Re: [help] porting brian on MIPS and POWER, or dropping support

On Sat, 30 Jan, 2021, 8:14 pm Étienne Mollier, wrote: > Hi again, > > Nevermind that: > > Étienne Mollier, on 2021-01-30 14:33:41 +0100: > > * I curiously couldn't locate mipsel builds in my backups, but > > from what I recall I got results very similar to mips64el. > > The build goes throu

hyphy - amd64 Test failures

Hi Michael, Thanks for your work on hyphy. It seems that with your last upload, CI tests are failing on amd64, but working everywhere else, as can be seen on tracker here[1] The log for amd64 on debci[2] seems to have compliance with salsa CI[3] I see the binaries generated as desired on correspo

Re: [RFR] brian 2.4.2-4

Hi, On Thu, 4 Feb, 2021, 5:54 pm Étienne Mollier, wrote: > Hi all, > > yesterday I missed my upload to experimental and it blocked the > package brian in Sid. I readied a 2.4.2-4 build to erase my > faulty build which ought to be uploaded to experimental. Before > I go further, I would like to

[Help Needed] umap-learn

Hi, umap-learn seems to fail its autopkgtests in i386[1] and armhf[2]. Looking at it, looks like the core functionality itself is broken. I initially had a perception that this is because of the broken numba. But now that numba is fixed and migrated to testing, and I re-triggered CI for umap-lear

Plan for Soft Freeze?

Hi all, Freeze step-2 a.k.a soft freeze starts roughly a week from now. As it seems, the majority of our key packages are in good shape right now. Thanks to all! :-) I had two questions: - From the start of soft freeze, should we be uploading most of the stuff to experimental instead of unstabl

Mark q2-* regressions on armhf and i386

Hi, Looks like q2-feature-classifier, q2-quality-filter*, *q2-quality-control, q2-taxa haven't migrated to testing yet due to regressions on armhf and i386. This is so because they (transitively)depend on python3-skbio which does not support these arches. I see that Etienne filed ROM --RM for tw

Re: Mark q2-* regressions on armhf and i386

On Sat, 6 Feb 2021 at 18:04, Étienne Mollier wrote: > Thanks, will give a try to the autopkgtest skip-not-installable > flag on q2-feature-classifier and upload q2-* friends if it does > what I am understanding at the moment. > I just uploaded q2-taxa. Just a note: Anything uploaded after noon

Re: [RFS] jalview

Hi Pierre, Thanks for your work on jalview. However, it seems that the autopkgtest fails on i386, which will prevent migration to testing. It looks like a memalloc problem so maybe this can be simply skipped. Or if I'm mistaken, please consider fixing this and uploading. PS: Please upload with ur

Re: [RFS] jalview

Seems relevant. Although the autopkgtest will reduce the delay to 2 days > in any case. > Yes, however it doesn't seem to be happening for a few of my packages that I noticed, for example vsearch[1] and kma[2] both of which have autopkgtests. Not sure of the reason though. [1]: https://tracker.de

Workflow for releasing new upstream versions to experimental?

Hi, Since soft freeze is around the corner, and new upstream versions which are **not** targeted fixes is _discouraged_[1] I plan uploading all new upstream versions till the release of bullseye to experimental. Hence I wanted to ask, is it sane to directly commit things to "master" branch with c

Re: Workflow for releasing new upstream versions to experimental?

On Tue, 9 Feb 2021 at 23:05, Nilesh Patra wrote: > Hi, > > Since soft freeze is around the corner, and new upstream versions which > are **not** targeted fixes is _discouraged_[1] > This is ofcourse, for packages in testing already

Re: Validating debian/upstream/metadata for debian-med projects

Your work (including critique as far as it concerns me) is perfectly > welcome and absolutely needed. > +1. Thank you, Andrius! This looks really cool. Andreas, do you think we can integrate/use this with routine-update? Nilesh

Re: bioawk - may I ask for a review?

Hi Steffen, On Thu, 11 Feb 2021 at 20:48, Steffen Möller wrote: > Hello, > > https://salsa.debian.org/med-team/bioawk > I did the following: * Added autopkgtests (this has a bit of hard-coding in d/tests/run-unit-tests but it should probably be OK) * Added manpage for bioawk * Add d/u/metadata

Re: bioawk - may I ask for a review?

