[med-svn] [Git][med-team/python-pbh5tools][master] 16 commits: Imported Upstream version 0.8.0+dfsg
Andreas Tille
gitlab at salsa.debian.org
Wed Oct 31 20:31:50 GMT 2018
Andreas Tille pushed to branch master at Debian Med / python-pbh5tools
Commits:
8611b48f by Afif Elghraoui at 2015-11-15T11:02:36Z
Imported Upstream version 0.8.0+dfsg
- - - - -
63bc9b4d by Andreas Tille at 2018-10-31T18:24:31Z
Use git mode in watch file
- - - - -
1a3d7389 by Andreas Tille at 2018-10-31T18:24:56Z
New upstream version 0.8.0+git20170929.58d54ff+dfsg
- - - - -
18c08b0c by Andreas Tille at 2018-10-31T18:25:02Z
Update upstream source from tag 'upstream/0.8.0+git20170929.58d54ff+dfsg'
Update to upstream version '0.8.0+git20170929.58d54ff+dfsg'
with Debian dir 998fe96c4d6173582f25179f626cecc4541a71c3
- - - - -
8d6be788 by Andreas Tille at 2018-10-31T18:27:10Z
debhelper 11
- - - - -
422b73c1 by Andreas Tille at 2018-10-31T18:28:08Z
Point Vcs fields to salsa.debian.org
- - - - -
eb97f174 by Andreas Tille at 2018-10-31T18:28:09Z
Standards-Version: 4.2.1
- - - - -
a162cd37 by Andreas Tille at 2018-10-31T18:28:09Z
Secure URI in copyright format
- - - - -
1af8ca33 by Andreas Tille at 2018-10-31T18:28:31Z
Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
- - - - -
c39d57ad by Andreas Tille at 2018-10-31T18:28:31Z
Build-Depends: s/python-sphinx/python3-sphinx/
- - - - -
b8d094f8 by Andreas Tille at 2018-10-31T18:36:58Z
Fix changelog
- - - - -
9ef6e625 by Andreas Tille at 2018-10-31T18:37:47Z
DEP3
- - - - -
33296162 by Andreas Tille at 2018-10-31T18:38:16Z
Remove unused patch
- - - - -
30553618 by Andreas Tille at 2018-10-31T18:39:20Z
hardening=+all
- - - - -
971281e1 by Andreas Tille at 2018-10-31T20:27:00Z
New (Build-)Depends: python-h5py
- - - - -
ff6ed10f by Andreas Tille at 2018-10-31T20:30:32Z
Upload to unstable
- - - - -
9 changed files:
- README.md
- debian/changelog
- debian/compat
- debian/control
- debian/copyright
- − debian/patches/enable-nosetests
- debian/patches/multiarch-module-path.patch
- debian/rules
- debian/watch
Changes:
=====================================
README.md
=====================================
@@ -4,3 +4,7 @@ Biosciences. Specifically, this package provides functionality for
manipulating and extracting data from "cmp.h5" and "bas.h5" files.
[Detailed documentation here](doc/index.rst).
+
+DISCLAIMER
+----------
+THIS WEBSITE AND CONTENT AND ALL SITE-RELATED SERVICES, INCLUDING ANY DATA, ARE PROVIDED "AS IS," WITH ALL FAULTS, WITH NO REPRESENTATIONS OR WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT OR FITNESS FOR A PARTICULAR PURPOSE. YOU ASSUME TOTAL RESPONSIBILITY AND RISK FOR YOUR USE OF THIS SITE, ALL SITE-RELATED SERVICES, AND ANY THIRD PARTY WEBSITES OR APPLICATIONS. NO ORAL OR WRITTEN INFORMATION OR ADVICE SHALL CREATE A WARRANTY OF ANY KIND. ANY REFERENCES TO SPECIFIC PRODUCTS OR SERVICES ON THE WEBSITES DO NOT CONSTITUTE OR IMPLY A RECOMMENDATION OR ENDORSEMENT BY PACIFIC BIOSCIENCES.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,18 @@
+pbh5tools (0.8.0+git20170929.58d54ff+dfsg-1) unstable; urgency=medium
+
+ * Team upload.
+ * Use git mode in watch file
+ * debhelper 11
+ * Point Vcs fields to salsa.debian.org
+ * Standards-Version: 4.2.1
+ * Secure URI in copyright format
+ * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+ * Build-Depends: s/python-sphinx/python3-sphinx/
+ * hardening=+all
+ * New (Build-)Depends: python-h5py
+
+ -- Andreas Tille <tille at debian.org> Wed, 31 Oct 2018 21:27:08 +0100
+
pbh5tools (0.8.0+dfsg-5) unstable; urgency=medium
* Rename source package to match primary binary package
=====================================
debian/compat
=====================================
@@ -1 +1 @@
-9
+11
=====================================
debian/control
=====================================
@@ -1,28 +1,28 @@
Source: pbh5tools
-Section: science
-Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Afif Elghraoui <afif at debian.org>
-Build-Depends: debhelper (>= 9),
- dh-python,
- python,
- python-setuptools,
- python-pbcore,
- python-sphinx,
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 11~),
+ dh-python,
+ python,
+ python-setuptools,
+ python-pbcore,
+ python-h5py,
+ python3-sphinx,
python-nose,
- python-cram,
-Standards-Version: 3.9.7
+ python-cram
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/pbh5tools
+Vcs-Git: https://salsa.debian.org/med-team/pbh5tools.git
Homepage: https://github.com/PacificBiosciences/pbh5tools
-Vcs-Git: https://anonscm.debian.org/git/debian-med/pbh5tools.git
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/pbh5tools.git
Package: pbh5tools
Architecture: all
-Depends:
- ${misc:Depends},
- ${python:Depends},
- python-pbh5tools (>= ${binary:Version}),
- python-pkg-resources,
+Depends: ${misc:Depends},
+ ${python:Depends},
+ python-pbh5tools (>= ${binary:Version}),
+ python-pkg-resources
Description: tools for manipulating Pacific Biosciences HDF5 files
This package provides functionality for manipulating and extracting data
from cmp.h5 and bas.h5 files produced by the Pacific Biosciences sequencers.
