From cc9480313b5e032e7c87e759a25472776bfd07e7 Mon Sep 17 00:00:00 2001
From: Zach Foltz <zfoltz3@gmail.com>
Date: Fri, 21 Apr 2023 16:15:02 -0600
Subject: [PATCH 01/16] fixed bug for issue #3755 when the figure object
 contains subplots

---
 .../python/plotly/plotly/basedatatypes.py     | 25 +++++++++++++++----
 1 file changed, 20 insertions(+), 5 deletions(-)

diff --git a/packages/python/plotly/plotly/basedatatypes.py b/packages/python/plotly/plotly/basedatatypes.py
index bf5eac3dfa..489010be63 100644
--- a/packages/python/plotly/plotly/basedatatypes.py
+++ b/packages/python/plotly/plotly/basedatatypes.py
@@ -1563,13 +1563,28 @@ def _add_annotation_like(
                 raise ValueError(
                     """
 Cannot add {prop_singular} to secondary y-axis of subplot at position ({r}, {c})
-because subplot does not have a secondary y-axis"""
+because subplot does not have a secondary y-axis""".format(
+                        prop_singular=prop_singular, r=row, c=col
+                    )
                 )
-            if secondary_y:
-                xaxis, yaxis = refs[1].layout_keys
+            # If the new_object was created with an xref specified, the specified xref should be used otherwise assign the xref from the layout_keys
+            if new_obj.xref is None:
+                if secondary_y:
+                    xaxis = refs[1].layout_keys[0]
+                else:
+                    xaxis = refs[0].layout_keys[0]
+                xref = xaxis.replace("axis", "")
+            else:
+                xref = new_obj.xref
+            # If the new_object was created with an xref specified, the specified xref should be used otherwise assign the xref from the layout_keys
+            if new_obj.yref is None:
+                if secondary_y:
+                    yaxis = refs[1].layout_keys[1]
+                else:
+                    yaxis = refs[0].layout_keys[1]
+                yref = yaxis.replace("axis", "")
             else:
-                xaxis, yaxis = refs[0].layout_keys
-            xref, yref = xaxis.replace("axis", ""), yaxis.replace("axis", "")
+                yref = new_obj.yref
             # if exclude_empty_subplots is True, check to see if subplot is
             # empty and return if it is
             if exclude_empty_subplots and (

From ebb3808223d647c15bfef7ed4c647149e348811a Mon Sep 17 00:00:00 2001
From: Zach Foltz <zfoltz3@gmail.com>
Date: Fri, 21 Apr 2023 16:21:45 -0600
Subject: [PATCH 02/16] fixed bug for issue #3755 when the figure object does
 not contain subplots

---
 packages/python/plotly/plotly/basedatatypes.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/packages/python/plotly/plotly/basedatatypes.py b/packages/python/plotly/plotly/basedatatypes.py
index 489010be63..e9e3338bda 100644
--- a/packages/python/plotly/plotly/basedatatypes.py
+++ b/packages/python/plotly/plotly/basedatatypes.py
@@ -4060,10 +4060,13 @@ def _process_multiple_axis_spanning_shapes(
             ):
                 # this was called intending to add to a single plot (and
                 # self.add_{layout_obj} succeeded)
-                # however, in the case of a single plot, xref and yref are not
-                # specified, so we specify them here so the following routines can work
+                # however, in the case of a single plot, xref and yref MAY not be
+                # specified, IF they are not specified we specify them here so the following routines can work
                 # (they need to append " domain" to xref or yref)
-                self.layout[layout_obj][-1].update(xref="x", yref="y")
+                if self.layout[layout_obj][-1].xref is None:
+                    self.layout[layout_obj][-1].update(xref="x")
+                if self.layout[layout_obj][-1].yref is None:
+                    self.layout[layout_obj][-1].update(yref="y")
             new_layout_objs = tuple(
                 filter(
                     lambda x: x is not None,

From d0522f5ed6eed9153e04cc4b5f8038210a79bbd0 Mon Sep 17 00:00:00 2001
From: Zach Foltz <zfoltz3@gmail.com>
Date: Fri, 21 Apr 2023 17:29:03 -0600
Subject: [PATCH 03/16] incorrect use of 'is' changed to '=='

---
 packages/python/plotly/plotly/basedatatypes.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/packages/python/plotly/plotly/basedatatypes.py b/packages/python/plotly/plotly/basedatatypes.py
index e9e3338bda..04bc45080c 100644
--- a/packages/python/plotly/plotly/basedatatypes.py
+++ b/packages/python/plotly/plotly/basedatatypes.py
@@ -1568,7 +1568,7 @@ def _add_annotation_like(
                     )
                 )
             # If the new_object was created with an xref specified, the specified xref should be used otherwise assign the xref from the layout_keys
-            if new_obj.xref is None:
+            if new_obj.xref == None:
                 if secondary_y:
                     xaxis = refs[1].layout_keys[0]
                 else:
@@ -1577,7 +1577,7 @@ def _add_annotation_like(
             else:
                 xref = new_obj.xref
             # If the new_object was created with an xref specified, the specified xref should be used otherwise assign the xref from the layout_keys
-            if new_obj.yref is None:
+            if new_obj.yref == None:
                 if secondary_y:
                     yaxis = refs[1].layout_keys[1]
                 else:

