Re: Debian for Systems Biology

Ciao Luca, Is there anybody interested to packaging software for systems biology? you mean in already packaged software :-) I'm a bioinformatics student, and I noticed nobody within Debian is packaging systems biology-related tools (there is only an old ITP for libsbml). It is mine. I have a

Re: Torque in Debian?

Hi Jordi, Jordi Mallach wrote: On Sat, Dec 19, 2009 at 07:58:29PM +0100, Steffen Moeller wrote: Now 2.4 is out and there should only be a single 2.4 branch left. I understand 2.4 is now stable and the packaging is what can be found in trunk. However, I don't see any recent changes to trunk,

Re: NARVAL ENX : two potential new packages

Hi Andreas, Andreas Tille wrote: On Mon, Mar 22, 2010 at 01:28:30PM +0100, Xavier Grave wrote: My idea to have NARVAL related to debian-science was to ease promote Debian in science area where for the moment we have Scientific Linux. SL has the backing of some large (!) and prominent (!)

Re: Big problems with scientifc use of amd64

On 06/17/2010 06:00 PM, Yaroslav Halchenko wrote: just as a sidenote I would like to echo Gudjon's reply: we use lenny on our little cluster, with backports (backports.org and neuro.debian.net) whenever feasable. And in addition to all that has been said I wish to mention that backports.org

packaging jmol, was Re: I want to contribute

Hello, On 07/14/2010 02:44 PM, Andreas Tille wrote: On Wed, Jul 14, 2010 at 11:53:10AM +0200, Egon Willighagen wrote: I am sure you would make many Debian users happy if you would package Jmol (http://jmol.org/) for Debian. (I am/was lead developer for both, and reside in Uppsala).

Re: packaging jmol, was Re: I want to contribute

On 07/16/2010 11:31 AM, Michael Banck wrote: Hi, On Wed, Jul 14, 2010 at 10:14:05PM +0200, Andreas Tille wrote: On Wed, Jul 14, 2010 at 11:04:15PM +0800, Alex John wrote: I'm Alex and I'd like to help package jmol if anyone is willing to introduce me to the procedure (first time

while sponsoring, patch against qcad - don't have permissions

Hello, I thought I could commit everywhere as a DD, but apparently not. Someone please fix this for me. Howard, the upload is coming Steffen $ cat 0001-typo.patch From 8b9b6acc2d0eb05542c3d91a88bc4c018e770d14 Mon Sep 17 00:00:00 2001 From: Steffen Moeller moel...@debian.org Date: Sun, 18 Jul

backports

Hello, how do you feel towards the idea that with the advent of backports as an official service of the distribution, we should use that in routine for the more frequently updated tools? In science, there is rarely (i.e. except for comparisons or for continuity) the need to use an older

Re: Qt3 removal rational

On 02/10/2011 09:10 PM, Michael Banck wrote: If qt3 is really popular with scientific apps, which presumably are slow moving targets which are not esaily /quickly ported to qt4, it should be enough motivation for the people who need qt3 to take on the maintenance, so no need to

Re: Removal requests submitted for CERNLIB packages

On 03/05/2011 02:57 AM, Lifeng Sun wrote: Hi Kevin, The FTBFS bug of CERNLIB is actually an issue of diffutils, when I built it after squeeze released last month, the bug disappeared, so I think this bug could be closed now. I would like to adopt the CERNLIB-related packages if allowed.

Re: Debian and Scientific Linux

On 03/05/2011 05:34 PM, Juergen Salk wrote: * Juergen Salk juergen.s...@gmx.de [110305 15:46]: That they have Scientific Linux and are Open Source already is per se already quite remarkable. [...] The main goal of Scientific Linux is *not* to be as scientific as possible, e.g. in terms of

Re: Scientific software packaging

Hello, On 05/23/2011 01:30 PM, Yngve Inntjore Levinsen wrote: On Monday 23 May 2011 12.29.15 Gürkan Sengün wrote: That sounds fantastic, do you already have ready packages that I could test? You can test the ROOT packages which we distribute from CERN (unofficially) here:

