cjdrake / gvmagic Goto Github PK

Hi

I am running Jupyter Lab Version 1.2.4. I recently cranked up a Jupyter Notebook that was about two years old, and %%dot didn't work :( ( I got the broken object icon, instead of the rendered SVG).

I found the fix was to convert the dot output (svg script) from a byte array to a string, like so in the function run_graphviz :

    dot = Popen(cmd, stdin=PIPE, stdout=PIPE, stderr=PIPE,  shell=True)
    stdoutdata, stderrdata = dot.communicate(s.encode('utf-8'))
    status = dot.wait()
    if status == 0:
        # convert byte array into string
        return stdoutdata.decode('utf-8')

I guess iPython has become more strict in what it accepts (or has dropped support for Python 2.*)

happy to supply more info if needed
Don

I'm attaching two patch files for gvmagic.py, which you should be able to apply using git. They do the following:

1. Find the dot executable in the user's shell, and invoke it by absolute pathname. This addresses #1
2. Ensure that run_graphviz returns a string. Under at least some conditions it will return a bytearray instead of a string, and then jupyter won't properly display the SVG image.

0001-Fix-invocation-of-dot-executable.patch.txt
0002-Ensure-run_graphviz-returns-string.patch.txt

Hi

I am running Jupyterlab Version 0.31.8 in Python 3.6 (3.6.3 | packaged by conda-forge | (default, Nov 4 2017, 10:10:42) [MSC v.1900 64 bit (AMD64)]), running on windows 10 (Windows-10-10.0.16299-SP0)

I installed graphviz 2.38.0 and python-graphviz 0.8.2 via anaconda navigator.

The dot shell command reports the dot version as:
dot - graphviz version 2.38.0 (20140413.2041)

I downloaded gvmagic.py from:
https://raw.githubusercontent.com/cjdrake/ipython-magic/master/gvmagic.py

on 7th March 2018

The magic commands:
%reload_ext gvmagic

%%dot

graph{
a -- b;
b -- c;
a -- c;
d -- c;
e -- c;
e -- a;
}

then fail with a Windows 'File not found' on the subprocess.Popen call that runs dot.

If I add the parameter shell=True to this call, then it all works fine:
IE dot = Popen(cmd, stdin=PIPE, stdout=PIPE, stderr=PIPE, shell=True)

happy to run more tests, if needed

Cheers
Don

I am running Jupyterlab Version 0.31.8 in Python 3.6 (3.6.3 | packaged by conda-forge | (default, Nov 4 2017, 10:10:42) [MSC v.1900 64 bit (AMD64)]), running on windows 10 (Windows-10-10.0.16299-SP0)

I installed graphviz 2.38.0 and python-graphviz 0.8.2 via anaconda navigator.

The dot shell command reports the dot version as:
dot - graphviz version 2.38.0 (20140413.2041)

Jupyterlab is running in Microsoft Edge 41.16299.248.0

the simple %%dot file

 %%dot

 graph {

  server1 [image="server.bmp", label="", shape=none]
  server2

  server1--server2
  }

fails to display the image in the output cell, and converting the notebook to HTML also yields an empty node (with no image).

Running the equivalent dot command from the command line works fine (image is displayed in node).

The format of the image (bmp, png, etc) does not seem to affect the result (all fail to display inside the node in the diagram in the notebook output cell).

Please note that I am setting shell=True in the gvmagic Popen call, as per issue previously raised.

happy to run more tests

Don