nauty 2.7r1+ds-1 uploaded

2020-08-26 Thread Andrius Merkys
Hi Doug,

Yesterday I reviewed and uploaded your packaging of nauty 2.7r1+ds-1.
Thanks a lot for your work!

Best,
Andrius



Re: Please delete science-team/ete3

2020-07-09 Thread merkys
On 2020-07-09 09:10, PICCA Frederic-Emmanuel wrote:
> done

Thanks!
Andrius



Please delete science-team/ete3

2020-07-09 Thread merkys
Hello,

Could someone with appropriate rights delete empty repository science-team/ete3 
from salsa? This one has been named incorrectly, and was replaced with 
med-team/python-ete3.

Thanks,
Andrius



Re: RFS ete

2020-07-03 Thread merkys
On 2020-07-03 13:50, zhao feng wrote:
> Thanks for your help. I can build the package on buster and bullyseye.
> Which distribution do you use? I find the version of softwares like
> python is quite new.

The package fails to build on clean sid chroot. Most likely some Python
dependencies are missing from debian/control.

> The upstream uses `ete` as the name of repository but they call the
> Python package `ete3`. In their paper, they explain the number 3 is
> the version and in their roadmap they plan to release `ete4`.
> (https://github.com/etetoolkit/ete/wiki/ROADMAP). I think using a
> version independent name like `ete` for source package and
> `python3-ete` for library is convenient. How to do think about it?

I agree that the source package could stay named 'ete'. However, after
reading the Debian Python naming conventions [1] I became even more
convinced to name the package 'python3-ete3'.

[1]
https://www.debian.org/doc/packaging-manuals/python-policy/module_packages.html#package_names

> 2-5 has been fixed now.

The copyright entry for 'SQLite-Levenshtein' seems still missing from
debian/copyright. Could you please add it?

> I have created a directory in
> https://salsa.debian.org/science-team/ete3 but I do not have
> privileges to create a branch. Can you help on it?

I see you have named the repository 'ete3'. This means you want to name
the source package 'ete3' as well, or was this unintentional?

By the way, packaging of 'ete3' seems to be ongoing in Debian Med team
as well (adding Andreas in CC):
https://salsa.debian.org/med-team/python-ete3. I suggest getting in
touch with them to keep duplicate efforts minimal.

Best wishes,
Andrius



Re: RFS ete

2020-07-02 Thread merkys
Hello,

On 2020-07-02 17:23, zhao feng wrote:
> ok, the warning has been fixed by 3.1.1-3

Thanks for fixing lintian issues. I have cloned your repository, tried
to build it, and ran into the following problem:

   dh_auto_test -O--buildsystem=pybuild
pybuild --test -i python{version} -p 3.8
I: pybuild base:217: cd
/home/andrius/debian-packages/ete/.pybuild/cpython3_3.8_ete/build;
python3.8 -m pytest -k "not test_ncbiquery and not test_skbio and not
test_ncbi_compare and not test_get_topology and not
test_01tree_annotation and not test_00_update_database"
ete3/test/test_api.py
= test session starts
==
platform linux -- Python 3.8.4rc1, pytest-4.6.11, py-1.8.1, pluggy-0.13.0
rootdir: /home/andrius/debian-packages/ete
plugins: timeout-1.3.3, cov-2.8.1
collected 51 items / 6 deselected / 45 selected

ete3/test/test_api.py Aborted
E: pybuild pybuild:352: test: plugin distutils failed with: exit
code=134: cd
/home/andrius/debian-packages/ete/.pybuild/cpython3_3.8_ete/build;
python3.8 -m pytest -k "not test_ncbiquery and not test_skbio and not
test_ncbi_compare and not test_get_topology and not
test_01tree_annotation and not test_00_update_database"
ete3/test/test_api.py
dh_auto_test: error: pybuild --test -i python{version} -p 3.8 returned
exit code 13
make: *** [debian/rules:9: build] Error 25
dpkg-buildpackage: error: debian/rules build subprocess returned exit
status 2
debuild: fatal error at line 1182:
dpkg-buildpackage -us -uc -ui -i -I failed
gbp:error: 'debuild -i -I -uc -us' failed: it exited with 29

Do you know what might be the reason?

