debian/changelog

+python-skbio (0.5.5-2) unstable; urgency=medium
+
+  * Upstream has fixed numpy issue
+    Closes: #917693, #918213
+  * debhelper 12
+  * Standards-Version: 4.3.0
+
+ -- Andreas Tille <tille@debian.org>  Tue, 12 Feb 2019 19:34:10 +0100
+
 python-skbio (0.5.5-1) unstable; urgency=medium
 
   * New upstream version

debian/compat

-11
+12

debian/control

@@ -5,7 +5,7 @@ Uploaders: Tim Booth <tbooth@ceh.ac.uk>,
            Kevin Murray <kdmfoss@gmail.com>
 Section: python
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper (>= 12~),
                dh-python,
                ipython3,
                python3-all-dev,
@@ -28,7 +28,7 @@ Build-Depends: debhelper (>= 11~),
                python3-sphinx,
                python3-sphinx-bootstrap-theme,
                libssw-dev
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/python-skbio
 Vcs-Git: https://salsa.debian.org/med-team/python-skbio.git
 Homepage: https://github.com/biocore/scikit-bio

debian/patches/6497020.patch

+From 649702053821de88dfa4e8bb3c25f9fe683c1179 Mon Sep 17 00:00:00 2001
+From: Evan Bolyen <ebolyen@gmail.com>
+Date: Mon, 11 Feb 2019 15:56:16 -0700
+Bug-Debian: https://bugs.debian.org/917693
+Bug-Upstream: https://github.com/biocore/scikit-bio/issues/1648
+Origin: https://github.com/biocore/scikit-bio/commit/6497020
+Subject: [PATCH] BUG: fix ownership for byte/string literals
+
+---
+ skbio/sequence/_sequence.py | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/skbio/sequence/_sequence.py b/skbio/sequence/_sequence.py
+index 91950ae5a..15fad55bd 100644
+--- a/skbio/sequence/_sequence.py
++++ b/skbio/sequence/_sequence.py
+@@ -630,7 +630,7 @@ def __init__(self, sequence, metadata=None, positional_metadata=None,
+                                 type(sequence).__name__)
+ 
+             sequence = s
+-            self._owns_bytes = True
++            self._owns_bytes = False
+ 
+             self._set_bytes(sequence)
+ 

debian/patches/series

@@ -2,3 +2,4 @@ mathjax-path
 0002-use-libsww-as-library-not-embedded-src.patch
 0003-Cherry-pick-upstream-fix-for-numpy-transition.patch
 no_privacy_breach_logo.patch
+6497020.patch