debian/changelog

 python-pbcore (1.6.5+dfsg-1) UNRELEASED; urgency=medium
 
+  [ Andreas Tille ]
   * Team upload.
   * Recommends: python-h5py (its considered an "optional dependency")
   * Upstream is now tagging releases - adjust watch file
@@ -9,6 +10,13 @@ python-pbcore (1.6.5+dfsg-1) UNRELEASED; urgency=medium
   * Remove trailing whitespace in debian/changelog
   * Build-Depends: s/python-sphinx/python3-sphinx/
 
+  [ Drew Parsons ]
+  * add fix_numpy_1.16_9c065b7.patch applying upstream commit
+    9c065b724 to fix dtypes for build against numpy 1.16.
+    Closes: #918212, #917670.
+  * Standards-Version: 4.3.0
+  * debhelper compatibility level 12
+
  -- Andreas Tille <tille@debian.org>  Wed, 31 Oct 2018 18:45:13 +0100
 
 python-pbcore (1.5.0+git20180606.43fcd9d+dfsg-2) unstable; urgency=medium

debian/compat

-11
+12

debian/control

@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Afif Elghraoui <afif@debian.org>
 Section: python
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper (>= 12),
                dh-python,
                python-all,
                python-setuptools,
@@ -27,7 +27,7 @@ Build-Depends: debhelper (>= 11~),
 #               python3-uritools <!nocheck>,
 #               pylint3,
 #               python3-coverage
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/python-pbcore
 Vcs-Git: https://salsa.debian.org/med-team/python-pbcore.git
 Homepage: https://github.com/PacificBiosciences/pbcore

debian/patches/fix_numpy_1.16_9c065b7.patch

+From 9c065b724ddfa2b78ddf3e2e6671cd30a50b0a66 Mon Sep 17 00:00:00 2001
+From: David Seifert <dseifert@pacificbiosciences.com>
+Date: Wed, 9 Jan 2019 17:56:40 +0100
+Subject: [PATCH] Fixes for numpy 1.16
+
+Fixes #120
+---
+ pbcore/io/BasH5IO.py | 5 ++++-
+ 1 file changed, 4 insertions(+), 1 deletion(-)
+
+diff --git a/pbcore/io/BasH5IO.py b/pbcore/io/BasH5IO.py
+index 5db9e80..89d59e6 100644
+--- a/pbcore/io/BasH5IO.py
++++ b/pbcore/io/BasH5IO.py
+@@ -281,7 +281,10 @@ def _makeOffsetsDataStructure(h5Group):
+ def _makeRegionTableIndex(regionTableHoleNumbers):
+     #  returns a dict: holeNumber -> (startRow, endRow)
+     diffs = np.ediff1d(regionTableHoleNumbers,
+-                       to_begin=[1], to_end=[1])
++                       to_begin=np.array([1],
++                                         dtype=regionTableHoleNumbers.dtype),
++                       to_end=np.array([1],
++                                       dtype=regionTableHoleNumbers.dtype))
+     changepoints = np.flatnonzero(diffs)
+     startsAndEnds = zip(changepoints[:-1],
+                         changepoints[1:])

debian/patches/series

@@ -5,3 +5,4 @@ relax_test_constraint.patch
 accept_debian_packaged_pylint.patch
 exclude_test_missing_data.patch
 # python3_support.patch
+fix_numpy_1.16_9c065b7.patch