Re: Scientific software packaging

Hello Yngve, On 05/23/2011 04:42 PM, Yngve Inntjore Levinsen wrote: On Monday 23 May 2011 14.19.44 Steffen Möller wrote: Hello, On 05/23/2011 01:30 PM, Yngve Inntjore Levinsen wrote: On Monday 23 May 2011 12.29.15 Gürkan Sengün wrote: That sounds fantastic, do you already have ready

Re: Proposal: Debian Science mailing lists

On 06/22/2011 02:36 PM, Brett Viren wrote: Andreas Tille andr...@an3as.eu writes: While I *personally* do not have a problem with the current situation I agree with Sylvestre that currently debian-science@l.d.o is not kind of missing link between developers and users. Because I think we

Re: ROOT 5.32/00 for Debian Squeeze

On 01/10/2012 03:06 AM, Sylvestre Ledru wrote: Hello Ricardo, Le mercredi 04 janvier 2012 à 09:20 -0800, Ricardo Yanez a écrit : Hi everyone, I have created a repository with the latest ROOT pro version (5.32.00) for Squeeze (i386, powerpc64 upcoming). The packages are built by me by

Re: ROOT 5.32/00 for Debian Squeeze

On 01/10/2012 05:44 PM, Ricardo Yanez wrote: Hello Ricardo, Le mercredi 04 janvier 2012 à 09:20 -0800, Ricardo Yanez a écrit : Hi everyone, I have created a repository with the latest ROOT pro version (5.32.00) for Squeeze (i386, powerpc64 upcoming). The packages are built by me by

Re: Debian at ESRF

On 04/18/2012 10:14 PM, Andreas Tille wrote: On Wed, Apr 18, 2012 at 09:39:30AM +0200, Sylvestre Ledru wrote: Following Yaroslav's message, I would like to advertize the migration of the European Synchrotoron (http://www.esrf.eu) at Grenoble to Debian6; succeeding to RedHat4 and Centos5. For

Re: Kudos to High Energy Physics packagers (Re: r3479 - /projects/science/trunk/debian-science/tasks/highenergy-physics)

Hello, On 07/13/2012 06:48 PM, Lifeng Sun wrote: Unfortunately, Herwig++ is also missed and failed to enter Wheezy, although I filed RFS more than one month ago. Args. I presume the answer to Herwig and to all those tools seeing new important versions will be backports.debian.org. We have

Aw: Re: DebConf 13: Call for Papers

¹ http://debconf13.debconf.org/ Has somebody volunteered to organize a science track yet? In general, I would volunteer if nobody else steps up, but I am not sure it makes sense as the deadline for abstract submission is nearby and I don't know if we have any science related submissions

Aw: Xeon Phi

Hello, I was wondering if there is a motivation to package the driver its software suite for the Xeon Phi: This would be nice, indeed. I am using the NVidia packages of Debian a lot and like them. And the Phi is long on my wishlist. ... This represents more or less 1GB of source code,

Aw: Re: Request for Ideas - Astronomy working group

Hello, at first thanks for all your great work on astronomy packages. On Thu, Jan 09, 2014 at 10:41:42PM +0100, Ole Streicher wrote: Dear all (astrophysicists, amateurs, scientists, other), there are now quite some people around that are interested in using Debian for astronomy

team building Aw: Re: Request for Ideas - Astronomy working group

Hello, I have already met Christian (professionally close to space), Andreas (physically close to space - as in living withing a mountainous area) and I (envious) have already met. The focus should be on those who do not know each other, yet, and give those this extra opportunity to increase

Aw: Re: wxAstroCapture / Astronomy working group

Hi Peter, hi Ole, Von: Оlе Ѕtrеісhеr debian-de...@liska.ath.cx Peter Cock p.j.a.c...@googlemail.com writes: (b) Bundle the generated Makefile with the Debian (c) Include the generated Makefile in the upstream repository This is not possible since then you dont build the package from

