[MoM] Re: bart - tools for computational magnetic resonance imaging
Hi Martin, I just officially added you to the MoM wiki. On Tue, Dec 01, 2015 at 04:33:19PM +, Uecker, Martin wrote: > > Thanks for letting me know. Please try at least to get ssh access > > > > ssh git.debian.org > > > > via ssh key and commit the repository. I'll check what changes might be > > needed and let you know. The MoM project is in the first place to lower > > the barrier for asking questions the student might be afraid about to be > > qualified as "stupid". Just feel free to ask anything you wonder about > > since I do not remember any stupid question here. ;-) > > Ok, I put it in /git/debian-med/bart.git as described in the > debian-med policy. I checked this out and added Vcs fields and Homepage to Debian control (please pull). I noticed that the pristine-tar branch is missing in the git repository. You can get this easily by redoing gbp import-orig --pristine-tar your_orig_tar_gz (just make sure you use the --pristine-tar option) and push the pristine-tar branch. The rationale is that we can both easily work on a byte identical tarball right from the Git archive. I assume that the debian/control file is missing other Build-Depends than just debhelper. I'd also recommend to use cme fix dpkg-control which would bump your Standards-Version to 3.9.6 (which you can also do manually but cme is a nifty tool I'd like to introduce to newcomers). Kind regards Andreas. -- http://fam-tille.de
Re: Removal of mummy and activiz.net
Hi Gert, On Tue, Dec 01, 2015 at 07:22:06PM +0100, Gert Wollny wrote: > considering that these two packages won't see any fixes, (they require > the abandoned gccxml), I guess that apart from tagging the related bugs > as wontfix (done), I also should request the removal of the packages. Thanks. > What I'm wondering now is how this is done for a team packages? Since I > am not in the uploaders list of these two packages (and also not yet > DD) I doubt that I can simply tag the request ROM. I guess ftpmaster is sane enough to accept this also from you on behalf of the team but I filed #806818 (for mummy) and an according bug for activiz.net. (This might give you an additional time slice to possibly have a short look on aeskulap. ;-)) Kind regards and thanks for your work on this Andreas. PS: Dcmtk is currently building. -- http://fam-tille.de
aeskulap, was: Re: Removal of mummy and activiz.net
On Tue, Dec 01, 2015 at 09:33:28PM +0100, Andreas Tille wrote: > (This might give you an additional time slice to possibly > have a short look on aeskulap. ;-)) YES ! Please do ! That would help A LOT ! :-) Karsten -- GPG key ID E4071346 @ eu.pool.sks-keyservers.net E167 67FD A291 2BEA 73BD 4537 78B9 A9F9 E407 1346
Re: bart - tools for computational magnetic resonance imaging
Am Dienstag, den 01.12.2015, 15:16 + schrieb Ghislain Vaillant: > On 01/12/15 15:04, Uecker, Martin wrote: > > Ghislain Vaillant: > > > >> > >> Hi Martin, > >> > >> Let me know if you need assistance on the packaging side. > >> > >> Glad to see more MRI reconstruction software being packaged for Debian. > >> > >> Cheers, > >> > >> Ghis > > > > > > Thank you, Ghis! > > > > I am sure that I will need some help. I see that you have already > > packaged the ismrmrd library (which we aim to properly support at > > some point in BART). > > Indeed. Still need to find time for Gadgetron as well, but it is a much > bigger piece of work ^^. > > Nice to hear you are planning to support ISMRMRD. FYI, Michael's team is > currently working on the next major release (2.x), so I would suggest to > wait a bit. Your call. I will wait. I made that mistake before... > 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. Martin
Re: bart - tools for computational magnetic resonance imaging
