PATH variable defines the directories which are searched when executing commands. However when you execute python sleep_plotter.py 113testCtM113.txt, sleep_plotter.py is an argument to the python program (command). Shell uses PATH to find python, but not its arguments.

You can add an executable attribute to your script:

$ chmod +x /Users/myname/python_functions/bin/sleep_plotter.py

Add a shebang sequence to the top (first line) of your Python script:

#!/usr/bin/env python

And run the script directly as a command:

$ sleep_plotter.py 113testCtM113.txt

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

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.

Typically, the environment variable $PYTHONPATH is empty (try echo $PYTHONPATH). The actual list of folders python searches for libraries can be found with (in python):

import sys
print(sys.path)

This will consist (in search order) of the current directory, any directories in your $PYTHONPATH, and finally the default library directories, set by site.py. The main default locations are (where X.Y is the python version, eg 2.7):

/usr/lib/pythonX.Y (python system libraries, eg re, urllib)
/usr/lib/pythonX.Y/dist-packages (python libraries installed with deb packages)

If you use pip install --user or similar to install libraries as yourself, it will also contain the user library directory:

/home/USERNAME/.local/lib/pythonX.Y/site-packages

You can manipulate the PYTHONPATH by either setting the environment variable before you launch python (PYTHONPATH=$PYTHONPATH:/foo/bar), or by editing sys.path once you've started python (import sys; sys.path = ["/foo/bar"] + sys.path).

However, if you want to play with your own python libraries, a good idea is to create a virtualenv. This is a directory in which you can play around with your own versions of python libraries without any risk of messing up the python libraries used by the system. See How to set up and use a virtual python environment in Ubuntu? for information about creating and using a virtualenv.

I suggest not to rely on the raw PYTHONPATH because it can vary depending on the OS.

Instead of the PYTHONPATH value in the os.environ dict, use sys.path from the sys module. This is preferrrable, because it is platform independent:

import sys
print(sys.path)

The value of sys.path is initialized from the environment variable PYTHONPATH, plus an installation-dependent default (depending on your OS). For more info see

https://docs.python.org/2/library/sys.html#sys.path

https://docs.python.org/3/library/sys.html#sys.path