From 24ad4c7af3028b19f659afdfd231df02168a3526 Mon Sep 17 00:00:00 2001
From: Zach Foltz <zfoltz3@gmail.com>
Date: Sat, 22 Apr 2023 08:42:38 -0600
Subject: [PATCH 04/16] added some conditionals to help find bug in subplot
 shapes

---
 debug.py                                      | 41 ++++++++++++++++++
 debugtesting.py                               | 43 +++++++++++++++++++
 .../python/plotly/plotly/basedatatypes.py     | 15 ++++++-
 3 files changed, 97 insertions(+), 2 deletions(-)
 create mode 100644 debug.py
 create mode 100644 debugtesting.py

diff --git a/debug.py b/debug.py
new file mode 100644
index 0000000000..06511a2b57
--- /dev/null
+++ b/debug.py
@@ -0,0 +1,41 @@
+import plotly.express as px
+import plotly.graph_objects as go
+import numpy as np
+from plotly import subplots
+
+test_subplots = True
+use_OP = False
+
+df = px.data.iris()
+if use_OP:
+    fig = px.scatter(df, x="petal_length", y="petal_width")
+    fig.add_traces(go.Scatter(y=np.arange(1, 7), mode="lines+markers", yaxis="y2"))
+
+    fig.update_layout(
+        yaxis2=dict(
+            title="yaxis2 title",
+            overlaying="y",
+            side="right",
+        )
+    )
+else:
+    trace1 = go.Scatter(x=df["petal_length"], y=df["petal_width"], mode="markers")
+    trace2 = go.Scatter(
+        x=[0, 1, 2, 3, 4, 5], y=np.arange(1, 7), mode="lines+markers", yaxis="y2"
+    )
+    data = [trace1, trace2]
+    layout = go.Layout(
+        yaxis=dict(title="yaxis1"),
+        yaxis2=dict(title="yaxis2 title", overlaying="y", side="right"),
+    )
+    fig = go.Figure(data=data, layout=layout)
+if test_subplots:
+    fig = subplots.make_subplots(rows=1, cols=2, shared_yaxes=False)
+
+fig.add_hline(
+    y=2,
+    line_dash="dash",
+    line_color="Red",  # yref='y2'
+    # secondary_y=True
+)
+fig.show()
diff --git a/debugtesting.py b/debugtesting.py
new file mode 100644
index 0000000000..71a9bd47e0
--- /dev/null
+++ b/debugtesting.py
@@ -0,0 +1,43 @@
+import plotly.express as px
+import plotly.graph_objects as go
+import numpy as np
+from plotly.subplots import make_subplots
+
+
+for k, fun, d, fun2, d2 in [
+    (
+        "shapes",
+        go.Figure.add_shape,
+        dict(type="rect", x0=1.5, x1=2.5, y0=3.5, y1=4.5),
+        # add a different type to make the check easier (otherwise we might
+        # mix up the objects added before and after fun was run)
+        go.Figure.add_annotation,
+        dict(x=1, y=2, text="A"),
+    ),
+    (
+        "annotations",
+        go.Figure.add_annotation,
+        dict(x=1, y=2, text="A"),
+        go.Figure.add_layout_image,
+        dict(x=3, y=4, sizex=2, sizey=3, source="test"),
+    ),
+    (
+        "images",
+        go.Figure.add_layout_image,
+        dict(x=3, y=4, sizex=2, sizey=3, source="test"),
+        go.Figure.add_shape,
+        dict(type="rect", x0=1.5, x1=2.5, y0=3.5, y1=4.5),
+    ),
+]:
+    # make a figure where not all the subplots are populated
+    fig = make_subplots(2, 2)
+    fig.add_trace(go.Scatter(x=[1, 2, 3], y=[5, 1, 2]), row=1, col=1)
+    fig.add_trace(go.Scatter(x=[1, 2, 3], y=[2, 1, -7]), row=2, col=2)
+    fun2(fig, d2, row=1, col=2)
+    # add a thing to all subplots but make sure it only goes on the
+    # plots without data or layout objects
+    fun(fig, d, row="all", col="all", exclude_empty_subplots="anything_truthy")
+    assert len(fig.layout[k]) == 3
+    assert fig.layout[k][0]["xref"] == "x" and fig.layout[k][0]["yref"] == "y"
+    assert fig.layout[k][1]["xref"] == "x2" and fig.layout[k][1]["yref"] == "y2"
+    assert fig.layout[k][2]["xref"] == "x4" and fig.layout[k][2]["yref"] == "y4"
diff --git a/packages/python/plotly/plotly/basedatatypes.py b/packages/python/plotly/plotly/basedatatypes.py
index 04bc45080c..fae8b9b9fc 100644
--- a/packages/python/plotly/plotly/basedatatypes.py
+++ b/packages/python/plotly/plotly/basedatatypes.py
@@ -1567,6 +1567,7 @@ def _add_annotation_like(
                         prop_singular=prop_singular, r=row, c=col
                     )
                 )
+            #'''
             # If the new_object was created with an xref specified, the specified xref should be used otherwise assign the xref from the layout_keys
             if new_obj.xref == None:
                 if secondary_y:
@@ -1585,6 +1586,14 @@ def _add_annotation_like(
                 yref = yaxis.replace("axis", "")
             else:
                 yref = new_obj.yref
+            #'''
+            """
+            if secondary_y:
+                xaxis, yaxis = refs[1].layout_keys
+            else:
+                xaxis, yaxis = refs[0].layout_keys
+            xref, yref = xaxis.replace("axis", ""), yaxis.replace("axis", "")
+            """
             # if exclude_empty_subplots is True, check to see if subplot is
             # empty and return if it is
             if exclude_empty_subplots and (
@@ -4063,10 +4072,12 @@ def _process_multiple_axis_spanning_shapes(
                 # however, in the case of a single plot, xref and yref MAY not be
                 # specified, IF they are not specified we specify them here so the following routines can work
                 # (they need to append " domain" to xref or yref)
-                if self.layout[layout_obj][-1].xref is None:
+                if self.layout[layout_obj][-1].xref == None:
                     self.layout[layout_obj][-1].update(xref="x")
-                if self.layout[layout_obj][-1].yref is None:
+                # self.layout[layout_obj][-1].update(xref="x")
+                if self.layout[layout_obj][-1].yref == None:
                     self.layout[layout_obj][-1].update(yref="y")
+                # self.layout[layout_obj][-1].update(yref='y')
             new_layout_objs = tuple(
                 filter(
                     lambda x: x is not None,