@@ -32,11 +32,12 @@ Description: tools for manipulating Pacific Biosciences HDF5 files
This package is part of the SMRTAnalysis suite.
Package: python-pbh5tools
-Section: python
Architecture: any
+Section: python
Depends: ${shlibs:Depends},
- ${misc:Depends},
- ${python:Depends},
+ ${misc:Depends},
+ ${python:Depends},
+ python-h5py
Description: tools for manipulating Pacific Biosciences HDF5 files -- Python 2 library
This package provides functionality for manipulating and extracting data
from cmp.h5 and bas.h5 files produced by the Pacific Biosciences sequencers.
@@ -47,11 +48,11 @@ Description: tools for manipulating Pacific Biosciences HDF5 files -- Python 2 l
Python 2 backend library
Package: python-pbh5tools-doc
-Section: doc
Architecture: all
+Section: doc
Depends: ${misc:Depends},
- libjs-jquery,
- libjs-underscore
+ libjs-jquery,
+ libjs-underscore
Description: tools for manipulating HDF5 files produced by Pacific Biosciences (doc)
This package provides functionality for manipulating and extracting data
from cmp.h5 and bas.h5 files produced by the Pacific Biosciences sequencers.
=====================================
debian/copyright
=====================================
@@ -1,4 +1,4 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: pbh5tools
Source: https://github.com/PacificBiosciences/pbh5tools
Files-Excluded: doc/pacbio-theme/*
=====================================
debian/patches/enable-nosetests deleted
=====================================
@@ -1,20 +0,0 @@
-Description: Configure nosetests to run with setup.py test
-Author: Afif Elghraoui <afif at ghraoui.name>
-Forwarded: not-needed
-Last-Update: 2015-08-12
---- python-pbh5tools.orig/setup.py
-+++ python-pbh5tools/setup.py
-@@ -26,6 +26,7 @@
- 'bin/cmph5tools.py'],
- packages = find_packages("."),
- package_dir = {'':'.'},
-+ test_suite = 'nose.collector',
- ext_modules=[Extension('pbh5tools/ci', ['pbh5tools/ci.c'],
- extra_compile_args=["-O3","-shared"])],
- zip_safe = False,
---- /dev/null
-+++ python-pbh5tools/setup.cfg
-@@ -0,0 +1,3 @@
-+[nosetests]
-+verbosity=2
-+where=tests
=====================================
debian/patches/multiarch-module-path.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Afif Elghraoui
+Last-Update: 2016-03-20 00:45:22 -0700
+Description: Enable multiarch
+
--- python-pbh5tools.orig/pbh5tools/Indexer.py
+++ python-pbh5tools/pbh5tools/Indexer.py
@@ -32,10 +32,11 @@
=====================================
debian/rules
=====================================
@@ -7,6 +7,8 @@ BINDIR=$(CURDIR)/debian/pbh5tools/usr/bin
export PYBUILD_NAME = pbh5tools
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
%:
LC_ALL=C.UTF-8 dh $@ --with python2 --buildsystem=pybuild
@@ -23,9 +25,11 @@ override_dh_install:
mv debian/python-pbh5tools/usr/bin/cmph5tools.py $(BINDIR)/cmph5tools
override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
PYBUILD_SYSTEM=custom \
PYBUILD_TEST_ARGS="PATH=$(CURDIR)/build/scripts-2.7:$$PATH $(MAKE) test" \
dh_auto_test
+endif
override_dh_auto_clean:
dh_auto_clean
=====================================
debian/watch
=====================================
@@ -1,2 +1,7 @@
-# Upstream currently does not tag versions in their github repository
-version=3
+version=4
+
+opts="mode=git,pretty=0.8.0+git%cd.%h,repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz" \
+ https://github.com/PacificBiosciences/pbh5tools.git HEAD
+
+# Issue asking for release tags:
+# https://github.com/PacificBiosciences/pbh5tools/issues/30
View it on GitLab: https://salsa.debian.org/med-team/python-pbh5tools/compare/6965eeaf38e6f16526b073423fedb470caf0ca1a...ff6ed10ff65865fe7ed52ea69e961501d8be3e52
--
View it on GitLab: https://salsa.debian.org/med-team/python-pbh5tools/compare/6965eeaf38e6f16526b073423fedb470caf0ca1a...ff6ed10ff65865fe7ed52ea69e961501d8be3e52
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