Debian Bug report logs - #909707
hyphy: Please provide autopkgtest

Toggle useless messages

Message #5 received at submit@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <tille@debian.org>

To: Debian Bug Tracking System <submit@bugs.debian.org>

Subject: hyphy: Please provide autopkgtest

Date: Thu, 27 Sep 2018 08:00:53 +0200

Package: hyphy
Severity: minor
Tags: newcomer

Please provide autopkgtest for this package.

-- System Information:
Debian Release: 9.5
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 4.9.0-6-amd64 (SMP w/1 CPU core)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8), LANGUAGE=de_DE.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Message #10 received at 909707@bugs.debian.org (full text, mbox, reply):

From: Ioannis Valasakis <code@wizofe.uk>

To: "909707" <909707@bugs.debian.org>

Subject: hyphy: autopkgtest

Date: Thu, 18 Oct 2018 02:46:14 +0100

[Message part 1 (text/plain, inline)]

I am interested in getting assigned this bug and getting to know the process of creating an autopkg test :) Regards ioannis

[Message part 2 (text/html, inline)]

Message #15 received at 909707@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <andreas@an3as.eu>

To: code@wizofe.uk, 909707@bugs.debian.org

Cc: Debian Med Project List <debian-med@lists.debian.org>

Subject: [outreachy] Re: Bug#909707: hyphy: autopkgtest

Date: Thu, 18 Oct 2018 09:03:20 +0200

Hi Ioannis,

On Thu, Oct 18, 2018 at 02:46:14AM +0100, Ioannis Valasakis wrote:
> I am interested in getting assigned this bug

There is no technical way to assign a bug - but readers of the bug log
will know now that somebody is working on it.

> and getting to know the process of creating an autopkg test :) Regards ioannis

The general description of best practices is in Debian Wiki:

   https://wiki.debian.org/ContinuousIntegration/AutopkgtestBestPractices

In the packaging template I've created for Debian Med packages there is
also a boilerplate for an autopkgtest:

   https://salsa.debian.org/med-team/community/package_template/tree/master/debian/tests

Please note: We usually install the run-unit-test script in the docs of
a package to enable users to run the test as an example on the local
machine.

In the Debian Med policy

   https://med-team.pages.debian.net/policy/

you get general hints about packaging inside the Debian Med team.
Writing an autopkgtest boils down to adding the debian/tests dir to
the packaging.

Hope this helps as first hints - keep on asking here if something
remains unclear

       Andreas.

-- 
http://fam-tille.de

Message #20 received at 909707@bugs.debian.org (full text, mbox, reply):

From: Ioannis Valasakis <code@wizofe.uk>

To: 909707@bugs.debian.org

Cc: tille@debian.org

Subject: hyphy: Please provide autopkgtest

Date: Mon, 5 Nov 2018 23:58:45 +0000

Dear Andreas, 

I send a PR for the autopkgtest boilerplate for hyphy. You can review it here: https://salsa.debian.org/med-team/hyphy/merge_requests/1

It's a WIP (sorry for being late but it was my last essay for the semester, phew!). If you are happy to include my contribution I'll be allowed to send an application to be considered for Outreachy and I am going to implement the tests (as I comment on my PR that would be for a started the existing tests on run_tests.sh on the root folder)!

Actually, if you give me some extra help, I can also finish it today;
let me know if you have the time for that though. I would like to find
out what's the best way to test the autopkgtests myself? Do you usually
do this via chroot? Also let's say that I want to include the tests on
the /usr/share/doc directory, do I need to copy the whole dir with the
Examples there as well?

Best
ioannis

Message #25 received at 909707@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <tille@debian.org>

To: Ioannis Valasakis <code@wizofe.uk>, 909707@bugs.debian.org

Subject: Re: Bug#909707: hyphy: Please provide autopkgtest

Date: Sun, 9 Dec 2018 08:00:19 +0100

Hi Ioannis,

sorry for my (too?) late answer.  I was on vacation and now I'm catching
up with old tasks.  I checked the Pull Request but it does not contain
any commit.  Am I missing something?

Kind regards

       Andreas.

