Note: for anyone are experiencing the same issue, a temporary work around I am using is found here Bokeh, how to change column used for glyph colors with CustomJS callbacks? although this is not sufficient as the interact feature is needed
Any help and suggestions are appreciated! :) However, do keep in mind I may be restricted due to the setup of our systems. I have provided as extensive help information as I could, do let me know if any other information will help.
I am creating a template for my company with Jupyter notebook and Bokeh. I have been successful so far until this particular issue. The 'interact' method which would allow for a user to change e.g. the colour of the datapoints via a dropdown menu does not load. I have tried many solutions, most of which are consistent with the following:
jupyter nbextension enable --py widgetsnbextension
jupyter nbextension enable --py --sys-prefix widgetsnbextension
Furthermore, I have also tried solutions requested on the following url all the way through but had no luck: https://github.com/jupyter-widgets/ipywidgets/issues/1745
Code that errors:
import pandas as pd
import numpy as np
#import exmaple dataset
from sklearn import datasets
#import clustering methods
from sklearn.cluster import KMeans
from sklearn.cluster import SpectralClustering
#import Bokeh
import bokeh
from bokeh.plotting import figure
from bokeh.io import output_notebook, show
from bokeh.layouts import widgetbox, gridplot
from bokeh.models import Select, CustomJS, ColumnDataSource
from bokeh.models.widgets import Dropdown
from ipywidgets import interact
from bokeh.io import push_notebook
#Initialise Bokeh into the notebook to display graphs with interactive toolbar
output_notebook()
p3 = figure(title="test", plot_height=300, plot_width=600)
colors = [colormap[x] for x in y]
p3.circle(f1, f2, size=10, color=colors)
h = show(p3, notebook_handle=True)
def update(f):#f=["Actual", "Kmeans", "Spectral"]
colormap = {1: 'red', 2: 'green', 0: 'blue'}
if f == "Actual":
the_x = np.array(list(zip(f1, f2)))
the_y = y
colors = [colormap[x] for x in the_y]
elif f == "Kmeans":
the_x = np.array(list(zip(f1, f2)))
kmeans = KMeans(n_clusters=3)
# Fitting the input data
kmeans = kmeans.fit(the_x)
# Getting the cluster labels
the_y = kmeans.predict(the_x)
colors = [colormap[x] for x in the_y]
elif f == "Spectral":
the_x = np.array(list(zip(f1, f2)))
clustering = SpectralClustering(n_clusters=3, assign_labels="discretize", random_state=0).fit(the_x)
the_y = clustering.labels_
colors = [colormap[x] for x in the_y]
#p3.circle(f1, f2, size=10, color=colors)
push_notebook(handle=h)
interact(update, f=["Actual", "Kmeans", "Spectral"])#this line here
Error displayed:
<function __main__.update(f)>
Versions Information
conda --version
conda 4.5.4
conda info
active environment : bokeh_test_2_1
active env location : /home/xxxxxxx/.conda/envs/bokeh_test_2_1
shell level : 1
user config file : /home/xxxxxxx/.condarc
populated config files : /home/xxxxxxx/.condarc