Aw: Re: Re: wxAstroCapture / Astronomy working group

Hi Ole, Steffen Möller steffen_moel...@gmx.de writes: I have just come up with some initial packaging for cbp2make and placed it on Debian-Science. It should possibly at some point move elsewhere, but since there is nothing outside Debian-Science using this at the moment, it may

Aw: Re: Re: wxAstroCapture / Astronomy working group

Hello again, Von: Steffen Möller steffen_moel...@gmx.de Steffen Möller steffen_moel...@gmx.de writes: I have just come up with some initial packaging for cbp2make and placed it on Debian-Science. It should possibly at some point move elsewhere, but since there is nothing outside

Aw: Re: Looking for sponsorship: libfann, pyevolve (updates)

Hi Christian, On 2014-03-04 15:31, Christian Kastner wrote: I've secured sponsorship for some packages already, but would still require sponsorship for the two packages libfann and pyevolve. Both packages had the DM-Upload-Allowed field set. That field has been obsoleted by the new

Aw: Re: Request for Ideas - Astronomy working group

Hallo, Andreas Tille andr...@an3as.eu writes: On Thu, Mar 13, 2014 at 11:32:50AM +0100, Оlе Ѕtrеісhеr wrote: I'd prefer debian-astronomy or -astrophysics. Otherwise we will have discussions about the inclusion of astrology software. debian-astrophysics may soound too professional and

Preparing packages Freifunk (WLAN mesh) gateways for Debian

Hello, local students and resident geeks have collected a series of technologies on top of OpenWRT to establish an IPv6 mesh of Wifi routers. A subset of machines of a mesh island links to the InterNet and all nodes together form a private network. More on http://www.freifunk.net (German). There

Aw: healpix-cxx: stuck in testing due to slow unit tests on mips builder

Hello, I noticed that healpix-cxx hasn't been able to migrate into testing because of a build failure on mips. It looks like the build timed out during unit tests. See build log: https://buildd.debian.org/status/logs.php?arch=mipspkg=healpix-cxx However, I just built it successfully

Aw: Re: healpix-cxx: stuck in testing due to slow unit tests on mips builder

Hi Leo, On May 8, 2014, at 4:18 AM, Steffen Möller steffen_moel...@gmx.de wrote: I noticed that healpix-cxx hasn't been able to migrate into testing because of a build failure on mips. It looks like the build timed out during unit tests. See build log: https://buildd.debian.org

Aw: Re: Location for CWL tool descriptions

Hello, I am happy to see this. I tend to agree that /usr/share/cwl sounds like the right place for everything coming through upstream. To accomodate for local user (or Debian package maintainer) additions, I suggest to also allow for /etc/cwl.d/ . Some /etc/cwl.conf may have an option to

Aw: Re: Re: Location for CWL tool descriptions

Hello Michael, by all means, /usr/local/share/cwl sounds like right, too, just let me attemt to quickly serialise all the input my mind gives me: * In my perception these CWL instructions are mostly independent of the installed software. As such I do not feel the urge to connect those too

Aw: Re: debian-science sprint?

I can only support Christian - get it off. The downside is that "Seaside during Winter" is a Debian Med theme already :) Could we possibly have "Mountains and Spring", instead? Andreas? Ole may know such venues with a large telescope that possibly even have Internet.   Best,   Steffen  

Re: RFS: openbsc/0.15.0-1 [ITP]

;openbsc": > > Package name: openbsc > Version: 0.15.0-1 > Upstream author: Osmocom > License: Mainly AGPL-3+ > > > Andreas Tille and Steffen Möller have helped me sponsoring all the libraries > needed by OpenBSC, and now the

Re: RFS: openbsc/0.15.0-1 [ITP]

I have changed my mind and just uploaded. Just contact Ruben, anyway :) Steffen On 26/02/16 11:45, Steffen Möller wrote: > Hello, > > Ruben's packages are typically just ready to upload. And the OpenBSC is > a mind-boggling Open Source movement with consequences that we do not

Aw: request for review: new yosys packages

Hi Sebastian, > Gesendet: Freitag, 25. März 2016 um 05:51 Uhr > Von: "Sebastian Kuzminsky" > An: debian-science@lists.debian.org > Betreff: request for review: new yosys packages > > Hi folks, I'm a new member joining the debian-science team. I've been > working with Ruben

Re: Why is libosmocore maintained in Debian Science?

