Develop Reference

Make Python module available for all Linux users

I have a Python 2.7 question, if somebody can help.
When we install a Python module using pip, how do we make it available to all users? Please, see the example below (with module faker). The import works when I am root, but doesn’t work when I am ubuntu user.
I have already tried to install using option --system, and also changing umask, as recommended in some articles I have found. Didn’t work so far. Any ideas?
If we run "which python", both users point to the same one.
root#ip-172-30-244-157:/home/ubuntu#
root#ip-172-30-244-157:/home/ubuntu# python
Python 2.7.17 (default, Sep 30 2020, 13:38:04)
[GCC 7.5.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import faker
>>>
>>> exit()
root#ip-172-30-244-157:/home/ubuntu#
root#ip-172-30-244-157:/home/ubuntu#
root#ip-172-30-244-157:/home/ubuntu# exit
exit
ubuntu#ip-172-30-244-157:~$
ubuntu#ip-172-30-244-157:~$
ubuntu#ip-172-30-244-157:~$ python
Python 2.7.17 (default, Sep 30 2020, 13:38:04)
[GCC 7.5.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import faker
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: No module named faker
>>>

Ok, I solved the issue.
In my case, the problematic module was "faker". But, when we install the faker, another additional module is installed as well (in this case - text-unidecode).
Then I uninstalled both modules, ran "umask 022" and re-installed the faker.
This solved the issue for all other users.
Thanks all for the help!

Accessing Python Modules Installed with Brew

I am trying to access "rdkit" module in python, but my python install doesn't seem to find the module. I installed it using brew as suggested here. I included the commands I use to reproduce the problem.
Is a simple fix just adding the "/usr/local/Cellar" to the python path? Symlinc the site-packages to the cellar? Candidly I did not understand the difference between pip and brew when updating my python, so my first thought is that the python path is not correct. Any suggestions greatly appreciated.
X:~\ python3 Python 3.8.1 (v3.8.1:1b293b6006, Dec 18 2019, 14:08:53) [Clang 6.0 (clang-600.0.57)] on darwin Type "help", "copyright", "credits" or "license" for more information.
>>> import rdkit Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'rdkit'
X:~\ which python3
/Library/Frameworks/Python.framework/Versions/3.8/bin/python3
X:~\ python3
Python 3.8.1 (v3.8.1:1b293b6006, Dec 18 2019, 14:08:53)
[Clang 6.0 (clang-600.0.57)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> print(sys.path)
['',
'/Library/Frameworks/Python.framework/Versions/3.8/lib/python38.zip',
'/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8',
'/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload',
'/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages']
**#:/usr/local/Cellar\** ls
boost/ gettext/ libffi/ numpy/ sip/
boost-python3/ glew/ libidn2/ openblas/ sqlite/
cmake/ glib/ libmpc/ openssl#1.1/ tcl-tk/
ddclient/ glm/ libpng/ pandoc/ tree/
eigen/ gmp/ libtiff/ pcre/ webp/
fontconfig/ graphviz/ libtool/ pkg-config/ wget/
freeglut/ gts/ libunistring/ pyqt/ xz/
freetype/ icu4c/ mmtf-cpp/ python/
gcc/ isl/ mpfr/ qt/
gd/ jasper/ msgpack/ **rdkit/**
gdbm/ jpeg/ netpbm/ readline/
Details:
OS Catalina: 10.15.3

How to import bitarray using pypy?

