1. PYTHONPATH is an environment variable which you can set to add additional directories where python will look for modules and packages. e.g.:

   # make python look in the foo subdirectory of your home directory for   
   # modules and packages 
   export PYTHONPATH=${PYTHONPATH}:${HOME}/foo 
   

   Here I use the sh syntax. For other shells (e.g. csh,tcsh), the syntax would be slightly different. To make it permanent, set the variable in your shell's init file (usually ~/.bashrc).

2. Ubuntu comes with python already installed. There may be reasons for installing other (independent) python versions, but I've found that to be rarely necessary.

3. The folder where your modules live is dependent on PYTHONPATH and where the directories were set up when python was installed. For the most part, the installed stuff you shouldn't care about where it lives -- Python knows where it is and it can find the modules. Sort of like issuing the command ls -- where does ls live? /usr/bin? /bin? 99% of the time, you don't need to care -- Just use ls and be happy that it lives somewhere on your PATH so the shell can find it.

4. I'm not sure I understand the question. 3rd party modules usually come with install instructions. If you follow the instructions, python should be able to find the module and you shouldn't have to care about where it got installed.

5. Configure PYTHONPATH to include the directory where your module resides and python will be able to find your module.

I'm assuming that when you installed anaconda 2, you manually set the PYTHONPATH environment variable, by putting something like

PYTHONPATH=/home/user/anaconda2/python
export PYTHONPATH

in your .bash_profile or .bash_rc.

But since you deleted the /home/user/anacanda2/ directory, that path no longer exists.

Thus you want to change PYTHONPATH to point to the executable in /usr/lib, by changing the above to

PYTHONPATH=/usr/lib/my_python_distribution
export PYTHON

PYTHONPATH is somewhat of a hack as far as package management is concerned. A "pretty" solution would be to package your library and install it.

This could sound more tricky than it is, so let me show you how it works.

Let us assume your "package" has a single file named wow.py and you keep it in /home/user/mylib/wow.py.

Create the file /home/user/mylib/setup.py with the following content:

from setuptools import setup

setup(name="WowPackage",
      packages=["."],
)

That's it, now you can "properly install" your package into the Python distribution of your choice without the need to bother about PYTHONPATH. As far as "proper installation" is concerned, you have at least three options:

• "Really proper". Will copy your code to your python site-packages directory:

  $ python setup.py install
  

• "Development". Will only add a link from the python site-packages to /home/user/mylib. This means that changes to code in your directory will have effect.

  $ python setup.py develop
  

• "User". If you do not want to write to the system directories, you can install the package (either "properly" or "in development mode") to /home/user/.local directory, where Python will also find them on its own. For that, just add --user to the command.

  $ python setup.py install --user
  $ python setup.py develop --user
  

To remove a package installed in development mode, do

$ python setup.py develop -u

or

$ python setup.py develop -u --user

To remove a package installed "properly", do

 $ pip uninstall WowPackage

If your package is more interesting than a single file (e.g. you have subdirectories and such), just list those in the packages parameter of the setup function (you will need to list everything recursively, hence you'll use a helper function for larger libraries). Once you get a hang of it, make sure to read a more detailed manual as well.

In the end, go and contribute your package to PyPI -- it is as simple as calling python setup.py sdist register upload (you'll need a PyPI username, though).

You're absolutely right, they use different PYTHONPATHs.

You can think of Python 2.x and Python 3.x as completely different programming environments. And yes, they store their packages in different locations.

To get numpy working, you can type:

sudo apt-get install python3-numpy

If you want to find out where exactly a package is kept, you can look at the module objects __path__ attribute:

>>> import numpy
>>> numpy.__path__
['/usr/local/lib/python3.5/site-packages/numpy']

You can also install python3-pip and then run pip3 install whatever to install packages for Python 3 with Pip, for packages that aren't available in Ubuntu as python3-whatever.

In case you're confused about the difference between distutils, setuptools, easy_install, pip and the rest, use pip. That's the cool one. :)

Try appending to PYTHONPATH instead of overwriting it completely.

export PYTHONPATH=$PYTHONPATH:/home/dev/python-files

References:

According to the the Python documentation on PYTHONPATH

Augment the default search path for module files. [...]

The default search path is installation dependent, but generally begins with prefix/lib/pythonversion (see PYTHONHOME above). It is always appended to PYTHONPATH.

meaning that some values exist in PYTHONPATH and the default search path is also only appended.

Additionally, this blog post (Archive.org link) also explains clearly why you need to append to PYTHONPATH and not overwrite it. Scrolling down to the section - Special cases and examining the search path explains it clearly (unfortunately no relative URL to that link so you'll have to scroll). Although the user gives the examples on a mac they are very much relevant to any platform

You would probably also want this:

import sys
print(sys.path)

Or as a one liner from the terminal:

python -c "import sys; print('\n'.join(sys.path))"

Caveat: If you have multiple versions of Python installed you should use a corresponding command python2 or python3.

The environment variable PYTHONPATH is actually only added to the list of locations Python searches for modules. You can print out the full list in the terminal like this:

python -c "import sys; print(sys.path)"

Or if want the output in the UNIX directory list style (separated by :) you can do this:

python -c "import sys; print(':'.join(x for x in sys.path if x))"

Which will output something like this:

/usr/local/lib/python2.7/dist-packages/feedparser-5.1.3-py2.7.egg:/usr/local/lib/
python2.7/dist-packages/stripogram-1.5-py2.7.egg:/home/qiime/lib:/home/debian:/us
r/lib/python2.7:/usr/lib/python2.7/plat-linux2:/usr/lib/python2.7/lib-tk:/usr/lib
/python2.7/lib-old:/usr/lib/python2.7/lib- dynload:/usr/local/lib/python2.7/dist-
packages:/usr/lib/python2.7/dist-packages:/usr/lib/python2.7/dist-packages/PIL:/u
sr/lib/python2.7/dist-packages/gst-0.10:/usr/lib/python2.7/dist-packages/gtk-2.0:
/usr/lib/pymodules/python2.7

It's not good to change the default python. Many system programs depends on python2 not python3. if you want to use python3, you just type the command python3.