On Sun, May 31, 2009 at 01:06:38AM -0700, Jenny Qing Qian wrote:
-> > Somewhat separately, on the 'doc_alignments' branch,
-> >
-> > http://github.com/ctb/pygr/commits/doc_alignments/
-> >
-> > I've started rewriting the 'alignments' tutorial, and making it into a
-> > doctest. You can see the Sphinxified results here,
-> >
-> >
-> >
http://lyorn.idyll.org/~t/transfer/doc_alignments/tutorials/alignment.html<http://lyorn.idyll.org/%7Et/transfer/doc_alignments/tutorials/alignment.html>
-> >
-> > Comments are extremely welcome! I'm doing this mostly offline (I'm
-> > travelling & away from Internet for much of the time) so I haven't
-> > necessarily got all the formatting down correctly.
->
-> Hi Titus,
->
-> I in general like your doctests very much. However, do you think it's a
-> good idea to load the datasets used by the doctests to the doc page?
-> Otherwise, the doctests won't work.
->
-> I can reconstruct the gapping.fa dataset since the two sample sequences are
-> printed out. But I am not clear about the 'sp_all_hbb' dataset.
Hey Jenny,
thanks for looking at them! I thought about moving everything into
doc/, but for now all of the data files are under tests/: if you run
the doctests in the tests/ directory, they will work. I have to
hack on the doctest runner a bit in order to get it to change to the
correct directory.
I've attached my 'run-doctests.py' script which you can use to run the
doctests from within the tests/ directory:
cd pygr/tests
python run-doctests.py ../doc/rest/tutorials/alignment.rst
cheers,
--titus
--
C. Titus Brown, c...@msu.edu
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#! /usr/bin/env python
import doctest
import sys
for filename in sys.argv[1:]:
print '... running doctests on', filename
doctest.testfile(filename)
print '*** SUCCESS ***'
