Why doesn't python setup.py build/install work?

Question

I'm trying to install a python package here, called pips. https://github.com/jbloom/pips-1.0#using-pips

I follow all the directions, using:

python setup.py build
python setup.py install

as root. I then try to load pips in python (ipython), using:

import pips

However, it doesn't recognize this program. My python installation is 2.7, which should be compatible with the package. Am I doing something wrong?

Edit: The output I get to the setup.py install is:

[root@tawfik pips-1.0-master]# python setup.py install
running install
running build
running build_py
running build_ext
running build_scripts
running install_lib
running install_scripts
changing mode of /usr/bin/pips_consensus.py to 775
changing mode of /usr/bin/pips_run_cupsat.py to 775
changing mode of /usr/bin/pips_build_tree_and_alignment.py to 775
changing mode of /usr/bin/pips_analysis.py to 775
changing mode of /usr/bin/pips_run_foldx.py to 775
changing mode of /usr/bin/pips_correlate_selected_mutations.py to 775
changing mode of /usr/bin/pips_analyze_selected_mutations.py to 775
running install_egg_info
Removing /usr/lib64/python2.6/site-packages/pips-1.0-py2.6.egg-info
Writing /usr/lib64/python2.6/site-packages/pips-1.0-py2.6.egg-info

My guess is pip installs to a different interpreter. This is a common issue. What is the output of which pip and which python (assuming you are on Unix)? — mbatchkarov
– mbatchkarov, Commented Oct 15, 2014 at 11:19
It says there is no pips when I search with 'which pips'. This is strange because it doesn't give me an error when I run the installation code. — Devinity
– Devinity, Commented Oct 15, 2014 at 11:26
@mbatchkarov: he is installing the pips package, not using the python-pip tool. @Devinity: can you give the output of your run of python setup.py install? — Dettorer
– Dettorer, Commented Oct 15, 2014 at 11:31
[root@tawfik pips-1.0-master]# python setup.py install running install running build running build_py running build_ext running build_scripts running install_lib running install_scripts changing mode of /usr/bin/pips_consensus.py to 775 changing mode of /usr/bin/pips_run_cupsat.py to 775 changing mode of /usr/bin/pips_build_tree_and_alignment.py to 775 changing mode of /usr/bin/pips_analysis.py to 775 changing mode of /usr/bin/pips_run_foldx.py to 775 changing mode of /usr/bin/pips_correlate_selected_mutations.py to 775 — Devinity
– Devinity, Commented Oct 15, 2014 at 11:38
ipython setup.py build then ipython setup.py install should work. — Dettorer
– Dettorer, Commented Oct 15, 2014 at 12:36

Devinity · Accepted Answer · 2014-10-15 12:39:10Z

1

The problem here is, as noted in the discussion, that there are two versions of my python installed in my system. One the OS (centos 6.4) uses, the other is used by my ipython distribution. I needed to install using ipython, rather than the OS python.

answered Oct 15, 2014 at 12:39

Devinity

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