From 8bb24b9e731de31dd5769ba5a364591eb2000037 Mon Sep 17 00:00:00 2001
From: Zach Foltz <zfoltz3@gmail.com>
Date: Wed, 26 Apr 2023 15:27:02 -0600
Subject: [PATCH 05/16] fixed bug which was causing shapes to be all drawn on
 the same axis

---
 .../python/plotly/plotly/basedatatypes.py     | 35 +++++++++++++------
 1 file changed, 24 insertions(+), 11 deletions(-)

diff --git a/packages/python/plotly/plotly/basedatatypes.py b/packages/python/plotly/plotly/basedatatypes.py
index fae8b9b9fc..812631c063 100644
--- a/packages/python/plotly/plotly/basedatatypes.py
+++ b/packages/python/plotly/plotly/basedatatypes.py
@@ -1559,6 +1559,7 @@ def _add_annotation_like(
                         subplot_type=refs[0].subplot_type,
                     )
                 )
+            '''
             if len(refs) == 1 and secondary_y:
                 raise ValueError(
                     """
@@ -1567,26 +1568,33 @@ def _add_annotation_like(
                         prop_singular=prop_singular, r=row, c=col
                     )
                 )
+            '''
+
             #'''
-            # If the new_object was created with an xref specified, the specified xref should be used otherwise assign the xref from the layout_keys
-            if new_obj.xref == None:
-                if secondary_y:
-                    xaxis = refs[1].layout_keys[0]
-                else:
-                    xaxis = refs[0].layout_keys[0]
-                xref = xaxis.replace("axis", "")
-            else:
-                xref = new_obj.xref
-            # If the new_object was created with an xref specified, the specified xref should be used otherwise assign the xref from the layout_keys
-            if new_obj.yref == None:
+            # If the new_object was created with an yref specified, the specified yref should be used otherwise assign the xref from the layout_keys
+            if new_obj.yref == None or new_obj.yref == "y":
+                if len(refs) == 1 and secondary_y:
+                    raise ValueError(
+                        """
+    Cannot add {prop_singular} to secondary y-axis of subplot at position ({r}, {c})
+    because subplot does not have a secondary y-axis""".format(
+                            prop_singular=prop_singular, r=row, c=col
+                        )
+                    )
                 if secondary_y:
                     yaxis = refs[1].layout_keys[1]
+                    xaxis = refs[1].layout_keys[0]
                 else:
                     yaxis = refs[0].layout_keys[1]
+                    xaxis = refs[0].layout_keys[0]
                 yref = yaxis.replace("axis", "")
+                xref = xaxis.replace("axis", "")
             else:
                 yref = new_obj.yref
+                xaxis = refs[0].layout_keys[0]
+                xref = xaxis.replace("axis", "")
             #'''
+
             """
             if secondary_y:
                 xaxis, yaxis = refs[1].layout_keys
@@ -1594,6 +1602,7 @@ def _add_annotation_like(
                 xaxis, yaxis = refs[0].layout_keys
             xref, yref = xaxis.replace("axis", ""), yaxis.replace("axis", "")
             """
+
             # if exclude_empty_subplots is True, check to see if subplot is
             # empty and return if it is
             if exclude_empty_subplots and (
@@ -1615,6 +1624,10 @@ def _add_domain(ax_letter, new_axref):
             new_obj.update(xref=xref, yref=yref)
 
         self.layout[prop_plural] += (new_obj,)
+        # The 'new_obj.xref' and 'new_obj.yref' parameters need to be reset otherwise it
+        # will appear as if user supplied yref params and will force annotation to
+        # be on the axis of the last drawn annotation (they all end up on the same axis)
+        new_obj.update(xref=None, yref=None)
 
         return self
 

From 1d1db35c9ca6ab0daa8a10b2bb259896c1416309 Mon Sep 17 00:00:00 2001
From: Zach Foltz <zfoltz3@gmail.com>
Date: Wed, 26 Apr 2023 15:28:52 -0600
Subject: [PATCH 06/16] removed some no longer needed files that were being
 used to find the bug on the previous commit

