Re: Fwd: heudiconv FTBFS on i386

Hi Alexandre, Do we know any details on how much memory we have on that i386 box? meanwhile I made a record against nibabel https://github.com/nipy/nibabel/issues/1307 on this. Here -- we could potentially just skip (announce xfail) that particular test (test_reproin_largely_smoke) on i386?

Re: Bug#1065841: Taking over datalad to either Debian Med or Debian Science team

Hi Andreas, Let's keep DataLad under our (NeuroDebian) umbrella for now, since we are also upstream there and project is active. We are also working with Vasyl (CCed) to experiment with some semi-automation for package updates/backports (for neurodebian) and datalad (and some of its ecosystem)

Re: Do we need pynwb - if yes please care for its new dependency

Hi Andreas, Thank you for taking care about upgrades of pynwb and hdmf! FWIW popcon is likely small because we never packaged downstream packages which use pynwb and usually just instructed people to "pip install" them. And as a developer, I usually had to do the same anyways. The reason for

Re: included git submodules

On Fri, 21 Oct 2022, Maarten L. Hekkelman wrote: > Suggestions, opinions? What is done with other packages that rely on > submodules? those feel like worth their own packages or you could establish your own "mhekkel-toolkit" library "upstream" to contain those two and any other similar one if

Re: Heudiconv moved to Debian Med repository

On Wed, 17 Nov 2021, Nilesh Patra wrote: > > Argh, that was what I intended to mention: I just uploaded heudiconv > > 0.9.0-3. I checked 0.10.0 but there were build time issues thus I did > > not bumped the version to be able to upload. > I fixed the tests an uploaded. coolio, thanks! will

Re: Heudiconv moved to Debian Med repository

On Wed, 17 Nov 2021, Andreas Tille wrote: > > I thought we were up to date with connectome-workbench ... yeap - we > > are. Upstream is "involved" with uploads so we keep it uptodate afaik. > > Also upstream (in both cases, we are the upstream of heudiconv) is > > interested in neurodebian

Re: Heudiconv moved to Debian Med repository

thank you very much Andreas! May be worth uploading new version (even if only to announce the move) so if we forget about the move we have a better chance to detect it? I thought we were up to date with connectome-workbench ... yeap - we are. Upstream is "involved" with uploads so we keep it

Re: Progress in merging neurodebian team?

On Sat, 13 Nov 2021, Andreas Tille wrote: > > Do we have a, sort of ETA to do this? > I do it >A) if I have time _and_ >B) I find some specific issue on a package > Issues can be RC bugs, package not in testing, broken watch file etc. > There are packages I gave up. For instance I

Re: Introduction

Hi Enric, thank you for reaching out! I just want to follow up on one aspect: even without any coding/packaging, everyone can contribute to the big long lasting positive effect for Debian and "Open" science/software/health/... by promoting open practices, software and licenses to apply and

Re: Should we offer Debian Med workflow-containers?

On Mon, 18 Jan 2021, Andreas Tille wrote: > Hi Yaroslav, > thanks a lot for the valuable information. > On Mon, Jan 18, 2021 at 09:15:16AM -0500, Yaroslav Halchenko wrote: > > May be would be of some help/information > You could join our Debian Med sprint and than we talk

Re: Should we offer Debian Med workflow-containers?

On Mon, 18 Jan 2021, Alex Mestiashvili wrote: > But we have a great success with singularity definition files. Forgot also to mention a project, which is despite "neuro" in its name, is not that much "neuro": https://github.com/ReproNim/neurodocker/ Neurodocker is a command-line

Re: Should we offer Debian Med workflow-containers?

On Sun, 17 Jan 2021, Steffen Möller wrote: > Hello, > Our HPC environment does not offer Docker, but Singularity > (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0177459) > is supported. I thought I should give it a shot. Is anybody using this > already on this list? FWIW,

Re: Ants taken over from Neurodebian team but it does not build - any volunteer?

On Mon, 07 Dec 2020, Andreas Tille wrote: > Hi, > since we take over packages in our tasks files from Neurodebian step by > step I did so with ants[1] which is unmaintained since a long time[2]. > I upgraded the packaging to Debian Med standards and injected the latest > upstream version.

