Latest bleeding-edge test bug? about khmer

[emcd]

All tests passed on my dev machine. I assume you did "git pull", "make
clean", and rebuilt before running the test suite....

Will try a fresh clone to see if I can reproduce the problem - thanks for
the report.

On Fri, Apr 5, 2013 at 6:26 PM, C. Titus Brown [email protected]:

....................................................................................................................................................................E.E............................................... ERROR:
tests.test_read_parsers.test_read_pair_iterator_in_error_mode

Traceback (most recent call last):
File
"/Users/t/dev/ipy/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
line 197, in runTest
self.test(*self.arg)
File "/Users/t/dev/khmer/tests/test_read_parsers.py", line 189, in
test_read_pair_iterator_in_error_mode
in rparser.iter_read_pairs( ReadParser.PAIR_MODE_ERROR_ON_UNPAIRED ):
AttributeError: type object 'ReadParser' has no attribute
'PAIR_MODE_ERROR_ON_UNPAIRED'
ERROR: tests.test_read_parsers.test_read_pair_iterator_in_ignore_mode

Traceback (most recent call last):
File
"/Users/t/dev/ipy/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
line 197, in runTest
self.test(*self.arg)
File "/Users/t/dev/khmer/tests/test_read_parsers.py", line 219, in
test_read_pair_iterator_in_ignore_mode
in rparser.iter_read_pairs( ReadParser.PAIR_MODE_IGNORE_UNPAIRED ):
AttributeError: type object 'ReadParser' has no attribute

'PAIR_MODE_IGNORE_UNPAIRED'

Ran 214 tests in 10.756s

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/40
.

Eric McDonald
HPC/Cloud Software Engineer
for the Institute for Cyber-Enabled Research (iCER)
and the Laboratory for Genomics, Evolution, and Development (GED)
Michigan State University
P: 517-355-8733

[ctb]

This is on a Mac; not sure if that matters. Will try again.

[emcd]

From a fresh clone on my dev machine:

tests.test_read_parsers.test_iterator_identities ... ok
tests.test_read_parsers.test_read_pair_iterator_in_error_mode ... ok
tests.test_read_parsers.test_read_pair_iterator_in_error_mode_xfail ... ok
tests.test_read_parsers.test_read_pair_iterator_in_ignore_mode ... ok

Shouldn't matter on a Mac... but, which Python version and is it a
framework build or a Homebrew/Fink/DarwinPorts/whatever build?

Thanks.

On Fri, Apr 5, 2013 at 7:28 PM, C. Titus Brown [email protected]:

This is on a Mac; not sure if that matters. Will try again.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/40#issuecomment-15986231
.

Eric McDonald
HPC/Cloud Software Engineer
for the Institute for Cyber-Enabled Research (iCER)
and the Laboratory for Genomics, Evolution, and Development (GED)
Michigan State University
P: 517-355-8733

[emcd]

Also, do you see any interesting warnings during compilation of
_khmermodule.cc or the linking of _khmer.so?

On Fri, Apr 5, 2013 at 7:34 PM, Eric McDonald [email protected] wrote:

From a fresh clone on my dev machine:

tests.test_read_parsers.test_iterator_identities ... ok
tests.test_read_parsers.test_read_pair_iterator_in_error_mode ... ok
tests.test_read_parsers.test_read_pair_iterator_in_error_mode_xfail ... ok
tests.test_read_parsers.test_read_pair_iterator_in_ignore_mode ... ok

Shouldn't matter on a Mac... but, which Python version and is it a
framework build or a Homebrew/Fink/DarwinPorts/whatever build?

Thanks.

On Fri, Apr 5, 2013 at 7:28 PM, C. Titus Brown [email protected]:

This is on a Mac; not sure if that matters. Will try again.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/40#issuecomment-15986231
.