Hi Andreas, Andreas Tille: > Hi Martin, > > On Tue, Dec 01, 2015 at 03:00:25PM +, Uecker, Martin wrote: > > thank you for your answer! > > You are welcome. :-) > > > Andreas Tille: > > > I have not yet checked out this and before I do I would like to suggest > > > that you move the actual Debian packaging to git.debian.org where all > > > our packaging code resides. This as several advantages (if interested > > > I could list them - one example would be that your work could be listed > > > on our imaging page[1] even in this stage). > > > > Ok, I created an account and applied for debian-med membership. > > Accepted. > > > > My suggestion would be that you check out our team policy[2] that > > > explains how to maintain a package in our packaging Git. Since we have > > > also a mentoring program called Mentoring of the Month[3] and there is a > > > free slot for December I wonder whether you like to become a MoM > > > student. Considering that you are obviously comfortable with gbp I'm > > > quite positive that we will succeede in way less than a month. > > > > > > What to you think about this? > > > > Sounds good. I am fairly busy though, so I am not sure how well > > the mentoring would work - there will be times where I am not > > going to be able to respond at all. But I will try to spend some > > time packaging this project, and could certainly use a > > lot of advise. > > Thanks for letting me know. Please try at least to get ssh access > > ssh git.debian.org > > via ssh key and commit the repository. I'll check what changes might be > needed and let you know. The MoM project is in the first place to lower > the barrier for asking questions the student might be afraid about to be > qualified as "stupid". Just feel free to ask anything you wonder about > since I do not remember any stupid question here. ;-) Ok, I put it in /git/debian-med/bart.git as described in the debian-med policy. Martin
Sponsoring request DCMTK-3.6.1~20150924
Dear all, I've prepared the new upstream snapshot of dcmtk. Important changes are: - the package is now build in git [1] - upstream dropped the www support, i.e. the removed the related perl scripts and programs from the source. Hence the package dcmtk-www will no longer be build. - new so-name, hence the library package is now called libdcmtk5 Because of the ABI change and the dropping og dcmtk-www I would suggest to first upload this version to experimental. Especially that latter is a bit ugly, because popcorn reports some installations of dcmtk-www. many thanks, Gert [1] git://git.debian.org/debian-med/dcmtk.git
Removal of mummy and activiz.net
Hi all, considering that these two packages won't see any fixes, (they require the abandoned gccxml), I guess that apart from tagging the related bugs as wontfix (done), I also should request the removal of the packages. What I'm wondering now is how this is done for a team packages? Since I am not in the uploaders list of these two packages (and also not yet DD) I doubt that I can simply tag the request ROM. many thanks. Gert
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. > Perfect. Don't hesitate to ping me once you are happy with the > current state of your packaging work. I am happy to help you on the > final touch before review. > Good luck and thanks for your contribution to Debian. Indeed thanks in advance Martin. And thanks Ghislain -- since of relevance, I have uploaded backports of ismrmrd to NeuroDebian, happen you need them on some older debian/ubuntu. Whenever bart package gets into Debian -- can do the same to it ;) Cheers! -- 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 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik
Re: Bug#777043: Shark / libshark packaging status
On 30/11/15 12:42, Goswin von Brederlow wrote: Go ahead and work on. I packaged this as it was a dependency for something one of our customers wanted but interest seems to have been reduced since then. So I'm happy passing this on to someone else. MfG Goswin Thanks for passing this on to me. Is there any further action to take on this ITP as a result ? Ghis
Re: bart - tools for computational magnetic resonance imaging
On 01/12/15 00:15, Uecker, Martin wrote: Hi all, I would love to see our image reconstruction software for magnetic resonance imaging included in Debian. I filed an ITP with more information here: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=806762 The source code is on Github: https://github.com/mrirecon/bart I already added a debian branch with the debian control files. Using gbp I can build a package with: gbp buildpackage --git-debian-branch=debian --git-upstream-tree=master but it probably needs more work... and a sponsor. Martin Hi Martin, Let me know if you need assistance on the packaging side. Glad to see more MRI reconstruction software being packaged for Debian. Cheers, Ghis
Jessie backports request
I was wondering if it would be possible to backport the latest `figtree' version 1.4.2 to Jessie backports. Thanks. Joseph.
