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Activity
    Jake Fenton
    @bocajnotnef
    ======================================================================
FAIL: tests.test_scripts.test_unique_kmers_stream_out
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/bocajnotnef/git/env/local/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/home/bocajnotnef/git/khmer/tests/test_scripts.py", line 3298, in test_unique_kmers_stream_out
    assert 'Writing to stdout' in err, err
AssertionError: 
|| This is the script 'unique-kmers.py' in khmer.
|| You are running khmer version 2.0-rc1+119.gf55bd1f
|| You are also using screed version 0.9
||
|| If you use this script in a publication, please cite EACH of the following:
||
||   * MR Crusoe et al., 2014. http://dx.doi.org/10.6084/m9.figshare.979190
||   * A. D\xf6ring et al. http://dx.doi.org:80/10.1186/1471-2105-9-11
||   * Irber and Brown, unpublished
||
|| Please see http://khmer.readthedocs.org/en/latest/citations.html for details.

Estimated number of unique 20-mers in -: 3950
Total estimated number of unique 20-mers: 3950

-------------------- >> begin captured stdout << ---------------------
running: unique-kmers.py in: /tmp/khmertest_rpcL1J
arguments cat /tmp/khmertest_rpcL1J/random-20-a.fa | python /home/bocajnotnef/git/khmer/tests/../scripts/unique-kmers.py -k 20 -e 0.01 --stream-out -

--------------------- >> end captured stdout << ----------------------

----------------------------------------------------------------------
Ran 572 tests in 32.963s

FAILED (failures=1)
Makefile:226: recipe for target 'test' failed
make: *** [test] Error 1
    it's failing in a clean env for me
    Luiz Irber
    @luizirber
    assert 'Writing to stdout' in err, err
    Did you add this assertion?
    Jake Fenton
    @bocajnotnef
    sigh
    yes.
    Luiz Irber
    @luizirber
    and, well, the test is correct, I don't see this in the output =]
    bocajnotnef @bocajnotnef headdesks
    Jake Fenton
    @bocajnotnef
    wait, no, that's not... in mine...
    ....
    whaaat the nuts
    Luiz Irber
    @luizirber
    remove any .pyc files
    find . -iname "*.pyc" -delete
    Jake Fenton
    @bocajnotnef
    Huzzah!
    Thanks!
    Luiz Irber
    @luizirber
    yw
    I'll go home, be I'll be online later
    cya
    Jake Fenton
    @bocajnotnef
    Cheers!
    Jake Fenton
    @bocajnotnef
    @mr-c neither make test, ./setup.py develop nor make install make pylint behave
    Jake Fenton
    @bocajnotnef
    @mr-c You about?
    Michael R. Crusoe
    @mr-c
    Yes
    Jake Fenton
    @bocajnotnef
    Hmmm
    Jake Fenton
    @bocajnotnef
    I am copying code everywhere
    which is concerning
    Jake Fenton
    @bocajnotnef
    my attempt to put useful things in one place instead has normalize-by-median puking stdout everywhere
    WOOO
    wonder if I just hacked a way around the tests capturing stdout
    hope not
    that'd be messy to fix
    Jake Fenton
    @bocajnotnef
    getting this error: TypeError: coercing to Unicode: need string or buffer, instance found
    am confused because dropping into PDB and typing the thing it's coercing shows it's already unicode
    wait
    waaaiiit
    Jake Fenton
    @bocajnotnef
    just realized #1186 is gonna cause all kinds of fun conflicts with the compressed output pull
    WHEEE
    Jake Fenton
    @bocajnotnef
    Aaaand I just typo'd my way up to filling up ~12 build threads. Whoops.
    Jake Fenton
    @bocajnotnef
    woo gonna break all the things
    oxli/functions is so sad now...
    Jake Fenton
    @bocajnotnef
    Aaalright
    refactoring extract-partitions
    (or, starting to, anyway)
    thing 1: We scan through alll the files three times over. That's just... SIlly.
    Let's see if we can do it all at once.
    Jake Fenton
    @bocajnotnef
    just got that abund thread test failure
    https://imgur.com/wJtP0f1
    Jake Fenton
    @bocajnotnef
    problem: could factor out code that checks to see if all files are of consistent format, but if I moved it it'd happen AFTER we scan through all the files, which could take a while for some datasets
    So if we want it to fail off the bat then it's not really easily refactor-able
    Alternatively, we could try promoting fasta data to fastq data, but doing that without asking seems bad
    Luiz Irber
    @luizirber
    @bocajnotnef not sure if it is cleaner, but you can use contextlib.contextmanager: https://github.com/dib-lab/khmer/compare/rfact/extract-part...rfact/extract-part_sugg