On Thu, 11 Feb 2021 at 22:56, Steffen Möller wrote: > Thanks! Is this no longer tested by lintian? > Lintian emits an "I: hardening-no-fortify" however, it is blhc which should be used to actually make a check of where exactly hardening opts are missing. > Thank you tons and - please upload. >

Some q2 friends are still not in testing (Was: Mark q2-* regressions on armhf and i386)

Hi Étienne Looks like majority of the q2-* migrated to bullseye. However, q2-quality-control and q2-feature-classifier haven't. The reason is at the tracker. Please consider uploading the fix and maybe we could request testing migration. PS: I'd have tried tracking and uploading a fix myself but

Re: [RFS] vsearch 2.25.2-3 arm64 port (Was: Some q2 friends are still not in testing)

On Sat, 13 Feb, 2021, 4:54 am Étienne Mollier, wrote: > Hi again, > > Étienne Mollier, on 2021-02-12 22:47:56 +0100: > > 2. port vsearch on arm64. > > Good news, this option turns out to work out of the box! :) > > Assuming this kind of change is welcome in Soft Freeze, would it > be possible t

Re: Help with autopkgtest for Seqsero and python-loompy

Hi, On Tue, 23 Feb 2021 at 22:25, Shruti Sridhar wrote: > Hi, > > I was trying to write autopkgtests for Seqsero and python-loompy. I have > been facing some errors. Could someone please have a look and let me know > what I can do : > > 1. Seqsero : I

Re: [RFS] libbio-db-embl-perl 1.7.4-4

On Tue, 23 Feb 2021 at 23:30, Étienne Mollier wrote: > Changes are available > below[1] for review and upload. > Granted you upload rights, upload when you feel like doing so

Re: Help with autopkgtest for Seqsero and python-loompy

Hi Andreas On Wed, 24 Feb 2021 at 13:40, Andreas Tille wrote: > > In any case, you can enable salsa CI on your personal fork to track this. > > Hmmm, I think we should not propagate personal forks. I'm afraid that > some fork might feature interesting commits but will be lost somewhere. > So I'

Re: Differences in salsa access (was: Help with autopkgtest for Seqsero and python-loompy)

On Wed, 24 Feb 2021 at 14:05, Juhani Numminen wrote: > Hi, > > Nilesh Patra kirjoitti 23.2.2021 klo 19.39: > > Hi, > > > > On Tue, 23 Feb 2021 at 22:25, Shruti Sridhar <mailto:shruti.sridha...@gmail.com>> wrote: > > > [...] I couldn't push m

[Request for review] rna-star

Hi Michael and other folks, The version 2.7.8a of rna-star which Steffen uploaded a couple of days ago seems to use intel intrinsics which leads unfortunately builds on non-amd64 Since simde is a good way to mitigate this, I tried using this -- on testing on a arm64 porter box, build goes green an

Re: [Request for review] rna-star

Hi Michael On Mon, 1 Mar, 2021, 5:06 pm Michael Crusoe, wrote: > Hello Nilesh! > > Thank you for noticing this. > > Please add entries to debian/changelog in the future. I use `dch 'changed > a thing'` followed by `debcommit -a` instead of using `git commit`, to > ensure I document my changes. >

Re: MRtrix3

Hi On Wed, 3 Mar, 2021, 5:10 pm Julien Lamy, wrote: > Hi all, > I've updated the Salsa repository for MRtrix3 so that the package now > builds correctly. There are still a couple of issues : > > Lintian complains about unnecessary-team-upload. Please add your work to the changelog and make you

Re: MRtrix3

On Thu, 4 Mar, 2021, 5:16 pm Andreas Tille, wrote: > On Thu, Mar 04, 2021 at 12:32:30PM +0100, Julien Lamy wrote: > > Le 03/03/2021 à 20:13, Andreas Tille a écrit : > > > Just a slight hint that there is a Blends-workaround for name > > > space conflicts which is described for instance here: > >

Re: Outreachy project: complete workflows of tools

Hi, On Fri, 5 Mar, 2021, 9:40 pm Tassia Camoes Araujo, wrote: > Hi all, > > On 2021-03-04 16:19, Steffen Möller wrote: > > I am very confident that Tony would be a wonderful mentor. I happily > > help by co- or co-co-mentoring - we had discussed Qiime at the very last > > minutes of our Sprint i

Re: Help with autopkgtest for Seqsero and python-loompy

On Sun, 7 Mar, 2021, 11:58 pm Shruti Sridhar, wrote: > Hi, > > Thank you so much! I haven't had a chance to work on loompy yet, but I > have added tests to Seqsero. Please review and sponsor. > Please remove the "ubuntu1" from changelog header. @Andreas, I'm not sure if it should be uploaded at

Which columns should we start working on?