Re: bart - tools for computational magnetic resonance imaging
Ghislain Vaillant: > > Hi Martin, > > Let me know if you need assistance on the packaging side. > > Glad to see more MRI reconstruction software being packaged for Debian. > > Cheers, > > Ghis Thank you, Ghis! I am sure that I will need some help. I see that you have already packaged the ismrmrd library (which we aim to properly support at some point in BART). Martin
Re: December
On Tue, Dec 01, 2015 at 03:41:50PM +0100, Gert Wollny wrote: > Hello, > > On Tue, > > > Maybe some of the "won't fix" can be resolved as well. > > I consider #798165, #797651, #805360, #705270 to be such cases. They > all relate to mummy and activit.net. As far as i can see both packages > are no longer used to generated .NET bindings (i.e. in gdcm Mathieu > provided the patch to change this, and I'm not aware of other packages > that used them). > > As far as i can see these packages are also abandoned upstream. > > If nobody on the list doesn't voice any objections, I'll add the > according tags & comments. Just go for it ... > I also intent to look into #803595 (vtk-dicom depends on vtk5) and #73 > 3629 ( Convenient lib: double-conversion in ITK4). Good. (Please beat me in fixing bugs and get a $DRINK once we might meet again. ;-)) Kind regards Andreas. -- http://fam-tille.de
Re: Jessie backports request
Hi, I've just uploaded a new package version to unstable and plan to backport this to Jessie once it has hit testing. More wishes for backports welcome Andreas. On Tue, Dec 01, 2015 at 10:06:06AM -0500, Joseph Brown wrote: > I was wondering if it would be possible to backport the latest `figtree' > version 1.4.2 to > Jessie backports. > > Thanks. > Joseph. -- http://fam-tille.de
Re: bart - tools for computational magnetic resonance imaging
On 01/12/15 15:04, Uecker, Martin wrote: Ghislain Vaillant: Hi Martin, Let me know if you need assistance on the packaging side. Glad to see more MRI reconstruction software being packaged for Debian. Cheers, Ghis Thank you, Ghis! I am sure that I will need some help. I see that you have already packaged the ismrmrd library (which we aim to properly support at some point in BART). Indeed. Still need to find time for Gadgetron as well, but it is a much bigger piece of work ^^. Nice to hear you are planning to support ISMRMRD. FYI, Michael's team is currently working on the next major release (2.x), so I would suggest to wait a bit. Your call. 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. Ghis
Re: bart - tools for computational magnetic resonance imaging
Hi Andreas, thank you for your answer! Andreas Tille: > I have not yet checked out this and before I do I would like to suggest > that you move the actual Debian packaging to git.debian.org where all > our packaging code resides. This as several advantages (if interested > I could list them - one example would be that your work could be listed > on our imaging page[1] even in this stage). Ok, I created an account and applied for debian-med membership. > My suggestion would be that you check out our team policy[2] that > explains how to maintain a package in our packaging Git. Since we have > also a mentoring program called Mentoring of the Month[3] and there is a > free slot for December I wonder whether you like to become a MoM > student. Considering that you are obviously comfortable with gbp I'm > quite positive that we will succeede in way less than a month. > > What to you think about this? Sounds good. I am fairly busy though, so I am not sure how well the mentoring would work - there will be times where I am not going to be able to respond at all. But I will try to spend some time packaging this project, and could certainly use a lot of advise. Martin > Kind regards > > Andreas. > > > [1] http://blends.debian.org/med/tasks/imaging#pkgvcs-debs > [2] http://debian-med.alioth.debian.org/docs/policy.html > [3] https://wiki.debian.org/DebianMed/MoM >
Re: bart - tools for computational magnetic resonance imaging
Hi Martin, On Tue, Dec 01, 2015 at 03:00:25PM +, Uecker, Martin wrote: > thank you for your answer! You are welcome. :-) > Andreas Tille: > > I have not yet checked out this and before I do I would like to suggest > > that you move the actual Debian packaging to git.debian.org where all > > our packaging code resides. This as several advantages (if interested > > I could list them - one example would be that your work could be listed > > on our imaging page[1] even in this stage). > > Ok, I created an account and applied for debian-med membership. Accepted. > > My suggestion would be that you check out our team policy[2] that > > explains how to maintain a package in our packaging Git. Since we have > > also a mentoring program called Mentoring of the Month[3] and there is a > > free slot for December I wonder whether you like to become a MoM > > student. Considering that you are obviously comfortable with gbp I'm > > quite positive that we will succeede in way less than a month. > > > > What to you think about this? > > Sounds good. I am fairly busy though, so I am not sure how well > the mentoring would work - there will be times where I am not > going to be able to respond at all. But I will try to spend some > time packaging this project, and could certainly use a > lot of advise. Thanks for letting me know. Please try at least to get ssh access ssh git.debian.org via ssh key and commit the repository. I'll check what changes might be needed and let you know. The MoM project is in the first place to lower the barrier for asking questions the student might be afraid about to be qualified as "stupid". Just feel free to ask anything you wonder about since I do not remember any stupid question here. ;-) Kind regards Andreas. -- http://fam-tille.de