A few more issues to address to address:

1. I am under the impression that the Python package should be named
'ete3', not 'ete'. After installing the .deb package Python command
'import ete3' fails.

2. Directory 'SQLite-Levenshtein' (SQLite extension for Levenshtein
algorithm) should not be present in the .deb package, at least not in
its current form. However, it could be packaged separately in the future.

3. If 'SQLite-Levenshtein' remains in the source, it should be mentioned
in debian/copyright.

4. The copyright for ETE is GPL-3+.

5. Please consider licensing debian/ directory under the same license
too to avoid possible license incompatibilities.

6. Please consider maintaining this package under the umbrella of Debian
Python or Science teams. To do so, join the appropriate team, move the
packaging repository to their namespace, and adjust Maintainer and
Uploaders fields in debian/control.

Thanks for your efforts to package ete.

Best wishes,
Andrius



Re: RFS ete

2020-07-02 Thread merkys
Hi,

I have tried building the package from the packaging repository on
salsa, however, 'upstream' and 'pristine-tar' branches are missing
there. Could you please push them with 'salsa push' or 'git push --all
&& git push --tags'?

On 2020-07-02 11:03, zhao feng wrote:
> feng@debian:~/ete$ lintian python3-ete_3.1.1-1.1_all.deb
> W: python3-ete: binary-without-manpage usr/bin/ete3
> W: python3-ete: copyright-has-url-from-dh_make-boilerplate
> W: python3-ete: description-synopsis-starts-with-article
> W: python3-ete: executable-not-elf-or-script
> usr/lib/python3/dist-packages/ete3/test/test_circle_label.py
> W: python3-ete: executable-not-elf-or-script
> usr/lib/python3/dist-packages/ete3/test/test_treeview/barchart_and_piechart_faces.py
> W: python3-ete: executable-not-elf-or-script
> usr/lib/python3/dist-packages/ete3/test/test_treeview/bubble_map.py
> W: python3-ete: executable-not-elf-or-script ... use
> --no-tag-display-limit to see all (or pipe to a file/program)
> W: python3-ete: file-in-unusual-dir usr/ete3/tools/ete_build.cfg
> W: python3-ete: non-standard-dir-in-usr usr/ete3/
> W: python3-ete: package-contains-vcs-control-file
> usr/lib/python3/dist-packages/ete3/ncbi_taxonomy/SQLite-Levenshtein/.gitignore
> feng@debian:~/ete$ lintian --version
> Lintian v2.80.0

These lintian warnings too should be fixed. Most of them are rather easy
to fix.

Best wishes,
Andrius



Re: RFS ete

2020-06-30 Thread merkys
Hello,

On 2020-06-30 11:56, zhao feng wrote:
> To access further information about this package, please visit the
> following URL:
> 
>   https://mentors.debian.net/package/ete

mentors.debian.net report lintian errors for this package. These have to
be addressed prior to sponsoring.

Best wishes,
Andrius



Re: [RFS] bibutils for an upload in experimental

2020-04-26 Thread merkys
Hi Pierre,

On 2020-04-26 12:39, Pierre Gruet wrote:
> Absolutely, the only non-Haskell reverse dependency is the binary bibutils.
> I have already filed a blocking bug, which I am going to raise to RC, and I
> will write to the list following your advice.

bibutils themselves should be fine. Haskell packages might require
either binNMU, or source uploads.

Best wishes,
Andrius



Re: [RFS] bibutils for an upload in experimental

2020-04-25 Thread merkys
Hi Pierre,

On 2020-04-25 15:53, Pierre Gruet wrote:
> The release team has just asked to go ahead after I submitted a transition
> bug [1]; I have prepared the upload to unstable in Salsa [2] (with
> UNRELEASED distribution), would you please mind uploading it, as you kindly
> offered?

