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

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

In addition to NeoTheThird's answer:

Ubuntu does not use ~/.bash_profile by default. You should use ~/.profile instead.

The path you should use is /home/john/Desktop/myscraper, though /home/john/Desktop/myscraper/ would also work. Paths that don't start with slashes are relative, not absolute, so will not work unless the working directory is /. More details here on Wikipedia.

You can put the definition and export statements together, and if PYTHONPATH is not already defined, you can leave off the $PYTHONPATH: at the start.

export PYTHONPATH=/home/john/Desktop/myscraper

If you're using bash (on a Mac or GNU/Linux distro), add this to your ~/.bashrc

export PYTHONPATH="${PYTHONPATH}:/my/other/path"

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()?