Package: python-skbio / 0.5.6-4

Metadata

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

Patch series

view the series file
Patch File delta Description
mathjax path | (download)

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

 set mathjax path to debian's copy
0002 use libsww as library not embedded src.patch | (download)

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

 use libsww as library, not embedded src
no_privacy_breach_logo.patch | (download)

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

 remove privacy breaching logo
simde | (download)

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
soften_test | (download)

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

 2.220446049250313e-16 is basically zero
pandas1.1 ordination fix.patch | (download)

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.


pandas1.1 valueerror.patch | (download)

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.


local_inventory | (download)

doc/source/conf.py | 12 6 + 6 - 0 !
1 file changed, 6 insertions(+), 6 deletions(-)

 use debian packages for intersphinx-links