Install python2.7.3 + numpy + scipy + matplotlib + scikits.statsmodels + pandas0.7.3 correctly

matplotlibpython

…using Linux (xubuntu).
How to install python2.7.3 + numpy + scipy + matplotlib + scikits.statsmodels + pandas0.7.3 correctly ? My final aim is to have them working. The problem:

~$ python --version
Python 2.7.3

so i already have a system-default 2.7.3, which is good!

~$ dpkg -s python-numpy
Package: python-numpy
Status: install ok installed

and i already have numpy installed! great! But…

~$ python
Python 2.7.3 (default, Oct 23 2012, 01:07:38) 
[GCC 4.6.1] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy as nmp
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named numpy

this module couldn't be find by python. The same with scipy, matplotlib. Why?

~$ sudo apt-get install python-numpy
[...] 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
python-numpy is already the newest version.
[...]

why it does not see numpy and others ?

update:

>>> import sys
>>> print sys.path
['', '/usr/local/lib/python27.zip', '/usr/local/lib/python2.7', '/usr/local/lib/python2.7/plat-linux2', '/usr/local/lib/python2.7/lib-tk', '/usr/local/lib/python2.7/lib-old', '/usr/local/lib/python2.7/lib-dynload', '/usr/local/lib/python2.7/site-packages']
>>>

so i do have /usr/local/lib/python2.7

~$ pip freeze
Warning: cannot find svn location for distribute==0.6.16dev-r0
BzrTools==2.4.0
CDApplet==1.0
[...]
matplotlib==1.0.1
mutagen==1.19
numpy==1.5.1
[...]
pandas==0.7.3
papyon==0.5.5
[...]
pytz==2012g
pyxdg==0.19
reportlab==2.5
scikits.statsmodels==0.3.1
scipy==0.11.0
[...]
zope.interface==3.6.1

as you can see, those modules are already installed! But! ls -la /usr/local/lib/ gives ONLY python2.7 dir. And still

~$ python -V
Python 2.7.3

and

import sys
sys.version
'2.7.3 (default, Oct 23 2012, 01:07:38) \n[GCC 4.6.1]'

updated:

Probably I've missed another instance… One at /usr/Python-2.7.3/ and second (seems to be installed "by hands" far far ago) at /usr/python2.7.3/Python-2.7.3/
But how two identical versions can work at the same time??? Probably, one of them is "disabled" (not used by any program, but I don't know how to check if any program uses it).

~$ ls -la /usr/bin/python*
lrwxrwxrwx 1 root root       9 2011-11-01 11:11 /usr/bin/python -> python2.7
-rwxr-xr-x 1 root root 2476800 2012-09-28 19:48 /usr/bin/python2.6
-rwxr-xr-x 1 root root    1452 2012-09-28 19:45 /usr/bin/python2.6-config
-rwxr-xr-x 1 root root 2586060 2012-07-21 01:42 /usr/bin/python2.7
-rwxr-xr-x 1 root root    1652 2012-07-21 01:40 /usr/bin/python2.7-config
lrwxrwxrwx 1 root root       9 2011-10-05 23:53 /usr/bin/python3 -> python3.2
lrwxrwxrwx 1 root root      11 2011-09-06 02:04 /usr/bin/python3.2 -> python3.2mu
-rwxr-xr-x 1 root root 2852896 2011-09-06 02:04 /usr/bin/python3.2mu
lrwxrwxrwx 1 root root      16 2011-10-08 19:50 /usr/bin/python-config -> python2.7-config

there is a symlink python->python2.7, maybe I can ln -f -s this link to exact /usr/Python-2.7.3/python destination without harm ?? And how correctly to remove the 'copy' of 2.7.3?
And else…

~$ ls -la /usr/bin/virtualenv 
-rwxr-xr-x 1 root root 58 2011-03-16 18:55 /usr/bin/virtualenv

but works only in this case:

~$ /usr/bin/python /usr/bin/virtualenv qenv
New python executable in qenv/bin/python
Installing distribute....................................................................................................................................................................................done.
Installing pip...............done.

and this doesn't work!

 python virtualenv.py pyenv

I will try to be more clear. Just questions. Why I can import numpy starting '/usr/bin/python' but can not by using only 'python'? If I want to install another version of python for different applications, what is the best way to do this? How to install packages into chosen pythonpath? I did not find a complete guide.

Thanks to everyone!
Solved it this way:

$ sudo nano /usr/share/python/debian_defaults
$ sudo mv /usr/bin/python /usr/bin/python2.Y_old
$ sudo ln -s -f /usr/bin/python2.7 /usr/bin/python

My default version was 2.7.3 and now it's 2.7.2+. I do not see huge difference, so I think it was quite safe. But I need to read more about

virtualenv

and

pip
and default
PATH

Best Answer

I strongly recomend you to use virtualenv. Virtualenv allows you to create python environment in per project basis. My workflow to begin a new project is

Create the project directory myapp
Download virtualenv from https://github.com/pypa/virtualenv/tarball/develop
Create a virtual environment: python virtualenv.py pyenv
Activate the virtualenv source pyenv/bin/activate
Install the packages in the virtual environment:

pip install -U numpy matplotlib pandas ...

With this setup, you can control the version, reinstall or remove the packages without have to depend on the version that is available in the repositories.

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I think you need to set PYTHONPATH after changing the links. On a fresh install of Ubuntu 10.10 I just did, I have:

evadeflow(57)% echo $PYTHONPATH 
/home/evadeflow/lib/python2.6/site-packages:/usr/lib/python2.6/site-packages

You should set this in your environment so it points to the version you want to use (i.e., change the 2.6 to 2.7...)

The suggested way to handle pip(easy_install) with homebrew

Maybe it is time to consider using virtualenv. Virtualenv creates self-contained python environments using the python version you specify. After activating the new virtual environment, everything you install using pip goes under that environment. This helps avoid situations like the one you described.

E.g. create and activate a new python environment using the default python:

# create environment
$ virtualenv --distribute myproject
New python executable in myproject/bin/python
Installing distribute...done.
Installing pip...done.

# activate environment
$ . ./myproject/bin/activate

# check default python
(myproject)$ which python
/Users/me/myproject/bin/python

It is suggested to use the --distribute options to indicate that distribute should be used for installing packages in the new environment instead of (the older) setuptools. After activation your command prompt changes to indicate which python environment is active.

Now install some package. The files will go into myproject directory:

# install django
(myproject)$ pip install django
...

# search for django dir
(myproject)$ find myproject -iname django
myproject/lib/python2.7/site-packages/django

Finally, deactivate:

# deactivate and check for default python
(myproject)$ deactivate
$ which python
/usr/bin/python

To create an environment using a non-default version of python:

$ virtualenv --distribute -p /path/to/custom/python mynewproject

By default virtualenv will copy to the new environment any packages installed for the python version you use to bootstrap it. To prevent this and create an empty environment use the --no-site-packages option. This is especially useful to create environments which can be exactly replicated e.g. from development to production.

Update: As of version 1.7 --no-site-packages has become the default behaviour of virtualenv.

If you want more details, there are plenty of tutorials and blog posts online. E.g.:

Notes on using pip and virtualenv with Django. (most of the post is not django-specific)
Working with virtualenv.

Give it a try and I'm sure you'll stick with it.

Note: Make sure that your executable scripts do not have the python interpreter hardcoded. I.e. their first line should be #!/usr/bin/env python and not something like #!/usr/bin/python.

Best Answer

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The suggested way to handle pip(easy_install) with homebrew

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