I'm trying to plot some geometric primitives in ipython (lines, circles, ellipses), following the sympy documentation.
I am using Sympy release 1.1.1 and python 3.5, on the CoCalc system, but can reproduce identical results on my own local installation of ipython and sympy (2.7 and 0.7.6). Here is my code:
from sympy import Point, Circle
from sympy.plotting.plot import Plot
p = Plot(axes='label_axes=True')
c = Circle(Point(0,0), 1)
p[0] = c
Now, when I enter p on an input line, ipython just returns the object but doesn't plot it:
In[2] = p
Out[2] = <sympy.plotting.plot.Plot at 0x7f2e64fe62e8>
The plot command works as expected, so the matplotlib backend is functional.
When I enter p.show(), I get the following error:
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-15-02f33f5f7a8f> in <module>()
----> 1 p.show()
/ext/anaconda3/lib/python3.5/site-packages/sympy/plotting/plot.py in show(self)
194 self._backend.close()
195 self._backend = self.backend(self)
--> 196 self._backend.show()
197
198 def save(self, path):
/ext/anaconda3/lib/python3.5/site-packages/sympy/plotting/plot.py in show(self)
1027
1028 def show(self):
-> 1029 self.process_series()
1030 #TODO after fixing https://github.com/ipython/ipython/issues/1255
1031 # you can uncomment the next line and remove the pyplot.show() call
/ext/anaconda3/lib/python3.5/site-packages/sympy/plotting/plot.py in process_series(self)
989 starts = [s.start for s in parent._series]
990 ends = [s.end for s in parent._series]
--> 991 self.ax.set_xlim(min(starts), max(ends))
992 if parent.ylim:
993 self.ax.set_ylim(parent.ylim)
ValueError: min() arg is an empty sequence
It displays and empty set of coordinate axes (without the circle). Also, p.save("foo.png") produces a similar error.
I have also tried p = Plot(Circle((0,0),1) (although this is not what the documentation suggests to do), and again nothing is shown, with p.show() producing another long error:
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-17-f1f858abbdb7> in <module>()
1 p = Plot(Circle((0,0),1))
----> 2 p.show()
/ext/anaconda3/lib/python3.5/site-packages/sympy/plotting/plot.py in show(self)
193 if hasattr(self, '_backend'):
194 self._backend.close()
--> 195 self._backend = self.backend(self)
196 self._backend.show()
197
/ext/anaconda3/lib/python3.5/site-packages/sympy/plotting/plot.py in __new__(cls, parent)
1065 matplotlib = import_module('matplotlib', min_module_version='1.1.0', catch=(RuntimeError,))
1066 if matplotlib:
-> 1067 return MatplotlibBackend(parent)
1068 else:
1069 return TextBackend(parent)
/ext/anaconda3/lib/python3.5/site-packages/sympy/plotting/plot.py in __init__(self, parent)
872 def __init__(self, parent):
873 super(MatplotlibBackend, self).__init__(parent)
--> 874 are_3D = [s.is_3D for s in self.parent._series]
875 self.matplotlib = import_module('matplotlib',
876 __import__kwargs={'fromlist': ['pyplot', 'cm', 'collections']},
/ext/anaconda3/lib/python3.5/site-packages/sympy/plotting/plot.py in <listcomp>(.0)
872 def __init__(self, parent):
873 super(MatplotlibBackend, self).__init__(parent)
--> 874 are_3D = [s.is_3D for s in self.parent._series]
875 self.matplotlib = import_module('matplotlib',
876 __import__kwargs={'fromlist': ['pyplot', 'cm', 'collections']},
AttributeError: 'Circle' object has no attribute 'is_3D'
Those examples are from "pygletplot" module which basically doesn't work (certainly not under Python 3), and hasn't been tested or developed for years. What SymPy can plot:
graphs y=f(x), with plot
parametric curves, with plot_parametric
implicit curves, with plot_implicit
3D graphs z=f(x, y), with plot3d
parametric curves in 3D, with plot3d_parametric_line
parametric surface, with plot3d_parametric_surface
Related
I am trying to read a GML file using the following code:
import geopandas as gpd
G = gpd.read_file('extract/top10nl_gebouw.gml', driver='gml')
But the following error is raised:
---------------------------------------------------------------------------
CPLE_AppDefinedError Traceback (most recent call last)
Input In [4], in <cell line: 3>()
1 import geopandas as gpd
----> 3 G = gpd.read_file('extract/top10nl_gebouw.gml', driver='gml')
File ~/opt/anaconda3/lib/python3.9/site-packages/geopandas/io/file.py:253, in _read_file(filename, bbox, mask, rows, engine, **kwargs)
250 path_or_bytes = filename