---
 debug.py        | 41 -----------------------------------------
 debugtesting.py | 43 -------------------------------------------
 2 files changed, 84 deletions(-)
 delete mode 100644 debug.py
 delete mode 100644 debugtesting.py

diff --git a/debug.py b/debug.py
deleted file mode 100644
index 06511a2b57..0000000000
--- a/debug.py
+++ /dev/null
@@ -1,41 +0,0 @@
-import plotly.express as px
-import plotly.graph_objects as go
-import numpy as np
-from plotly import subplots
-
-test_subplots = True
-use_OP = False
-
-df = px.data.iris()
-if use_OP:
-    fig = px.scatter(df, x="petal_length", y="petal_width")
-    fig.add_traces(go.Scatter(y=np.arange(1, 7), mode="lines+markers", yaxis="y2"))
-
-    fig.update_layout(
-        yaxis2=dict(
-            title="yaxis2 title",
-            overlaying="y",
-            side="right",
-        )
-    )
-else:
-    trace1 = go.Scatter(x=df["petal_length"], y=df["petal_width"], mode="markers")
-    trace2 = go.Scatter(
-        x=[0, 1, 2, 3, 4, 5], y=np.arange(1, 7), mode="lines+markers", yaxis="y2"
-    )
-    data = [trace1, trace2]
-    layout = go.Layout(
-        yaxis=dict(title="yaxis1"),
-        yaxis2=dict(title="yaxis2 title", overlaying="y", side="right"),
-    )
-    fig = go.Figure(data=data, layout=layout)
-if test_subplots:
-    fig = subplots.make_subplots(rows=1, cols=2, shared_yaxes=False)
-
-fig.add_hline(
-    y=2,
-    line_dash="dash",
-    line_color="Red",  # yref='y2'
-    # secondary_y=True
-)
-fig.show()
diff --git a/debugtesting.py b/debugtesting.py
deleted file mode 100644
index 71a9bd47e0..0000000000
--- a/debugtesting.py
+++ /dev/null
@@ -1,43 +0,0 @@
-import plotly.express as px
-import plotly.graph_objects as go
-import numpy as np
-from plotly.subplots import make_subplots
-
-
-for k, fun, d, fun2, d2 in [
-    (
-        "shapes",
-        go.Figure.add_shape,
-        dict(type="rect", x0=1.5, x1=2.5, y0=3.5, y1=4.5),
-        # add a different type to make the check easier (otherwise we might
-        # mix up the objects added before and after fun was run)
-        go.Figure.add_annotation,
-        dict(x=1, y=2, text="A"),
-    ),
-    (
-        "annotations",
-        go.Figure.add_annotation,
-        dict(x=1, y=2, text="A"),
-        go.Figure.add_layout_image,
-        dict(x=3, y=4, sizex=2, sizey=3, source="test"),
-    ),
-    (
-        "images",
-        go.Figure.add_layout_image,
-        dict(x=3, y=4, sizex=2, sizey=3, source="test"),
-        go.Figure.add_shape,
-        dict(type="rect", x0=1.5, x1=2.5, y0=3.5, y1=4.5),
-    ),
-]:
-    # make a figure where not all the subplots are populated
-    fig = make_subplots(2, 2)
-    fig.add_trace(go.Scatter(x=[1, 2, 3], y=[5, 1, 2]), row=1, col=1)
-    fig.add_trace(go.Scatter(x=[1, 2, 3], y=[2, 1, -7]), row=2, col=2)
-    fun2(fig, d2, row=1, col=2)
-    # add a thing to all subplots but make sure it only goes on the
-    # plots without data or layout objects
-    fun(fig, d, row="all", col="all", exclude_empty_subplots="anything_truthy")
-    assert len(fig.layout[k]) == 3
-    assert fig.layout[k][0]["xref"] == "x" and fig.layout[k][0]["yref"] == "y"
-    assert fig.layout[k][1]["xref"] == "x2" and fig.layout[k][1]["yref"] == "y2"
-    assert fig.layout[k][2]["xref"] == "x4" and fig.layout[k][2]["yref"] == "y4"

From d95d8ee7fbef3075f20c4f81ac92ba91c0f432c1 Mon Sep 17 00:00:00 2001
From: Zach Foltz <zfoltz3@gmail.com>
Date: Wed, 26 Apr 2023 16:35:04 -0600
Subject: [PATCH 07/16] added tests

---
 .../test_update_annotations.py                | 56 +++++++++++++++++++
 1 file changed, 56 insertions(+)

diff --git a/packages/python/plotly/plotly/tests/test_core/test_update_objects/test_update_annotations.py b/packages/python/plotly/plotly/tests/test_core/test_update_objects/test_update_annotations.py
index 23c3af2796..58af8cb6fc 100644
--- a/packages/python/plotly/plotly/tests/test_core/test_update_objects/test_update_annotations.py
+++ b/packages/python/plotly/plotly/tests/test_core/test_update_objects/test_update_annotations.py
@@ -5,6 +5,7 @@
 
 import plotly.graph_objs as go
 from plotly.subplots import make_subplots
+import plotly.express as px
 import pytest
 
 
@@ -351,6 +352,61 @@ def test_no_exclude_empty_subplots():
         assert fig.layout[k][3]["xref"] == "x4" and fig.layout[k][3]["yref"] == "y4"
 