Hi Steffen, I'm mostly addressing you specifically here for the new "workflow based" packages we should start working on -- as you mentioned at the sprints. Since freeze work should _mostly_ be done by now, we could focus on new packages :-) Would you have any workflow package that you'd like hel

fsm-lite -- should binaries down from sse4.2 to baseline be compiled on amd64?

Hi, fsm-lite seems to pass in -msse4.2 for amd64. From the conversation I had in debian-cross@l.d.o this is probably a baseline violation -- please check this mail[1] Probably the best way forward is to build sse4.2 down to no vectorized operations, like it is done in simde-based builds? I'm not

Moving packages removed in the archive to /attic?

Hi, There are some packages that have been removed from the archive, but their repositories still reside on the med-team salsa namespace. It might be helpful to preserve such repositories in case someone in future might want to re-introduce them, but at the same time probably keeping it at s.d.o/

Re: Moving packages removed in the archive to /attic?

On Wed, Mar 10, 2021 at 05:03:31PM +0200, Andrius Merkys wrote: > Hi, > > On 2021-03-10 16:48, Robbi Nespu wrote: > > On 3/10/21 10:14 PM, Nilesh Patra wrote: > >> There are some packages that have been removed from the archive, but > >> their repositories s

Re: Communication: bullseye release notes

Hi, On Thu, 11 Mar, 2021, 9:22 pm Tassia Camoes Araujo, wrote: > Hi, > > I was exploring the team's salsa and found a project with past release > notes. Isn't it time to write something for bullseye? > Which project project exactly are you talking about, and what are the "release notes" you tal

Re: My upcomming talks and workshops

On 12 March 2021 11:27:23 am IST, Andreas Tille wrote: >Hi, > >I'll be active on Chemnitzer Linuxtage (this Saturday) and >FOSSASIA Summit 2021 following weekend. > >In German language: > > Samstag, 13.3. 11:00-14:00 (CET) >Debian Paketier Workshop > https://chemnitzer.linux-tage.de/2021/

Re: [RFS] hyphy 2.5.28+dfsg-3 (closes: #985284)

On Wed, Mar 17, 2021 at 12:06:28AM +0100, Étienne Mollier wrote: > Please could you consider reviewing changes, and upload or grant > dm permission, as you feel would be the most appropriate ? Done. Please make sure that you upload *only* the changes in the debdiff Nilesh

Re: [RFS] xdffileio 0.3-4 (closes #985290)

On 17 March 2021 8:29:08 pm IST, "Étienne Mollier" wrote: >need dm grants on it; please consider applying the option you >feel the most appropriate. > Done. BTW I wonder why there are several piuparts bugs identified right now. I also wonder how this migrated to testing in the first place w

Re: [RFS] xdffileio 0.3-4 (closes #985290)

On 18 March 2021 1:01:27 pm IST, Andreas Tille wrote: >On Wed, Mar 17, 2021 at 09:10:58PM +0530, Nilesh Patra wrote: >> BTW I wonder why there are several piuparts bugs identified right >now. I also wonder how this migrated to testing in the first place with >bad piuparts. >

Request for review -- radiant

Hi, radiant upgrade from buster seems to have a broken symlink as reported in #985523. I tried fixing this with hints from previous scripts, and taking a look at dpkg's maintscripts manpage. However, I'm not sure if these fixes are right. Please consider to review and upload, or give me a green s

Re: Autopkgtest for Changeo

On Fri, Mar 19, 2021 at 09:53:27PM +0530, Shruti Sridhar wrote: > Hi, > > I have added autopkgtests for Changeo. Please review. The size of the autopkgtest data is 1.3M, which is a bit too much and blows out of proportion with the size of the original package. Please embed the data instead, ref

Re: Request for review -- radiant

Hi, On Fri, 19 Mar 2021 at 23:07, Étienne Mollier wrote: > Hi Nilesh, > > Nilesh Patra, on 2021-03-19 21:15:35 +0530: > > radiant upgrade from buster seems to have a broken symlink as reported > > in #985523. I tried fixing this with hints from previous scripts, and > &

Re: [RFS] odin 2.0.4-2 (closes: #985508)

On Sat, 20 Mar 2021 at 01:51, Étienne Mollier wrote: > > Please consider review and sponsor or dm grants at your > convenience. The package has no autopkgtest, so I will fill the > required unblock request to the attention of the release team. > Done. Thanks for your work on this Nilesh

Re: python3-scanpy 1.6.0 patched, could you take a look?

