Re: [Numpy-discussion] doctest fortran I/O synchronization

10 Oct 2003

      On Fri, Oct 10, 2003 at 10:17:54AM -0400, Todd Miller wrote:
...
I'm trying to make a doctest to verify that the different flow patterns
of f2py interfaces work with different varieties of numarrays (normal,
byte-swapped, misaligned, dis-contiguous, type-converted).  I'm trying
to test this out under Linux with g77, and (it seems like) I'm having
trouble synchronizing the Fortran I/O with Python's C I/O.
Given foo.f:
subroutine in_c(a,m,n)
      real*8 a(n,m)
Cf2py intent(in,c) a
Cf2py depend(a) ::  n=shape(a,0),  m=shape(a,1)
      do j=1,m
         do i=1,n
            write (6,1) a(i,j)
 1          format( $, 1F3.0, ', ')
         enddo
         print *,''
      enddo
      end
And given f2py_tests.py:
"""
...
...
...
foo.in_f(a)
 0.,  5., 10.,
 1.,  6., 11.,
 2.,  7., 12.,
 3.,  8., 13.,
 4.,  9., 14.,
"""
import foo, numarray
def test():
    import doctest
    global a
    t = doctest.Tester(globs=globals())
    a = numarray.arange(15., shape=(3,5))
    t.runstring(__doc__, "c_array")
    return t.summarize()
I get this:
[jmiller@halloween ~/f2py_tests]$ python f2py_tests.py
 0.,  5., 10.,
 1.,  6., 11.,
 2.,  7., 12.,
 3.,  8., 13.,
 4.,  9., 14.,
*****************************************************************
Failure in example: foo.in_f(a)
from line #1 of c_array
Expected:
 0.,  5., 10.,
 1.,  6., 11.,
 2.,  7., 12.,
 3.,  8., 13.,
 4.,  9., 14.,
Got:
*****************************************************************
1 items had failures:
   1 of   1 in c_array
***Test Failed*** 1 failures.
Where it appears that the output from the first example somehow escapes
the C I/O system I presume doctest is using.  The actual test I'm
doctest uses Python's I/O system: it assigns a new object to
sys.stdout. Your code uses Fortran's output, which would go the same
place a printf in C would: to the program's stdout (file descriptor 1).

You'd need to run the code in a separate process, and capture the
output. Something along the lines of this:

import commands
def test_f2py():
    """
    put your doctest here
    """
    output = commands.getoutput('python f2pytest1.py')
    print output

Or, set your test up to write output to a file instead of stdout, then
read that file (that's probably better).
...
writing has multiple examples, and the fortran I/O *does* make it into
the doctest after the first example  but remains out of sync.
It's out of sync because it's not going through Python; Python has
absolutely no clue that the Fortran code wrote anything.

-- 
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|David M. Cooke                      http://arbutus.physics.mcmaster.ca/dmc/
|cookedm@physics.mcmaster.ca