From c87929631838d30283042e631f1e893373966b39 Mon Sep 17 00:00:00 2001
From: Kyle Conroy <kyleconroy@gmail.com>
Date: Wed, 5 Apr 2023 14:51:14 -0400
Subject: [PATCH 01/12] fix error raised when spectrum uncertainty is None

---
 jdaviz/core/helpers.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/jdaviz/core/helpers.py b/jdaviz/core/helpers.py
index cda5e91d20..5b988a1a89 100644
--- a/jdaviz/core/helpers.py
+++ b/jdaviz/core/helpers.py
@@ -418,10 +418,11 @@ def _handle_display_units(data, use_display_units):
                     flux_unit = self.app._get_display_unit('flux')
                     # TODO: any other attributes (meta, wcs, etc)?
                     # TODO: implement uncertainty.to upstream
+                    new_uncert = data.uncertainty.__class__(data.uncertainty.quantity.to(flux_unit)) if data.uncertainty is not None else None  # noqa
                     data = Spectrum1D(spectral_axis=data.spectral_axis.to(spectral_unit,
                                                                           u.spectral()),
                                       flux=data.flux.to(flux_unit),
-                                      uncertainty=data.uncertainty.__class__(data.uncertainty.quantity.to(flux_unit)))  # noqa
+                                      uncertainty=new_uncert)
                 else:  # pragma: nocover
                     raise NotImplementedError(f"converting {data.__class__.__name__} to display units is not supported")  # noqa
             return data

From 970836dd208162448284ee4ec9a72b26f7c8bfe8 Mon Sep 17 00:00:00 2001
From: Kyle Conroy <kyleconroy@gmail.com>
Date: Wed, 5 Apr 2023 14:51:32 -0400
Subject: [PATCH 02/12] fix RTD build failure because of missing mixin
 available in import

---
 jdaviz/core/template_mixin.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/jdaviz/core/template_mixin.py b/jdaviz/core/template_mixin.py
index 4092724239..ded3170d26 100644
--- a/jdaviz/core/template_mixin.py
+++ b/jdaviz/core/template_mixin.py
@@ -28,6 +28,7 @@
 
 
 __all__ = ['show_widget', 'TemplateMixin', 'PluginTemplateMixin',
+           'ViewerPropertiesMixin',
            'BasePluginComponent', 'SelectPluginComponent', 'UnitSelectPluginComponent',
            'PluginSubcomponent',
            'SubsetSelect', 'SpatialSubsetSelectMixin', 'SpectralSubsetSelectMixin',

From c1e19b7a7ee7aff9eea687b95758f30e37b4d1f9 Mon Sep 17 00:00:00 2001
From: Kyle Conroy <kyleconroy@gmail.com>
Date: Wed, 5 Apr 2023 14:53:52 -0400
Subject: [PATCH 03/12] fix test setting display unit now that um is preferred
 to micron

---
 jdaviz/configs/specviz/tests/test_helper.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/jdaviz/configs/specviz/tests/test_helper.py b/jdaviz/configs/specviz/tests/test_helper.py
index f3041ab734..2be9d6cb9c 100644
--- a/jdaviz/configs/specviz/tests/test_helper.py
+++ b/jdaviz/configs/specviz/tests/test_helper.py
@@ -293,7 +293,7 @@ def test_get_spectral_regions_unit_conversion(specviz_helper, spectrum1d):
     assert label_mouseover.icon == ''
 
     # Convert the wavelength axis to micron
-    new_spectral_axis = "micron"
+    new_spectral_axis = "um"
     spec_viewer.state.x_display_unit = new_spectral_axis
     spec_viewer.set_plot_axes()
 

From b4e5d3e7f0cc46d1446bf2a1131af806a431fbd1 Mon Sep 17 00:00:00 2001
From: Kyle Conroy <kyleconroy@gmail.com>
Date: Wed, 5 Apr 2023 15:06:18 -0400
Subject: [PATCH 04/12] add disabled unit conversion plugin to mosviz

