Running gvmagic extension on jupyter notebook returning FileNotFounError - ipython

Question

I am developing Python 3.5.3 using the jupyter notebook in Anaconda 2.5.0 (64-bit) on a Windows 10 machine. I am trying to use an extension called 'gvmagic', which is used for viewing graphs. The extension seems to load, but returns a FileNotFoundError instead of a graph.
My input code is (Note: 'visualize_de_bruijn_graph' is a custom code that builds a de Bruijn graph from a string):
dbg = visualize_de_bruijn_graph('ACGCGTCG', 3)
print(dbg)
Which returns graph:
digraph "DeBruijn Graph" {
CG [label="CG"] ;
TC [label="TC"] ;
GC [label="GC"] ;
AC [label="AC"] ;
GT [label="GT"] ;
AC -> CG ;
CG -> GC ;
GC -> CG ;
CG -> GT ;
GT -> TC ;
TC -> CG ;
}
Trying to visualize the graph with the following code:
%load_ext gvmagic
%dotstr dbg
returns the error below. I cannot figure out what file is missing, as all the files referenced are where they are suppose to be.
FileNotFoundError Traceback (most recent call last)
<ipython-input-17-d138faf6c47c> in <module>()
----> 1 get_ipython().magic('dotstr dbg')
C:\Users\username\Anaconda3\lib\site-packages\IPython\core\interactiveshell.py in magic(self, arg_s)
2161 magic_name, _, magic_arg_s = arg_s.partition(' ')
2162 magic_name = magic_name.lstrip(prefilter.ESC_MAGIC)
-> 2163 return self.run_line_magic(magic_name, magic_arg_s)
2164
2165 #-------------------------------------------------------------------------
C:\Users\username\Anaconda3\lib\site-packages\IPython\core\interactiveshell.py in run_line_magic(self, magic_name, line)
2082 kwargs['local_ns'] = sys._getframe(stack_depth).f_locals
2083 with self.builtin_trap:
-> 2084 result = fn(*args,**kwargs)
2085 return result
2086
<decorator-gen-126> in dotstr(self, line)
C:\Users\username\Anaconda3\lib\site-packages\IPython\core\magic.py in <lambda>(f, *a, **k)
191 # but it's overkill for just that one bit of state.
192 def magic_deco(arg):
--> 193 call = lambda f, *a, **k: f(*a, **k)
194
195 if callable(arg):
C:\Users\username\Anaconda3\lib\site-packages\IPython\extensions\gvmagic.py in dotstr(self, line)
50 #line_magic
51 def dotstr(self, line):
---> 52 self._from_str(line, 'dot')
53
54 #line_magic
C:\Users\username\Anaconda3\lib\site-packages\IPython\extensions\gvmagic.py in _from_str(self, line, layout_engine)
151 def _from_str(self, line, layout_engine):
152 s = self.shell.ev(line)
--> 153 data = run_graphviz(s, layout_engine)
154 if data:
155 display_svg(data, raw=True)
C:\Users\username\Anaconda3\lib\site-packages\IPython\extensions\gvmagic.py in run_graphviz(s, layout_engine)
30 cmd = ['dot', '-Tsvg', '-K', layout_engine]
31
---> 32 dot = Popen(cmd, stdin=PIPE, stdout=PIPE, stderr=PIPE)
33 stdoutdata, stderrdata = dot.communicate(s.encode('utf-8'))
34 status = dot.wait()
C:\Users\username\Anaconda3\lib\subprocess.py in __init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds)
674 c2pread, c2pwrite,
675 errread, errwrite,
--> 676 restore_signals, start_new_session)
677 except:
678 # Cleanup if the child failed starting.
C:\Users\username\Anaconda3\lib\subprocess.py in _execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, unused_restore_signals, unused_start_new_session)
953 env,
954 cwd,
--> 955 startupinfo)
956 finally:
957 # Child is launched. Close the parent's copy of those pipe
FileNotFoundError: [WinError 2] The system cannot find the file specified

Answer 1

You have to install the Graphviz software on your PC. For Windows, for example, download this https://graphviz.gitlab.io/_pages/Download/Download_windows.html.
In your IPython session, you have to point to the install location, for example:
import os
os.environ["PATH"] += os.pathsep + 'C:/Program Files (x86)/Graphviz2.38/bin'
%load_ext gvmagic
dbg = visualize_de_bruijn('ACGCGTCG', 3)
%dotstr dbg
And now it should work for you, just as it does for me! You can probably set the PATH variable on your PC instead of having to do it inside IPython each time.