[BUG] nan_color argument in LinearColorMapper is not used

ALL software version info (bokeh, python, notebook, OS, browser, any other relevant packages)

bokeh.version: 1.3.0 python: 3.7.3 OS: Windows 10 browser: all

Description of expected behavior and the observed behavior

LinearColorMapper has the option to set nan_color. It is however not used. Instead it sets the color of the nan entry to be the lowest color in the range.

In the example below you should see the center region as black, but instead it shows as lowest color in the range.

Complete, minimal, self-contained example code that reproduces the issue

To run, download this file: provinces.zip

import geopandas as gpd 
import numpy as np
from bokeh.palettes import Reds
from bokeh.models import GeoJSONDataSource, LinearColorMapper
from bokeh.plotting import figure, show

geodf = gpd.read_file("provinces.geojson")
geodf.loc[6, 'index'] = np.nan
print(geodf)
color_mapper = LinearColorMapper(palette=Reds[9][::-1], nan_color='black')

p = figure()
geo_source = GeoJSONDataSource(geojson=geodf.to_json())
p.patches('xs', 'ys', fill_alpha=1, 
              fill_color={'field': 'index', 'transform': color_mapper}, 
              line_color='white', line_width=0.5, 
              source=geo_source)

show(p)

Stack traceback and/or browser JavaScript console output

Data frame that is plotted

Screenshots or screencasts of the bug in action

[bryevdv]

Yes, brilliant this small change fixes:

diff --git a/bokehjs/src/lib/models/sources/geojson_data_source.ts b/bokehjs/src/lib/models/sources/geojson_data_sourc
index a7918a425..661a011d9 100644
--- a/bokehjs/src/lib/models/sources/geojson_data_source.ts
+++ b/bokehjs/src/lib/models/sources/geojson_data_source.ts
@@ -31,6 +31,10 @@ export namespace GeoJSONDataSource {

 export interface GeoJSONDataSource extends GeoJSONDataSource.Attrs {}

+function orNaN(v: number | undefined) {
+  return v != null ? v : NaN
+}
+
 export class GeoJSONDataSource extends ColumnarDataSource {
   properties: GeoJSONDataSource.Props

@@ -75,16 +79,12 @@ export class GeoJSONDataSource extends ColumnarDataSource {
     for (const property in properties) {
       if (!data.hasOwnProperty(property))
         data[property] = this._get_new_nan_array(item_count)
-      data[property][i] = properties[property]
+      data[property][i] = orNaN(properties[property])
     }
   }

   private _add_geometry(geometry: GeoItem, data: GeoData, i: number): void {

-    function orNaN(v: number | undefined) {
-      return v != null ? v : NaN
-    }
-
     function flatten(acc: Position[], item: Position[]) {
       return acc.concat([[NaN, NaN, NaN]]).concat(item)
     }

_add_properties tried to handle this by pre-populating nan arrays for the values but it did not all “orNan” on each value, so nulls that made it over would just overwrite the nans. I will add a PR for this later this week unless someone else gets to it first (needs a unit test that maintains nulls in properties end up as nans in the columns)

[harmbuisman]

@bryevdv, great to read you found a solution, thanks for the quick turnaround!