---
 jdaviz/configs/mosviz/mosviz.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/jdaviz/configs/mosviz/mosviz.yaml b/jdaviz/configs/mosviz/mosviz.yaml
index b5a846350c..98f842b08b 100644
--- a/jdaviz/configs/mosviz/mosviz.yaml
+++ b/jdaviz/configs/mosviz/mosviz.yaml
@@ -22,6 +22,7 @@ tray:
   - g-gaussian-smooth
   - g-slit-overlay
   - g-model-fitting
+  - g-unit-conversion
   - g-line-list
   - specviz-line-analysis
   - g-export-plot

From f6058f2fc93ac6da8a7e19a40dd42add32bd0503 Mon Sep 17 00:00:00 2001
From: Kyle Conroy <kyleconroy@gmail.com>
Date: Wed, 5 Apr 2023 15:15:35 -0400
Subject: [PATCH 05/12] avoid unit-conversion error in cubeviz tests

---
 jdaviz/core/helpers.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/jdaviz/core/helpers.py b/jdaviz/core/helpers.py
index 5b988a1a89..ed353d141c 100644
--- a/jdaviz/core/helpers.py
+++ b/jdaviz/core/helpers.py
@@ -415,6 +415,12 @@ def _handle_display_units(data, use_display_units):
                     spectral_unit = self.app._get_display_unit('spectral')
                     if not spectral_unit:
                         return data
+                    if self.app.config == 'cubeviz' and spectral_unit == 'deg':
+                        # this happens before the correct axis is set for the spectrum-viewer
+                        # and would result in a unit-conversion error if attempting to convert
+                        # to the display units.  This should only ever be temporary during
+                        # app intialization.
+                        return data
                     flux_unit = self.app._get_display_unit('flux')
                     # TODO: any other attributes (meta, wcs, etc)?
                     # TODO: implement uncertainty.to upstream

From 83994c83c515475946d53420f82c6c8b94c37765 Mon Sep 17 00:00:00 2001
From: Kyle Conroy <kyleconroy@gmail.com>
Date: Thu, 13 Apr 2023 09:17:23 -0400
Subject: [PATCH 06/12] bump versions of glue/glue-jupyter

---
 setup.cfg | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index 575c6555c2..6e03f9b7c6 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -24,8 +24,8 @@ install_requires =
     traitlets>=5.0.5
     bqplot>=0.12.37
     bqplot-image-gl>=1.4.11
-    glue-core>=1.9.0
-    glue-jupyter>=0.15.0
+    glue-core>=1.9.1
+    glue-jupyter>=0.16.2
     echo>=0.5.0
     ipykernel>=6.19.4
     ipyvue>=1.6

From 36901433758c13179e4f6f5089788213e3621a75 Mon Sep 17 00:00:00 2001
From: Kyle Conroy <kyleconroy@gmail.com>
Date: Thu, 13 Apr 2023 13:06:18 -0400
Subject: [PATCH 07/12] fix deg intialization in cubeviz slice plugin

---
 jdaviz/configs/cubeviz/plugins/slice/slice.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/jdaviz/configs/cubeviz/plugins/slice/slice.py b/jdaviz/configs/cubeviz/plugins/slice/slice.py
index 57026f9d63..0ff906af8c 100644
--- a/jdaviz/configs/cubeviz/plugins/slice/slice.py
+++ b/jdaviz/configs/cubeviz/plugins/slice/slice.py
@@ -171,7 +171,8 @@ def _on_global_display_unit_changed(self, msg):
             return
         prev_unit = self.wavelength_unit
         self.wavelength_unit = msg.unit.to_string()
-        if self._x_all is None or prev_unit == '':
+        # original unit during init can be blank or deg (before axis is set correctly)
+        if self._x_all is None or prev_unit in ['deg', '']:
             return
         self._update_data((self._x_all * u.Unit(prev_unit)).to(msg.unit, u.spectral()))
 