 
+def test_supplied_yref_on_single_plot_subplot():
+    ### test a (1,1) subplot figure object from px.scatter
+    fig = px.scatter(x=[1, 2, 3, 4], y=[1, 2, 2, 1])
+    fig.add_trace(go.Scatter(x=[1, 2, 3, 4], y=[4, 3, 2, 1], yaxis="y2"))
+    fig.update_layout(
+        yaxis=dict(title="yaxis1 title"),
+        yaxis2=dict(title="yaxis2 title", overlaying="y", side="right"),
+    )
+    # add horizontal line on y2. Secondary_y can be True or False
+    fig.add_hline(y=3, yref="y2", secondary_y=True)
+    assert fig.layout["shapes"][0]["yref"] == "y2"
+
+
+def test_supplied_yref_on_non_subplot_figure_object():
+    ### test a non-subplot figure object from go.Figure
+    trace1 = go.Scatter(x=[1, 2, 3, 4], y=[1, 2, 2, 1])
+    trace2 = go.Scatter(x=[1, 2, 3, 4], y=[4, 3, 2, 1], yaxis="y2")
+    data = [trace1, trace2]
+    layout = go.Layout(
+        yaxis=dict(title="yaxis1 title"),
+        yaxis2=dict(title="yaxis2 title", overlaying="y", side="right"),
+    )
+    fig = go.Figure(data=data, layout=layout)
+    # add horizontal line on y2. Secondary_y can be True or False
+    fig.add_hline(y=3, yref="y2", secondary_y=False)
+    assert fig.layout["shapes"][0]["yref"] == "y2"
+
+
+def test_supplied_yref_on_multi_plot_subplot():
+    ### test multiple subploted figure object with subplots.make_subplots
+    fig = make_subplots(
+        rows=1,
+        cols=2,
+        shared_yaxes=False,
+        specs=[[{"secondary_y": True}, {"secondary_y": True}]],
+    )
+    fig.add_trace(go.Scatter(x=[1, 2, 3], y=[1, 2, 3]), row=1, col=1)
+    fig.add_trace(
+        go.Scatter(x=[1, 2, 3], y=[3, 2, 1], yaxis="y2"), row=1, col=1, secondary_y=True
+    )
+    fig.add_trace(go.Scatter(x=[1, 2, 3], y=[1, 2, 3], yaxis="y"), row=1, col=2)
+    fig.add_trace(
+        go.Scatter(x=[1, 2, 3], y=[1, 1, 2], yaxis="y2"), row=1, col=2, secondary_y=True
+    )
+    # add a horizontal line on both subplots secondary y.
+    # When using the subplots.make_subplots() method yref parameter should not be supplied to add_hline()
+    # Instead Secondary_y MUST be True to plot on secondary y
+    fig.add_hline(y=2, row=1, col=1, secondary_y=True)
+    fig.add_hline(y=1, row=1, col=2, secondary_y=True)
+    assert fig.layout["shapes"][0]["yref"] == "y2"
+    assert fig.layout["shapes"][0]["xref"] == "x domain"
+    assert fig.layout["shapes"][1]["yref"] == "y4"
+    assert fig.layout["shapes"][1]["xref"] == "x2 domain"
+
+
 @pytest.fixture
 def select_annotations_integer():
     fig = make_subplots(2, 3)

From f92dc6e1089e12559c8610c086a271d01be74d87 Mon Sep 17 00:00:00 2001
From: Zach Foltz <zfoltz3@gmail.com>
Date: Wed, 26 Apr 2023 17:54:31 -0600
Subject: [PATCH 08/16] added comments and cleaned up code

---
 .../python/plotly/plotly/basedatatypes.py     | 39 ++++---------------
 .../test_update_annotations.py                |  8 ++--
 2 files changed, 13 insertions(+), 34 deletions(-)

diff --git a/packages/python/plotly/plotly/basedatatypes.py b/packages/python/plotly/plotly/basedatatypes.py
index 812631c063..380a3e740b 100644
--- a/packages/python/plotly/plotly/basedatatypes.py
+++ b/packages/python/plotly/plotly/basedatatypes.py
@@ -1559,19 +1559,8 @@ def _add_annotation_like(
                         subplot_type=refs[0].subplot_type,
                     )
                 )
-            '''
-            if len(refs) == 1 and secondary_y:
-                raise ValueError(
-                    """
-Cannot add {prop_singular} to secondary y-axis of subplot at position ({r}, {c})
-because subplot does not have a secondary y-axis""".format(
-                        prop_singular=prop_singular, r=row, c=col
-                    )
-                )
-            '''
 
-            #'''
-            # If the new_object was created with an yref specified, the specified yref should be used otherwise assign the xref from the layout_keys
+            # If the new_object was created with an yref specified, the specified yref should be used otherwise assign the xref and yref from the layout_keys
             if new_obj.yref == None or new_obj.yref == "y":
                 if len(refs) == 1 and secondary_y:
                     raise ValueError(
@@ -1582,27 +1571,14 @@ def _add_annotation_like(
                         )
                     )
                 if secondary_y:
-                    yaxis = refs[1].layout_keys[1]
-                    xaxis = refs[1].layout_keys[0]
+                    xaxis, yaxis = refs[1].layout_keys
                 else:
-                    yaxis = refs[0].layout_keys[1]
-                    xaxis = refs[0].layout_keys[0]
-                yref = yaxis.replace("axis", "")
-                xref = xaxis.replace("axis", "")
+                    xaxis, yaxis = refs[0].layout_keys
+                xref, yref = xaxis.replace("axis", ""), yaxis.replace("axis", "")
             else:
                 yref = new_obj.yref
                 xaxis = refs[0].layout_keys[0]
                 xref = xaxis.replace("axis", "")
-            #'''
-
-            """
-            if secondary_y:
-                xaxis, yaxis = refs[1].layout_keys
-            else:
-                xaxis, yaxis = refs[0].layout_keys
-            xref, yref = xaxis.replace("axis", ""), yaxis.replace("axis", "")
-            """
-
             # if exclude_empty_subplots is True, check to see if subplot is
             # empty and return if it is
             if exclude_empty_subplots and (
@@ -1625,8 +1601,9 @@ def _add_domain(ax_letter, new_axref):
 