Hi Andreas, On Mon, Mar 22, 2021 at 09:24:56AM +0100, Andreas Tille wrote: > At first we should consider the name of the source package. If this > software is just a Python module (and thus we only create python3-scanpy > binary package and no additional scanpy package) I'd recommend to rename >

Re: Which columns should we start working on?

> Hi Steffen, > I'm mostly addressing you specifically here for the new "workflow based" > packages we should start working on -- as you mentioned at the sprints. > Since freeze work should _mostly_ be done by now, we could focus on new > packages :-) > Would you have any workflow package that

Re: python3-scanpy 1.6.0 patched, could you take a look?

On 2021-03-22 17:24, u...@debian.org wrote: > Nilesh Patra writes: > >> [1]: >> https://www.debian.org/doc/packaging-manuals/python-policy/index.html#module-package-names > > By my reading, this documents how binary package names should related to > module names (as

Re: python3-scanpy 1.6.0 patched, could you take a look?

On 2021-03-23 12:18, Andreas Tille wrote: > I was pointed in some mails (which I'm to busy to seek for) by members > of the Python team to prefix source package names by 'python-' and I'm > following this recommendation. I see > I know there are counter-examples but > it also fits my personal ta

Re: Re: Which columns should we start working on?

Hi Steffen, Thanks for your reply. This is a lot of information, so I'll just quote specific sections. > There are some tools that block many columns from being completed. To > mention here in particular are the workflow engines, and here it is > nextflow that seems like being a beast to package.

Free software license for MEME?

Hi, Thanks for all your work on MEME :-) We actually were willing to package MEME inside Debian, so that folks using Debian or derivatives could simply: "$sudo apt-get install meme" And use your great work with ease! However, we experience a problem - The current license for MEME states: """ Th

Re: Any volunter to write a test for bamclipper?

On 2021-03-26 01:58, Andreas Tille wrote: > Hi folks, > > I have packaged bamclipper[1] since it is a precondition for the > pipeline covpipe[2] which is developed and used in my institute. > (@Steffen, possibly another column in the spreadsheet.) > > Despite bamclipper is pretty easy I would lov

Re: Any volunter to write a test for bamclipper?

Hi Steffen, On 26 March 2021 6:35:13 am IST, "Steffen Möller" wrote: > >> I found those files here[1] inside examples/ dir -- it also has >> outputted *.primer.bam* files, so I think it is sensible >> to assume that these files work. >> I follow this in other packages as well, when on adding

Re: Any volunter to write a test for bamclipper?

On Fri, 26 Mar 2021 at 02:48, Andreas Tille wrote: > I'll do so for every package I'm touching and would have probably done > soon for this package. However, what I would love even more if someone > would fix inject-into-salsa-git to approach this automatically. > I wonder if there is a central

[Request for review] nthash

Hi, I packages nthash which lives in the salsa repository here[1] Salsa CI shows all good, and it also cross-builds successfully in my schroot. Please consider doing a review and upload, or give me a green signal and I'll do so. [1]: https://salsa.debian.org/med-team/nthash Nilesh

Re: nthash is fine - please review two other packages. :-) (Was: [Request for review] nthash)

Hi Andreas, On 3/27/21 2:03 AM, Andreas Tille wrote: > Hi Nilesh, > > On Fri, Mar 26, 2021 at 09:02:27PM +0530, Nilesh Patra wrote: >> I packages nthash which lives in the salsa repository here[1] >> Salsa CI shows all good, and it also cross-builds successfully in my >

[RFS] fastani

Hi, I've packaged fastani[1], which looks good, with everything passing. I confirmed that it also cross-builds in my schroot (with my patches applied) Please consider doing a review and upload this one -- I need more resources to upload this one which I do not have currently -- so sponsorship wo

Re: nthash is fine - please review two other packages. :-)

On 2021-03-27 02:43, Andreas Tille wrote: > On Sat, Mar 27, 2021 at 02:33:03AM +0530, Nilesh Patra wrote: >> > Please check the probably >> > unneeded empty file debian/tests/test1. Feel free to upload yourself. >> > It looks good from my point. >> I uploaded,