Re: mrtrix3

On Thu, 26 Nov 2020, Andreas Tille wrote: > /usr/bin/env: 'python': No such file or directory > make[1]: *** [debian/rules:68: override_dh_clean] Error 127 > make[1]: Leaving directory > '/home/andreas/debian-maintain/salsa/med-team/build-area/mrtrix3-3.0.2' > I think its just because I

mrtrix3

Could someone takes a look for final step to cross the line for mrtrix3. I have pushed added new 3.0.2 release and completely disabled tests since seems to require data now which is not shipped along AFAIK (but may be I overreacted). Might just need tune up for python3 though

Re: getData - could it be heaven? Was: Sepp : including a dataset?

On Fri, 09 Oct 2020, Steffen Möller wrote: > > On Fri, 09 Oct 2020, Steffen Möller wrote: > >> I added datalad-crawler to > >> https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit#gid=401910682 > >> . > > thanks! requested write access to contribute (no

getData - could it be heaven? Was: Sepp : including a dataset?

Please pardon me in advance -- came out long again. TL;DR summary: - would be great to merry getData and datalad to benefit from knowledge getData possess ATM on data sources, but then gain (many) benefits from git/git-annex/datalad, especially while thinking about "research process", data

Re: Sepp : including a dataset?

On Wed, 07 Oct 2020, Andreas Tille wrote: > On Wed, Oct 07, 2020 at 10:30:34PM +0200, Pierre Gruet wrote: > > I have almost finished the initial packaging of sepp [0]. Beside the > > sepp program, upstream also provides the tipp program in the same > > tarball. Basically, tipp classifies

Re: mCaller - Unicode error - anybody who has encountered this before/having an instant idea?

On Fri, 04 Sep 2020, Steffen Möller wrote: >  File "./mCaller.py", line 59, in distribute_threads >     >

Re: Datalad (Was: How to package human, mouse and viral genomes?)

On Fri, 04 Sep 2020, Andreas Tille wrote: > On Thu, Sep 03, 2020 at 05:25:51PM -0400, Yaroslav Halchenko wrote: > > > PS: Yaroslav, I have not seen yet any commit of yours to add datalad > > > to the science tasks. > > guilty as charged! > :-) >

Re: How to package human, mouse and viral genomes?

On Fri, 04 Sep 2020, Steffen Möller wrote: >  * sharing data between colleagues - can you have two different versions > at the same time? sure, similar to git... well -- it is git ;) so multiple versions across collaborators, multiple versions on your own box etc -- all possible. When you

Re: Datalad (Was: How to package human, mouse and viral genomes?)

On Thu, 03 Sep 2020, Andreas Tille wrote: > On Thu, Sep 03, 2020 at 08:30:54PM +0200, Steffen M�ller wrote: > > I looked at datasets.datalad.org. > I'd strongly recommend the very entertaining talk from DebConf > >

Re: How to package human, mouse and viral genomes?

On Thu, 03 Sep 2020, Steffen Möller wrote: > The name "datalad" (https://www.thesaurus.com/browse/lad) I definitely like. ;-) The history goes: it was called datagit, but naive Yarik decided to asks FSF for a permission... so we had to come up with a new name, I flew into Germany, we drank

Re: How to package human, mouse and viral genomes?

On Thu, 03 Sep 2020, Steffen Möller wrote: > I looked at datasets.datalad.org. I could well imagine to use your > technology for other (larger) databases like Pfam or UniProt or PDB. For > cute little genomes my initial reaction was that I felt overwhelmed. > Your pointer will certainly help to

Re: How to package human, mouse and viral genomes?

You might like to listen to debconf20 talk on DataLad ;-) At some point I have started even to establish some kind of dh-datalad helper so that .deb package would contain a datalad dataset (git/git-annex repo), and would just `get` data files upon installation... So -- yes, they would not be

Re: dcm2niix -- I have an intent to take over (still under Debian Med team), objections?

On Tue, 04 Dec 2018, Andreas Tille wrote: > On Tue, Dec 04, 2018 at 06:39:15AM +0100, Ghislain Vaillant wrote: > > > I would be happy to move it to salsa. I just pointed to it as the one > > > we currently use > > > I guess I would then move it to dcm2niix-epoch1 smth like that (on salsa > >

Re: dcm2niix -- I have an intent to take over (still under Debian Med team), objections?