         self.layout[prop_plural] += (new_obj,)
         # The 'new_obj.xref' and 'new_obj.yref' parameters need to be reset otherwise it
-        # will appear as if user supplied yref params and will force annotation to
-        # be on the axis of the last drawn annotation (they all end up on the same axis)
+        # will appear as if user supplied yref params when looping through subplots and
+        # will force annotation to be on the axis of the last drawn annotation
+        # i.e. they all end up on the same axis.
         new_obj.update(xref=None, yref=None)
 
         return self
@@ -4084,7 +4061,7 @@ def _process_multiple_axis_spanning_shapes(
                 # self.add_{layout_obj} succeeded)
                 # however, in the case of a single plot, xref and yref MAY not be
                 # specified, IF they are not specified we specify them here so the following routines can work
-                # (they need to append " domain" to xref or yref)
+                # (they need to append " domain" to xref or yref). If they are specified, we leave them alone.
                 if self.layout[layout_obj][-1].xref == None:
                     self.layout[layout_obj][-1].update(xref="x")
                 # self.layout[layout_obj][-1].update(xref="x")
diff --git a/packages/python/plotly/plotly/tests/test_core/test_update_objects/test_update_annotations.py b/packages/python/plotly/plotly/tests/test_core/test_update_objects/test_update_annotations.py
index 58af8cb6fc..56e6a1cdb7 100644
--- a/packages/python/plotly/plotly/tests/test_core/test_update_objects/test_update_annotations.py
+++ b/packages/python/plotly/plotly/tests/test_core/test_update_objects/test_update_annotations.py
@@ -388,17 +388,19 @@ def test_supplied_yref_on_multi_plot_subplot():
         shared_yaxes=False,
         specs=[[{"secondary_y": True}, {"secondary_y": True}]],
     )
+    ### Add traces to the first subplot
     fig.add_trace(go.Scatter(x=[1, 2, 3], y=[1, 2, 3]), row=1, col=1)
     fig.add_trace(
         go.Scatter(x=[1, 2, 3], y=[3, 2, 1], yaxis="y2"), row=1, col=1, secondary_y=True
     )
+    ### Add traces to the second subplot
     fig.add_trace(go.Scatter(x=[1, 2, 3], y=[1, 2, 3], yaxis="y"), row=1, col=2)
     fig.add_trace(
         go.Scatter(x=[1, 2, 3], y=[1, 1, 2], yaxis="y2"), row=1, col=2, secondary_y=True
     )
-    # add a horizontal line on both subplots secondary y.
-    # When using the subplots.make_subplots() method yref parameter should not be supplied to add_hline()
-    # Instead Secondary_y MUST be True to plot on secondary y
+    # add a horizontal line on both subplots on their respective secondary y.
+    # When using the subplots.make_subplots() method yref parameter should NOT be supplied per docstring instructions.
+    # Instead secondary_y specs and secondary_y parameter MUST be True to plot on secondary y
     fig.add_hline(y=2, row=1, col=1, secondary_y=True)
     fig.add_hline(y=1, row=1, col=2, secondary_y=True)
     assert fig.layout["shapes"][0]["yref"] == "y2"

From 9f0650910517a9d696412589a3c396d2f953427e Mon Sep 17 00:00:00 2001
From: Zach Foltz <zfoltz3@gmail.com>
Date: Wed, 26 Apr 2023 18:05:05 -0600
Subject: [PATCH 09/16] more comments

---
 .../test_core/test_update_objects/test_update_annotations.py  | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/packages/python/plotly/plotly/tests/test_core/test_update_objects/test_update_annotations.py b/packages/python/plotly/plotly/tests/test_core/test_update_objects/test_update_annotations.py
index 56e6a1cdb7..7c35c0aee5 100644
--- a/packages/python/plotly/plotly/tests/test_core/test_update_objects/test_update_annotations.py
+++ b/packages/python/plotly/plotly/tests/test_core/test_update_objects/test_update_annotations.py
@@ -360,7 +360,7 @@ def test_supplied_yref_on_single_plot_subplot():
         yaxis=dict(title="yaxis1 title"),
         yaxis2=dict(title="yaxis2 title", overlaying="y", side="right"),
     )
-    # add horizontal line on y2. Secondary_y can be True or False
+    # add horizontal line on y2. Secondary_y can be True or False when yref is supplied
     fig.add_hline(y=3, yref="y2", secondary_y=True)
     assert fig.layout["shapes"][0]["yref"] == "y2"
 
@@ -375,7 +375,7 @@ def test_supplied_yref_on_non_subplot_figure_object():
         yaxis2=dict(title="yaxis2 title", overlaying="y", side="right"),
     )
     fig = go.Figure(data=data, layout=layout)
-    # add horizontal line on y2. Secondary_y can be True or False
+    # add horizontal line on y2. Secondary_y can be True or False when yref is supplied
     fig.add_hline(y=3, yref="y2", secondary_y=False)
     assert fig.layout["shapes"][0]["yref"] == "y2"
 