252 if engine == "fiona":
--> 253 return _read_file_fiona(
254 path_or_bytes, from_bytes, bbox=bbox, mask=mask, rows=rows, **kwargs
255 )
256 elif engine == "pyogrio":
257 return _read_file_pyogrio(
258 path_or_bytes, bbox=bbox, mask=mask, rows=rows, **kwargs
259 )
File ~/opt/anaconda3/lib/python3.9/site-packages/geopandas/io/file.py:301, in _read_file_fiona(path_or_bytes, from_bytes, bbox, mask, rows, **kwargs)
293 with fiona_env():
294 with reader(path_or_bytes, **kwargs) as features:
295
296 # In a future Fiona release the crs attribute of features will
297 # no longer be a dict, but will behave like a dict. So this should
298 # be forwards compatible
299 crs = (
300 features.crs["init"]
--> 301 if features.crs and "init" in features.crs
302 else features.crs_wkt
303 )
305 # handle loading the bounding box
306 if bbox is not None:
File ~/opt/anaconda3/lib/python3.9/site-packages/fiona/collection.py:215, in Collection.crs(self)
213 """Returns a Proj4 string."""
214 if self._crs is None and self.session:
--> 215 self._crs = self.session.get_crs()
216 return self._crs
File fiona/ogrext.pyx:742, in fiona.ogrext.Session.get_crs()
File fiona/_err.pyx:291, in fiona._err.exc_wrap_pointer()
CPLE_AppDefinedError: Cannot import 28992 due to ALLOW_FILE_ACCESS=NO
I have tried installing and uninstalling different versions of GeoPandas and Fiona, but nothing seems to fix the issue. My colleague who runs the exact same code (with Fiona 1.8.6) is not experiencing any issues.
Hey I am pretty new to SymPy. I am trying to use SymPy's built-in plotting to plot some functions. My codes are as follows:
from sympy import Symbol, sin, Function, pi,exp
from sympy.plotting import plot
t = Symbol('t')
source = t**2
plot(source,(t,0,1))
This works perfectly. However, notice that I have also imported functions such as sin and exp above. However, I am finding anything involving these functions, SymPy will not plot. For example,
source1 = exp(t)
source2= sin(t)
plot(source1,(t,0,1))
plot(source2,(t,0,1))
Neither of these will work. The error I received is as follows, using the case with sin as an example:
TypeError Traceback (most recent call last)
/usr/local/lib/python3.6/dist-packages/sympy/plotting/experimental_lambdify.py in __call__(self, args, kwargs)
194 #The result can be sympy.Float. Hence wrap it with complex type.
--> 195 result = complex(self.lambda_func(args))
196 if abs(result.imag) > 1e-7 * abs(result):
TypeError: complex() first argument must be a string or a number, not 'FunctionClass'
During handling of the above exception, another exception occurred:
AttributeError Traceback (most recent call last)
<ipython-input-45-85c4f08c25e4> in <module>
1 f0 = 15
2 source = sin(t)
----> 3 plot(exp(t),(t,0,1))
/usr/local/lib/python3.6/dist-packages/sympy/plotting/plot.py in plot(*args, **kwargs)
1556 plots = Plot(*series, **kwargs)
1557 if show:
-> 1558 plots.show()
1559 return plots
1560
/usr/local/lib/python3.6/dist-packages/sympy/plotting/plot.py in show(self)
189 self._backend.close()
190 self._backend = self.backend(self)
--> 191 self._backend.show()
192
193 def save(self, path):
/usr/local/lib/python3.6/dist-packages/sympy/plotting/plot.py in show(self)
1246
1247 def show(self):
-> 1248 self.process_series()
1249 #TODO after fixing https://github.com/ipython/ipython/issues/1255
1250 # you can uncomment the next line and remove the pyplot.show() call
/usr/local/lib/python3.6/dist-packages/sympy/plotting/plot.py in process_series(self)
1243 if isinstance(self.parent, PlotGrid):
1244 parent = self.parent.args[i]
-> 1245 self._process_series(series, ax, parent)
1246
1247 def show(self):
/usr/local/lib/python3.6/dist-packages/sympy/plotting/plot.py in _process_series(self, series, ax, parent)
1072 # Create the collections
1073 if s.is_2Dline:
-> 1074 collection = self.LineCollection(s.get_segments())
1075 ax.add_collection(collection)
1076 elif s.is_contour:
/usr/local/lib/python3.6/dist-packages/sympy/plotting/plot.py in get_segments(self)
661 list_segments.append([p, q])
662
--> 663 f_start = f(self.start)
664 f_end = f(self.end)
665 sample(np.array([self.start, f_start]),
/usr/local/lib/python3.6/dist-packages/sympy/plotting/experimental_lambdify.py in __call__(self, args, kwargs)
234 ' problematic. We are trying a failback method'
235 ' that may still work. Please report this as a bug.')