Heya, I personally like it in Debian Science. What came to mind is a friendly bunch of people, some of which also associated with Debian Science, of https://alioth.debian.org/projects/pkg-fso/ . The repository is not overly active, anyway, _if_ you feel like moving it then this may be a good new

Re: Looking for a sponsor : openmeca package [ITP: #850590]

Hello Damien, On 17.04.17 22:12, dada wrote: > Hello all, > I am looking for a sponsor for the openmeca software : > https://gitlab.com/damien.andre/openmeca I like it, thank you for preparing your package. > I open an > - ITP : https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=850590 > - RFS :

Re: It's not exactly science, but...

On 25.08.17 21:39, Andreas Tille wrote: > Hi, > > On Sat, Jul 29, 2017 at 08:13:53PM -0500, JohnT wrote: >> I've noticed that there aren't any clearcut metapackages or distros >> focused on business (office mgmt, contact lists of customers, prospects, >> vendors, etc, specialized software for

Re: Package for Apache SINGA - a deep learning library

Hello, On 01.11.17 16:37, Moaz Reyad wrote: > Hi All, > > About two months ago, I submitted a RFS for SINGA: > > https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=873459 > > > But I did not find any sponsor until now. > > SINGA is an

Uploaded maeparser to salsa for internal review

Hello, I had addressed an update rdkit which prompted me with a couple of new dependencies - maeparser is one of them. I named it "schroedinger-maeparser" since I had felt to be much clearer for those who have no immediate association of mae with the .mae ending of Maestro files. Like me. The

Science-supporting Crypto Currency - an issue for Debian Science?

Hello, I discovered Gridcoins for me (https://www.gridcoin.us). They have a package for Ubuntu and I have toyed with the thought to bring their wallet also to Debian - too busy, have instead created an Ubuntu instance with some cloud provider. And it works. It works nicely. So nicely, that I

Testing parallel execution Re: h5py and hdf5-mpi

How do autotests work for MPI? We simply configure the test script to invoke the same tests using mpirun. This is a bigger issue.  We have test suites that test MPI features without checking MPI processor counts (eg the Magics /Metview code). One workaround is to enable oversubscribe to

Re: h5py and hdf5-mpi

On 13.08.19 06:01, Drew Parsons wrote: On 2019-08-13 03:51, Steffen Möller wrote: Hello, There are a few data formats in bioinformatics now depending on hdf5 and h5py is used a lot. My main concern is that the user should not need to configure anything, like a set of hostnames

Re: h5py and hdf5-mpi

Hello, On 12.08.19 18:15, Ghislain Vaillant wrote: Le lun. 12 août 2019 à 17:04, Mo Zhou a écrit : Hi Drew, thanks for the commits to h5py. On 2019-08-12 03:10, Drew Parsons wrote: We need to change h5py to support hdf5-mpi. h5py is somewhat crippled as serial-only. I didn't even notice

e4s - there is so much out there - too much for us to cope

Hello, I just came across https://e4s-project.github.io/ and am both fascinated and shocked about how free HPC software much I am not aware of. Their answer to everything are containers. Does anyone on this list have any ties with these folks? Would Debian (and Ubuntu with it) benefit from

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

Hello, 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. Many thanks Steffen

Re: Interested in packaging nextpnr

Heyho, On 11.05.20 23:41, Kurt Kremitzki wrote: Hi Nate, On Monday, May 11, 2020 3:45:10 PM CDT Nathaniel Graff wrote: <-snip-> I welcome and appreciate any feedback! Thanks, Nate Graff It's funny, I just purchased an iCEBreaker FPGA over the weekend, was looking at the state of supporting

Re: Welcoming Mo Zhou as GSoC student

+1 On 05.05.20 10:33, Ole Streicher wrote: Congratulations, Mo! This is really great and will improve the Debian science ecosystem a lot! I look forward to this! Best regards Ole Andreas Tille writes: Hi, I've got confirmation that Mo Zhou is accepted as GSoC student for the topic

Re: p4c in debian-science?

