz/configs/specviz2d/tests/test_helper.py
@@ -1,4 +1,6 @@
+import pytest
 from specutils import Spectrum1D
+
 from jdaviz import Specviz
 
 
@@ -13,6 +15,8 @@ def test_helper(specviz2d_helper, mos_spectrum2d):
     assert isinstance(returned_data, Spectrum1D)
 
 
+# Some API might be going through deprecation, so ignore the warning.
+@pytest.mark.filterwarnings("ignore::DeprecationWarning")
 def test_plugin_user_apis(specviz2d_helper):
     for plugin_name, plugin_api in specviz2d_helper.plugins.items():
         plugin = plugin_api._obj
diff --git a/jdaviz/core/template_mixin.py b/jdaviz/core/template_mixin.py
index 4bfeaebee0..4b5136cf16 100644
--- a/jdaviz/core/template_mixin.py
+++ b/jdaviz/core/template_mixin.py
@@ -1,20 +1,19 @@
-from astropy.coordinates.sky_coordinate import SkyCoord
-from astropy.nddata import NDData
-from astropy.table import QTable
-from astropy.table.row import Row as QTableRow
-import astropy.units as u
-import bqplot
-from contextlib import contextmanager
-import numpy as np
 import inspect
-import logging
 import os
 import threading
 import time
 import warnings
+from contextlib import contextmanager
+from functools import cached_property
 
+import astropy.units as u
+import bqplot
+import numpy as np
+from astropy.coordinates.sky_coordinate import SkyCoord
+from astropy.nddata import NDData
+from astropy.table import QTable
+from astropy.table.row import Row as QTableRow
 from echo import delay_callback
-from functools import cached_property
 from ipyvuetify import VuetifyTemplate
 from glue.config import colormaps
 from glue.core import Data, HubListener
@@ -31,16 +30,15 @@
 from glue_jupyter.bqplot.image import BqplotImageView
 from glue_jupyter.registries import viewer_registry
 from glue_jupyter.widgets.linked_dropdown import get_choices as _get_glue_choices
+from ipywidgets import widget_serialization
+from ipypopout import PopoutButton
+from ipypopout.popout_button import get_kernel_id
 from photutils.aperture import CircularAperture, EllipticalAperture, RectangularAperture
 from regions import PixelRegion
 from specutils import Spectrum1D
 from specutils.manipulation import extract_region
 from traitlets import Any, Bool, Dict, Float, HasTraits, List, Unicode, observe
 
-from ipywidgets import widget_serialization
-from ipypopout import PopoutButton
-from ipypopout.popout_button import get_kernel_id
-
 from jdaviz.components.toolbar_nested import NestedJupyterToolbar
 from jdaviz.configs.cubeviz.plugins.viewers import WithSliceIndicator
 from jdaviz.core.custom_traitlets import FloatHandleEmpty
@@ -472,8 +470,11 @@ def get_api_text(name, obj):
             if type(obj).__name__ == 'method':
                 return f"{name}{inspect.signature(obj)}"
             return name
-        self.api_methods = sorted([get_api_text(name, obj)
-                                   for name, obj in inspect.getmembers(self.user_api)])
+        with warnings.catch_warnings():
+            # Some API might be going through deprecation, so ignore the warning.
+            warnings.filterwarnings("ignore", category=DeprecationWarning)
+            self.api_methods = sorted([get_api_text(name, obj)
+                                       for name, obj in inspect.getmembers(self.user_api)])
 
     def new(self):
         new = self.__class__(app=self.app)
@@ -4522,7 +4523,7 @@ def _on_value_changed(self, msg):
             setattr(self.plugin, self._spinner, True)
 
         if self._glue_name == 'color_mode' and msg['new'] == 'Monochromatic':
-            logging.warning("DeprecationWarning: 'Monochromatic' renamed to 'Color'")
+            warnings.warn("'Monochromatic' renamed to 'Color'", DeprecationWarning)
             self.value = 'One color per layer'
             return
 
diff --git a/jdaviz/core/user_api.py b/jdaviz/core/user_api.py
index b4ed875481..a98d5c654c 100644
--- a/jdaviz/core/user_api.py
+++ b/jdaviz/core/user_api.py
@@ -1,4 +1,5 @@
-import logging
+import warnings
+
 import astropy.units as u
 
 __all__ = ['UserApiWrapper', 'PluginUserApi', 'ViewerUserApi']
@@ -36,7 +37,7 @@ def __getattr__(self, attr):
             return super().__getattribute__(attr)
 
         if attr in self._deprecated:
-            logging.warning("DeprecationWarning: %s is deprecated" % attr)
+            warnings.warn(f"{attr} is deprecated", DeprecationWarning)
 
         exp_obj = getattr(self._obj, attr)
         return getattr(exp_obj, 'user_api', exp_obj)
@@ -141,7 +142,7 @@ def __init__(self, plugin, expose=[], readonly=[], excl_from_dict=[], deprecated
 
     def __repr__(self):
         if self._deprecation_msg:
-            logging.warning("DeprecationWarning: %s" % self._deprecation_msg)
+            warnings.warn(self._deprecation_msg, DeprecationWarning)
             super().__setattr__('_deprecation_msg', None)
         return f'<{self._obj._registry_label} API>'
 
@@ -164,12 +165,12 @@ def __repr__(self):
 
     def __getattr__(self, *args, **kwargs):
         if super().__getattr__('_deprecation_msg'):
-            logging.warning(f"DeprecationWarning: {self._deprecation_msg}")
+            warnings.warn(self._deprecation_msg, DeprecationWarning)
             super().__setattr__('_deprecation_msg', None)
         return super().__getattr__(*args, **kwargs)
 
     def __setattr__(self, *args, **kwargs):
         if hasattr(self, '_deprecation_msg') and self._deprecation_msg:
-            logging.warning(f"DeprecationWarning: {self._deprecation_msg}")
+            warnings.warn(self._deprecation_msg, DeprecationWarning)
             super().__setattr__('_deprecation_msg', None)
         return super().__setattr__(*args, **kwargs)