Done. Thanks for your contribution!

I see that the most of the reverse dependencies of bibutils belong to
Haskell team. As I am not a member of that team, please contact them for
sponsoring haskell-* packages.

Best wishes,
Andrius



Re: [RFS] bibutils for an upload in experimental

2020-04-14 Thread Andrius Merkys
Hi Pierre,

On Tue, 14 Apr 2020, 18:54 Pierre Gruet,  wrote:

> Thanks a lot for reviewing my work, correcting this mistake and uploading
> the package to experimental!
>

Happy to help!

I will now wait for it to exit NEW and then launch the transition procedure.


Sure! Ping me when you need an upload to unstable for this.

Best wishes,
Andrius


Re: [RFS] bibutils for an upload in experimental

2020-04-13 Thread merkys
Hi Pierre,

On 2020-04-08 19:59, Pierre Gruet wrote:
> Some days ago I worked on the packaging of bibutils, which is maintained in
> the team. I had to bump the SONAME and therefore I ask for sponsorship to
> put it in *experimental* in order to begin a transition procedure, having
> identified four reverse-dependencies.
>
> If time permits, I would be happy to get feedback on my packaging and to
> have the package uploaded.

I have uploaded bibutils to experimental today. I have just changed a
line in the debian/changelog saying that libraries are placed in
/usr/share, when indeed they seem to be placed in /usr/lib.

Thanks a lot for your contribution!

Best,
Andrius



Re: Request to source-only upload https://salsa.debian.org/science-team/ricks-amdgpu-utils/

2020-04-08 Thread merkys
Hi Steffen,

On 2020-04-08 20:03, Steffen Möller wrote:
> My GPG key expired, could someone please source-only upload Rick's
> AMDGPU utils from
> https://salsa.debian.org/science-team/ricks-amdgpu-utils/ ? I have run
> it through cowbuilder. 

Done.

Best,
Andrius



Re: Insufficient privileges on Salsa to create a default branch

2019-04-25 Thread merkys
On 2019-04-25 16:45, Emmanuel Arias wrote:
> If you need work, meanwhile you can create your own repo.
> Then, when you have privileges you can transfer the repo.

Sure, thanks.

Andrius

-- 
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
LT-10257 Vilnius, Lithuania



Insufficient privileges on Salsa to create a default branch

2019-04-25 Thread merkys
Hello,

it seems that my current privileges in Debian Science group on Salsa
('Developer') are sufficient to create new projects, but insufficient to
create default branches for them:

remote: GitLab:
remote: A default branch (e.g. master) does not yet exist for
science-team/coot-reference-structures
remote: Ask a project Owner or Maintainer to create a default branch:
remote:
remote:  
https://salsa.debian.org/science-team/coot-reference-structures/project_members
remote:
To salsa.debian.org:science-team/coot-reference-structures.git
 ! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to
'g...@salsa.debian.org:science-team/coot-reference-structures.git'

Could I be promoted to Maintainer status? My Salsa login is 'merkys'.

Thanks,
Andrius

-- 
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
LT-10257 Vilnius, Lithuania



Re: mmdb transition

2018-05-05 Thread Andrius Merkys
On 05/05/2018 03:30 PM, PICCA Frederic-Emmanuel wrote:
> Is it possible to add a get-orig-source target in order to deal with the ccp4 
> release process workflow.
> using bzr in order to get the latest trunk branch of mmdb ?.

This should be doable, but I have to find some more time to look into it. I'm 
not common with bzr.

Best,
Andrius

-- 
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
LT-10257 Vilnius, Lithuania



Re: mmdb transition

2018-05-05 Thread Andrius Merkys
On 05/05/2018 03:15 PM, PICCA Frederic-Emmanuel wrote:
> It was uploaded into experimental.