On Mon, 03 Dec 2018, Andreas Tille wrote: > Hi Yaroslav, > On Mon, Dec 03, 2018 at 03:36:19PM -0500, Yaroslav Halchenko wrote: > > Chris asked me to take over maintenance in Debian as well, and Ghislain > > blessed me as well. > Fine for me. > > To minimize a

dcm2niix -- I have an intent to take over (still under Debian Med team), objections?

Dear Team Comrades, Upon blessing from Ghislain Antony Vaillant (previous team maintainer) and Chris Rorden (upstream, CCed) I would like to take over the maintenance of dcm2niix. And I would like to do it largely by taking the dcm2niix packaging setup we have in NeuroDebian. bits of history -

Re: mrtrix3 is "coming". Howto tests?

On Fri, 07 Sep 2018, Andreas Tille wrote: > > to recreate it from git tree. Without awareness of submodules, it would > > need > > to keep the delta for the entire submodule tree. Not sure if that is worth > > to > > breed across commits, since it would just keep adding those 16MB with

Re: mrtrix3 is "coming". Howto tests?

On Thu, 06 Sep 2018, Andreas Tille wrote: > On Wed, Sep 05, 2018 at 04:12:55PM -0400, Yaroslav Halchenko wrote: > > > I know there is some way to create pristine-tar from plain Git packaging. > > > I'd be really happy if you would consider this since it enables oth

Re: mrtrix3 is "coming". Howto tests?

On Wed, 05 Sep 2018, Andreas Tille wrote: > Hi Yaroslav, > On Tue, Sep 04, 2018 at 07:51:52PM -0400, Yaroslav Halchenko wrote: > > The interesting aspect is that upstream repo provides git submodule > > testing/data . It is not that large - just 15 MB compressed but it

mrtrix3 is "coming". Howto tests?

Hello Team, We have mrtrix 0.2.x series in Debian which is still used by some. Upstream worked hard and soon (hopefully) will push out 3.0 release as mrtrix3. I've migrated and tuned up packaging for it (for 3.0~rc3+git86-g4b523b413) which is now at https://salsa.debian.org/med-team/mrtrix3 The

Re: Using recent packages on stable systems (Was: Depends available in other PPA's)

On Fri, 09 Mar 2018, Andreas Tille wrote: > > > > - a lot of people are going to show up running ubuntu.� What might you > > > > all > > > > recommend?� In theory ubuntu people could add debian testing to > > > > `apt/sources.list.d`. > > > I do not think that it is a good idea to mix Debian

Re: Sprint-derived paper now out:

On Fri, 17 Nov 2017, Steffen Möller wrote: > Dear all, > this paper has now surfaced > Möller, Steffen; Prescott, Stuart W.; Wirzenius, Lars; Reinholdtsen, > Petter; Chapman, Brad; Prins, Pjotr; Soiland-Reyes, Stian; Klötzl, > Fabian; Bagnacani, Andrea; Kalaš, Matúš; Tille, Andreas; Crusoe,

Re: Auto creation of docker images from Debian (Med) packages?

On Thu, 12 Oct 2017, Andreas Tille wrote: > > we auto generate docker images using their stock utility (stockbrew or what > > it became), see https://github.com/neurodebian/dockerfiles > > For singularity, we auto generate just one "ultimate one" - > >

Re: Bug#862361: RFS: dcm2niix/1.0.20170429-1 [experimental]

On Thu, 11 May 2017, Ghislain Vaillant wrote: > Package: sponsorship-requests > Severity: normal > Dear mentors, > I am looking for a sponsor for the following package: > * Package name: dcm2niix >   Version : 1.0.20170429-1 >   Upstream Author : Chris Rorden > * URL :

Re: [Neurodebian-devel] Help needed for pandas bug: Could anybody verify the suspicion that tzdata might have some influence?