Re: Autopkgtest for Changeo

Hi Shruti, On Mon, Mar 29, 2021 at 10:26:46PM +0530, Shruti Sridhar wrote: > I have embedded the data and changed the autopkgtest. > Kindly review. * Looks like you missed to commit the -data tarball to pristine-tar which the salsa CI job showed[1] - I fixed this one, CI looks better now. * Plea

[Request for review] r-bioc-ioniser

Hi, Please consider doing a review for: https://salsa.debian.org/r-pkg-team/r-bioc-ioniser And upload or give me a grean flag and I'll do so. I was rather confident and going to push it to NEW, however it has a few fast5 data (binary) files in inst/extdata/* and I'm not sure if it is acceptable

Re: Please track you new packages in Blends tasks (Was: pullseq_1.0.2-1_amd64.changes is NEW)

Hi Andreas, On Tue, Mar 30, 2021 at 03:30:51PM +0200, Andreas Tille wrote: > Hi Nilesh, > > I'm very happy to see your performance to add new packages to the pool. > That's really cool. It would be nice if you would add packages you > are working on to the relevent Debian Med task even if it is

[Request for review] ntcard

Hi, Please consider doing a review for: https://salsa.debian.org/med-team/ntcard (Specifically the copyrights) Please note: this has a build-dep on libnthash-dev (src:nthash) which is still in NEW (repo here: https://salsa.debian.org/med-team/nthash) hence build accordingly. Either upload to NEW

[Request for review] nxtrim

Hi, Please consider reviewing nxtrim[1] - mainly for licensing stuff and upload, or give me a green signal so I'll do so [1]: https://salsa.debian.org/med-team/nxtrim/ Nilesh signature.asc Description: PGP signature

Re: Re: Please track you new packages in Blends tasks (Was: pullseq_1.0.2-1_amd64.changes is NEW)

Hi Andreas, Apologies for late reply, I missed to reply to this mail (see below) >> Since these NEW packages are not yet accepted, is >> adding in "Recommends:" still OK? > Definitely. The toolset will deal with this. The code to generate the > metapackages will decrease any Recommends that ca

last-align: Baseline violation on amd64?

Hi Michael, Whilst compiling last-align for new upstream release, I noticed that last-align binaries are not being generated for baseline amd64, i.e. without sse/avx et. al. More specifically, there's no instruction to build the "-plain" binaries while the same is actually present for i386[1] So i

Fixing d/watch Teamwide

Hi, GitHub lately decided to change it's tarball locations from archive/version to archive/ref/tag/version - or something similar. This ended up breaking a lot of d/watch files which fetch stuff from github. There was a discussion on -devel[1] regarding fixing d/watch for github URLs, a few nice s

Re: Fixing d/watch Teamwide

On Fri, 23 Apr, 2021, 7:07 am Robbi Nespu, wrote: > > On 4/23/21 5:02 AM, Nilesh Patra wrote: > > Hi, > > > > GitHub lately decided to change it's tarball locations from > > archive/version to archive/ref/tag/version - or something similar. > > This ended

Re: Fixing d/watch Teamwide

On Fri, 23 Apr, 2021, 7:07 am Robbi Nespu, wrote: On 4/23/21 5:02 AM, Nilesh Patra wrote: > Hi, > > GitHub lately decided to change it's tarball locations from > archive/version to archive/ref/tag/version - or something similar. > This ended up breaking a lot of d/watch fil

Re: [RFS] dipy/1.3.0-3

Allowed, thanks On Sun, 25 Apr 2021 at 16:47, Étienne Mollier wrote: > Hi all, > > I brought some changes in dipy/1.3.0-3[1] to address RC bugs > #987453[2] and #987517[3], and I am preparing an unblock request > for the release team, debdiff in attachment. Salsa CI raises no > complaints, but

Re: Bug#987771: ITP: capsule-nextflow -- packaging and deployment tool for Java applications

On 4/29/21 7:24 PM, Andreas Tille wrote: > Hi Pierre, > > On Thu, Apr 29, 2021 at 11:08:04AM +0200, Pierre Gruet wrote: >> Package: wnpp >> Severity: wishlist >> Owner: Debian-med team >> X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org >> >> * Package name: capsule-n

Re: sponsor for medphys manual and calculator

On 10 May 2021 10:18:19 am IST, name wrote: >Greetings, > >Would you or someone you know be interested in sponsoring a medical >physics reference manual and (second-check) calculator for inclusion in > >the Debian repository? I am thinking to write one as a useful >compendium >of references a

