WestHealth
google colab
Hi, great package! I was wondering if you had any tips for getting the graph to load in google colab. Currently, I get 'localhost refused to connect' as an error.
Same here. It'd be great to have it working in Colab (ps it works if you just save to a file)
I ended up using a binder notebook to demo the stuff I was working on.
the other option is to save the html file locally, open the 'files' sidebar, right click + download and then open it locally. laborious but it works..
The problem is the files for the underlying library vis.js are being linked from the web at the visualization time. This poses a limitation when using the library in environments with no internet connection. It would be great to offer the user an option to specify the location of the required files or, even better, embed the required files into the library. Right know it is possible to patch the template.html file but that should not be the way to go. Is there any licensing reason for not doing so?
@masdeseiscaracteres do you think that it'd be enough to add a local copy of visjs in the same folder as the html template, and then updating the link?
I don't think so. That's the first thing I tried and failed miserably.
It fails because when you run
g.show('example.html')
a file called example.html is created in your working directory based on the HTML template. Your browser needs to be able to get to the location where you have your visjs files stored based on the link in that HTML file.
What I did so far was embedding the whole visjs into the HTML template so that no links are required. I guess there has to be a cleaner way to do it.
BTW, this is how plotly.py is doing to allow the user to create plots that work offline: https://github.com/plotly/plotly.py/blob/master/packages/python/plotly/plotly/offline/offline.py#L458-L492
that makes sense and prob the way to go. I'm overstretched at the moment but can't wait to have time to hack something together ...
I finally got it to work. I did two things
a) modify the html template so that all JS is included.
b) create a custom version of pyvis.Network so that the template path points at the new template and the show method checks if we are in Colab and if so it return a IPython.display.HTML object instead of an IFrame.
This has been implemented as part of another library I'm working on (dimcli), but the gist of it is generic enough:
try:
from google.colab import files
COLAB_ENV = True
except:
COLAB_ENV = False
class NetworkViz(PyvisNetwork):
"""Extend PyVis class so that we can use a modified template that works in Colab.
"""
def __init__(self,
height="500px",
width="500px",
directed=False,
notebook=False,
bgcolor="#ffffff",
font_color=False,
layout=None):
# call super class init
PyvisNetwork.__init__(self,
height,
width,
directed,
notebook,
bgcolor,
font_color,
layout)
# override template location - update as per installation
self.path = os.path.abspath(os.path.join(os.path.dirname( __file__ ), '..', 'templates/pyvis_inline.html'))
# fun copied from pyvis to skip imports
def check_html(self, name):
"""
Given a name of graph to save or write, check if it is of valid syntax
:param: name: the name to check
:type name: str
"""
assert len(name.split(".")) >= 2, "invalid file type for %s" % name
assert name.split(
".")[-1] == "html", "%s is not a valid html file" % name
# fun extended for colab
def show(self, name):
"""
Writes a static HTML file and saves it locally before opening.
:param: name: the name of the html file to save as
:type name: str
"""
self.check_html(name)
if self.template is not None:
if not COLAB_ENV:
# write file and return IFrame
return self.write_html(name, notebook=True)
else:
# write file and return HTML
self.write_html(name, notebook=True)
return IPython.display.HTML(filename=name)
else:
self.write_html(name)
webbrowser.open(name)
See it in action in this Colab notebook https://drive.google.com/file/d/188vea7vRsLjWvHd0RBnufXOatt43uBcC/view?usp=sharing
PS it'd be nice if @boludo00 or one of the maintainers would consider changing pyvis so that Google Colab is supported by default...
I don't know if something has changed in the last couple of years but it looks like on Colab you just need to perform an extra step to display the generated HTML:
from IPython.core.display import display, HTML
g.show('network.html')
display(HTML('network.html'))
The problem is in the html file that it generates:
<!-- < link rel="stylesheet" href="../node_modules/vis/dist/vis.min.css" type="text/css" />
<script type="text/javascript" src="../node_modules/vis/dist/vis.js"> </script>-->
It fails with 'vis is not defined' because, as you see, vis library is included with a relative path, which is, obviously, is missing in the notebooks. Not to mention, that it is commented out, lol.
The fix would be to include it from cdn, like the rest of js in the file. WHOEVER HAS ACCESS TO THE CODE -> FIX IT!!!
I don't know if something has changed in the last couple of years but it looks like on Colab you just need to perform an extra step to display the generated HTML:
from IPython.core.display import display, HTML g.show('network.html') display(HTML('network.html'))
I got it to work by passing in cdn_resources = 'remote'
net = Network(notebook = True, cdn_resources = 'remote')
Possibly helpful to others - as of today, this works with default packages and versions, building on this thread and others.
` #pyvis 0.3.2 !pip install pyvis
from pyvis.network import Network import networkx as nx from IPython.core.display import display, HTML net = Network(notebook = True, cdn_resources = 'in_line')
#build graph nx_graph = nx.cycle_graph(10) nx_graph.nodes[1]['title'] = 'Number 1' nx_graph.nodes[1]['group'] = 1 nx_graph.nodes[3]['title'] = 'I belong to a different group!' nx_graph.nodes[3]['group'] = 10 nx_graph.add_node(20, size=20, title='couple', group=2) nx_graph.add_node(21, size=15, title='couple', group=2) nx_graph.add_edge(20, 21, weight=5) nx_graph.add_node(25, size=25, label='lonely', title='lonely node', group=3)
#populates the nodes and edges data structures net.from_nx(nx_graph) net.show('nx.html') display(HTML('nx.html')) `