On Tue, 28 Mar 2017, Andreas Tille wrote: > > - I have already stated many times that if you want to move any of the > > core packages under bigger (-med, -science, etc) maintenance -- I > > don't mind. But it shouldn't complicate my own work on those > > packages. Someone's "mess" might

Re: Help needed for pandas bug: Could anybody verify the suspicion that tzdata might have some influence?

eurodebian/pandas.git > > is not even featuring the latest uploads - last changelog entry is > > pandas (0.19.2-2) unstable; urgency=medium > > * Exclude a number of tests while running on non-amd64 platforms > > due to bugs in numpy/pandas > > -- Yaroslav Halche

Re: dcm2niix

On Wed, 11 Jan 2017, Ghislain Vaillant wrote: > On Wed, 2017-01-11 at 11:22 -0500, Yaroslav Halchenko wrote: > > Hi Ghislain, > > Thanks for packaging and uploading to dcm2niix! > You're welcome. > > It is a pity though that we duplicated the effort somewhat since &g

Re: upload aghermann-1.1.0, fix #824574 and #828008

xes but also > with a more cme-compliant debian/control. > Cheers, > Andrei > On 26 August 2016 at 01:29, andrei zavada <johnhom...@gmail.com> wrote: > > Thanks muchly! > > On 26 August 2016 at 01:26, Yaroslav Halchenko <deb...@onerussian.com> > > wrote: > >>

Re: Shall we develop a Debian Med Tutorial? Fwd: [BC2-conference] Call for workshop and tutorial proposals open now.

On Wed, 30 Nov 2016, Steffen Möller wrote: > Hello, > much like many of you I just received this invitation to come up with a > tutorial and/or workshop for the Basel (Switzerland) conference. The > ISMB (next time in Prague (CZ) if I recall correctly) I expect to send > the same around any

Re: RRID: a namespace for research software

Related (although we yet to "support" RRIDs) - have a look at http://duecredit.org , might be of interest if you are looking into sitting surviving methods and contributions, not only entire package On June 28, 2016 5:57:00 PM GMT+02:00, Michael Crusoe wrote: >On

Re: Open-source MRI hardware initiative project

I just want to complement (inlined with original email below) to already good responses, and hope that you Broche would continue the discussion by providing your feedback to our feedback ;) On Sat, 09 Apr 2016, Broche, Lionel wrote: > Hello Debian-Med team, > I am a researcher in MRI hardware at

Re: Bug#814000: ITP: cwltool -- Common workflow language reference implementation

On Wed, 20 Apr 2016, Andreas Tille wrote: > Hi Afif, > On Tue, Apr 19, 2016 at 10:12:40PM -0700, Afif Elghraoui wrote: > > > and the reason is given in the description of the task: > > >Note that there is no according metapackage created since the packages > > >might be to different to

Re: [MoM] Fwd: Outreachy project (CI for all biological applications inside Debian)

Fwiw, for all packages I maintain, wherever upstream provides tests, I am executing them at build time (scikit-learn, stats models, pymvpa2 are few random ones for eg). For many, I (or contributors) also started to enable autopkgtests, see eg pandas. Depending on where to draw the line for bio,

Re: bart - tools for computational magnetic resonance imaging

On Tue, 01 Dec 2015, Ghislain Vaillant wrote: > >>I can set the packaging repository up on d-med and push your initial > >>work to it if you like. That would make collaborative work with members > >>of d-med much easier, myself included. > >So I tried to do it myself. See my mail to Andreas. >

Re: Debian Med usage or download stats

On Tue, 17 Nov 2015, ti...@debian.org wrote: >http://blends.debian.org/med/tasks/bio#emboss > Emboss seems to be the most frequently used package maintained by the > Debian Med team. We have no number of those users who are disabling > popcon and also no numbers who are using derivatives

Re: debian-med (possibly + -science) hackathon 2016 dates?

On Fri, 16 Oct 2015, Steffen Möller wrote: > Hello, > On 15.10.2015 23:52, Yaroslav Halchenko wrote: > > Hi Andreas, > > Sorry for me forgetting, when will it happen? May be time to start > > planing ... ;) > Indeed. I put up > https://wiki.debian.org/Sprints/

debian-med (possibly + -science) hackathon 2016 dates?

Hi Andreas, Sorry for me forgetting, when will it happen? May be time to start planing ... ;) -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834

Re: About backports.

On Mon, 10 Aug 2015, Charles Plessy wrote: Like you indicated, that's not the only concern. On behalf of stable release users, I think making a recent version of samtools available in stable-backports is important-- I think the backports repository is a huge reason why Debian stable is

Re: sponsor upload aghermann-1.0.4 please?

