Drew Parsons pushed to branch master at Debian Med / python-pbcore
Commits: 9f8a0d4c by Drew Parsons at 2019-01-09T21:57:10Z add fix_numpy_1.16_9c065b7.patch applying upstream commit Upstream commit 9c065b724ddfa2b78ddf3e2e6671cd30a50b0a66 fixes dtypes for build against numpy 1.16. Upstream issue #120. Closes: #918212, #917670. - - - - - 9e7d1186 by Drew Parsons at 2019-01-09T22:01:56Z Standards-Version: 4.3.0 - - - - - a562cc4e by Drew Parsons at 2019-01-09T22:02:56Z debhelper compatibility level 12 - - - - - 5 changed files: - debian/changelog - debian/compat - debian/control - + debian/patches/fix_numpy_1.16_9c065b7.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,5 +1,6 @@ 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 <[email protected]> Wed, 31 Oct 2018 18:45:13 +0100 python-pbcore (1.5.0+git20180606.43fcd9d+dfsg-2) unstable; urgency=medium ===================================== debian/compat ===================================== @@ -1 +1 @@ -11 +12 ===================================== debian/control ===================================== @@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Afif Elghraoui <[email protected]> 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 ===================================== @@ -0,0 +1,26 @@ +From 9c065b724ddfa2b78ddf3e2e6671cd30a50b0a66 Mon Sep 17 00:00:00 2001 +From: David Seifert <[email protected]> +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 View it on GitLab: https://salsa.debian.org/med-team/python-pbcore/compare/7c621d51a101903060853b08d7a29ede354f9bd6...a562cc4efc0d4523c613010dc2717e2bc682b7f4 -- View it on GitLab: https://salsa.debian.org/med-team/python-pbcore/compare/7c621d51a101903060853b08d7a29ede354f9bd6...a562cc4efc0d4523c613010dc2717e2bc682b7f4 You're receiving this email because of your account on salsa.debian.org.
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