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Bug#858318: marked as done (unblock: python-cutadapt/1.12-2)

Your message dated Tue, 21 Mar 2017 09:29:27 +0100
with message-id <5e1f5c16-abba-3ddc-63e9-fcaf23fc4312@debian.org>
and subject line Re: Bug#858318: unblock: python-cutadapt/1.12-2
has caused the Debian Bug report #858318,
regarding unblock: python-cutadapt/1.12-2
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

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-- 
858318: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=858318
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message --- 
Package: release.debian.org
Severity: normal
User: release.debian.org@packages.debian.org
Usertags: unblock

Please unblock package python-cutadapt

Cutadapt now (Build-)Depends python-xopen where I filed an unblock
request #858317 which should be resolved before unblocking
python-cutadapt to make sure it will be installable in testing.

Upstream has simply split of the xopen code (see #858053) and the
latest uploader of python-cutadapt has not realised this change.

I took the freedom of not only fixing this but also added build time
tests to the packaging to make sure that this will not happen in the
future again.  Thus the attached debdiff contains

  1. Fix for bug #858053 by adding python-xopen dependency
  2. Build time test to prove that the bug is really fixed

Thanks for your work as release team

      Andreas.

unblock python-cutadapt/1.12-2

-- System Information:
Debian Release: 8.7
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 3.16.0-4-amd64 (SMP w/1 CPU core)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

diff -Nru python-cutadapt-1.12/debian/changelog python-cutadapt-1.12/debian/changelog
--- python-cutadapt-1.12/debian/changelog	2016-12-02 03:56:33.000000000 +0100
+++ python-cutadapt-1.12/debian/changelog	2017-03-20 16:49:26.000000000 +0100
@@ -1,3 +1,11 @@
+python-cutadapt (1.12-2) unstable; urgency=medium
+
+  * Depends: python-xopen
+    Closes: #858053
+  * Run build time tests
+
+ -- Andreas Tille <tille@debian.org>  Mon, 20 Mar 2017 16:49:26 +0100
+
 python-cutadapt (1.12-1) unstable; urgency=medium
 
   * New upstream version 1.12 (Closes: #846471)
diff -Nru python-cutadapt-1.12/debian/control python-cutadapt-1.12/debian/control
--- python-cutadapt-1.12/debian/control	2016-12-02 03:56:33.000000000 +0100
+++ python-cutadapt-1.12/debian/control	2017-03-20 16:49:26.000000000 +0100
@@ -10,11 +10,15 @@
                python-all,
                python-all-dev,
                python-setuptools,
+               python-nose,
+               python-xopen,
                cython,
                python3-all,
                python3-all-dev,
                python3-setuptools,
                python3-six,
+               python3-nose,
+               python3-xopen,
                cython3
 Standards-Version: 3.9.8
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/python-cutadapt.git
diff -Nru python-cutadapt-1.12/debian/patches/0003_fixtest.patch python-cutadapt-1.12/debian/patches/0003_fixtest.patch
--- python-cutadapt-1.12/debian/patches/0003_fixtest.patch	1970-01-01 01:00:00.000000000 +0100
+++ python-cutadapt-1.12/debian/patches/0003_fixtest.patch	2017-03-20 16:49:26.000000000 +0100
@@ -0,0 +1,37 @@
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Fri, 17 Mar 2017 21:20:50 +0100
+Description: Make sure test suite will find utils
+
+--- a/tests/testcolorspace.py
++++ b/tests/testcolorspace.py
+@@ -3,7 +3,7 @@ from __future__ import print_function, d
+ 
+ from cutadapt.colorspace import encode, decode
+ from cutadapt.scripts.cutadapt import main
+-from .utils import run, datapath
++from utils import run, datapath
+ 
+ # If there are any unknown characters in the test sequence,
+ # round tripping will only work if all characters after the
+--- a/tests/testpaired.py
++++ b/tests/testpaired.py
+@@ -4,7 +4,7 @@ from __future__ import print_function, d
+ import shutil
+ from nose.tools import raises
+ from cutadapt.scripts import cutadapt
+-from .utils import run, files_equal, datapath, cutpath, redirect_stderr, temporary_path
++from utils import run, files_equal, datapath, cutpath, redirect_stderr, temporary_path
+ 
+ def run_paired(params, in1, in2, expected1, expected2):
+ 	if type(params) is str:
+--- a/tests/tests.py
++++ b/tests/tests.py
+@@ -9,7 +9,7 @@ import sys
+ from nose.tools import raises
+ from cutadapt.scripts import cutadapt
+ from cutadapt.compat import StringIO
+-from .utils import run, files_equal, datapath, cutpath, redirect_stderr, temporary_path
++from utils import run, files_equal, datapath, cutpath, redirect_stderr, temporary_path
+ 
+ def test_example():
+ 	run('-N -b ADAPTER', 'example.fa', 'example.fa')
diff -Nru python-cutadapt-1.12/debian/patches/series python-cutadapt-1.12/debian/patches/series
--- python-cutadapt-1.12/debian/patches/series	2016-12-02 03:56:33.000000000 +0100
+++ python-cutadapt-1.12/debian/patches/series	2017-03-20 16:49:26.000000000 +0100
@@ -1,2 +1,3 @@
 cython_version.patch
 0002-Fix-encoding-issue-in-setup.py.patch
+0003_fixtest.patch
diff -Nru python-cutadapt-1.12/debian/rules python-cutadapt-1.12/debian/rules
--- python-cutadapt-1.12/debian/rules	2016-12-02 03:56:33.000000000 +0100
+++ python-cutadapt-1.12/debian/rules	2017-03-20 16:49:26.000000000 +0100
@@ -20,6 +20,8 @@
 
