Fix #20 for Python 2/3 compatibility

[nigiord]

Related to #20 Allow to install and use MicrobeCensus in Python3. Unittests run ok for Python 2.7.15 and Python 3.5.5.

$ python tests/test_microbe_census.py 
...
----------------------------------------------------------------------
Ran 3 tests in 36.410s

OK

Details

There were only two problems with Python 3:

• in setup.py, octal number were defined as 0555 and 07777. Since Python 2.6, one shall use 0o555 and 0o7777. The old notation is no longer accepted in Python 3.
• in microbe_census.py, the error from process.communicate() was not decoded (apparently it returns a byte-like object in Python 3, that you have to decode() into a string)

Also in Python 3, tests/test_microbe_census.py was complaining about unclosed files (lot of warnings). I fixed the code so all opened files are properly closed when no longer used.

Finally, tests/test_microbe_census.py and microbe_census/microbe_census.py presented a mix of tab and 4-space indentations. I converted everything to 4-space indentation.

Best, Nils

[snayfach]

Looks good - I'll merge. Thanks!