From ee12c73d5a7bf980ab2c74c9fe514775dd193fc3 Mon Sep 17 00:00:00 2001
From: Kyle Conroy <kyleconroy@gmail.com>
Date: Thu, 13 Apr 2023 13:10:54 -0400
Subject: [PATCH 08/12] add LinesAutoUnit to __all__ so RTD can find it

---
 jdaviz/core/marks.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/jdaviz/core/marks.py b/jdaviz/core/marks.py
index 08ffba76b9..95b29843f0 100644
--- a/jdaviz/core/marks.py
+++ b/jdaviz/core/marks.py
@@ -14,7 +14,7 @@
 
 __all__ = ['OffscreenLinesMarks', 'BaseSpectrumVerticalLine', 'SpectralLine',
            'SliceIndicatorMarks', 'ShadowMixin', 'ShadowLine', 'ShadowLabelFixedY',
-           'PluginMark', 'PluginLine', 'PluginScatter',
+           'PluginMark', 'LinesAutoUnit', 'PluginLine', 'PluginScatter',
            'LineAnalysisContinuum', 'LineAnalysisContinuumCenter',
            'LineAnalysisContinuumLeft', 'LineAnalysisContinuumRight',
            'LineUncertainties', 'ScatterMask', 'SelectedSpaxel', 'MarkersMark']

From c4bb23d9b6a666126f178071f0f47fde65caf183 Mon Sep 17 00:00:00 2001
From: Kyle Conroy <kyleconroy@gmail.com>
Date: Thu, 13 Apr 2023 13:18:23 -0400
Subject: [PATCH 09/12] add use_display_units kwarg to get_spectral_regions

---
 jdaviz/configs/specviz/helper.py            |  9 +++++++--
 jdaviz/configs/specviz/tests/test_helper.py | 14 +++++++++-----
 2 files changed, 16 insertions(+), 7 deletions(-)

diff --git a/jdaviz/configs/specviz/helper.py b/jdaviz/configs/specviz/helper.py
index 7692ec04be..e3cd24495b 100644
--- a/jdaviz/configs/specviz/helper.py
+++ b/jdaviz/configs/specviz/helper.py
@@ -128,18 +128,23 @@ def get_spectra(self, data_label=None, subset_to_apply=None, apply_slider_redshi
 
             return output_spectra
 
-    def get_spectral_regions(self):
+    def get_spectral_regions(self, use_display_units=False):
         """
         A simple wrapper around the app-level call to retrieve only spectral
         subsets, which are now returned as SpectralRegions by default.
 
+        Parameters
+        ----------
+        use_display_units: bool, optional
+            Whether to convert to the display units defined in the <unit-conversion> plugin.
+
         Returns
         -------
         spec_regs : dict
             Mapping from the names of the subsets to the subsets expressed
             as `specutils.SpectralRegion` objects.
         """
-        return self.app.get_subsets(spectral_only=True)
+        return self.app.get_subsets(spectral_only=True, use_display_units=use_display_units)
 
     def x_limits(self, x_min=None, x_max=None):
         """Sets the limits of the x-axis
diff --git a/jdaviz/configs/specviz/tests/test_helper.py b/jdaviz/configs/specviz/tests/test_helper.py
index 2be9d6cb9c..53e8122dbd 100644
--- a/jdaviz/configs/specviz/tests/test_helper.py
+++ b/jdaviz/configs/specviz/tests/test_helper.py
@@ -294,16 +294,20 @@ def test_get_spectral_regions_unit_conversion(specviz_helper, spectrum1d):
 
     # Convert the wavelength axis to micron
     new_spectral_axis = "um"
-    spec_viewer.state.x_display_unit = new_spectral_axis
-    spec_viewer.set_plot_axes()
+    specviz_helper.plugins['Unit Conversion'].spectral_unit = new_spectral_axis
 
     spec_viewer.apply_roi(XRangeROI(0.6, 0.7))
 