I am traveling but I believe it was build and I just forgot about uploading it.. unfortunately laptop refuses to connect atm so if not uploaded by tomorrow I will do that in the morning Cheers On May 11, 2015 10:50:02 PM GMT+01:00, andrei zavada johnhom...@gmail.com wrote: Hi Andreas, As my

Re: sponsor upload aghermann-1.0.4 please?

On Tue, 12 May 2015, Andreas Tille wrote: Hi, On Tue, May 12, 2015 at 12:17:21AM +0100, Yaroslav Halchenko wrote: I am traveling but I believe it was build and I just forgot about uploading it.. unfortunately laptop refuses to connect atm so if not uploaded by tomorrow I will do

Re: Debian Med Sprint in Montreal @ PyCon 2015?

On Thu, 12 Feb 2015, Michael Crusoe wrote: Is there interest in having a Debian Med Sprint at PyCon 2015? The dates are Monday, April 13th 2015 - Thursday, April 16th 2015. I'll be there running a Sprint for the khmer project but I would be happy to have Debian folk (both

Re: aghermann-1.0.3, reproducible builds

On Tue, 03 Feb 2015, andrei zavada wrote: Hi Yaroslav, I see some red ink appearing on my QA page, this time suggesting to avoid using __DATE__ and __TIME__ macros in order to ensure reproducible builds: https://wiki.debian.org/ReproducibleBuilds/TimestampsFromCPPMacros. To address this,

Re: preparing insighttookit 4.7

On Tue, 27 Jan 2015, Steve M. Robbins wrote: Ha! Good point. That reminds me: some years ago I considered creating a new source package for the ITK docs. Never got further than considering it, but that would solve the builder problem, anyway. BTW, the i386 pbuilder build also

Re: Task for MRI (Magnetic Resonance Imaging) development

On Mon, 08 Dec 2014, Ghislain Vaillant wrote: Dear all, I originally started to contribute to the Debian ecosystem to help make available some of the development library, such as [1], necessary to work with MRI data. In the field of MRI processing, we are currently witnessing

Re: Big data needed for unit test

On Mon, 01 Dec 2014, Corentin Desfarges wrote: I'm still working on the packaging of fw4spl, and I'm faced with a new problematic : One of the unit tests needs to load an important data file, which has a big size (~200 Mo). such large data arrays are worth their own packages... then

Re: please upload cnrun2

On Tue, 25 Nov 2014, andrei zavada wrote: On Mon, 24 Nov 2014 15:23:20 -0500 Yaroslav Halchenko deb...@onerussian.com wrote: On Mon, 24 Nov 2014, andrei zavada wrote: On Mon, 24 Nov 2014 14:59:24 -0500 Yaroslav Halchenko deb...@onerussian.com wrote: On Sun, 23 Nov 2014, andrei

upstream metadata bib

I remember seeing somewhere a compiled bibtex from the upstream metadata we have been feeding our packages with... could someone remind me a url? do we have already a tool to collate a .bib file given a list of software in question? Thank in advance! -- Yaroslav O. Halchenko, Ph.D.

Re: Compiling binaries on package installation

On Tue, 14 Oct 2014, Michael Banck wrote: Or should I point out how to compile your own, like it is done in the Building an optimized OpenBLAS packages on your architecture in the README.Debian file of openblas-base? Not sure what's in those files, but I suggest to support

Re: Compiling binaries on package installation

On Tue, 14 Oct 2014, Michael Banck wrote: Or should I point out how to compile your own, like it is done in the Building an optimized OpenBLAS packages on your architecture in the README.Debian file of openblas-base? Not sure what's in those files, but I suggest to support

Re: Compiling binaries on package installation

On Tue, 14 Oct 2014, Michael Banck wrote: If you bundle a please rebuild my packages with optimization script with a local .deb archive, you'd only need to do it once on a frontend box. and initially expose those as an apt repository, adjust apt configuration on every node... Then

Re: sponsor upload aghermann-1.0.2 fixing #764820

On Wed, 15 Oct 2014, andrei zavada wrote: Hi Yaroslav, Laurent, There was a bug (#764820) reported last week for aghermann-1.0.1, about menu entries missing icons. So here's 1.0.2 with a fix (also for some lesser issues raised by current lintian), which I am humbly asking you to sponsor

