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I've installed several external Python modules in the QGIS Python environement (I use the last nightly build of QGIS dev) including geopandas and osmnx.
My code is working properly from the windows command line (using QGIS version of python 3.6) but when using the QSGIS python command line I keep having an error that I can't understand. Here is a simplified version of it using geopandas and osmnx:

Console Python
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import matplotlib
matplotlib.use('agg') # just to avoid osmnx to change matplotlib backend to tkinter which seems touchy in QGIS Python
import matplotlib.pyplot as plt
import geopandas as gpd
polygonShape = gpd.read_file("D:\\software\\OSGeo4W64\\apps\\qgis-dev\\python\\plugins\\dhcoptimzier\\data\\antwerp.shp") # I joined the file which is very simple

print(polygonShape)
district geometry
0 antwerp POLYGON ((4.394025849609361 51.21877037018072,...

import osmnx as ox
graph = ox.graph_from_polygon(polygonShape['geometry'][0], network_type='all')

Traceback (most recent call last):
File "D:\software\OSGeo4W64\apps\Python36\lib\code.py", line 91, in runcode
exec(code, self.locals)
File "<input>", line 1, in <module>
File "D:\software\OSGeo4W64\apps\Python36\lib\site-packages\osmnx\core.py", line 1680, in graph_from_polygon
G_buffered = truncate_graph_polygon(G_buffered, polygon_buffered, retain_all=True, truncate_by_edge=truncate_by_edge)
File "D:\software\OSGeo4W64\apps\Python36\lib\site-packages\osmnx\core.py", line 1125, in truncate_graph_polygon
points_within_geometry = intersect_index_quadrats(gdf_nodes, polygon, quadrat_width=quadrat_width, min_num=min_num, buffer_amount=buffer_amount)
File "D:\software\OSGeo4W64\apps\Python36\lib\site-packages\osmnx\core.py", line 1043, in intersect_index_quadrats
multipoly = quadrat_cut_geometry(geometry, quadrat_width=quadrat_width, buffer_amount=buffer_amount, min_num=min_num)
File "D:\software\OSGeo4W64\apps\Python36\lib\site-packages\osmnx\core.py", line 1007, in quadrat_cut_geometry
lines_buffered = [line.buffer(buffer_size) for line in lines]
File "D:\software\OSGeo4W64\apps\Python36\lib\site-packages\osmnx\core.py", line 1007, in <listcomp>
lines_buffered = [line.buffer(buffer_size) for line in lines]
File "D:\software\OSGeo4W64\apps\Python36\lib\site-packages\shapely\geometry\base.py", line 584, in buffer
return geom_factory(self.impl['buffer'](self, distance, res))
File "D:\software\OSGeo4W64\apps\Python36\lib\site-packages\shapely\topology.py", line 78, in call
return self.fn(this._geom, *args)
OSError: exception: access violation writing 0x00007FF9A3E58A30

I don't get where the memory access violation comes from (I've tried to run as administrator as well).
Here is my pip freeze for my QGIS Python:
alabaster==0.7.10
Babel==2.5.3
certifi==2018.1.18
chardet==3.0.4
click==6.7
click-plugins==1.0.3
cligj==0.4.0
colorama==0.3.9
cycler==0.10.0
decorator==4.2.1
descartes==1.1.0
docutils==0.14
Fiona==1.7.11
future==0.16.0
GDAL==2.2.2
geopandas==0.3.0
geopy==1.11.0
httplib2==0.10.2
idna==2.6
imagesize==1.0.0
ipython-genutils==0.2.0
Jinja2==2.9.4
joblib==0.11
jsonschema==2.6.0
jupyter-core==4.4.0
MarkupSafe==0.23
matplotlib==2.1.1
mock==2.0.0
munch==2.2.0
nbformat==4.4.0
networkx==2.1
nose2==0.6.5
numpy==1.14.1
osmnx==0.6
OWSLib==0.14.0
packaging==16.8
pandas==0.22.0
pb-tool==3.0.6
pbr==1.10.0
pipdeptree==0.10.1
plotly==2.4.1
psycopg2==2.7.3.2
PuLP==1.6.8
Pygments==2.2.0
pyparsing==2.2.0
pyproj==1.9.5.1
python-dateutil==2.6.1
pytz==2018.3
PyYAML==3.12
requests==2.18.4
Rtree==0.8.3
Shapely==1.6.4.post1
six==1.11.0
snowballstemmer==1.2.1
Sphinx==1.7.0
sphinxcontrib-websupport==1.0.1
traitlets==4.3.2
urllib3==1.22

Thanks in advance !

Maxime