--> 236 if abs(result.imag) > 1e-7 * abs(result):
237 return None
238 else:
AttributeError: type object 'exp' has no attribute 'imag'
This might be something trivial, but as a beginner I am having quite a hard time figuring these out. Really appreciate your help!!
I want to use ggplot2 within Jupyter Notebook. However, when I try to make an R magic cell and introduce a variable, I get an error.
Here is the code (one paragraph indicates one cell):
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
import rpy2
%matplotlib inline
from rpy2.robjects import pandas2ri
pandas2ri.activate()
%load_ext rpy2.ipython
%%R
library(ggplot2)
data = pd.read_csv('train_titanic.csv')
%%R -i data -w 900 -h 480 -u px
With this last cell, I get the following error (incl traceback):
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
~/anaconda3/envs/catenv/lib/python3.7/site-packages/rpy2/robjects/pandas2ri.py in py2rpy_pandasdataframe(obj)
54 try:
---> 55 od[name] = conversion.py2rpy(values)
56 except Exception as e:
~/anaconda3/envs/catenv/lib/python3.7/functools.py in wrapper(*args, **kw)
839
--> 840 return dispatch(args[0].__class__)(*args, **kw)
841
~/anaconda3/envs/catenv/lib/python3.7/site-packages/rpy2/robjects/pandas2ri.py in py2rpy_pandasseries(obj)
125 if type(x) is not homogeneous_type:
--> 126 raise ValueError('Series can only be of one type, or None.')
127 # TODO: Could this be merged with obj.type.name == 'O' case above ?
ValueError: Series can only be of one type, or None.
During handling of the above exception, another exception occurred:
TypeError Traceback (most recent call last)
~/anaconda3/envs/catenv/lib/python3.7/site-packages/rpy2/rinterface_lib/sexp.py in from_object(cls, obj)
367 try:
--> 368 mv = memoryview(obj)
369 res = cls.from_memoryview(mv)
TypeError: memoryview: a bytes-like object is required, not 'Series'
During handling of the above exception, another exception occurred:
AttributeError Traceback (most recent call last)
<ipython-input-14-75e210679e4a> in <module>
----> 1 get_ipython().run_cell_magic('R', '-i data -w 900 -h 480 -u px', '\n\n')
~/anaconda3/envs/catenv/lib/python3.7/site-packages/IPython/core/interactiveshell.py in run_cell_magic(self, magic_name, line, cell)
2360 with self.builtin_trap:
2361 args = (magic_arg_s, cell)
-> 2362 result = fn(*args, **kwargs)
2363 return result
2364
</home/morgan/anaconda3/envs/catenv/lib/python3.7/site-packages/decorator.py:decorator-gen-130> in R(self, line, cell, local_ns)
~/anaconda3/envs/catenv/lib/python3.7/site-packages/IPython/core/magic.py in <lambda>(f, *a, **k)
185 # but it's overkill for just that one bit of state.