Re: insighttoolkit4 backport on wheezy 32bit -- 2 tests failures

On Fri, 30 May 2014, Gert Wollny wrote: About the failing tests: The test itkTIFFImageIOCompression_RGBTestImageJPEG_JPEG also fails on wheezy amd64. The error TIFFImageIO: error out of disk space is nonsense though, this is the default ITK response to a failing

Re: insighttoolkit4 backport on wheezy 32bit -- 2 tests failures

On Fri, 30 May 2014, Gert Wollny wrote: On Fri, 2014-05-30 at 08:57 -0400, Yaroslav Halchenko wrote: Considering this, one could indeed disable this test but then one should probably also disable the corresponding functionality. indeed. What would be a preferable way to disable

insighttoolkit4 backport on wheezy 32bit -- 2 tests failures

Hi Guys, I have (again) tried to provide a backport build of itk4 for wheezy (to be shipped from NeuroDebian) and got those 2 tests to fail. 926 - itkTIFFImageIOCompression_RGBTestImageJPEG_JPEG (Failed) 2168 - itkOtsuThresholdImageFilterTestShort (Failed) Would you be so kind

Re: insighttoolkit4 backport on wheezy 32bit -- 2 tests failures

On Thu, 29 May 2014, Gert Wollny wrote: Hello Yaroslav, On Thu, 2014-05-29 at 10:33 -0400, Yaroslav Halchenko wrote: I have (again) tried to provide a backport build of itk4 for wheezy (to be shipped from NeuroDebian) and got those 2 tests to fail. 926

Re: Fwd: paper: Custom software development for use in a clinical laboratory

very interesting -- thanks for sharing. I wondered though, if such an in-lab software releases under FOSS license could then it be re-used or better built-upon in another lab without violating FDA/etc regulations? In-house developments resting on the work of FOSS projects are nice but is there a

Re: Q-Leap Networks contributes to Debian Med

On Thu, 24 Apr 2014, r...@q-leap.de wrote: Tony We appreciated the pizza, of course, but your interest in Tony supporting Debian Med is very welcome indeed. I've just moved Tony house, and I don't yet have a broadband connection. However, Tony when I get reconnected, I'll

Re: Q-Leap Networks contributes to Debian Med

On Thu, 24 Apr 2014, r...@q-leap.de wrote: Yaroslav == Yaroslav Halchenko deb...@onerussian.com writes: Yaroslav On Thu, 24 Apr 2014, r...@q-leap.de wrote: Tony We appreciated the pizza, of course, but your interest in Tony supporting Debian Med is very welcome indeed. I've

Re: Q-Leap Networks contributes to Debian Med

On Thu, 24 Apr 2014, r...@q-leap.de wrote: Yaroslav == Yaroslav Halchenko deb...@onerussian.com writes: Yaroslav On Thu, 24 Apr 2014, r...@q-leap.de wrote: Yaroslav == Yaroslav Halchenko deb...@onerussian.com writes: Yaroslav On Thu, 24 Apr 2014, r...@q-leap.de wrote

Re: Q-Leap Networks contributes to Debian Med

On Thu, 24 Apr 2014, r...@q-leap.de wrote: You're right. How about the added note on: https://www.qlustar.com/download much better -- thanks! -- Yaroslav O. Halchenko, Ph.D. http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org Senior Research Associate, Psychological

Re: Presentation of Debian Med on local Next Generation Sequencing workshop (April)

On Fri, 21 Mar 2014, Charles Plessy wrote: For packages without upstream tests, in the meantime, even the most simple tests like running the command with the --help option, are potentially useful. +10 ;) I also try to run some Demo or Example script if such is provided (often via xvfb) to

Re: Presentation of Debian Med on local Next Generation Sequencing workshop (April)

On Wed, 19 Mar 2014, Carlos Borroto wrote: I lost some of my initial excitement about contributing to Debian Med. If I cannot use the results of my effort in the system where I actually do my job quick side question: which are running ? -- Yaroslav O. Halchenko, Ph.D.