Re: Re: sponsor for medphys manual and calculator

> A medical *calculator* is a useful tool, especially if it > makes adjusting/calculating dosage instructions intuitive and > foolproof (this female child of such and such weight and/or > age is to receive so many drops of medication X with a > concentration of this grams per that milliliters of so

Re: Welcome Shruti Sridhar to the GSoC project

On 5/18/21 1:17 AM, Andreas Tille wrote: > Hi Shruti, > > your are accepted to our project "Quality Assurance and Continuous > Integration for Applications in Life Sciences and Medicine" as Google > Summer of Code student. Congratulations for this. > > You are kindly invited to ask any questio

Re: PyEnsembl - how does that help us?

On 5/18/21 6:16 PM, Steffen Möller wrote: > Hello, > > I just packaged xpore, which points to > https://github.com/openvax/pyensembl to get various sorts of sequencing > data, also complete genomes. I like that and address its packaging now. > New packages are uploaded to PyPi, not release tagge

Re: PyEnsembl - how does that help us?

On 20 May 2021 3:42:20 am IST, "Steffen Möller" wrote: >Quick update - I have package all dependencies fo xpore (and of >pyensembl with it) , packages are tagged orange on the spreadsheet's >"Nanopore" tab >(https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edi

Re: PyEnsembl - how does that help us?

On Thu, 20 May, 2021, 3:45 pm Steffen Möller, wrote: > > Am 20.05.21 um 11:42 schrieb Andreas Tille: > > On Thu, May 20, 2021 at 11:00:59AM +0530, Nilesh Patra wrote: > >> This can be uploaded to NEW right now, no? > > +1 > My fear was that this would take en

Re: RFS Prime-phylo

Hi Shruti, On 5/20/21 4:56 PM, Shruti Sridhar wrote: > Hi, > > I have added autopkgtests for prime-phylo. > (https://salsa.debian.org/med-team/prime-phylo) > Kindly review and sponsor Looks nice. However, * We are in deep freeze right now[1] I'll happily sponsor when bullseye is out. * You have

Re: PyEnsembl - how does that help us?

Hi, On 5/20/21 4:09 PM, Steffen Möller wrote: > > Am 20.05.21 um 12:19 schrieb Nilesh Patra: >> >> >> On Thu, 20 May, 2021, 3:45 pm Steffen Möller, > <mailto:steffen_moel...@gmx.de>> wrote: >> >> >> Am 20.05.21 um 11:42 schrieb Andreas Ti

Re: PyEnsembl - how does that help us?

On 5/20/21 8:38 PM, Steffen Möller wrote: > > Am 20.05.21 um 16:36 schrieb Nilesh Patra: >> Hi, >> >> On 5/20/21 4:09 PM, Steffen Möller wrote: >>> Am 20.05.21 um 12:19 schrieb Nilesh Patra: >>>> >>>> On Thu, 20 May, 2021, 3:45 pm S

Re: PyEnsembl - how does that help us?

On 5/20/21 8:38 PM, Steffen Möller wrote: >>> datacache: https://salsa.debian.org/med-team/python-datacache Regarding datacache, I suppose the copyright holder should be "Mount Sinai School of Medicine" instead of "Alex Rubinsteyn " -- since the former is what is written in all the files. If yo

Re: PyEnsembl - how does that help us?

Hi Steffen, I believe I have uploaded all 7 packages after making lintian happy and doing a few QA checks. I haven't added autopkgtest to xpore yet. It seems doable, will try doing it in the next upload (after it gets accepted) Thanks a lot for all your work! Nilesh signature.asc Description

[RFS] libstreamvbyte and vbz-compression

Hi, libstreamvbyte: has been in salsa for a while, but it was never uploaded. I did a few minor changes, and its good to go. Please review and upload. vbz-compression: It took more effort to get this one building, but I'm not particularly sure if it's done right. Upstream beuild rules look just

Re: CuteSV (Was: PyEnsembl - how does that help us?)

On 5/23/21 2:54 AM, Andreas Tille wrote: > On Sat, May 22, 2021 at 09:10:46AM +0200, Andreas Tille wrote: >> On Fri, May 21, 2021 at 09:26:48PM +0200, Steffen Möller wrote: >>> >>> If someone needs a stimulus to package something - cuteSV >>> (https://github.com/tjiangHIT/cuteSV), please. >> >> I

Re: libvbz-hdf-plugin (Was: CuteSV (Was: PyEnsembl - how does that help us?))

