scripts/print_qiime_config.py | 3 1 + 2 - 0 !
1 file changed, 1 insertion(+), 2 deletions(-)

---

qiime/denoiser/utils.py | 5 3 + 2 - 0 !
1 file changed, 3 insertions(+), 2 deletions(-)

 fix path to binary helper for denoiser

qiime/assign_taxonomy.py | 20 13 + 7 - 0 !
scripts/assign_taxonomy.py | 5 5 + 0 - 0 !
2 files changed, 18 insertions(+), 7 deletions(-)

 this patch twists qiime's arm to accept running a newer version
 of the RDP classifier by setting RDP_JAR_VERSION_OK, which is done
 by the QIIME wrapper.
 This is a nasty hack and hopefully the patch can be dropped for QIIME 1.6

qiime/util.py | 5 3 + 2 - 0 !
1 file changed, 3 insertions(+), 2 deletions(-)

 this may be a much simpler fix than patching every single mention
 of support_files, but I'm not sure what else this function is used
 to find?

scripts/print_qiime_config.py | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 enable proper detection of mathplotlib

scripts/print_qiime_config.py | 6 3 + 3 - 0 !
1 file changed, 3 insertions(+), 3 deletions(-)

 enable running more tests successfully by relaxing version number

doc/_templates/layout.html | 8 1 + 7 - 0 !
1 file changed, 1 insertion(+), 7 deletions(-)

 remove google addsense from user documentation
 to save user privacy

qiime/test.py | 6 4 + 2 - 0 !
tests/all_tests.py | 3 3 + 0 - 0 !
2 files changed, 7 insertions(+), 2 deletions(-)

 enhancing unit tests

setup.py | 10 3 + 7 - 0 !
1 file changed, 3 insertions(+), 7 deletions(-)

 do not try to download uclust at build time

tests/test_align_seqs.py | 258 129 + 129 - 0 !
tests/test_assign_taxonomy.py | 92 46 + 46 - 0 !
tests/test_pick_otus.py | 502 251 + 251 - 0 !
3 files changed, 426 insertions(+), 426 deletions(-)

 exclude tests that need to fail
 uclust is non-free and can not be packaged.  The QIIME package just contains
 a wrapper telling this fact the user and thus the tests will fail.  To avoid
 useless failures these tests are excluded.