Merge remote-tracking branch 'origin/master' into kaleido

Author: jonmmease

Diff for: doc/python/multiple-axes.md

@@ -22,7 +22,7 @@ jupyter:
     pygments_lexer: ipython3
     version: 3.7.2
   plotly:
-    description: How to make a graph with multiple axes in python.
+    description: How to make a graph with multiple axes (dual y-axis plots, plots with secondary axes) in python.
     display_as: file_settings
     language: python
     layout: base
@@ -225,4 +225,4 @@ fig.show()
 ```
 
 #### Reference
-All of the y-axis properties are found here: https://plotly.com/python/reference/#YAxis.  For more information on creating subplots see the [Subplots in Python](/python/subplots/) section.
+All of the y-axis properties are found here: https://plotly.com/python/reference/#YAxis.  For more information on creating subplots see the [Subplots in Python](/python/subplots/) section.

Diff for: doc/python/tick-formatting.md

@@ -98,7 +98,7 @@ fig.update_layout(yaxis_tickformat = '%')
 fig.show()
 ```
 
-#### Using Tickformat Atttribute - Date/Time
+#### Using Tickformat Attribute - Date/Time
 
 
 For more date/time formatting types, see: https://github.com/d3/d3-time-format/blob/master/README.md
@@ -194,4 +194,4 @@ fig.show()
 ```
 
 #### Reference
-See https://plotly.com/python/reference/#layout-xaxis for more information and chart attribute options!
+See https://plotly.com/python/reference/#layout-xaxis for more information and chart attribute options!

Diff for: doc/python/time-series.md

@@ -184,6 +184,8 @@ fig.show()
 
 The `rangebreaks` attribute available on x- and y-axes of type `date` can be used to hide certain time-periods. In the example below, we show two plots: one in default mode to show gaps in the data, and one where we hide weekends and holidays to show an uninterrupted trading history. Note the smaller gaps between the grid lines for December 21 and January 4, where holidays were removed. Check out the reference for more options: https://plotly.com/python/reference/#layout-xaxis-rangebreaks
 
+> Note: a known limitation of this feature is that it does not support `scattergl` traces. When using this feature on plots with more than a few hundred data points with `px.scatter` or `px.line` or `px.area`, you may need to pass in `render_mode="svg"` to ensure that the underlying trace type is `scatter` and not `scattergl`.
+
 ```python
 import plotly.express as px
 import pandas as pd
@@ -208,4 +210,4 @@ fig.update_xaxes(
     ]
 )
 fig.show()
-```
+```

Diff for: packages/python/plotly/plotly/express/_doc.py

@@ -538,7 +538,7 @@ def make_docstring(fn, override_dict={}, append_dict={}):
         param_desc_list = param_doc[1:]
         param_desc = (
             tw.fill(" ".join(param_desc_list or ""))
-            if param in docs
+            if param in docs or param in override_dict
             else "(documentation missing from map)"
         )
 

Diff for: packages/python/plotly/plotly/figure_factory/_dendrogram.py

@@ -25,14 +25,21 @@ def create_dendrogram(
     color_threshold=None,
 ):
     """
-    Function that returns a dendrogram Plotly figure object.
+    Function that returns a dendrogram Plotly figure object. This is a thin
+    wrapper around scipy.cluster.hierarchy.dendrogram.
 
     See also https://dash.plot.ly/dash-bio/clustergram.
 
     :param (ndarray) X: Matrix of observations as array of arrays
     :param (str) orientation: 'top', 'right', 'bottom', or 'left'
     :param (list) labels: List of axis category labels(observation labels)
-    :param (list) colorscale: Optional colorscale for dendrogram tree
+    :param (list) colorscale: Optional colorscale for the dendrogram tree.
+                              Requires 8 colors to be specified, the 7th of
+                              which is ignored.  With scipy>=1.5.0, the 2nd, 3rd
+                              and 6th are used twice as often as the others.
+                              Given a shorter list, the missing values are
+                              replaced with defaults and with a longer list the
+                              extra values are ignored.
     :param (function) distfun: Function to compute the pairwise distance from
                                the observations
     :param (function) linkagefun: Function to compute the linkage matrix from
@@ -160,8 +167,8 @@ def __init__(
         if len(self.zero_vals) > len(yvals) + 1:
             # If the length of zero_vals is larger than the length of yvals,
             # it means that there are wrong vals because of the identicial samples.
-            # Three and more identicial samples will make the yvals of spliting center into 0 and it will \
-            # accidentally take it as leaves.
+            # Three and more identicial samples will make the yvals of spliting
+            # center into 0 and it will accidentally take it as leaves.
             l_border = int(min(self.zero_vals))
             r_border = int(max(self.zero_vals))
             correct_leaves_pos = range(
@@ -185,6 +192,9 @@ def get_color_dict(self, colorscale):
 
         # These are the color codes returned for dendrograms
         # We're replacing them with nicer colors
+        # This list is the colors that can be used by dendrogram, which were
+        # determined as the combination of the default above_threshold_color and
+        # the default color palette (see scipy/cluster/hierarchy.py)
         d = {
             "r": "red",
             "g": "green",
@@ -193,26 +203,58 @@ def get_color_dict(self, colorscale):
             "m": "magenta",
             "y": "yellow",
             "k": "black",
+            # TODO: 'w' doesn't seem to be in the default color
+            # palette in scipy/cluster/hierarchy.py
             "w": "white",
         }
         default_colors = OrderedDict(sorted(d.items(), key=lambda t: t[0]))
 
         if colorscale is None:
-            colorscale = [
+            rgb_colorscale = [
                 "rgb(0,116,217)",  # blue
                 "rgb(35,205,205)",  # cyan
                 "rgb(61,153,112)",  # green
                 "rgb(40,35,35)",  # black
                 "rgb(133,20,75)",  # magenta
                 "rgb(255,65,54)",  # red
                 "rgb(255,255,255)",  # white
-                "rgb(255,220,0)",
-            ]  # yellow
+                "rgb(255,220,0)",  # yellow
+            ]
+        else:
+            rgb_colorscale = colorscale
 
         for i in range(len(default_colors.keys())):
             k = list(default_colors.keys())[i]  # PY3 won't index keys
-            if i < len(colorscale):
-                default_colors[k] = colorscale[i]
+            if i < len(rgb_colorscale):
+                default_colors[k] = rgb_colorscale[i]
+
+        # add support for cyclic format colors as introduced in scipy===1.5.0
+        # before this, the colors were named 'r', 'b', 'y' etc., now they are
+        # named 'C0', 'C1', etc. To keep the colors consistent regardless of the
+        # scipy version, we try as much as possible to map the new colors to the
+        # old colors
+        # this mapping was found by inpecting scipy/cluster/hierarchy.py (see
+        # comment above).
+        new_old_color_map = [
+            ("C0", "b"),
+            ("C1", "g"),
+            ("C2", "r"),
+            ("C3", "c"),
+            ("C4", "m"),
+            ("C5", "y"),
+            ("C6", "k"),
+            ("C7", "g"),
+            ("C8", "r"),
+            ("C9", "c"),
+        ]
+        for nc, oc in new_old_color_map:
+            try:
+                default_colors[nc] = default_colors[oc]
+            except KeyError:
+                # it could happen that the old color isn't found (if a custom
+                # colorscale was specified), in this case we set it to an
+                # arbitrary default.
+                default_colors[n] = "rgb(0,116,217)"
 
         return default_colors