Thursday, May 1, 2014

Python doctest and functions that do file I/O

Some of my code contains functions that read data from files in chunks, process them, and then write data out to other files. I thought it was silly and expensive to first read the data into a list/array, work on them, write out the results to another list and then write the list out to files. But how do you write doctests for such functions?

One way would be to explicitly open files for reading/writing but this is a pain because you have to first create the file, process them, check the answers and then remember to clean up (delete) the files afterwards. You could use the wonderful Python tempfile module, but ...

In my case I was passing file handles to the functions. One convenient way to test such functions without creating physical files on disk is to use io.BytesIO(). This function returns a data structure that has all the characteristics of a file but resides in memory.

For example, suppose you have a cool function that reads in a file and writes out every second byte.

def skip_a_byte(fin, fout):
  b = fin.read(1)
  while b:
    if fin.tell() % 2:
      fout.write(b)
    b = fin.read(1)

We could outfit with a doctest harness as follows:

def skip_a_byte(fin, fout):
  """
  >>> import io; \
  data = 'Haopwf gNqojwj jBlrmowwjnl BCloRwT'; \
  f1 = io.BytesIO(data); \
  f2 = io.BytesIO(); \
  skip_a_byte(f1, f2); \
  _ = f2.seek(0); \
  print f2.read()
  How Now Brown Cow
  """
  b = fin.read(1)
  while b:
    if fin.tell() % 2:
      fout.write(b)
    b = fin.read(1)

if __name__ == "__main__":
  import doctest
  doctest.testmod()

Oh, BTW, I would like to give a shoutout to PyCharm for being very cool: they recognize the code in the docstring, and can do code analysis on it!

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