packages.txt
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Review modules and import 

Given module foo with attribute x, x could be variable, function, class, ...

import foo       # loads all contents of foo module file into foo module object
... foo.x ...    # module name prefix distinguishes x, foo.x, bar.x, ...
                 
import foo as f  # 'nickname': loads contents of foo into f module object
... f.x ...      # maintains prefix, but saves space (and your fingers)

from foo import x  # loads x from foo into current module
... x ...          # NO prefix, but what if there was an x here already?

from foo import *  # puts all contents of module foo into current module
... x ...          # NOT recommended in module, can be OK in interactive session








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Finding modules

Python can tell you where it found a module.  For example, the regular
expression module re

>>> import re
>>> re
<module 're' from '/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/re.pyc'>

Python looks for the module in all the directories in sys.path

>>> import sys
>>> sys.path
['', '/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python27.zip', '/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7', ...
... 

sys.path is set by several things, including the PYTHONPATH environment variable
(but PYTHONPATH is only a subset of sys.path)




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Loading modules with the python -m option

You can start a Python session by loading a module with -m.

Python will search sys.path for the module.  For example, regular expressions:

Jonathans-MacBook-Pro:fall_2011 jon$ python -i -m re
...
>>> dir()
['DEBUG', 'DOTALL', 'I', 'IGNORECASE', 'L', 'LOCALE', 'M', 'MULTILINE', 'S', 'Scanner', 'T', 'TEMPLATE', 'U', 'UNICODE', 'VERBOSE', 'X', '_MAXCACHE', '__all__',
...












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Packages 

Packages provide dotted (hierarchical) module names

import Bio.Entrez               # import package (a module in another package)
import Bio.Entrez.Parser        # import module from package
from Bio.Entrez import Parser   # import module from package into current module
import Bio.Entrez.Parser as ep  # import module from package with nickname

A package is a module that contains other modules (and maybe more packages)

Modules are files, packages are directories + contents

A package P is a directory named P that contains a file named __init__.py

Other modules in directory P are the modules of package P

Some of those modules can themselves be packages (dirs with own __init__.py)








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Inside a package

Sample: BioPython /Library/Python/2.7/site-packages/Bio on my system

__init__.py can be empty or just a docstring, or can include any code

Modules in package can import other modules in same package without package prefix

So you can easily turn a directory containing modules into a package at any time, 
just add __init__.py (which can be empty)















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Installation

Where do installed packages live?  Usually in .../site_packages

There might be several

 Windows: C:\Python26\lib\site-packages

 Mac: /Library/Python/2.6/site-packages, but also
/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages

How does the python interpreter find site-packages?  sys.path

Installation should put packages in the right place, update sys.path as needed