Bug#961319: ITP: ncbi-acc-download -- Download genome files from NCBI by accession
Package: wnpp Severity: wishlist Owner: Sao I Kuan * Package name: ncbi-acc-download Version : 0.2.6 Upstream Author : Kai Blin * URL : https://github.com/kblin/ncbi-acc-download * License : Apache-2.0 Programming Lang: Python Description : Download genome files from NCBI by accession This package provides a script to download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API. This package is a dependency of idseq-bench (#956033) and will be team-maintained with Debian Med Packaging Team.
Bug#961330: ITP: yuview -- QT based YUV player with an advanced analytic toolset
Package: wnpp Severity: wishlist Owner: Roger Shimizu * Package name: yuview Version : 2.6 Upstream Author : Institut für Nachrichtentechnik * URL : https://github.com/IENT/YUView * License : GPL-3+ with OpenSSL exception Programming Lang: C++ Description : QT based YUV player with an advanced analytic toolset YUView is a YUV player and analysis tool. However, it can do so much more: * simple navigation/zooming in the video * support for a wide variety of YUV formats using various subsamplings and bit depts * support for raw RGB files, image files and image sequences * direct decoding of raw h.265/HEVC bitstreams with visualization of internals like prediction modes and motion vectors and many more * interface with visualization for the reference software decoders HM and JEM * support for opening almost any file using FFmpeg * image comparison using side-by-side and comparison view * calculation and display of differences (in YUV or RGB colorspace) * save and load playlists * overlay the video with statistics data
Bug#961331: ITP: insilicoseq -- A sequencing simulator producing realistic illumina reads
Package: wnpp Severity: wishlist Owner: Sao I Kuan * Package name: insilicoseq Version : 1.4.6 Upstream Author : Hadrien Gourle * URL : http://github.com/HadrienG/InSilicoSeq * License : Expat Programming Lang: Python Description : A sequencing simulator producing realistic illumina reads Primarily intended for simulating metagenomic samples, it can also be used to produce sequencing data from a single genome. . InSilicoSeq is written in python, and use kernel density estimators to model the read quality of real sequencing data. . InSilicoSeq support substitution, insertion and deletion errors. If you don't have the use for insertion and deletion error a basic error model is provided. This package is a dependency of idseq-bench (#956033) and will be team-maintained with Debian Med Packaging Team.
Bug#961342: ITP: libmu-tiny-perl -- minimal variant of Mu
Package: wnpp Owner: gregor herrmann Severity: wishlist X-Debbugs-CC: debian-devel@lists.debian.org, debian-p...@lists.debian.org * Package name: libmu-tiny-perl Version : 0.01 Upstream Author : mst - Matt S. Trout (cpan:MSTROUT) * URL : https://metacpan.org/release/Mu-Tiny * License : Artistic or GPL-1+ Programming Lang: Perl Description : minimal variant of Mu Mu::Tiny is the bare minimum subset of Mu, a wrapper around Moo, the Minimalist Object Orientation library. Mu::Tiny supports read-only attributes and lazy builders. The package will be maintained under the umbrella of the Debian Perl Group. -- Generated with the help of dpt-gen-itp(1) from pkg-perl-tools. signature.asc Description: Digital Signature
Re: Survey: DebConf20 and COVID-19
On 23/05/2020 14:05, Antonio Terceiro wrote: > Dear Debian community, > > Back when the COVID-19 outbreak became a global issue, we considered > whether to cancel or postpone DebConf20. At the time we had very little > evidence about what the future might look like, so we decided to come to > a decision by the beginning of June. It's time for us to make that > decision, to keep or cancel the conference. So, we are trying to gather > as much information as we can. > > Please provide your input through the following survey: > > https://surveys.debian.net/index.php?r=survey/index&sid=832462&lang=en > Thanks for this and have filled in the survey. Paul
Bug#961348: ITP: sphinx-tabs -- Tabbed views for Sphinx
Package: wnpp Severity: wishlist Owner: Pierre-Elliott Bécue * Package name: sphinx-tabs Version : 1.1.13 Upstream Author : Alex Collins * URL : https://github.com/djungelorm/sphinx-tabs * License : MIT Programming Lang: Python Description : Tabbed views for Sphinx Sphinx Tabs is a Sphinx extension that allows one to create tabbed content in a Sphinx documentation built in HTML. The current features are: - Simple tabs - Groupped tabs (synchronize the tabs between multiple areas of the page) - Code tabs This package is a documentation requirement for python-coverage 5, and provides features not built in the current sphinx releases. It would be maintained in DPMT.