Re: Bug#777043: Shark / libshark packaging status
On 01/12/15 10:33, Andreas Tille wrote: On Tue, Dec 01, 2015 at 09:24:12AM +, Ghislain Vaillant wrote: Thanks for passing this on to me. Is there any further action to take on this ITP as a result ? Uploading? :-P Which might be happening soon, upstream has been very responsive to my initial packaging feedback. Once again, I will require some of your sponsorship magic when the time comes ;-) Ghis
December
Hi everybody, the time has come and in order to carry on a tradition, I want to remind everybody of our combined efforts to take care of some poor souls at this time of the year. The days are closing in, the year is drawing to an end and we should think of all those, that are not around with their own kind. Again, during the last few months, lots of volunteers all around the world tracked down those poor souls and put their cases in the database. We should take care of those needy. This year, there are about 260 cases which are relevant to Debian Med[1] (28 being serious[2]). So please feel pity for them and allow the transition of as many as possible poor souls to their final destination, the retirement community in the Archive. Maybe some of the "won't fix" can be resolved as well. Furthermore I would like to mention another page[3] with lots of information about Debian Med packages. Besides the list of RC bugs you can also see packages that can not be built on a Debian architecture, packages that are not allowed to migrate from unstable to testing (and thus won't be included in the next release) and packages with a new upstream version. I think those packages need some care as well. As soon as I get the notice of a closed case I will record that in our Advent calendar[4]. In contrast to normal calendars, let us fill this special one with lots of good deeds. Maybe we can hide at least one number of a closed case behind every door and I am sure we will be much better than last year. Have fun, Thorsten [1]http://bugs.debian.org/cgi-bin/pkgreport.cgi?which=maint=debian-med-packaging%40lists.alioth.debian.org=no=yes=yes=fixed=done [2]http://bugs.debian.org/cgi-bin/pkgreport.cgi?which=maint=debian-med-packaging%40lists.alioth.debian.org=no=done=critical=grave=serious [3]http://udd.debian.org/dmd.cgi?email=debian-med-packag...@lists.alioth.debian.org [4]http://debian-med.alteholz.de/advent
Re: December
Hello, On Tue, > Maybe some of the "won't fix" can be resolved as well. I consider #798165, #797651, #805360, #705270 to be such cases. They all relate to mummy and activit.net. As far as i can see both packages are no longer used to generated .NET bindings (i.e. in gdcm Mathieu provided the patch to change this, and I'm not aware of other packages that used them). As far as i can see these packages are also abandoned upstream. If nobody on the list doesn't voice any objections, I'll add the according tags & comments. I also intent to look into #803595 (vtk-dicom depends on vtk5) and #73 3629 ( Convenient lib: double-conversion in ITK4). Best, Gert
Re: December
Hi Thorsten, On Tue, Dec 01, 2015 at 01:45:20PM +0100, Thorsten Alteholz wrote: > As soon as I get the notice of a closed case I will record that in our > Advent calendar[4]. Thanks a lot for your all year quality assurance push in this cute form. This is really appreciated. For NEWCOMERS (and not so new comers but people who have no idea how to squash bugs) I promise to help kindly into all not so secret but may be hidden facts needed to squash some bugs. every helping hand is welcome and I think everybody can really help. > In contrast to normal calendars, let us fill this special one with lots of > good deeds. I started today with #801043, #785374 and #806743. :-) > Maybe we can hide at least one number of a closed case behind > every door and I am sure we will be much better than last year. I need to admit that last year I was concentrating on other RC bugs to get the release out. By nature they were more tricky and not so much in our focus. May be others did so as well? But this year there is no excuse. Please people, check your packages and squash bugs! Thanks for the calender and have fun yourself by helping us closing our ITP bugs ;-)) Andreas (just "working" on #804578 which is so brain dead easy as several others - you just need to *do* it ...) > [1]http://bugs.debian.org/cgi-bin/pkgreport.cgi?which=maint=debian-med-packaging%40lists.alioth.debian.org=no=yes=yes=fixed=done > [2]http://bugs.debian.org/cgi-bin/pkgreport.cgi?which=maint=debian-med-packaging%40lists.alioth.debian.org=no=done=critical=grave=serious > [3]http://udd.debian.org/dmd.cgi?email=debian-med-packag...@lists.alioth.debian.org > [4]http://debian-med.alteholz.de/advent -- http://fam-tille.de
Re: bart - tools for computational magnetic resonance imaging
On 01/12/15 16:37, Uecker, Martin 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. Perfect. Don't hesitate to ping me once you are happy with the current state of your packaging work. I am happy to help you on the final touch before review. Good luck and thanks for your contribution to Debian. Ghis