     # Retrieve the Subset
-    subsets = specviz_helper.get_spectral_regions()
+    subsets = specviz_helper.get_spectral_regions(use_display_units=False)
+    reg = subsets.get('Subset 1')
+    assert reg.lower.unit == u.Angstrom
+    assert reg.upper.unit == u.Angstrom
+
+    subsets = specviz_helper.get_spectral_regions(use_display_units=True)
     reg = subsets.get('Subset 1')
-    assert reg.lower.unit == u.micron
-    assert reg.upper.unit == u.micron
+    assert reg.lower.unit == u.um
+    assert reg.upper.unit == u.um
 
     # Coordinates info panel should show new unit
     label_mouseover._viewer_mouse_event(spec_viewer,

From a41c92f8012eb987d537eb3ddfd653b0cfb3cbbb Mon Sep 17 00:00:00 2001
From: Kyle Conroy <kyleconroy@gmail.com>
Date: Thu, 13 Apr 2023 13:33:40 -0400
Subject: [PATCH 10/12] fix setting display units for unitless data

---
 jdaviz/configs/specviz/plugins/viewers.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/jdaviz/configs/specviz/plugins/viewers.py b/jdaviz/configs/specviz/plugins/viewers.py
index a917fb4578..7b77e93d6b 100644
--- a/jdaviz/configs/specviz/plugins/viewers.py
+++ b/jdaviz/configs/specviz/plugins/viewers.py
@@ -361,8 +361,10 @@ def add_data(self, data, color=None, alpha=None, **layer_state):
         result = super().add_data(data, color, alpha, **layer_state)
 
         if reset_plot_axes:
-            self.state.x_display_unit = data.get_component(self.state.x_att.label).units
-            self.state.y_display_unit = data.get_component("flux").units
+            x_units = data.get_component(self.state.x_att.label).units
+            y_units = data.get_component("flux").units
+            self.state.x_display_unit = x_units if len(x_units) else None
+            self.state.y_display_unit = y_units if len(y_units) else None
             self.set_plot_axes()
 
         self._plot_uncertainties()
@@ -489,7 +491,8 @@ def _plot_uncertainties(self):
     def set_plot_axes(self):
         # Set axes labels for the spectrum viewer
         flux_unit_type = "Flux density"
-        x_unit = u.Unit(self.state.x_display_unit)
+        x_disp_unit = self.state.x_display_unit
+        x_unit = u.Unit(x_disp_unit) if x_disp_unit is not None else u.dimensionless_unscaled
         if x_unit.is_equivalent(u.m):
             spectral_axis_unit_type = "Wavelength"
         elif x_unit.is_equivalent(u.Hz):

From f030cce1c140a2ebee4615ff93913bf28b1f34a5 Mon Sep 17 00:00:00 2001
From: Kyle Conroy <kyleconroy@gmail.com>
Date: Thu, 13 Apr 2023 14:53:56 -0400
Subject: [PATCH 11/12] Apply suggestions from code review

Co-authored-by: P. L. Lim <2090236+pllim@users.noreply.github.com>
---
 jdaviz/app.py                                 | 4 ++--
 jdaviz/configs/cubeviz/plugins/slice/slice.py | 2 +-
 jdaviz/configs/specviz/helper.py              | 4 ++--
 jdaviz/configs/specviz/plugins/viewers.py     | 2 +-
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/jdaviz/app.py b/jdaviz/app.py
index c7341fc606..6e6216cdad 100644
--- a/jdaviz/app.py
+++ b/jdaviz/app.py
@@ -886,8 +886,8 @@ def get_subsets(self, subset_name=None, spectral_only=False,
         object_only : bool
             Return only object relevant information and
             leave out the region class name and glue_state.
-        use_display_units: bool, optional
-            Whether to convert to the display units defined in the <unit-conversion> plugin.
+        use_display_units : bool, optional
+            Whether to convert to the display units defined in the Unit Conversion plugin.
 