conda version : 4.5.4
conda-build version : 3.0.27
python version : 2.7.14.final.0
base environment : /opt/cloudera/parcels/Anaconda (read only)
channel URLs : xxxxxxx/current/anaconda-suite/pkgs/linux-64
xxxxxxx/current/anaconda-suite/pkgs/noarch
package cache : /opt/cloudera/parcels/Anaconda/pkgs
/home/xxxxxxx/.conda/pkgs
envs directories : /home/xxxxxxx/.conda/envs
/opt/cloudera/parcels/Anaconda/envs
platform : linux-64
user-agent : conda/4.5.4 requests/2.18.4 CPython/2.7.14 Linux/3.10.0-862.11.6.el7.x86_64 rhel/7.5 glibc/2.17
UID:GID : xxxxxxx
netrc file : None
offline mode : False
jupyter nbextension list
Known nbextensions:
config dir: /home/xxxxxxxx/.conda/envs/bokeh_test_2_1/etc/jupyter/nbconfig
notebook section
jupyter-js-widgets/extension enabled
- Validating: OK
jupyter --paths
config:
/home/xxxxxxxx/.jupyter
/home/xxxxxxxx/.conda/envs/bokeh_test_2_1/etc/jupyter
/usr/local/etc/jupyter
/etc/jupyter
data:
/home/xxxxxxxx/.local/share/jupyter
/home/xxxxxxxx/.conda/envs/bokeh_test_2_1/share/jupyter
/usr/local/share/jupyter
/usr/share/jupyter
runtime:
/home/xxxxxxxx/.local/share/jupyter/runtime
(bokeh_test_2_1) xxxx@xxxx-xxxxxxxxx $ conda list
# packages in environment at /home/xxxxxxxx/.conda/envs/bokeh_test_2_1:
#
# Name Version
_tflow_180_select 3.0
absl-py 0.2.2
astor 0.6.2
backcall 0.1.0
blas 1.0
bleach 1.5.0
bokeh 0.12.16
ca-certificates 2018.03.07
certifi 2018.4.16
dbus 1.13.2
decorator 4.3.0
entrypoints 0.2.3
expat 2.2.5
fontconfig 2.12.6
freetype 2.8
gast 0.2.0
glib 2.56.1
gmp 6.1.2
grpcio 1.11.0
gst-plugins-base 1.14.0
gstreamer 1.14.0
h5py 2.8.0
hdf5 1.10.2
html5lib 0.9999999
icu 58.2
intel-openmp 2018.0.0
ipykernel 4.8.2
ipython 6.4.0
ipython_genutils 0.2.0
ipywidgets 7.2.1
jedi 0.12.0
jinja2 2.10
jpeg 9b
jsonschema 2.6.0
jupyter 1.0.0
jupyter_client 5.2.3
jupyter_console 5.2.0
jupyter_core 4.4.0
keras 2.1.6
libedit 3.1.20170329
libffi 3.2.1
libgcc-ng 7.2.0
libgfortran-ng 7.2.0
libpng 1.6.34
libprotobuf 3.5.2
libsodium 1.0.16
libstdcxx-ng 7.2.0
libxcb 1.13
libxml2 2.9.8
markdown 2.6.11
markupsafe 1.0
mistune 0.8.3
mkl 2018.0.2
mkl_fft 1.0.1
mkl_random 1.0.1
nbconvert 5.3.1
nbformat 4.4.0
ncurses 6.1
notebook 5.5.0
numpy 1.14.3
numpy-base 1.14.3
openssl 1.0.2o
packaging 17.1
pandas 0.23.0
pandoc 1.19.2.1
pandocfilters 1.4.2
parso 0.2.0
pcre 8.42
pexpect 4.5.0
pickleshare 0.7.4
pip 10.0.1
prompt_toolkit 1.0.15
protobuf 3.5.2
ptyprocess 0.5.2
py4j 0.10.6
pygments 2.2.0
pyparsing 2.2.0
pyqt 5.9.2
pyspark 2.3.0
python 3.6.5
python-dateutil 2.7.3
pytz 2018.4
pyyaml 3.12
pyzmq 17.0.0
qt 5.9.5
qtconsole 4.3.1
readline 7.0
scikit-learn 0.19.1
scipy 1.1.0
send2trash 1.5.0
setuptools 39.2.0
simplegeneric 0.8.1
sip 4.19.8
six 1.11.0
sqlite 3.23.1
tensorboard 1.8.0
tensorflow 1.8.0
tensorflow-base 1.8.0
termcolor 1.1.0
terminado 0.8.1
testpath 0.3.1
tk 8.6.7
tornado 5.0.2
traitlets 4.3.2
wcwidth 0.1.7
werkzeug 0.14.1
wheel 0.31.1
widgetsnbextension 3.2.1
xz 5.2.4
yaml 0.1.7
zeromq 4.2.5
zlib 1.2.11