 export PYBUILD_NAME=cutadapt
 
+PYTHON2 := $(shell pyversions -r)
+PYTHON3 := $(shell py3versions -r)
 
 # main packaging script based on dh7 syntax
 %:
@@ -31,5 +33,12 @@
 	mv debian/python3-cutadapt/usr/bin/cutadapt debian/cutadapt/usr/bin/
 	rm -f debian/python-cutadapt/usr/bin/cutadapt
 
-
-
+override_dh_auto_test:
+ifeq ($(filter nocheck,$(DEB_BUILD_OPTIONS)),)
+	for py in $(PYTHON2) ; do\
+	    $$py setup.py nosetests -v ; \
+	done
+	for py in $(PYTHON3) ; do\
+	    $$py setup.py nosetests -v ; \
+	done
+endif

--- End Message ---
--- Begin Message --- 
On 21/03/17 08:07, Andreas Tille wrote:
> Package: release.debian.org
> Severity: normal
> User: release.debian.org@packages.debian.org
> Usertags: unblock
> 
> Please unblock package python-cutadapt
> 
> Cutadapt now (Build-)Depends python-xopen where I filed an unblock
> request #858317 which should be resolved before unblocking
> python-cutadapt to make sure it will be installable in testing.
> 
> Upstream has simply split of the xopen code (see #858053) and the
> latest uploader of python-cutadapt has not realised this change.
> 
> I took the freedom of not only fixing this but also added build time
> tests to the packaging to make sure that this will not happen in the
> future again.  Thus the attached debdiff contains
> 
>   1. Fix for bug #858053 by adding python-xopen dependency
>   2. Build time test to prove that the bug is really fixed
> 
> Thanks for your work as release team
> 
>       Andreas.
> 
> unblock python-cutadapt/1.12-2

+override_dh_auto_test:
+ifeq ($(filter nocheck,$(DEB_BUILD_OPTIONS)),)

You don't need that, debhelper does it for you. That's harmless though.

Anyway this is already unblocked:

Hints in place:
==> ivodd
  # 20170320
  # #858053
  unblock python-cutadapt/1.12-2
  age-days 5 python-cutadapt/1.12-2

Cheers,
Emilio

--- End Message ---
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