186 def magic_deco(arg):
--> 187 call = lambda f, *a, **k: f(*a, **k)
188
189 if callable(arg):
~/anaconda3/envs/catenv/lib/python3.7/site-packages/rpy2/ipython/rmagic.py in R(self, line, cell, local_ns)
721 raise NameError("name '%s' is not defined" % input)
722 with localconverter(converter) as cv:
--> 723 ro.r.assign(input, val)
724
725 tmpd = self.setup_graphics(args)
~/anaconda3/envs/catenv/lib/python3.7/site-packages/rpy2/robjects/functions.py in __call__(self, *args, **kwargs)
190 kwargs[r_k] = v
191 return (super(SignatureTranslatedFunction, self)
--> 192 .__call__(*args, **kwargs))
193
194
~/anaconda3/envs/catenv/lib/python3.7/site-packages/rpy2/robjects/functions.py in __call__(self, *args, **kwargs)
111
112 def __call__(self, *args, **kwargs):
--> 113 new_args = [conversion.py2rpy(a) for a in args]
114 new_kwargs = {}
115 for k, v in kwargs.items():
~/anaconda3/envs/catenv/lib/python3.7/site-packages/rpy2/robjects/functions.py in <listcomp>(.0)
111
112 def __call__(self, *args, **kwargs):
--> 113 new_args = [conversion.py2rpy(a) for a in args]
114 new_kwargs = {}
115 for k, v in kwargs.items():
~/anaconda3/envs/catenv/lib/python3.7/functools.py in wrapper(*args, **kw)
838 '1 positional argument')
839
--> 840 return dispatch(args[0].__class__)(*args, **kw)
841
842 funcname = getattr(func, '__name__', 'singledispatch function')
~/anaconda3/envs/catenv/lib/python3.7/site-packages/rpy2/robjects/pandas2ri.py in py2rpy_pandasdataframe(obj)
59 'The error is: %s'
60 % (name, str(e)))
---> 61 od[name] = StrVector(values)
62
63 return DataFrame(od)
~/anaconda3/envs/catenv/lib/python3.7/site-packages/rpy2/robjects/vectors.py in __init__(self, obj)
382
383 def __init__(self, obj):
--> 384 super().__init__(obj)
385 self._add_rops()
386
~/anaconda3/envs/catenv/lib/python3.7/site-packages/rpy2/rinterface_lib/sexp.py in __init__(self, obj)
286 super().__init__(obj)
287 elif isinstance(obj, collections.abc.Sized):
--> 288 super().__init__(type(self).from_object(obj).__sexp__)
289 else:
290 raise TypeError('The constructor must be called '
~/anaconda3/envs/catenv/lib/python3.7/site-packages/rpy2/rinterface_lib/sexp.py in from_object(cls, obj)
370 except (TypeError, ValueError):
371 try:
--> 372 res = cls.from_iterable(obj)
373 except ValueError:
374 msg = ('The class methods from_memoryview() and '
~/anaconda3/envs/catenv/lib/python3.7/site-packages/rpy2/rinterface_lib/conversion.py in _(*args, **kwargs)
26 def _cdata_res_to_rinterface(function):
27 def _(*args, **kwargs):
---> 28 cdata = function(*args, **kwargs)
29 # TODO: test cdata is of the expected CType
30 return _cdata_to_rinterface(cdata)
~/anaconda3/envs/catenv/lib/python3.7/site-packages/rpy2/rinterface_lib/sexp.py in from_iterable(cls, iterable, populate_func)
317 if populate_func is None:
318 cls._populate_r_vector(iterable,
--> 319 r_vector)
320 else:
321 populate_func(iterable, r_vector)
~/anaconda3/envs/catenv/lib/python3.7/site-packages/rpy2/rinterface_lib/sexp.py in _populate_r_vector(cls, iterable, r_vector)
300 r_vector,
301 cls._R_SET_VECTOR_ELT,
--> 302 cls._CAST_IN)
303
304 #classmethod
~/anaconda3/envs/catenv/lib/python3.7/site-packages/rpy2/rinterface_lib/sexp.py in _populate_r_vector(iterable, r_vector, set_elt, cast_value)
237 def _populate_r_vector(iterable, r_vector, set_elt, cast_value):
238 for i, v in enumerate(iterable):
--> 239 set_elt(r_vector, i, cast_value(v))
240
241
~/anaconda3/envs/catenv/lib/python3.7/site-packages/rpy2/rinterface_lib/sexp.py in _as_charsxp_cdata(x)
430 return x.__sexp__._cdata
431 else:
--> 432 return conversion._str_to_charsxp(x)
433
434
~/anaconda3/envs/catenv/lib/python3.7/site-packages/rpy2/rinterface_lib/conversion.py in _str_to_charsxp(val)
118 s = rlib.R_NaString
119 else:
--> 120 cchar = _str_to_cchar(val)
121 s = rlib.Rf_mkCharCE(cchar, _CE_UTF8)
122 return s
~/anaconda3/envs/catenv/lib/python3.7/site-packages/rpy2/rinterface_lib/conversion.py in _str_to_cchar(s, encoding)
97 def _str_to_cchar(s, encoding: str = 'utf-8'):
98 # TODO: use isStrinb and installTrChar
---> 99 b = s.encode(encoding)
100 return ffi.new('char[]', b)
101
AttributeError: 'float' object has no attribute 'encode'
So I find that it is not possible to even start an R magic cell while importing my pandas dataframe object. However, I have tried creating R vectors inside the cell, and find I can plot these using ggplot2 with no issues.