Bug#961349: ITP: sphinx-rst-builder -- A Sphinx builder for rST (reStructuredText) files
Package: wnpp Severity: wishlist Owner: Pierre-Elliott Bécue * Package name: sphinx-rst-builder Version : 0.0.3 Upstream Author : David Fritzsche * URL : https://github.com/davidfritzsche/sphinx-rst-builder * License : BSD-2-Clause Programming Lang: Python Description : A Sphinx builder for reST (reStructuredText) files Sphinx extension to build reST (reStructuredText) files. This extension is in particular useful to use in combination with the autodoc extension to automatically generate documentation for use by any rst parser (such as the GitHub wiki). In itself, the extension is fairly straightforward – it takes the parsed reST file from Sphinx and outputs it as reST. This library is needed to build python-coverage 5.1's doc and would be maintained under the DPMT
Bug#961358: ITP: vf1 -- command-line gopher client
Package: wnpp Severity: wishlist Owner: Ryan Kavanagh * Package name: vf1 Version : 0.0.11 Upstream Author : Solderpunk * URL : https://github.com/solderpunk/VF-1/ * License : BSD Programming Lang: Python 3 Description : command-line gopher client VF-1 is a full-featured gopher client. Its features include * Bookmarking * Configurable MIME-type handlers * line wrapping * TLS support * visiting a queue of links (the "tour" feature) * Veronica search vf-1 has been my primary gopher client for close to a year now. I intend to package it under the PAPT umbrella. -- |)|/ Ryan Kavanagh | GPG: 4E46 9519 ED67 7734 268F |\|\ https://rak.ac | BD95 8F7B F8FC 4A11 C97A signature.asc Description: PGP signature
Re: DebConf20 registration is now open (with caveats)
On Thu, May 21, 2020 at 10:44:01PM +0200, Daniel Lange wrote: > [1]: https://wiki.debian.org/DebConf/20/Faq This says: > The deadline for deciding on postponing, cancelling or changing the > format of the conference is June 8th. The announcement says: > To request bursaries (sponsorship) for food, accommodation, or travel, > you must be registered by Sunday, May 31st 2020. After this date, new > bursary applications won’t be considered. I'm perplexed by the deadline for the bursaries being earlier than the date in which there'll be a decision about what the format of the conference will be like. The call for registration implies that one would be registering to a similar format of conference as the previous years. As such, I will pass on the registration, and incidentally I resent that this pidgeonholes me as "the only thing you want to do is lay low". Can you however confirm that if on the 8th of June the format of the conference will change into something that one would instead feel motivated to attend, and such format would still requires expenses for which one could use a bursary, then the bursaries deadline will be extended? Otherwise, what I see is that you are effectively forcing people who would like to attend *some* form of DebConf, and aren't sure of their financial means, to apply to something they can't participate, in order not to lose the possibility of being funded for something they would like to. Enrico -- GPG key: 4096R/634F4BD1E7AD5568 2009-05-08 Enrico Zini signature.asc Description: PGP signature
Bug#961371: ITP: due -- Wrapper tool to create and run Docker container software build environments.