Oh, I overlooked 2.0.1-1~exp1. Currently experimental contains 2.0.5-1~exp1, 
which has libmmdb2-0-dbgsym debug symbols package, which superseded the -dbg 
one. Sorry. Fixed now.

Best,
Andrius

-- 
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
LT-10257 Vilnius, Lithuania



Re: mmdb transition

2018-05-05 Thread Andrius Merkys
On 05/05/2018 02:55 PM, PICCA Frederic-Emmanuel wrote:
> the migration is for the libmmdb2-0-dbg package and not the  libmmdb0-dbg one.

True indeed, but package 'libmmdb2-0-dbg' was never uploaded neither to 
unstable nor to testing. Therefore, there is no use of 'Breaks' or 'Replaces' 
indication for it. Or do I miss something?

Best,
Andrius

-- 
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
LT-10257 Vilnius, Lithuania



Re: mmdb transition

2018-05-05 Thread Andrius Merkys
On 05/05/2018 12:44 PM, PICCA Frederic-Emmanuel wrote:
> Can you do this before the upload ?

Done. I hope I did it right. Debug symbols package descriptions now contain 
correct Breaks and Replaces records.

Best,
Andrius

-- 
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
LT-10257 Vilnius, Lithuania




Re: mmdb transition

2018-05-05 Thread Andrius Merkys
Hi,

On 05/05/2018 12:16 PM, PICCA Frederic-Emmanuel wrote:
> You juts have to follow the instructions and remove all the -dbg packages and 
> add the dh command line options :)

Sounds really easy :)

> Yes, and did you subscribe to ccp4-dev mailinglist.
> It would be great also to work with the upstream in order to integrate the 
> relevant debian patches :).

True indeed. I have just subscribed to the list.

> Just tell me when it is ok for you, and I will upload mmdb first to start the 
> transition :).

I think that's OK with me right now :) Please proceed, and let me know should 
anything fail.

Best,
Andrius

-- 
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
LT-10257 Vilnius, Lithuania



Re: mmdb transition

2018-05-05 Thread Andrius Merkys
Hello,

On 05/04/2018 11:38 AM, PICCA Frederic-Emmanuel wrote:
> It would be great if you could add yourself to the Uploaders list.

done :)

> https://wiki.debian.org/AutomaticDebugPackages
>
> So it seems that you need to add the migration in the rules file :)

I see. OK, I was not aware of that.

> Is it possible for you to check with the ccp4 upstream on the ccp-dev mailing 
> list if it is possible to have the lastest sources packages of libccp4, mmdb, 
> ssm and clipper.
> I had to ask for them each time to Marcin Wojdyr

I saw your recent e-mail to the ccp4-dev mailing list. Let's hear what they 
will say.

> then I will upload the packages, once I build them with sbuild :))

Great!

Thanks,
Andrius

-- 
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
LT-10257 Vilnius, Lithuania




Re: mmdb transition

2018-05-03 Thread Andrius Merkys
Hi Frederic-Emmanuel,

I have reserved a transition slot 
(https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=897579) and updated the mmdb 
reverse dependencies. There were new upstream releases for ssm and clipper, I 
have packaged both of them.

I have updated topmost changelog entries, however, I signed them as myself to 
prevent lintian timewarp warnings. Feel free to replace my signatures with 
yours.

Moreover, I don't know what to do with '--ddeb-migration' dh options. Do you 
know, should they be removed before the transition? I have left them where they 
were.

Could you please upload updated mmdb, ssm, clipper and libccp4 packages to 
unstable if they are OK? If not, let me know what should I fix.