I am using Python 3.7.6, rpy2 3.1.0, jupyter-notebook 6.0.3and am using Ubuntu 18.04.2 LTS on Windows Subsystem for Linux.
The problem is most likely with one (or more) columns having more than one type - therefore it is impossible to transfer the data into an R vector (which can hold only one data type). The traceback may be overwhelming, but here is the relevant part:
ValueError: Series can only be of one type, or None.
Which column it is? Difficult to say without looking at the dataset that you load, but my general solution is to check the types in the columns:
types = data.applymap(type).apply(set)
types[types.apply(len) > 1]
Anything returned by the snippet above would be a candidate culprit. There are many different ways of dealing with the problem, depending on the exact nature of the data. Workarounds that I frequently use include:
calling data = data.infer_objects() - helps if the pandas did not catch up with a dtype change and still stores the data with (suboptimal) Python objects
filling NaN with an empty string or a string constant if you have missing values in a string column (e.g. str_columns = str_columns.fillna(''))
dates.apply(pd.to_datetime, axis=1) if you have datetime objects but the dtype is object
using df.applymap(lambda x: datetime.combine(x, datetime.min.time()) if not isinstance(x, datetime) else x) if you have a mixture of date and datetime objects
In some vary rare cases pandas stores the data differently than expected by rpy2 (following certain manipulations); then writing the dataframe down to a csv file and reading it from the disk again helps - but this is likely not what you are facing here, as you start from a newly read dataframe.
I just noticed there might be an even simpler reason for the problem. For some reason, pandas2ri requires you to call pandas2ri.activate()after importing it. This solved the problem for me.
I want to calculate distance between two lat/log point using geopandas series.distance and measure the result by unit meters, I know I should define crs first, but I tried several times to use to_crs(), but it is showing an error: b'no arguments in initialization list' seems like the function never worked. Anyone can help me on this problem?
def wgs84_to_CGCS2000(df,code):
result=df.to_crs(from_epsg(code))
return result
city=wgs84_to_CGCS2000(city,4549)
kfc=wgs84_to_CGCS2000(kfc,4549)
RuntimeError Traceback (most recent call last)
<ipython-input-42-c0d1c4e6af6a> in <module>
2 result=df.to_crs(from_epsg(code))
3 return result
----> 4 city=wgs84_to_CGCS2000(city,4549)
5 kfc=wgs84_to_CGCS2000(kfc,4549)
<ipython-input-42-c0d1c4e6af6a> in wgs84_to_CGCS2000(df, code)
1 def wgs84_to_CGCS2000(df,code):
----> 2 result=df.to_crs(from_epsg(code))
3 return result
4 city=wgs84_to_CGCS2000(city,4549)
5 kfc=wgs84_to_CGCS2000(kfc,4549)
C:\ProgramData\Anaconda3\lib\site-packages\geopandas\geodataframe.py in to_crs(self, crs, epsg, inplace)
441 else:
442 df = self.copy()
--> 443 geom = df.geometry.to_crs(crs=crs, epsg=epsg)
444 df.geometry = geom
445 df.crs = geom.crs
C:\ProgramData\Anaconda3\lib\site-packages\geopandas\geoseries.py in to_crs(self, crs, epsg)
302 except TypeError:
303 raise TypeError('Must set either crs or epsg for output.')
--> 304 proj_in = pyproj.Proj(self.crs, preserve_units=True)
305 proj_out = pyproj.Proj(crs, preserve_units=True)
306 project = partial(pyproj.transform, proj_in, proj_out)
C:\ProgramData\Anaconda3\lib\site-packages\pyproj\__init__.py in __new__(self, projparams, preserve_units, **kwargs)
360 # on case-insensitive filesystems).