Re: Presentation of Debian Med on local Next Generation Sequencing workshop (April)

On Wed, 19 Mar 2014, Diane Trout wrote: I think the more effort we spent in autopkgtest suites the more we will be able to come closer to reproducibility. I hope that this effort will be rewarded by such projects who for whatever reason do not (yet) trust our work. There's also the

Re: Presentation of Debian Med on local Next Generation Sequencing workshop (April)

On Wed, 19 Mar 2014, Carlos Borroto wrote: I lost some of my initial excitement about contributing to Debian Med. If I cannot use the results of my effort in the system where I actually do my job quick side question: which are running ? Are you asking about

Re: Presentation of Debian Med on local Next Generation Sequencing workshop (April)

On Wed, 19 Mar 2014, Diane Trout wrote: I think the more effort we spent in autopkgtest suites the more we will be able to come closer to reproducibility. I hope that this effort will be rewarded by such projects who for whatever reason do not (yet) trust our work. There's also the

Re: Presentation of Debian Med on local Next Generation Sequencing workshop (April)

Hi Steffen, On Tue, 18 Mar 2014, Steffen Möller wrote: I was invited to a local (Northern Germany) workshop on next generation sequencing https://sites.google.com/site/nexgenseqmv/home/workshop to give a quick overview on what Debian/Ubuntu/BioLinux can do for them. This is a very friendly

Re: ANTs Data file license in http://slicer.kitware.com/midas3/

On Thu, 27 Feb 2014, brian avants wrote: i havent followed the whole discussion but agree that it would be nice to separate our testing data entirely from the source, as yarik suggests, at least for ANTs. i have been struggling a bit with testing lately, specifically, testing

Re: ANTs Data file license in http://slicer.kitware.com/midas3/

On Wed, 26 Feb 2014, Matthew McCormick wrote: From what I can see (find ANTS -name '*.md5'), most if not all of the data is located in the slicer.kitware.com/BRAINSTools Midas Community [1]. @Hans, could a license notice be placed in the Info tab? Something like Creative Commons

Re: ANTs Data file license in http://slicer.kitware.com/midas3/

On Thu, 27 Feb 2014, Matthew McCormick wrote: @Yaroslav, the script we use for creating the ITK tarballs [3] may be a useful reference for creating an ANTS data tarball. Thank you Matthew, we might make use of its parts... but while at it I would like to raise a concern actually about

Re: Conflict between debian/upstream (DEP-12) debian/upstream/ (uscan)

of uscan using now debian/upstream/signing-key.*. Now such a rename in uscan is IMHO only brings even more confusion among debian/ files (debian/watch which uses debian/upstream/signing-key.*). On Sat, 22 Feb 2014, Yaroslav Halchenko wrote: Have I missed the background? is debian/watch getting

Re: should google-glog be ok with libunwind7-dev? [Was: Orthanc 0.7.2 backport of wheezy]

On Thu, 13 Feb 2014, Sebastien Jodogne wrote: Hi, Thanks to Daigo's -2 of glog with suggested tune up of build-depends, I have uploaded backport build of orthanc for wheezy straight into NeuroDebian wheezy just to give it a try... Fine! Could you give the link to the repository containing

Re: should google-glog be ok with libunwind7-dev? [Was: Orthanc 0.7.2 backport of wheezy]

, Yaroslav Halchenko wrote: Hi Daigo, I have looked at the packporting of orthanc for Wheezy. orthanc uses google-glog and that one currently build-depends on libunwind8-dev. It seems to build (including the build-time testing -- thanks for enabling those!) fine using libunwind7-dev, so I

Re: Python-mne uploaded

FWIW I have realized that I haven't uploaded 0.7.3 backport builds of mne-python to NeuroDebian -- done now Cheers, On Sun, 19 Jan 2014, Andreas Tille wrote: Hi Alexandre, I uploaded your preparation in Git with some changes: 1. You said it would be upstream version 0.7.3 but you had

Re: modulefiles for fis-gtm may be?

On Wed, 22 Jan 2014, Luis Ibanez wrote: Sounds good.                                  Yes, This looks great. We will appreciate anything that will reduce the barrier  of entry for learning M/MUMPS.   Certainly the need for setting those environment variables  (although

modulefiles for fis-gtm may be?

I have ran into Luis's recent blog post http://www.osehra.org/blog/backporting-fis-gtm-ubuntu-linux-distribution Environment Set Up Setting up the usual environment variables in the bash shell: export gtm_dist='/usr/lib/fis-gtm/V6.0-003-2~nd12.10_x86_64' # backported from NeuroDebian export

Re: Thank you Luis!