Thanks,
Andrius

On 05/02/2018 07:25 PM, PICCA Frederic-Emmanuel wrote:
> It would be nice tu update all these library to the lateste versions :))

-- 
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
LT-10257 Vilnius, Lithuania




Re: mmdb transition

2018-05-02 Thread Andrius Merkys
On 05/02/2018 07:25 PM, PICCA Frederic-Emmanuel wrote:
> It would be nice tu update all these library to the lateste versions :))

OK, I'll see what I can do :)

Best,
Andrius

-- 
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
LT-10257 Vilnius, Lithuania



Re: mmdb transition

2018-05-02 Thread Andrius Merkys
Hello,

On 05/02/2018 07:21 PM, PICCA Frederic-Emmanuel wrote:
> Not enough time from my side :((. If you want to take care of this. It is ok 
> for me.

sure, I would like to give it a try. Will you help me with uploading the 
packages once they're ready?

Best,
Andrius

-- 
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
LT-10257 Vilnius, Lithuania



mmdb transition

2018-05-02 Thread Andrius Merkys
Dear Frédéric-Emmanuel,
dear all,

I noticed that mmdb v2.0.5 was uploaded to experimental, however, the full 
transition of mmdb does not seem to be carried out yet. I wonder what were the 
showstoppers? All r-dependencies of mmdb 
(https://release.debian.org/transitions/html/auto-mmdb.html) seem to build 
successfully for me, therefore, I guess the transition could be initiated. mmdb 
>= 2 is a build dependency of coot, which I would like to see in Debian one day.

Best wishes,
Andrius

-- 
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
LT-10257 Vilnius, Lithuania




Re: [Debichem-devel] Membership and permissions for repository creation on salsa

2018-04-13 Thread Andrius Merkys
Dear Daniel,

On 04/13/2018 01:34 PM, Daniel Leidert wrote:
> We basically follow the same role principle as described in the debian-
> science policy. To create a new project, you can simply ask. Another
> possibility is to create the project in your personal workspace. As soon
> as you find it ready, tell us, and we can import it into the group space
> from there. Then we can also adjust the projects permissions if necessary.

thanks for the explanation. I prefer creating projects in my personal workspace 
and asking to be moved after they are done.

Best,
Andrius

-- 
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
LT-10257 Vilnius, Lithuania



Re: [Debichem-devel] Membership and permissions for repository creation on salsa

2018-04-12 Thread Andrius Merkys
Dear Boris,

On 04/12/2018 11:27 AM, Boris Pek wrote:
> It is briefly described in Debian Science Policy Manual:
> https://science-team.pages.debian.net/policy/#idm145

thanks for the link. I was not aware of this change of the policy.

Best wishes,
Andrius

-- 
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
LT-10257 Vilnius, Lithuania



Membership and permissions for repository creation on salsa

2018-04-12 Thread Andrius Merkys
Hello,

I am a member of Debian Science Team and Debichem, and as a "Member" I had 
permissions to create repositories on anonscm.debian.org in both projects. 
However, on salsa.debian.org I am "Developer", therefore I can not create new 
repositories in neither of the projects. How can I contribute new packages on 
salsa?

Best wishes,
Andrius

-- 
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
LT-10257 Vilnius, Lithuania




Re: Pushing commits to GitLab-Salsa not allowed

2018-01-11 Thread Andrius Merkys
Dear Boris,

On 01/11/2018 10:59 AM, Boris Pek wrote:
> Just join to Debian Science Team group:
> https://salsa.debian.org/science-team
> as a member with Developer level of access:
> https://docs.gitlab.com/ee/user/permissions.html

many thanks for the explanation! I have requested to join the Team and
now I am able to push my commits.

Best regards,
Andrius

-- 
Andrius Merkys
PhD student at Vilnius University Institute of Biotechnology, Saulėtekio al. 7, 
room V325
LT-10257 Vilnius, Lithuania



Pushing commits to GitLab-Salsa not allowed

2018-01-10 Thread Andrius Merkys
Dear all,

I used to own a guest account on Alioth, and with this account I have
created a few packaging GIT repositories. However, since the transition
to GitLab-Salsa I am unable to push my commits:

andrius@tasmanijos-velnias cod-tools $ git remote set-url origin
g...@salsa.debian.org:science-team/cod-tools.git
andrius@tasmanijos-velnias cod-tools $ git push
GitLab: You are not allowed to push code to this project.
fatal: Could not read from remote repository.