Package: wnpp Severity: wishlist Owner: adoyle * Package name: due Version : 1.3.1 Upstream Author : Alex Doyle * URL : https://github.com/CumulusNetworks/DUE * License : MIT Programming Lang: Bash Description : Wrapper tool to create and run Docker container software build environments. Dedicated User Environment (DUE) is a framework for creating preconfigured build/development environments in Docker containers. It serves two primary purposes: 1 - Maintains configurations for creating Docker images for any build environment, using any architecture of any Debian based release it can find an image for. For example, the Open Network Install Environment (https://github.com/opencomputeproject/onie) currently builds on Debian 8 and 9, but requires some Backports packages, and a program that isn't packaged for Debian. DUE maintains a configuration to get all of that added when the Docker image is created so ONIE can 'just build'. Apart from not requiring the end user to have to configure the build environment, it also allows all developers to use the same build environment when debugging - regardless of where they happen to be. 2 - It goes beyond 'just using a Dockerfile' by using a launcher application that supplies runtime configuration to Docker for the Docker images it has created. Apart from reducing typing and being smart about the containers that it runs (ex: containers building Debian packages mount the host directory _above_ the build directory so the resulting .debs aren't stored in the container), DUE preserves the user's identity in the container by creating an account for them with their user ID, and mounting their home directory so they can access their .config files. This creates a less intrusive development environment when the user is in a build/test/debug cycle. While the above are the most important features DUE provides, there are a lot more ways it makes using different development configurations easier, which are documented in the Readme.md (https://github.com/CumulusNetworks/DUE/blob/master/README.md) I also created a tutorial video using DUE to build ONIE as part of a talk I gave at OpenCompute here: https://www.youtube.com/watch?v=-5onRbZA0QQ&feature=youtu.be History: DUE came out of work I did at Cumulus Networks to provide build environments for teams of engineers building packages for Cumulus' Jessie and Buster based releases of Cumulus Linux. When I took over as ONIE Project Lead, I saw the opportunity to use it to create a standard way of setting up build environments for ONIE and any other software projects. Cumulus saw the value in any developer being able to use it and DUE was open sourced under the MIT license. Q&A: Why is this package useful/relevant? See above. Is it a dependency for another package? No. It does require a version ( Debian or upstream ) of Docker to work though. Do you use it? All. The. Time. Building packages at work, building ONIE, and if I just need an environment to quickly test configuration changes. This 'dogfooding' has provided insight into fixing program behaviors that initially seemed okay, and then became irritating through repeated use. If there are other packages providing similar functionality, how does it compare? I looked around for quite a while before starting on DUE ( why reinvent the wheel?), but couldn't find anything that had the combination of: - Consistent, user friendly interface - Easy build environment configuration - And support for Debian derivatives ...that I was looking for. I think the closest software to this would be using schroots, and while they can be functionally the same, the end user experience, especially for users that are new to Debian ( or are trying to build code that partially exists outside the Debian ecosystem ) has less of a learning curve, and is faster to set up. How do you plan to maintain it? I will be updating the upstream source and doing the work to make sure it is Debian compliant. Are you looking for co-maintainers? Not at the moment. Do you need a sponsor? Yes, as I am not a Debian Developer ( in the official sense, anyway :) ) Thank you for your consideration, Alex Doyle
Re: DebConf20 registration is now open (with caveats)
Hi Enrico, Am 23.05.20 um 18:41 schrieb Enrico Zini: I'm perplexed by the deadline for the bursaries being earlier than the date in which there'll be a decision about what the format of the conference will be like. That's because we need some time to evaluate bursary requests and if we give people approval too late, they will be unable to apply for Visa and get reasonable flights. So we'd exempt people that need a Visa for Israel inadvertently. The bursary decisions are scheduled to be announced as soon as possible after an eventual "go ahead" decision for the physical conference and the availability of an approved conference budget. The call for registration implies that one would be registering to a similar format of conference as the previous years. If you don't want to attend a physical conference, that is the right thing to do. We are currently only collecting registrations from people that are in the region or want to fly to Israel and estimate themselves that they will be likely be allowed to do so in August. Can you however confirm that if on the 8th of June the format of the conference will change into something that one would instead feel motivated to attend, and such format would still requires expenses for which one could use a bursary, then the bursaries deadline will be extended? An online format will be free of charge for people joining. If a community member needs specific hardware to attend and cannot afford it themselves, there is the normal DPL reimbursement process available. This would apply to the prior Online Mini-DC (End of May) already before DebConf20 (End of August). Kind regards, Daniel
