I wanted to draw a simple graph with networkx and graphviz but there seems to be a problem with pydot.
I'm using
- Ubuntu 18.04.4 LTS
- Python 3.6.9
- graphviz 0.14
- networkx 2.4
- the newest versions of pydot, pydot2, pydot3 and pydotplus
I tried to run:
import networkx as nx
G = nx.complete_graph(4)
pos = nx.nx_pydot.graphviz_layout(G)
pos = nx.nx_pydot.graphviz_layout(G, prog='dot')
but seem to get an error when no matter what pydot module I use and I do not know why.
for pydot2 1.0.33 I get:
Couldn't import dot_parser, loading of dot files will not be possible.
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
in
1 G = nx.complete_graph(4)
----> 2 pos = nx.nx_pydot.graphviz_layout(G)
3 pos = nx.nx_pydot.graphviz_layout(G, prog='dot')
/usr/local/lib/python3.6/dist-packages/networkx/drawing/nx_pydot.py in graphviz_layout(G, prog, root)
266 This is a wrapper for pydot_layout.
267 """
--> 268 return pydot_layout(G=G, prog=prog, root=root)
269
270
/usr/local/lib/python3.6/dist-packages/networkx/drawing/nx_pydot.py in pydot_layout(G, prog, root)
314 # List of low-level bytes comprising a string in the dot language converted
315 # from the passed graph with the passed external GraphViz command.
--> 316 D_bytes = P.create_dot(prog=prog)
317
318 # Unique string decoded from these bytes with the preferred locale encoding
/usr/local/lib/python3.6/dist-packages/pydot.py in (f, prog)
1800 self.__setattr__(
1801 'create_'+frmt,
-> 1802 lambda f=frmt, prog=self.prog : self.create(format=f, prog=prog))
1803 f = self.__dict__['create_'+frmt]
1804 f.__doc__ = '''Refer to the docstring accompanying the 'create' method for more information.'''
/usr/local/lib/python3.6/dist-packages/pydot.py in create(self, prog, format)
1964 tmp_fd, tmp_name = tempfile.mkstemp()
1965 os.close(tmp_fd)
-> 1966 self.write(tmp_name)
1967 tmp_dir = os.path.dirname(tmp_name )
1968
/usr/local/lib/python3.6/dist-packages/pydot.py in write(self, path, prog, format)
1893 prog = self.prog
1894
-> 1895 dot_fd = file(path, "w+b")
1896 if format == 'raw':
1897 data = self.to_string()
NameError: name 'file' is not defined
for pydot3 I get:
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
in
1 G = nx.complete_graph(4)
----> 2 pos = nx.nx_pydot.graphviz_layout(G)
3 pos = nx.nx_pydot.graphviz_layout(G, prog='dot')
/usr/local/lib/python3.6/dist-packages/networkx/drawing/nx_pydot.py in graphviz_layout(G, prog, root)
266 This is a wrapper for pydot_layout.
267 """
--> 268 return pydot_layout(G=G, prog=prog, root=root)
269
270
/usr/local/lib/python3.6/dist-packages/networkx/drawing/nx_pydot.py in pydot_layout(G, prog, root)
314 # List of low-level bytes comprising a string in the dot language converted
315 # from the passed graph with the passed external GraphViz command.
--> 316 D_bytes = P.create_dot(prog=prog)
317
318 # Unique string decoded from these bytes with the preferred locale encoding
/usr/local/lib/python3.6/dist-packages/pydot/__init__.py in (f, prog)
1798 self.__setattr__(
1799 'create_'+frmt,
-> 1800 lambda f=frmt, prog=self.prog : self.create(format=f, prog=prog))
1801 f = self.__dict__['create_'+frmt]
1802 f.__doc__ = '''Refer to the docstring accompanying the 'create' method for more information.'''
/usr/local/lib/python3.6/dist-packages/pydot/__init__.py in create(self, prog, format)
2011
2012 if stderr_output:
-> 2013 stderr_output = ''.join(stderr_output)
2014
2015 #pid, status = os.waitpid(p.pid, 0)
TypeError: sequence item 0: expected str instance, bytes found
for pydotplus 2.0.2 I get:
ModuleNotFoundError Traceback (most recent call last)
in
1 G = nx.complete_graph(4)
----> 2 pos = nx.nx_pydot.graphviz_layout(G)
3 pos = nx.nx_pydot.graphviz_layout(G, prog='dot')
/usr/local/lib/python3.6/dist-packages/networkx/drawing/nx_pydot.py in graphviz_layout(G, prog, root)
266 This is a wrapper for pydot_layout.
267 """
--> 268 return pydot_layout(G=G, prog=prog, root=root)
269
270
/usr/local/lib/python3.6/dist-packages/networkx/drawing/nx_pydot.py in pydot_layout(G, prog, root)
307
308 """
--> 309 import pydot
310 P = to_pydot(G)
311 if root is not None:
ModuleNotFoundError: No module named 'pydot'
for pydot I get a parsing error and for pydot2 I get a file not found error.