361 projstring = projstring.replace('EPSG','epsg')
--> 362 return _proj.Proj.__new__(self, projstring)
363
364 def __call__(self, *args, **kw):
_proj.pyx in _proj.Proj.__cinit__()
RuntimeError: b'no arguments in initialization list'
I'm recently install igraph on my windows machine running iPython through the Anaconda distribution. I have been following the tutorial on the igraph website to try and become familiar with igraph, as I typically use NetworkX. However, I'm having trouble actually drawing my graph.
At first, I realized it might be because I didn't enable pylab inline, and I was receiving the error: NameError: name 'plot' is not defined.
But after I enabled that and tried to plot the graph again, I got the error: TypeError: There is no line property "layout"
I simply want to draw my network in iPython, and I'm not sure what I'm doing wrong.
import igraph
import cairo
g = igraph.Graph([(0,1), (0,2), (2,3), (3,4), (4,2), (2,5), (5,0), (6,3), (5,6)])
cairo.__path__
Out[4]: ['C:\\Users\\Curtis\\Anaconda\\lib\\site-packages\\cairo']
layout = g.layout_kamada_kawai()
plot(g, layout = layout)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-6-df59bbbf0497> in <module>()
----> 1 plot(g, layout = layout)
NameError: name 'plot' is not defined
After enabling pylab inline:
pylab inline
Populating the interactive namespace from numpy and matplotlib
plot(g, layout = layout)

---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-8-df59bbbf0497> in <module>()
----> 1 plot(g, layout = layout)
C:\Users\Curtis\Anaconda\lib\site-packages\matplotlib\pyplot.pyc in plot(*args, **kwargs)
2985 ax.hold(hold)
2986 try:
-> 2987 ret = ax.plot(*args, **kwargs)
2988 draw_if_interactive()
2989 finally:
C:\Users\Curtis\Anaconda\lib\site-packages\matplotlib\axes.pyc in plot(self, *args, **kwargs)
4135 lines = []
4136
-> 4137 for line in self._get_lines(*args, **kwargs):
4138 self.add_line(line)
4139 lines.append(line)
C:\Users\Curtis\Anaconda\lib\site-packages\matplotlib\axes.pyc in _grab_next_args(self, *args, **kwargs)
315 return
316 if len(remaining) <= 3:
--> 317 for seg in self._plot_args(remaining, kwargs):
318 yield seg
319 return
C:\Users\Curtis\Anaconda\lib\site-packages\matplotlib\axes.pyc in _plot_args(self, tup, kwargs)
303 ncx, ncy = x.shape[1], y.shape[1]
304 for j in xrange(max(ncx, ncy)):
--> 305 seg = func(x[:, j % ncx], y[:, j % ncy], kw, kwargs)
306 ret.append(seg)
307 return ret
C:\Users\Curtis\Anaconda\lib\site-packages\matplotlib\axes.pyc in _makeline(self, x, y, kw, kwargs)
255 **kw
256 )
--> 257 self.set_lineprops(seg, **kwargs)
258 return seg
259
C:\Users\Curtis\Anaconda\lib\site-packages\matplotlib\axes.pyc in set_lineprops(self, line, **kwargs)
196 funcName = "set_%s" % key
197 if not hasattr(line, funcName):
--> 198 raise TypeError('There is no line property "%s"' % key)
199 func = getattr(line, funcName)
200 func(val)
TypeError: There is no line property "layout"
Your command
plot(g, layout = layout)
has the problem. In the first case there is no plot. In the second case you have loaded all sorts of stuff from matplotlib to the common namespace, and plot refers to matplotlib.pyplot.plot.
What you really want to call is the igraph.plot. So, replace the line above by
igraph.plot(g, layout=layout)
to use the correct function.
Just a minimal example:
import igraph
g = igraph.Graph([(0,1), (0,2), (2,3), (3,4), (4,2), (2,5), (5,0), (6,3), (5,6)])
igraph.plot(g, target="/tmp/igraph_demo.png")
creates:
Note that this creates a file. If your plot without the target="..." and do not get anything on the screen, it is a configuration issue. The solution depends on your OS. (igraph uses cairo for SVG plotting.)