## Package: python-skbio / 0.5.6-4

Package Version Patches format
python-skbio 0.5.6-4 3.0 (quilt)

### Patch series

view the series file
Patch File delta Description

doc/source/conf.py | 2 2 + 0 - 0 !
1 file changed, 2 insertions(+)

 set mathjax path to debian's copy


setup.py | 22 3 + 19 - 0 !
1 file changed, 3 insertions(+), 19 deletions(-)

 use libsww as library, not embedded src


doc/source/_templates/layout.html | 6 1 + 5 - 0 !
1 file changed, 1 insertion(+), 5 deletions(-)

 remove privacy breaching logo


setup.py | 13 9 + 4 - 0 !
skbio/alignment/_lib/ssw.c | 3 2 + 1 - 0 !
skbio/alignment/_lib/ssw.h | 5 3 + 2 - 0 !
3 files changed, 14 insertions(+), 7 deletions(-)

 add simd everywhere for non x86 support


skbio/tree/tests/test_nj.py | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 2.220446049250313e-16 is basically zero


CHANGELOG.md | 5 5 + 0 - 0 !
skbio/stats/ordination/tests/test_redundancy_analysis.py | 1 0 + 1 - 0 !
skbio/util/_testing.py | 59 39 + 20 - 0 !
3 files changed, 44 insertions(+), 21 deletions(-)

 ordination fix (#1720)

* skbio.stats.ordination tests have been relaxed.

* Fixes build errors for newer versions of NumPy, Pandas, and SciPy.

* Corrected a criticial bug in skbio.alignment.StripedSmithWaterman /
skbio.alignment.local_pairwise_align_ssw which would cause the
formatting of the aligned sequences to misplace gap characters by the
number of gap characters present in the opposing aligned sequence up
to that point. This was caused by a faulty implementation of CIGAR
string parsing, see
[#1679](https://github.com/biocore/scikit-bio/pull/1679) for full
details.



skbio/metadata/_testing.py | 7 5 + 2 - 0 !
1 file changed, 5 insertions(+), 2 deletions(-)

 update valueerror message assertion check

Fixes compatibility with Pandas 1.1.


 use debian packages for intersphinx-links