On Sun, 19 Jan 2014, Luis Ibanez wrote:                                             This is great ! Thanks for uploading the package to the NeuroDebian repository. It shows now at:          [2]http://neuro.debian.net/pkgs/fis-gtm.html#binary-pkg-fis-gtm Following the

Re: Thank you Luis!

On Tue, 14 Jan 2014, Luis Ibanez wrote:            Thank You All !    :-)    BTW,     we are now making progress     on the vista-foia package.         Luis BTW since fis-gtm backport builds nicely for wheezy and ubuntus = 12.04, would it be of any

Re: Thank you Luis!

On Tue, 14 Jan 2014, Andreas Tille wrote: BTW,  we are now making progress  on the vista-foia package.      Luis BTW since fis-gtm backport builds nicely for wheezy and ubuntus = 12.04, would it be of any value for you guys if we provided backports for it from

should google-glog be ok with libunwind7-dev? [Was: Orthanc 0.7.2 backport of wheezy]

Hi Daigo, I have looked at the packporting of orthanc for Wheezy. orthanc uses google-glog and that one currently build-depends on libunwind8-dev. It seems to build (including the build-time testing -- thanks for enabling those!) fine using libunwind7-dev, so I thought to check with you - if

Re: Orthanc 0.7.2 backport of wheezy

On Mon, 13 Jan 2014, Sebastien Jodogne wrote: I admit I'm quite lazy with backports and while I definitely think this is a reasonable task I somehow consider it Somebody Else's Problem. I simply need to restrict my field of work. Yes, you are perfectly right. Yaroslav, I have just

Re: Thank you Luis!

On Mon, 13 Jan 2014, Luis Ibanez wrote:         Thank You All !    :-) BTW,  we are now making progress  on the vista-foia package.      Luis BTW since fis-gtm backport builds nicely for wheezy and ubuntus = 12.04, would it be of any value for you guys if we provided

Re: Bug#728797: ITP: python-mne -- Python modules for MEG and EEG data analysis

it is intended to go and makes no sense for unstable i.e. proper Debian upload $ git show commit e1d70152267aedf2ba7f4f5be167d53854d5b2c2 Author: Yaroslav Halchenko deb...@onerussian.com Date: Sun Jan 12 10:03:16 2014 -0500 Boost X-Python-Version to = 2.7 to provide installable builds for wheezy

Orthanc 0.7.2 backport of wheezy

Hi Sebastien, Thank you for packaging orthanc -- it looks very interesting! I wonder -- are there big showstoppers which would forbid its backport for wheezy? At some point (0.4.0 iirc) I have tried to build it for wheezy but then got stuck while backporting also some of the dependencies...

Thank you Luis!

For a very nice post http://www.osehra.org/blog/packaging-fis-gtm-debian-linux-distribution-0 ;-) -- Yaroslav O. Halchenko, Ph.D. http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org Senior Research Associate, Psychological and Brain Sciences Dept. Dartmouth College, 419

Re: Bug#728797: ITP: python-mne -- Python modules for MEG and EEG data analysis

ah -- so the minimal supported Python is 2.7? then we should add X-Python-Version: =2.7 to source package paragraph (top) within debian/control then I am yet to furnish package for the new release... since it is backports/NeuroDebian specific -- I will do that... hopefully later today and push

Re: Bug#728797: ITP: python-mne -- Python modules for MEG and EEG data analysis

On Sat, 11 Jan 2014, Yaroslav Halchenko wrote: ah -- so the minimal supported Python is 2.7? then we should add X-Python-Version: =2.7 or may be you would prefer to adjust that one to stay 2.6 compatible? also for testing, I am usually trying to test with all supported versions, which could

Re: Fis-gtm accepted in unstable (Was: Packaging VistA - GT.M directories)

On Sun, 15 Dec 2013, Andreas Tille wrote: finally we have a nice Christmas gift for all people dealing with VistA: fis-gtm is now accepted in unstable. ... Thanks to everybody who has helped to let fis-gtm packages become available in official Debian hip hip hoorray -- go Team! ;) --

Re: Fis-gtm accepted in unstable (Was: Packaging VistA - GT.M directories)

On Sun, 15 Dec 2013, Bhaskar, K.S wrote: Yaroslav, how could I forget to mention you in my thanks! You drove several hours to our hackathon to help us get GT.M packaged. well -- that was so long ago now it seems, so it is not surprising that those sweet memories about the hackathon were not

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