Re: Maven packages in Debian (was Re: Progress in preparing the Bazel Build System for Debian (COVID-19 Biohackathon follow-up))
On Wed, May 13, 2020 at 7:33 PM Thorsten Glaser wrote: > > On Wed, 6 May 2020, Andreas Tille wrote: > > > > Or perhaps we need a webpage or wiki page generated by parsing the > > > Contents file and listing the matching Debian package for each class > > > or, at least, Java package (unless split across multiple packages)… > > > > I remember times when such a web page (actually some autogenerated text > > file) existed which was **extremely** helpful. I wished this would be > > back! > > > > > … I just volunteerd, didn’t I? > > Here you are: > > https://wiki.debian.org/Java/MavenPkgs > > Sponsored by ⮡ tarent, see below. > > This is step 1, the list of all Maven packages ⇒ Debian package name. > It doesn’t go as far as to map Java packages or even classes… yet. > For this I’d have to download all those packages, extract them and > look into the JARs. I’d prefer some central service to offer archive > contents if possible (diffoscope already extracts archives anyway). I have now made a list with package name, the jar files that it provides and the list of class that the jar provides. Not sure where to put that or if it is in an usable format. So, initial version is at: https://drive.google.com/open?id=1A0tnTNofdNFuMwzrxV_HQE6npfpUglcS I think, next I will make a sorted list so that it will be easy to make a diff of what has changed. -- Regards Sudip
Re: Maven packages in Debian (was Re: Progress in preparing the Bazel Build System for Debian (COVID-19 Biohackathon follow-up))
On Sat, 23 May 2020, Sudip Mukherjee wrote: > I have now made a list with package name, the jar files that it > provides and the list of class that the jar provides. This must be scripted/scriptable though… the list for stable is pretty much fixed, but the one for unstable (which is the relevant one for packaging) isn’t and needs to be redone every few weeks at least… > Not sure where to put that or if it is in an usable format. So, > initial version is at: > https://drive.google.com/open?id=1A0tnTNofdNFuMwzrxV_HQE6npfpUglcS Ouch, 33M… methinks this is more suited as a web application. Not all that easy… due to sheer size, at least. bye, //mirabilos -- tarent solutions GmbH Rochusstraße 2-4, D-53123 Bonn • http://www.tarent.de/ Tel: +49 228 54881-393 • Fax: +49 228 54881-235 HRB 5168 (AG Bonn) • USt-ID (VAT): DE122264941 Geschäftsführer: Dr. Stefan Barth, Kai Ebenrett, Boris Esser, Alexander Steeg
Re: DebConf20 registration is now open (with caveats)
On Thu, May 21, 2020 at 10:44:01PM +0200, Daniel Lange wrote: >... > We do suggest that attendees begin making travel arrangements as soon as > possible, of course. Please bear in mind that most air carriers allow > free cancellations and changes. >... Please bear in mind that this is not true. Free cancellation with cash refund if you book now for August but later choose not to travel is not what most air carriers offer (except in fare types that anyway permit it). Typically you are getting in the best case a voucher, sometimes a one-time opportunity to change the date of the flight to the booked destination, and in the worst case travels in August are not covered by "book with confidence" rules of the airline - it is mandatory to read the fine print before booking. cu Adrian
Re: Maven packages in Debian (was Re: Progress in preparing the Bazel Build System for Debian (COVID-19 Biohackathon follow-up))
On Sat, May 23, 2020 at 8:10 PM Thorsten Glaser wrote: > > On Sat, 23 May 2020, Sudip Mukherjee wrote: > > > I have now made a list with package name, the jar files that it > > provides and the list of class that the jar provides. > > This must be scripted/scriptable though… the list for stable is > pretty much fixed, but the one for unstable (which is the relevant > one for packaging) isn’t and needs to be redone every few weeks at > least… It was generated using a script. It will not be a problem to redo every week. > > > Not sure where to put that or if it is in an usable format. So, > > initial version is at: > > https://drive.google.com/open?id=1A0tnTNofdNFuMwzrxV_HQE6npfpUglcS > > Ouch, 33M… methinks this is more suited as a web application. > Not all that easy… due to sheer size, at least. Yes, I was thinking of making a Debian native package for it, the data will be in either sqlite or yaml and then an application to read from it. cmdline will accept either jar or class name and will list the package containing them. And if package name is given then it will list everything that the package contains. Just a thought for now. -- Regards Sudip