On Mon, Nov 05, 2018 at 11:58:45PM +0000, Ioannis Valasakis wrote:
> Dear Andreas, 
> 
> I send a PR for the autopkgtest boilerplate for hyphy. You can review it here: https://salsa.debian.org/med-team/hyphy/merge_requests/1
> 
> It's a WIP (sorry for being late but it was my last essay for the semester, phew!). If you are happy to include my contribution I'll be allowed to send an application to be considered for Outreachy and I am going to implement the tests (as I comment on my PR that would be for a started the existing tests on run_tests.sh on the root folder)!
> 
> Actually, if you give me some extra help, I can also finish it today;
> let me know if you have the time for that though. I would like to find
> out what's the best way to test the autopkgtests myself? Do you usually
> do this via chroot? Also let's say that I want to include the tests on
> the /usr/share/doc directory, do I need to copy the whole dir with the
> Examples there as well?
> 
> Best
> ioannis
> 
> _______________________________________________
> Debian-med-packaging mailing list
> Debian-med-packaging@alioth-lists.debian.net
> https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging

-- 
http://fam-tille.de

Message #30 received at 909707-close@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <tille@debian.org>

To: 909707-close@bugs.debian.org

Subject: Bug#909707: fixed in hyphy 2.5.1+dfsg-1

Date: Fri, 06 Dec 2019 22:21:22 +0000

Source: hyphy
Source-Version: 2.5.1+dfsg-1

We believe that the bug you reported is fixed in the latest version of
hyphy, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 909707@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated hyphy package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 1.8
Date: Fri, 06 Dec 2019 22:47:47 +0100
Source: hyphy
Binary: hyphy-pt hyphy-mpi hyphy-common
Architecture: source
Version: 2.5.1+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
 hyphy-common - Hypothesis testing using Phylogenies (common files)
 hyphy-mpi  - Hypothesis testing using Phylogenies (MPI version)
 hyphy-pt   - Hypothesis testing using Phylogenies (pthreads version)
Closes: 909707 943311
Changes:
 hyphy (2.5.1+dfsg-1) unstable; urgency=medium
 .
   [ Helmut Grohne ]
   * Add pkg-config to Build-Depends as FindMPI.cmake will need it for cross
     compilation. (Closes: #943311)
 .
   [ Andreas Tille ]
   * New upstream version
   * debhelper-compat 12
   * Secure URI in copyright format
   * Remove trailing whitespace in debian/changelog
   * New upstream version
   * Standards-Version: 4.4.1
   * Use secure URI in Homepage field.
   * Remove patches msse_option_only_if_available.patch that are missing
     from debian/patches/series.
   * Skip GTEST target for the moment since this is currently in flux
     see https://github.com/veg/hyphy/issues/1058
   * No need to rename executables any more since upstream is doing this now
   * Autopkgtest exists since last release - so close bug
     Closes: #909707
Checksums-Sha1:
 3d2f8e893dfae6d4ba2411ebf456f9d17b39f045 2171 hyphy_2.5.1+dfsg-1.dsc
 3e1253bf9f0d2b5537b3dc55e6fe73a75db9e0d2 2899360 hyphy_2.5.1+dfsg.orig.tar.xz
 9ed2a9ca4253a5070c66dce7b3769faf620d6ce2 10332 hyphy_2.5.1+dfsg-1.debian.tar.xz
Checksums-Sha256:
 0257eb0d590134ace1dff5aa1612b5caca094b6bc11c55a523c31e974f0ebc70 2171 hyphy_2.5.1+dfsg-1.dsc
 1ba52718825b34268f9b8ba2e9425f3450f5466750c2dadebc0238385bba989c 2899360 hyphy_2.5.1+dfsg.orig.tar.xz
 a8391b2b0acee18ff5650117f5d86bc2e8b1d88c1f685cbc0ffecff72d6dd0f1 10332 hyphy_2.5.1+dfsg-1.debian.tar.xz
Files:
 d7ea75f4ba58b7809972de077aa073b4 2171 science optional hyphy_2.5.1+dfsg-1.dsc
 512d3dc73c4c5ca19865627ff4317db5 2899360 science optional hyphy_2.5.1+dfsg.orig.tar.xz
 bdc2fab1276a9b2e78c74692c210fdaa 10332 science optional hyphy_2.5.1+dfsg-1.debian.tar.xz

-----BEGIN PGP SIGNATURE-----
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=F55d
-----END PGP SIGNATURE-----

Send a report that this bug log contains spam.