Please make sure you have the correct access rights

I have signed up on salsa.debian.org (@merkys-guest) and set up my SSH
key. Could this be because of me being absent from 'Project members' of
my package's project
(https://salsa.debian.org/science-team/cod-tools/project_members)? If
so, could I be added?

Best wishes,
Andrius

-- 
Andrius Merkys
PhD student at Vilnius University Institute of Biotechnology, Saulėtekio al. 7, 
room V325
LT-10257 Vilnius, Lithuania




Bug #864713: cod-tools package is ready

2017-09-29 Thread Andrius Merkys
Dear maintainers,

I have prepared the Debian package for cod-tools in its package
repository of Debian Science
(https://anonscm.debian.org/git/debian-science/packages/cod-tools.git/)
and I am looking for a sponsor. I think the package is suitable for
DebianScience/Chemistry metapackage.

Sincerely,
Andrius Merkys

-- 
Andrius Merkys
PhD student at Vilnius University Institute of Biotechnology, Saulėtekio al. 7, 
room V325
LT-10257 Vilnius, Lithuania




Re: Bug#864355: ITP: cod-tools -- tools for manipulation of Crystallographic Information Format v1.1 and v2.0 files

2017-06-13 Thread Andrius Merkys
Dear Andreas,

thank you for your message. I would gladly maintain my package in either
Debian Science or DebiChem team.

Best wishes,
Andrius


On 10/06/17 07:58, Andreas Tille wrote:
> Hi Andrius,
>
> thanks for this interesting ITP.  This package seems to fit nicely into
> the scope of Debian Science or DebiChem.  I'd like to suggest you should
> maintain the package in either of this team.
>
> Kind regards
>
>Andreas.
>
> On Wed, Jun 07, 2017 at 04:33:49PM +0300, Andrius Merkys wrote:
>> Package: wnpp
>> Severity: wishlist
>> Owner: Andrius Merkys <andrius.mer...@gmail.com>
>>
>> * Package name: cod-tools
>>   Version     : 2.0
>>   Upstream Author : Saulius Gražulis <grazu...@ibt.lt>, Andrius Merkys 
>> <andrius.mer...@gmail.com>, Antanas Vaitkus <antanas.vaitku...@gmail.com>
>> * URL : http://wiki.crystallography.net/cod-tools
>> * License : GPL 2.0
>>   Programming Lang: C, Perl, Python, Shell
>>   Description : tools for manipulation of Crystallographic Information 
>> Format v1.1 and v2.0 files
>>
>> The package contains Crystallographic Information Format (CIF) v1.1 and
>> v2.0 parser (parser of CIF v1.1 is compared to other parsers in Merkys et
>> al. 2016, doi:10.1107/S1600576715022396) and scripts for manipulating CIF
>> files. Package includes CIF parser bindings for C, Perl and Python. Tools
>> from the package are used in the development and maintenance of the
>> Crystallography Open Database (http://www.crystallography.net/cod/, usage
>> described in Gražulis et al. 2009, doi:10.1107/S0021889809016690 and
>> Gražulis et al. 2015, doi:10.1107/S1600576714025904). The tools follow
>> the same filter-like usage pattern as Netpbm.
>>
>> As I am an upstream author, I plan to maintain the package myself. As
>> this is my first submission, I will need a sponsor.
>>
>>

-- 
Andrius Merkys
PhD student at Vilnius University Institute of Biotechnology, Saulėtekio al. 7, 
room V325
LT-10257 Vilnius, Lithuania
Lecturer at Vilnius University Faculty of Mathematics and Informatics, 
Naugarduko g. 24
LT-03225 Vilnius, Lithuania