From 746b227d95300b2f928834b82ef3f4d7cc9ac94d Mon Sep 17 00:00:00 2001
From: Zach Foltz <zfoltz3@gmail.com>
Date: Wed, 26 Apr 2023 20:07:15 -0600
Subject: [PATCH 10/16] removed import plotly express from test

---
 .../test_update_objects/test_update_annotations.py         | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/packages/python/plotly/plotly/tests/test_core/test_update_objects/test_update_annotations.py b/packages/python/plotly/plotly/tests/test_core/test_update_objects/test_update_annotations.py
index 7c35c0aee5..d1c81a3113 100644
--- a/packages/python/plotly/plotly/tests/test_core/test_update_objects/test_update_annotations.py
+++ b/packages/python/plotly/plotly/tests/test_core/test_update_objects/test_update_annotations.py
@@ -5,7 +5,7 @@
 
 import plotly.graph_objs as go
 from plotly.subplots import make_subplots
-import plotly.express as px
+
 import pytest
 
 
@@ -353,8 +353,9 @@ def test_no_exclude_empty_subplots():
 
 
 def test_supplied_yref_on_single_plot_subplot():
-    ### test a (1,1) subplot figure object from px.scatter
-    fig = px.scatter(x=[1, 2, 3, 4], y=[1, 2, 2, 1])
+    ### test a (1,1) subplot figure object
+    fig = make_subplots(1, 1)
+    fig.add_trace(go.Scatter(x=[1, 2, 3, 4], y=[1, 2, 2, 1]))
     fig.add_trace(go.Scatter(x=[1, 2, 3, 4], y=[4, 3, 2, 1], yaxis="y2"))
     fig.update_layout(
         yaxis=dict(title="yaxis1 title"),

From 9f8c92d1c70298e7a1cb300ed2a07f3aed63ae9a Mon Sep 17 00:00:00 2001
From: Alex Johnson <alex@plot.ly>
Date: Fri, 5 May 2023 11:59:46 -0400
Subject: [PATCH 11/16] comment tweaks and remove commented-out code

---
 packages/python/plotly/plotly/basedatatypes.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/packages/python/plotly/plotly/basedatatypes.py b/packages/python/plotly/plotly/basedatatypes.py
index 380a3e740b..eb3e581092 100644
--- a/packages/python/plotly/plotly/basedatatypes.py
+++ b/packages/python/plotly/plotly/basedatatypes.py
@@ -1560,7 +1560,8 @@ def _add_annotation_like(
                     )
                 )
 
-            # If the new_object was created with an yref specified, the specified yref should be used otherwise assign the xref and yref from the layout_keys
+            # If new_obj was created with yref specified, the specified yref
+            # should be used, otherwise assign xref and yref from layout_keys
             if new_obj.yref == None or new_obj.yref == "y":
                 if len(refs) == 1 and secondary_y:
                     raise ValueError(
@@ -4062,12 +4063,10 @@ def _process_multiple_axis_spanning_shapes(
                 # however, in the case of a single plot, xref and yref MAY not be
                 # specified, IF they are not specified we specify them here so the following routines can work
                 # (they need to append " domain" to xref or yref). If they are specified, we leave them alone.
-                if self.layout[layout_obj][-1].xref == None:
+                if self.layout[layout_obj][-1].xref is None:
                     self.layout[layout_obj][-1].update(xref="x")
-                # self.layout[layout_obj][-1].update(xref="x")
-                if self.layout[layout_obj][-1].yref == None:
+                if self.layout[layout_obj][-1].yref is None:
                     self.layout[layout_obj][-1].update(yref="y")
-                # self.layout[layout_obj][-1].update(yref='y')
             new_layout_objs = tuple(
                 filter(
                     lambda x: x is not None,

From 8b2d4bf17633a91f09f0507f5aa4a51de757e1a6 Mon Sep 17 00:00:00 2001
From: Zach Foltz <zfoltz3@gmail.com>
Date: Tue, 9 May 2023 20:44:39 -0600
Subject: [PATCH 12/16] Fixed issued caused by a paper or domain, yref

---
 packages/python/plotly/plotly/basedatatypes.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/packages/python/plotly/plotly/basedatatypes.py b/packages/python/plotly/plotly/basedatatypes.py
index 380a3e740b..9e1f46bf68 100644
--- a/packages/python/plotly/plotly/basedatatypes.py
+++ b/packages/python/plotly/plotly/basedatatypes.py
@@ -1560,8 +1560,13 @@ def _add_annotation_like(
                     )
                 )
 
-            # If the new_object was created with an yref specified, the specified yref should be used otherwise assign the xref and yref from the layout_keys
-            if new_obj.yref == None or new_obj.yref == "y":
+            # If the new_object was created with a yref specified that did not include paper or domain, the specified yref should be used otherwise assign the xref and yref from the layout_keys
+            if (
+                new_obj.yref == None
+                or new_obj.yref == "y"
+                or "paper" in new_obj.yref
+                or "domain" in new_obj.yref
+            ):
                 if len(refs) == 1 and secondary_y:
                     raise ValueError(
                         """

From 872e3d5558bc4b8686761845c7ce19ae7599eefe Mon Sep 17 00:00:00 2001
From: Zach Foltz <zfoltz3@gmail.com>
Date: Tue, 9 May 2023 22:52:42 -0600
Subject: [PATCH 13/16] Added changelog entry