         Returns
         -------
diff --git a/jdaviz/configs/cubeviz/plugins/slice/slice.py b/jdaviz/configs/cubeviz/plugins/slice/slice.py
index 0ff906af8c..04ef23a59e 100644
--- a/jdaviz/configs/cubeviz/plugins/slice/slice.py
+++ b/jdaviz/configs/cubeviz/plugins/slice/slice.py
@@ -172,7 +172,7 @@ def _on_global_display_unit_changed(self, msg):
         prev_unit = self.wavelength_unit
         self.wavelength_unit = msg.unit.to_string()
         # original unit during init can be blank or deg (before axis is set correctly)
-        if self._x_all is None or prev_unit in ['deg', '']:
+        if self._x_all is None or prev_unit in ('deg', ''):
             return
         self._update_data((self._x_all * u.Unit(prev_unit)).to(msg.unit, u.spectral()))
 
diff --git a/jdaviz/configs/specviz/helper.py b/jdaviz/configs/specviz/helper.py
index e3cd24495b..ac1cb3d2f6 100644
--- a/jdaviz/configs/specviz/helper.py
+++ b/jdaviz/configs/specviz/helper.py
@@ -135,8 +135,8 @@ def get_spectral_regions(self, use_display_units=False):
 
         Parameters
         ----------
-        use_display_units: bool, optional
-            Whether to convert to the display units defined in the <unit-conversion> plugin.
+        use_display_units : bool, optional
+            Whether to convert to the display units defined in the Unit Conversion plugin.
 
         Returns
         -------
diff --git a/jdaviz/configs/specviz/plugins/viewers.py b/jdaviz/configs/specviz/plugins/viewers.py
index 7b77e93d6b..e1de39a615 100644
--- a/jdaviz/configs/specviz/plugins/viewers.py
+++ b/jdaviz/configs/specviz/plugins/viewers.py
@@ -492,7 +492,7 @@ def set_plot_axes(self):
         # Set axes labels for the spectrum viewer
         flux_unit_type = "Flux density"
         x_disp_unit = self.state.x_display_unit
-        x_unit = u.Unit(x_disp_unit) if x_disp_unit is not None else u.dimensionless_unscaled
+        x_unit = u.Unit(x_disp_unit) if x_disp_unit else u.dimensionless_unscaled
         if x_unit.is_equivalent(u.m):
             spectral_axis_unit_type = "Wavelength"
         elif x_unit.is_equivalent(u.Hz):

From 7bda40b1b62864a4e7b5a13dafdf255f0e8610d0 Mon Sep 17 00:00:00 2001
From: Kyle Conroy <kyleconroy@gmail.com>
Date: Thu, 13 Apr 2023 15:00:41 -0400
Subject: [PATCH 12/12] fix RTD link in API docstring

---
 jdaviz/app.py                    | 3 ++-
 jdaviz/configs/specviz/helper.py | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/jdaviz/app.py b/jdaviz/app.py
index 6e6216cdad..773c5706b7 100644
--- a/jdaviz/app.py
+++ b/jdaviz/app.py
@@ -887,7 +887,8 @@ def get_subsets(self, subset_name=None, spectral_only=False,
             Return only object relevant information and
             leave out the region class name and glue_state.
         use_display_units : bool, optional
-            Whether to convert to the display units defined in the Unit Conversion plugin.
+            Whether to convert to the display units defined in the
+            :ref:`Unit Conversion <unit-conversion>` plugin.
 
         Returns
         -------
diff --git a/jdaviz/configs/specviz/helper.py b/jdaviz/configs/specviz/helper.py
index ac1cb3d2f6..e5252ee985 100644
--- a/jdaviz/configs/specviz/helper.py
+++ b/jdaviz/configs/specviz/helper.py
@@ -136,7 +136,8 @@ def get_spectral_regions(self, use_display_units=False):
         Parameters
         ----------
         use_display_units : bool, optional
-            Whether to convert to the display units defined in the Unit Conversion plugin.
+            Whether to convert to the display units defined in the
+            :ref:`Unit Conversion <unit-conversion>` plugin.
 
         Returns
         -------