Eric McDonald
HPC/Cloud Software Engineer
for the Institute for Cyber-Enabled Research (iCER)
and the Laboratory for Genomics, Evolution, and Development (GED)
Michigan State University
P: 517-355-8733

Eric McDonald
HPC/Cloud Software Engineer
for the Institute for Cyber-Enabled Research (iCER)
and the Laboratory for Genomics, Evolution, and Development (GED)
Michigan State University
P: 517-355-8733

[emcd]

Just tested outside of my usual virtualenv and everything still worked, so
I think we can rule out any virtualenv pollution on my end. (I don't have
'khmer' or 'screed' installed into it anyway, so that never should've been
an issue... But, just to be extra paranoid, I checked anyway.)

On Fri, Apr 5, 2013 at 7:37 PM, Eric McDonald [email protected] wrote:

Also, do you see any interesting warnings during compilation of
_khmermodule.cc or the linking of _khmer.so?

On Fri, Apr 5, 2013 at 7:34 PM, Eric McDonald [email protected] wrote:

From a fresh clone on my dev machine:

tests.test_read_parsers.test_iterator_identities ... ok
tests.test_read_parsers.test_read_pair_iterator_in_error_mode ... ok
tests.test_read_parsers.test_read_pair_iterator_in_error_mode_xfail ... ok
tests.test_read_parsers.test_read_pair_iterator_in_ignore_mode ... ok

Shouldn't matter on a Mac... but, which Python version and is it a
framework build or a Homebrew/Fink/DarwinPorts/whatever build?

Thanks.

On Fri, Apr 5, 2013 at 7:28 PM, C. Titus Brown [email protected]:

This is on a Mac; not sure if that matters. Will try again.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/40#issuecomment-15986231
.

Eric McDonald
HPC/Cloud Software Engineer
for the Institute for Cyber-Enabled Research (iCER)
and the Laboratory for Genomics, Evolution, and Development (GED)
Michigan State University
P: 517-355-8733

Eric McDonald
HPC/Cloud Software Engineer
for the Institute for Cyber-Enabled Research (iCER)
and the Laboratory for Genomics, Evolution, and Development (GED)
Michigan State University
P: 517-355-8733

Eric McDonald
HPC/Cloud Software Engineer
for the Institute for Cyber-Enabled Research (iCER)
and the Laboratory for Genomics, Evolution, and Development (GED)
Michigan State University
P: 517-355-8733

[emcd]

Oh, almost forgot the obligatory question: was it built with Clang or g++?

On Fri, Apr 5, 2013 at 7:28 PM, C. Titus Brown [email protected]:

This is on a Mac; not sure if that matters. Will try again.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/40#issuecomment-15986231
.

Eric McDonald
HPC/Cloud Software Engineer
for the Institute for Cyber-Enabled Research (iCER)
and the Laboratory for Genomics, Evolution, and Development (GED)
Michigan State University
P: 517-355-8733

[ctb]

Found the problem: the items were set within assert statements, which were being no-oped in my build environment. Take a look at my fix and tell me what you think. Apologies for committing directly -- I wanted to see if I could close the issue with a commit message (apparently not ;(.

[emcd]

Oh... doh! My bad. Yes, that's what happens when you get too clever [by
half]. Thanks for fixing.

The issue will close when the commit is merged into 'master'. I think there
is a way you can target a specific branch with a close message, but I
haven't experimented with that yet.

On Sat, Apr 6, 2013 at 4:35 PM, C. Titus Brown [email protected]:

Found the problem: the items were set within assert statements, which were
being no-oped in my build environment. Take a look at my fix and tell me
what you think. Apologies for committing directly -- I wanted to see if I
could close the issue with a commit message (apparently not ;(.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/40#issuecomment-16003528
.

Eric McDonald
HPC/Cloud Software Engineer
for the Institute for Cyber-Enabled Research (iCER)
and the Laboratory for Genomics, Evolution, and Development (GED)
Michigan State University
P: 517-355-8733