On 23 May 2021 2:06:00 pm IST, Andreas Tille wrote: >Hi Nilesh, > >On Sun, May 23, 2021 at 03:32:55AM +0530, Nilesh Patra wrote: >> PS: Please check and upload vbz-compression whenever you have time >(after two days as you wrote would be fine anyway) >> I'll be ina

Re: CuteSV (Was: PyEnsembl - how does that help us?)

On 5/23/21 5:56 PM, Steffen Möller wrote: > > Am 23.05.21 um 00:02 schrieb Nilesh Patra: >> >> On 5/23/21 2:54 AM, Andreas Tille wrote: >>> On Sat, May 22, 2021 at 09:10:46AM +0200, Andreas Tille wrote: >>>> On Fri, May 21, 2021 at 09:26:48PM +0200, Steff

Re: CuteSV (Was: PyEnsembl - how does that help us?)

On 5/23/21 10:00 PM, tony mancill wrote: > On Sun, May 23, 2021 at 06:16:42PM +0200, Steffen Möller wrote: >> https://salsa.debian.org/med-team/catfishq >> is ready for review+sponsoring. >> Many thanks! > > Hello Steffen, hi Debian Med@ > > Since I have worked on the fastqc package in the past

Please keep enabling salsa CI for any packages you work on

Hi, Few days earlier I ran a script which changed the default file to d/salsa-ci.yml So basically every package in the med-team has the default config file set to d/salsa-ci.yml and pushing to any repository will trigger the CI [ **NOTE: please don't mass push to hundreds of repos at once** ] H

Re: CuteSV (Was: PyEnsembl - how does that help us?)

On Mon, 24 May, 2021, 11:00 am Andreas Tille, wrote: > On Mon, May 24, 2021 at 01:26:47AM +0200, Steffen Möller wrote: > > > > Should there be a bug report about the missing test data in the pypi > > tarball? > > May be. But to my observation it is very common that the PyPI tarball > is lacking

Re: Autopkgtests for quorum

Hi Shruti, On Mon, 24 May 2021 at 21:13, Shruti Sridhar wrote: > Hi, > > I have written autopkgtests for quorum ( > https://salsa.debian.org/med-team/quorum) > Kindly review, > Please consider adding the copyright information (I guess its BSD-3-Clause) for d/tests/data/* in d/copyright (it make

Re: libvbz-hdf-plugin (Was: CuteSV (Was: PyEnsembl - how does that help us?))

On 5/23/21 2:06 PM, Andreas Tille wrote: > Hi Nilesh, > > On Sun, May 23, 2021 at 03:32:55AM +0530, Nilesh Patra wrote: >> PS: Please check and upload vbz-compression whenever you have time (after >> two days as you wrote would be fine anyway) >> I'll be inact

Re: libvbz-hdf-plugin (Was: CuteSV (Was: PyEnsembl - how does that help us?))

On Tue, 25 May 2021 at 01:04, Andreas Tille wrote: > On Tue, May 25, 2021 at 12:15:37AM +0530, Nilesh Patra wrote: > > Ah, one thing: > > > > $ cat debian/libvbz-hdf-plugin-dev.install > > #!/usr/bin/dh-exec > > > > usr/lib/*/lib*.so > > vbz_plugin/*.

Re: htscodec has new upstream location

[I'm taking the liberty to answer your other questions] On 5/25/21 2:44 AM, Steffen Möller wrote: > How far away is our release, still? We don't know yet. The RC bugs in key packages[1] are 45, and this number seems to stay more-or-less, the same - I check this page daily and I do not blame any

Re: ont-fast5-api (Was: libvbz-hdf-plugin (Was: CuteSV))

Hi Andreas, On 5/24/21 2:34 AM, Andreas Tille wrote: > Hi Nilesh, > > On Sun, May 23, 2021 at 03:07:09PM +0530, Nilesh Patra wrote: >>> now and I've also uploaded to new. I admit I forgot for what >>> final target I was working on this lib. :-( >&g

Re: ont-fast5-api (Was: libvbz-hdf-plugin (Was: CuteSV))

On Wed, 26 May, 2021, 1:21 pm Andreas Tille, wrote: > Hi Nilesh, > > On Wed, May 26, 2021 at 03:22:21AM +0530, Nilesh Patra wrote: > > > I've commited some changes to ont-fast5-api. When I try to run any > > > of the scripts