Hi, Have you considered the electronics team? https://salsa.debian.org/electronics-team Best, Steffen On 25.08.20 23:19, itd wrote: > Hi, > > is p4c [1]---reference compiler for the P4 [2] programming > language---within scope for this team? (I am considering to package > p4c. Currently

Re: Tinyarray packaging

Hi Christoph, On 21.09.20 18:03, Christoph Groth wrote: > Hello, > > As mentioned [1], Steffen Möller and Andreas Tille helped to finish the > packaging of Tinyarray [2]. Here, I would like to continue off-list > discussions we had. > > Andreas Tille wrote: >

Re: [RFS] seaborn

Allowed. On 10.08.20 20:57, Nilesh Patra wrote: > Hi, > currently seaborn FTBFS as reported in: #966991 > I've fixed this temporarily with a patch which can be conveniently > dropped with the next upstream release. > My changes are pushed to the team repo[1]. > Please: > > gbp clone

Re: [RFS] sleef

allowed On 30.07.20 15:07, Nilesh Patra wrote: > Hi, > I've fixed gcc-10 FTBFS for sleef as reported here in RC bug #957809. > It now builds with passing tests. > I've pushed my changes to the team-repo[1] > Please: > > gbp clone --pristine-tar https://salsa.debian.org/science-team/sleef >

Done Re: [RFS] apertium-cy-en

I suggest you add a note in d/changelog that this team-upload fixes the migration to testing. And if it builds for you then close the bug with this upload. Best, Steffen Am 24.12.20 um 13:47 schrieb Nilesh Patra: > Hi, > > Currently apertium-cy-en seems to be blocking apertium's testing >

Re: RFS: robot-testing-framework/2.0.1-1 [ITP] -- Robot Testing Framework

@Nilesh, if you can help out with a Nilesh-typical review then I happily sponsor. Best, Steffen Am 15.12.20 um 09:57 schrieb Nilesh Patra: Hi Daniele On Tue, 15 Dec, 2020, 2:14 pm Daniele E. Domenichelli, mailto:ddomeniche...@drdanz.it>> wrote: Any other comment on this package?

Re: Fwd: stan packaging

Am 18.06.2021 um 13:33 schrieb Stéphane Glondu: Hello, Le 05/06/2021 à 14:51, Steffen Möller a écrit : You may have heard of R and a (fairly) new kid on the block, Julia, and there is something in between that is also tantalizingly different such that all math environments have interfaces

Re: Quick Poll: Debian to better support hardware acceleration?

Am 21.05.21 um 15:55 schrieb Thomas Schiex: > I'm a computer scientist working in AI and structural biology. I'm > sorry to say that CUDA has slowly invaded a lot of our scientific > pipelines, for Deep learning, convex optimization and molecular > simulations. > > I just could not vote for

Fwd: stan packaging

:Nilesh Patra An: Steffen Möller Kopie (CC): Debian Science On 04/06/21 10:27 PM, Steffen Möller wrote: Sigh. cmdstan needs stanc3 (to be packaged) which needs dune (available) which needs https://opam.ocaml.org/packages/ppx_jane/ppx_jane.v0.14.0/ (to be packaged). This is a bit

Re: stan packaging

, Steffen Möller wrote: Hi Mo, Thank you tons for you initiative on stan. I did a few smallish changes to the math library and have a few more of the same for the stan package that are triggered from the build tests. Now, I would like to proceed to https://github.com/stan-dev/cmdstan, so we have something

Aw: ASTM Lab equipment protocol

Hi Rob, > Which Debian packages support the ASTM lab equipment (over TCP) > protocol? An overview would be nice. Nothing in Debian, and nothing anywhere, so it felt. Found a Python package implementing the ASTM standard from 2013, which we could (help you to) maintain in Debian. But otherwise,

Datasets downloaded by scikit-learn as separate packages?

