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.

Rather than hardcoding paths in your Python script we should make use of the path operation from the module os.

os.path.expanduser(path) expands the path to the user's home directory
os.path.join(path1,*path2*,...) joins path elements with the appropriate separator
os.sep gives the OS dependent path separator (/ for Linux/Unix, \ for Windows)
os.getcwd() gives the current working directory
os.path.abspath(path) gives the OS dependent absolute path of a given path

Example:

>>>import os
>>>path = os.path.join(os.path.expanduser('~'), 'documents', 'python', 'file.txt')
>>>print (path)

Result

/home/user/documents/python/file.txt ## when on Ubuntu
C:\Users\user\documents\python\file.txt ## when running Windows

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

The site module documentation and Modifying Python's Search Path seem to be what you're looking for.

As far as I understand it, those entries are being added to sys.path by:

• /usr/lib/python2.6/site.py
• /usr/lib/python2.6/dist-packages/site.py
  (Change 2.6 to your version of Python.)

The easiest way to change it is to add a file /usr/local/lib/python2.6/dist-packages/site-packages.pth containing ../site-packages.

Alternatively, maybe you can teach the package to use site.getsitepackages()?