Re: Autopkgtests for quorum

On 5/26/21 5:18 PM, Shruti Sridhar wrote: > Hi,  > > I have taken the examples from filtlong and pushed the changes for quorum > (https://salsa.debian.org/med-team/quorum) Great stuff. > I have also added autopkgtests for Nanosv  > (https://salsa.debian.org/med-team/nanosv) Ah, this one is n

Re: [RFS] vtk-dicom/0.8.12-4

On 5/29/21 6:06 PM, Étienne Mollier wrote: > Greetings everyone, > > following up on the green light from Sebastian Ramacher on > unblock pre-approval request #988643[0], please would it be > possible to proceed to a sponsored upload of vtk-dicom 0.8.12-4 > to unstable? (Or to provide dm grants

Re: Autopkgtests for quorum

On 5/29/21 8:39 PM, Shruti Sridhar wrote: > Hi,  > > I have converted the .bam test data to .sam files, added the source of the > files to d/tests/README and d/copyright and pushed.  It looks like you changed the data instead, and used a file from samtools. The toy.sam file is already availab

Re: Stan statistics programming - interesting buut missing

Hi Steffen, On 6/1/21 7:57 AM, Steffen Möller wrote: > Hello, > > I need to add "Stan" to the list of languages to have a closer look at > (https://mc-stan.org).  We do not have a Debian package for this > statistics programming environment. R has rspan as an interface, so do > Python, Matlab, J

Re: Autopkgtests for yaha

Hi Shruti, On 6/3/21 2:08 PM, Shruti Sridhar wrote: > Hi,  > > I have written autopkgtests for yaha (https://salsa.debian.org/med-team/yaha) > Kindly review, The size of test data is 114M $ du -sh testdata 114Mtestdata Such large data should _never_ be installed w

Re: Static linking without using a Built-Using attribute

Hi Sébastien On Fri, 4 Jun, 2021, 2:15 pm Sébastien Jodogne, wrote: > > Adrian (Bunk) replied that "This is fixable with a +really version." > Unfortunately, this is visibly a non-trivial procedure that is out of > the scope of my personal experience. In particular, I don't understand > to wha

Re: Static linking without using a Built-Using attribute

On 04/06/21 06:37 PM, Sébastien Jodogne wrote: > Dear Nilesh, > > Thank you very much for your help! > > > On 4/06/21 11:45, Nilesh Patra wrote: > > Hi Sébastien > > > > On Fri, 4 Jun, 2021, 2:15 pm Sébastien Jodogne, > > mailto:s.jodo...@orthanc-

Re: Static linking without using a Built-Using attribute

On Fri, 4 Jun 2021 at 23:43, Étienne Mollier wrote: >orthanc (1.9.2+really1.9.1+dfsg-1) unstable; ... Ah, yeah, right. I overlooked the package name, thanks for bringing attention to this! > although I may have a different view on the package name to > specify to the Built-Using Nilesh

Re: Static linking without using a Built-Using attribute

On 6/5/21 5:39 PM, Étienne Mollier wrote: > Hi Sébastien, > > Sébastien Jodogne, on 2021-06-05: >> I'm obviously fine with your changes (to which I had a look), as they >> seem to be perfectly in line with Nilesh's explanations. >> >> It would indeed be great if you could do the team upload: Thi

Re: Autopkgtests for python - leidenalg

Hi, On 6/5/21 4:15 PM, Shruti Sridhar wrote: > Hi,  > > I have written autopkgtests for python-leidenalg   > (https://salsa.debian.org/med-team/python-leidenalg) > Kindly review, Since this package is not in testing, I did some minor changes and uploaded. You should get an accepted into unstabl

Request for Free software license for GramAlign

Hi David, Thanks for all your work on GramAlign! We (the Debian Med team - CC'ed in this email) actually were willing to package GramAlign inside Debian, so that folks using Debian or derivatives could simply: "$sudo apt-get install gramalign" And simply use the gramalign without having to compi

Re: Autopkgtests for Gramalign

On 6/8/21 6:45 PM, Shruti Sridhar wrote: > Hi,  > > I have written autopkgtests for gramalign  > (https://salsa.debian.org/med-team/gramalign) * Since this was never uploaded, we usually do not add entries in changelog except for "Initial Release" - no hard rule though * blhc was failing, I f

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