---
 CHANGELOG.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f17a4a7e17..2bd64b6a7d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,9 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 ### Fixed
   - Fixed another compatibility issue with Pandas 2.0, just affecting `px.*(line_close=True)` [[#4190](https://github.com/plotly/plotly.py/pull/4190)]
   - Added some rounding to the `make_subplots` function to handle situations where the user-input specs cause the domain to exceed 1 by small amounts https://github.com/plotly/plotly.py/pull/4153
+  - Fixed issue with shapes and annotations plotting on the wrong y axis when supplied with a specific axis in the `yref` parameter [[#4177](https://github.com/plotly/plotly.py/pull/4177)]
+  
+  
 
 ## [5.14.1] - 2023-04-05
 

From 76788127d73c3620c256b584631ba3830ed51b77 Mon Sep 17 00:00:00 2001
From: Zach Foltz <zfoltz3@gmail.com>
Date: Fri, 12 May 2023 10:13:46 -0600
Subject: [PATCH 14/16] fixed issue with annotation_text of an
 axis_spanning_shape being displayed on the primary y instead of the yref
 supplied with the axis_spanning_shape

---
 packages/python/plotly/plotly/basedatatypes.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/packages/python/plotly/plotly/basedatatypes.py b/packages/python/plotly/plotly/basedatatypes.py
index 812631c063..ba7196d127 100644
--- a/packages/python/plotly/plotly/basedatatypes.py
+++ b/packages/python/plotly/plotly/basedatatypes.py
@@ -4071,6 +4071,7 @@ def _process_multiple_axis_spanning_shapes(
                 row=row,
                 col=col,
                 exclude_empty_subplots=exclude_empty_subplots,
+                yref=shape_kwargs["yref"],
             )
         # update xref and yref for the new shapes and annotations
         for layout_obj, n_layout_objs_before in zip(

From c2860de16f00f6a705cf5578c56ebd5d942180ee Mon Sep 17 00:00:00 2001
From: Zach Foltz <zfoltz3@gmail.com>
Date: Fri, 12 May 2023 10:46:08 -0600
Subject: [PATCH 15/16] Added check to catch if no yref was supplied

---
 packages/python/plotly/plotly/basedatatypes.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/packages/python/plotly/plotly/basedatatypes.py b/packages/python/plotly/plotly/basedatatypes.py
index 0da2015079..1807212a13 100644
--- a/packages/python/plotly/plotly/basedatatypes.py
+++ b/packages/python/plotly/plotly/basedatatypes.py
@@ -4053,7 +4053,7 @@ def _process_multiple_axis_spanning_shapes(
                 row=row,
                 col=col,
                 exclude_empty_subplots=exclude_empty_subplots,
-                yref=shape_kwargs["yref"],
+                yref=shape_kwargs["yref"] if "yref" in shape_kwargs.keys() else "y",
             )
         # update xref and yref for the new shapes and annotations
         for layout_obj, n_layout_objs_before in zip(

From a8fa9dd4f711124ce4eef0d16a2a6707672eb8fd Mon Sep 17 00:00:00 2001
From: Alex Johnson <alex@plot.ly>
Date: Wed, 24 May 2023 10:19:05 -0400
Subject: [PATCH 16/16] Apply suggestions from code review

---
 CHANGELOG.md                                   | 3 +--
 packages/python/plotly/plotly/basedatatypes.py | 4 ++--
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7b3584e56b..8bc032c041 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,8 +6,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 ### Fixed
   - Fixed another compatibility issue with Pandas 2.0, just affecting `px.*(line_close=True)` [[#4190](https://github.com/plotly/plotly.py/pull/4190)]
-
-  - Added some rounding to the `make_subplots` function to handle situations where the user-input specs cause the domain to exceed 1 by small amounts https://github.com/plotly/plotly.py/pull/4153
+  - Added some rounding to the `make_subplots` function to handle situations where the user-input specs cause the domain to exceed 1 by small amounts [[#4153](https://github.com/plotly/plotly.py/pull/4153)]
   - Sanitize JSON output to prevent an XSS vector when graphs are inserted directly into HTML [[#4196](https://github.com/plotly/plotly.py/pull/4196)]
   - Fixed issue with shapes and annotations plotting on the wrong y axis when supplied with a specific axis in the `yref` parameter [[#4177](https://github.com/plotly/plotly.py/pull/4177)]
 
diff --git a/packages/python/plotly/plotly/basedatatypes.py b/packages/python/plotly/plotly/basedatatypes.py
index 1807212a13..8fa70e0ada 100644
--- a/packages/python/plotly/plotly/basedatatypes.py
+++ b/packages/python/plotly/plotly/basedatatypes.py
@@ -1562,7 +1562,7 @@ def _add_annotation_like(
 
             # If the new_object was created with a yref specified that did not include paper or domain, the specified yref should be used otherwise assign the xref and yref from the layout_keys
             if (
-                new_obj.yref == None
+                new_obj.yref is None
                 or new_obj.yref == "y"
                 or "paper" in new_obj.yref
                 or "domain" in new_obj.yref
@@ -4053,7 +4053,7 @@ def _process_multiple_axis_spanning_shapes(
                 row=row,
                 col=col,
                 exclude_empty_subplots=exclude_empty_subplots,
-                yref=shape_kwargs["yref"] if "yref" in shape_kwargs.keys() else "y",
+                yref=shape_kwargs.get("yref", "y"),
             )
         # update xref and yref for the new shapes and annotations
         for layout_obj, n_layout_objs_before in zip(