Create a Python3 environment with pyenv on Mac and display a NetworkX graph
Preamble
I tried to display the network diagram using NetworkX of Python in the Wikipedia link data that I imported earlier, but it took time to build the environment. So leave the steps. By the way, I learned about NetworkX at the Python Beginners' Gathering that came out last week.
Homebrew installation
Excuse me from a very rudimentary point, but check with the brew command whether the package management tool Homebrew for Mac is installed.
brew --version
If you haven't installed it yet, install Homebrew.
/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
/master/install)"
-Japanese page of Homebrew official website
If it was installed, update it to the latest version.
brew update
pyenv-Create virtualenv environment
What is pyenv-virtualenv?
The Mac has 2 Pythons from the beginning, but I want to keep this environment and make the project to be 3 3s, so I can automatically switch between multiple versions of Python environment [pyenv-virtualenv]( (https://github.com/yyuu/pyenv-virtualenv) is installed.
pyenv is a Python multi-environment switching tool (Simple Python version management) virtualenv is the official Python Virtual Python Environment builder.
It seems that pyenv-virtualenv is a library that uses virtualenv from pyenv. Anyway, with pyenv-virtualenv, you will be able to automatically switch any directory between Python 2 and 3.
Qiita already has a lot of explanations on building an environment for pyenv and pyenv-virtualenv.
-Pyenv + virtualenv on Mac -Building an environment with pyenv and virtualenv -Building Python 3.x environment with Pyenv (CentOS, Ubuntu)
Install pyenv-virtualenv
brew install pyenv-virtualenv
By the way, this installation will also automatically install the dependent pyenv.
$ brew install pyenv-virtualenv
==> Installing dependencies for pyenv-virtualenv: autoconf, pkg-config, openssl, readline, pyenv
pyenv-virtualenv settings
Set environment variables after installation
~/.bash_profile
export PYENV_ROOT=$HOME/.pyenv
export PATH=$PYENV_ROOT/bin:$PATH
eval "$(pyenv init -)"
eval "$(pyenv virtualenv-init -)"
Reflecting changes in environment variables
source ~/.bash_profile
Let's display the installable version with pyenv.
pyenv install --list
Find the latest version of Python 3 from the list and install it.
pyenv install 3.5.1
Python will be downloaded and installed from www.python.org like this.
$ pyenv install 3.5.1
Downloading Python-3.5.1.tgz...
-> https://www.python.org/ftp/python/3.5.1/Python-3.5.1.tgz
Installing Python-3.5.1...
When finished, reflect the changes in the environment variables again.
source ~/.bash_profile
Go to your working directory and have Python 3.5.1 running in that directory.
cd [Any working directory for Python 3]
pyenv local 3.5.1
When you're done, make sure the environment switches.
$ cd ~
$ python --version
Python 2.7.10
$ cd [Any working directory for Python 3]
$ python --version
Python 3.5.1
pip update
I'm about to install NetworkX, which uses pip, Python's package management system. In Python3, the pip command is attached by default, but if it is the default, it seems to be an old version, so I will update it.
cd [Any working directory for Python 3]
pip install --upgrade pip
$ pip list
Omission
pip (7.1.2)
Omission
$ pip install --upgrade pip
$ pip list
Omission
pip (8.0.2)
Omission
NetworkX installation
NetworkX is a library for dealing with complex networks in Python.
NetworkX is a Python language software package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.
cd [Any working directory for Python 3]
pip install networkx
After the installation, it seems that the networkx module is placed under .pyenv / versions / 3.5.1.
$ ls ~/.pyenv/versions/3.5.1/lib/python3.5/site-packages/networkx
__init__.py classes drawing generators relabel.py tests
__pycache__ convert.py exception.py linalg release.py utils
algorithms convert_matrix.py external readwrite testing version.py
$ ls ~/.pyenv/versions/3.5.1/share/doc/networkx-1.11/examples
3d_drawing advanced algorithms basic drawing graph multigraph pygraphviz
Try console display on NetworkX
As a test, let's run the First Sample on the NetrowkX site.
networkx-sample.py
import networkx as nx
G=nx.Graph()
G.add_node("spam")
G.add_edge(1,2)
print(G.nodes())
print(G.edges())
Create a networkx-sample.py script in the environment set in Python3 and execute it.
$ cd [Any working directory for Python 3]
$ python networkx-sample.py
['spam', 2, 1]
[(2, 1)]
The nodes and edges of the network are displayed in the console.
Install matplotlib
Next, I will try to find and execute the Sample that graphically displays the network from the official website. , It seems that the matplotlib library is required for graph display.
Also install with the pip command.
pip install matplotlib
If you run the sample as it is, an error will occur. Is the error message pointing to this page?
RuntimeError: Python is not installed as a framework. The Mac OS X backend will not be able to function correctly if Python is not installed as a framework.
See the Python documentation for more information on installing Python as a framework on Mac OS X. Please either reinstall Python as a framework, or try one of the other backends.
If you are Working with Matplotlib in a virtual enviroment see 'Working with Matplotlib in Virtual environments' in the Matplotlib FAQ
(The error message has a long line, so it has a line break.)
I did not solve it even if I did it as written, so I will search for a solution from Qiita. Reference: Cannot import matplotlib etc. in VirtualEnv environment
Create a new matplotlibrc file
~/.matplotlib/matplotlibrc
One line description in matplotlibrc
backend : TkAgg
Try to display the network diagram with NetworkX
Create a Python script by copying the sample Random Geometric Graph from the official website.
RandomGeometricGraph.py
import networkx as nx
import matplotlib.pyplot as plt
G=nx.random_geometric_graph(200,0.125)
# position is stored as node attribute data for random_geometric_graph
pos=nx.get_node_attributes(G,'pos')
# find node near center (0.5,0.5)
dmin=1
ncenter=0
for n in pos:
x,y=pos[n]
d=(x-0.5)**2+(y-0.5)**2
if d<dmin:
ncenter=n
dmin=d
# color by path length from node near center
p=nx.single_source_shortest_path_length(G,ncenter)
plt.figure(figsize=(8,8))
nx.draw_networkx_edges(G,pos,nodelist=[ncenter],alpha=0.4)
nx.draw_networkx_nodes(G,pos,nodelist=p.keys(),
node_size=80,
node_color=[float(v) for v in p.values()],
cmap=plt.cm.Reds_r)
plt.xlim(-0.05,1.05)
plt.ylim(-0.05,1.05)
plt.axis('off')
plt.savefig('random_geometric_graph.png')
plt.show()
It didn't work in Python3 as it was, so I changed one line.
original
node_color=p.values()
I changed it like this. I think it's the difference between 2 and 3 series, but it may be due to the version of matplotlib.
node_color=[float(v) for v in p.values()]
Run sample
When I ran the sample, somehow a network diagram was displayed and a random_geometric_graph.png file was created.
python RandomGeometricGraph.py
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