I am running pypy and after adding the path to the bitarray library to sys.path I still can't import the module:
Python 2.7.3 (87aa9de10f9ca71da9ab4a3d53e0ba176b67d086, Feb 10 2014, 05:26:49)
[PyPy 2.2.1 with GCC 4.7.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
And now for something completely different: ``every VM should come with neural
network trained to recognize microbenchmarks and randomly fluctuate them
+/-9000%''
>>>> import sys
>>>> sys.path.append('/usr/local/lib/python2.7/dist-packages/')
>>>> sys.path.append('/usr/local/lib/python2.7/dist-packages/bitarray/')
>>>> import bitarray
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python2.7/dist-packages/bitarray/__init__.py", line 11, in <module>
from bitarray._bitarray import _bitarray, bitdiff, bits2bytes, _sysinfo
ImportError: No module named bitarray._bitarray
In regular python (CPython installed from aptitude) importing bitarray works fine and I haven't made any modifications to the module after installing it with pip. What's wrong here?
Just in case you need it here is the content of the bitarray dir:
$ls /usr/local/lib/python2.7/dist-packages/bitarray/
_bitarray.so __init__.py __init__.pyc test_bitarray.py test_bitarray.pyc
UPDATE
After creating a virtualenv for pypy and installing bitarray with pip as Sunny suggested I still get an ImportError:
$ ls my-pypy-env/site-packages/bitarray
_bitarray.pypy-22.so __init__.py __init__.pyc test_bitarray.py test_bitarray.pyc
$ cd my-pypy-env/
~/my-pypy-env$ ./bin/activate
~/my-pypy-env$ pypy
Python 2.7.3 (87aa9de10f9ca71da9ab4a3d53e0ba176b67d086, Feb 10 2014, 05:26:49)
[PyPy 2.2.1 with GCC 4.7.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
And now for something completely different: ``__xxx__ and __rxxx__ vs operation
slots: particle quantum superposition kind of fun''
>>>> import sys
>>>> sys.path.append('/home/sofia/my-pypy-env/site-packages/bitarray')
>>>> import bitarray
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: No module named bitarray
UPDATE 2
Sunny's solution is correct. The new problem was appending /site-packages/bitarray
instead of just /site-packages/. I would have though that virtualenv would add this to the path automatically but it seems that it doesn't.

The _bitarray module looks like a CPython extension, which is written directly in C.
CPython extension modules does not work directly in PyPy without any changes. You either need to install PyPy compatible version of the module, or do the required changes manually.
To install pypy compatible version, use the following commands:
# If pypy is installed globally
/path/to/pypy/pypy-2.1/bin/pip install bitarray
# If using virtualenv
source /path/to/virtualenv/env/bin/activate
pip install bitarray
Here are a couple of links from PyPy FAQs about this issue:
http://doc.pypy.org/en/latest/faq.html#module-xyz-does-not-work-with-pypy-importerror
http://doc.pypy.org/en/latest/faq.html#do-cpython-extension-modules-work-with-pypy

Compile Z3python?

I want to have Z3python on my Ubuntu 12.04 64-bit. I downloaded Z3 source, and compiled like below:
$autoconf
$./configure
$sudo make
$sudo make a
$sudo make o
Everything went well, but then I tried:
$ python
Python 2.7.3 (default, Sep 26 2012, 21:51:14)
[GCC 4.7.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import z3
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: No module named z3
It seems Z3python is not installed yet? I followed exactly the instructions in README, but it seems to miss something regarding Python binding?

please ignore, what i got is the old version of Z3.
a recommendation: please provide the source code of the latest Z3 in the homepage. i couldnt find it anywhere, then wrongly got the old version. finally, i had to download the latest version from the SourceControl, which was a bit tricky.

problems with python 2.7.3 on Centos with sqlite3 module

i'm tying to play with sqlite3 on my centos server but it reports always the same error (module installed)....
Python 2.7.3 (default, Jun 29 2012, 19:03:18)
[GCC 4.4.6 20110731 (Red Hat 4.4.6-3)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import sqlite3
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "sqlite3/__init__.py", line 24, in <module>
from dbapi2 import *
File "sqlite3/dbapi2.py", line 27, in <module>
from _sqlite3 import *
ImportError: No module named _sqlite3
on ubuntu and so on works fine.... any ideas of what i'm missing here?
i recompile the 2.7.3 again and it catch the sqlite3 libs well.

If you are under RHEL/centos 6, you can try this:
cp /usr/lib64/python2.6/lib-dynload/_sqlite3.so /usr/local/lib/python2.7/sqlite3/

This will work for CentOS:
ln -s /usr/lib64/python2.6/lib-dynload/_sqlite3.so /usr/local/lib/python2.7/lib-dynload/
/usr/local/lib/python2.7/ is already on python's path. No need to duplicate the file or add the python's path.

first find:
find / -name _sqlite3.so
/usr/usr/lib/python2.6/lib-dynload/_sqlite3.so
/usr/local/service/python2.7/lib/python2.7/lib-dynload/_sqlite3.so
/usr/lib64/python2.6/lib-dynload/_sqlite3.so
next
cp /usr/local/service/python2.7/lib/python2.7/lib-dynload/_sqlite3.so /usr/local/lib/python2.7/sqlite3/
this centso 6.5 python2.7.10

If you're using Python 2.7.3 on a Red Hat 5 or CentOS 5 machine, there was a bug that prevented the SQLite modules from compiling properly when building Python from source; you should see an error message when running make. It's since been fixed in 2.7.4 so your best option is to upgrade.
If that's not possible, then there's a patch available. Here's the bug page and the patch.