Hello, This goes out to the good fellas who care about scikit-learn. There is tutorial for the qiime package that has classifier prepared that only works with the latest stable version (0.24.2). We are at 0.23.2 in Debian. I gave an update of Scikit-Learn a shot and while the main build was

Re: Contributing to yosys maintenance

Hi Daniel, On 30.12.21 22:38, Daniel Gröber wrote: Hi Anton and Steffen, On Thu, Dec 30, 2021 at 10:11:26PM +0100, Anton Gladky wrote: I have just added you to the group. Welcome on board! You can commit directly in git, but please coordinate your work with an active uploaders of this

Re: Contributing to yosys maintenance

Hi Daniel, On 30.12.21 21:08, Daniel Gröber wrote: I'm working on packaging the latest version of yosys and related packages for Debian. Nice. I was not aware of the many new releases - clifford.at seems down and https://github.com/YosysHQ/yosys is the new home? What's the procedure in

Re: Debian Math Team

While I agree, this may also be good thing. There will be more Sprints (I hope) with then more people that are brought to our community at large. And Debian so far does very well in keeping all those fragments together. Best, Steffen On 30.10.21 01:55, Anton Gladky wrote: Hi Doug, well, I

LinuxCNC in New Queue - upstream as an alternative to teams on salsa

Hello, LinuxCNC.org has its own Debian repository since a couple of decades. and I have worked as DDs with upstream over the past few weeks to eliminate a series of lintian errors and sidetracked ourselves here and there, but yesterday LinuxCNC arrived in the New Queue. Its runtime (suggested)

Re: alphafold Debian packaging ?

I am only aware of someone who got it to run on Debian :)  I agree that it would be nice to have. Very nice. Cheers, Steffen On 11.01.22 14:47, PICCA Frederic-Emmanuel wrote: Hello guyes, I would like to know if you are aware of an effort to package alphafold[1] on Debian ? Cheers Frederic

Re: alphafold Debian packaging ?

On 12.01.22 17:24, M. Zhou wrote: Even more complicated is the underlying software dependency tree. alphafold depends on dm-haiku, jax, tensorflow. dm-haiku depends on jax. jax depends on XLA from tensorflow. tensorflow still in NEW. Long way to go. Mhhh. That is what I had thought, too.

freecad - python autotests fail on arm+powerpc

Hello, following https://tracker.debian.org/pkg/freecad to https://ci.debian.net/data/autopkgtest/testing/armhf/f/freecad/19724334/log.gz I just don't grasp test_issue_4456 (parttests.regression_tests.RegressionTests) 0004456: Regression : Part.Plane.Intersect do not accept plane as argument ...

Re: Google Summer of Code, Debian Science

You are aware of https://wiki.debian.org/DebianScience/ROOT ? On 22.02.22 17:19, Stephan Lachnit wrote: On Mon, Feb 21, 2022 at 5:43 PM Anton Gladky wrote: If somebody wants to be a co-mentor or if you have better ideas for the project, please let me know. I would love to have a student to

RFS faber - build dependency for boost-python

Hello, This is about https://salsa.debian.org/python-team/packages/faber I had asked the Debian boost folks already to comment on that package but have not heard back. Faber is a build tool that the upstream boost community has elevated as the next thing for their Python interface. But it can

Re: RFS faber - build dependency for boost-python

Fantastic - thank you tons! Steffen On 11.02.22 11:44, Étienne Mollier wrote: Hi Steffen, Steffen Möller, on 2022-02-08: https://salsa.debian.org/python-team/packages/faber I had asked the Debian boost folks already to comment on that package but have not heard back. Faber is a build tool

Aw: Re: Removing ATLAS?

Hi all, EMMAX is (was) important https://genome.sph.umich.edu/wiki/EMMAX but I admittedly cannot invest into maintaining this or atlas. My suggestion would be to talk back to upstream about transitioning to an alternative. I have no idea about how difficult this would be to patch ourselves.