Debian Med Sprint 2025
An in-person meetup of volunteers to create and update packages of bioinformatics and other biomedical software in Debian as part of the DebianMed team.
If you would like to join our small meeting for bug squashing, or if you are a newcomer looking to get in touch with Debian people, you are perfectly welcome to add your name to the list of attendees as well!
Location, Date
- when: February 15th and 16th, 2025
- Venue will open at ~9AM, please ring the bell outside building number 22 ("DCSO" 2nd floor, main reception). If no one opens, please call organiser (+49 (0)151 54150155)
Venue
We will have access to one large (~15 people) and one small (~ 5 people) meeting room, so working in separate groups from time to time is definitely possible. A comfortable open space with coffee machine for socialising and relaxing is available.
Network and Wifi
There will be only public WiFi provided by DCSO. Sorry, no wired ethernet will be available.
Getting there
Berlin can be easily reached from within Germany using the DB train system (Berlin Hbf or Berlin-Südkreuz) or Flixbus long-distance bus service (Berlin ZOB or Alexanderplatz). There is also a major international airport: Berlin Brandenburg (BER) with good public transport connections to the rest of the city for 3.80 € per trip: https://ber.berlin-airport.de/en/orientation/getting-here/public-transport.html
The venue is easily reachable by S-Bahn (S1, Ringbahn S41/S42/S46) via Schöneberg station. There are also a couple of buses running (M46, 248). See https://sbahn.berlin/fahren/bahnhofsuebersicht/schoeneberg/ for more details. Südkreuz station (https://sbahn.berlin/fahren/bahnhofsuebersicht/suedkreuz/) would also be an alternative with a bit of walking.
Please avoid coming by car in favour of the environment and limited parking.
Accommodation
There are a variety of hotels and hostels just a couple of S-Bahn stations from the venue, e.g. near Potsdamer Platz or Anhalter Bahnhof: https://www.google.com/maps/search/hotels+near+euref-campus/@52.4884989,13.3415758,14z/data=!3m1!4b1!4m5!2m4!5m3!5m2!4m1!1i2
Examples:
Nearest and good experience: https://www.google.com/maps/place/the+niu+Dwarf/@52.4829201,13.3519029,16.42z
Within walking distance: https://www.google.com/maps/place/Hotel+Sch%C3%B6neberg/@52.4838617,13.3538017,17.5z/data=!4m8!3m7!1s0x0:0x7cbdc6094eb22597!5m2!4m1!1i2!8m2!3d52.4849925!4d13.3545083
Few S-Bahn stations away: https://www.google.com/maps/place/Hotel+Novotel+Suites+Berlin+City+Potsdamer+Platz/@52.5048022,13.3817308,16.54z/data=!4m8!3m7!1s0x0:0x1c4720a47f155c71!5m2!4m1!1i2!8m2!3d52.50457!4d13.38312 and others in the area
On campus: https://euref.de/en/euref-campus_en/campus-life/#overnight (only few spaces available, might go quickly)
Participants
Please add yourself to the list below if you wish to attend. There will be space for ~15 participants.
Please take care to register up to 2-3 days before the meeting, as we will need to prepare visitor passes and arrange the stay with DCSO's physical security provider.
No |
Name |
confirmed |
booked accom. |
Affiliation |
Country |
Arrival at |
Departure at |
|
1 |
Sascha Steinbiss |
Yes |
|
Debian, DCSO |
DE |
2025-02-15T09:00 |
2025-02-16T19:00 |
|
2 |
Andreas Tille |
Yes |
Done |
Debian |
DE |
2025-02-14 |
2025-02-17 |
|
3 |
Michael R. Crusoe |
Yes |
Local |
Debian |
DE |
|
|
|
4 |
Pierre Gruet |
Yes |
Done |
Debian |
FR |
2025-02-14T18:00 |
2025-02-16T19:00 |
|
5 |
Étienne Mollier |
Yes |
Done |
Debian, Viridien |
FR |
2025-02-14T18:00 |
2025-02-17T07:00 |
|
6 |
Karsten Schöke |
No |
Local |
|
DE |
|
|
Food
The venue is located in the "Rote Insel" district of Berlin (https://en.wikipedia.org/wiki/Rote_Insel) with many suitable and affordable lunch spots, e.g. good Korean and Indian restaurants, a South German Wirtshaus within very short walking distance, and various fast food options (with vegetarian menu items). There is also a nice Vietnamese restaurant right next to the S station Schoneberg (Viet Kitchen, Dominicusstraße 54, 10827 Berlin) with many vegan options.
Bring
Please consider bringing the following items:
- computers
- adaptors for EU power plugs, if necessary
- power strips
- energy bars 🍫
- video adapters/cables maybe?
Agendas
Andreas
- If there are newcomers I'm fine to teach packaging
- Provide some new insights into Debian I've gathered in the last 10 months
- Fix bugs
- Work with Pierre on a talk
- General discussion about a vision. I have the feeling we are just keeping the status quo since several years.
Michael
- RC bugs ; package version updates
Packages that use header-only libraries should document which version their binary packages were built with using Static-Built-Using: dh_builtusing:libsimde-dev or similar (along with adding dh-sequence-builtusing to their build dependency list)
Debian-Med team-maintained C/C++ header-only libraries (that are in the build-depends lists of other packages)
- libargs-dev
- libatomicbitvector-dev
- libbioparser-dev
- libbiosoup-dev
- libhnswlib-dev
- libips4o-dev
- librandom123-dev
- libreaderwriterqueue-dev
- libsavvy-dev
- libseqan2-dev
- libseqan3-dev
- libsimde-dev
- tao-json-dev
- tao-config-dev
- libtsl-hopscotch-map-dev
- libtoml11-dev
- libshrinkwrap-dev
Pierre
- Get scala back into testing to have our rdeps shipped into trixie
- Get sumaclust and genomicsdb into testing
- Fix bugs
- Work with Andreas on a talk
Sascha
- Work on community talk
- Find some time to do housekeeping on packages
Étienne
- Finish ongoing work on dcmtk
- Package globus-compute-common and globus-compute-sdk as part of newer python-parsl upgrades
- Package python_calamine as part of newer augur upgrades
- Continue tackling bugs.
Reports
Pierre
- Fixing #1091067 in scala
- Updating json-simple, documenting why we stay at version 2.x
- Working on #1092841 in genomicsdb
- Uploading new upstream version of jalview, snpeff
- Having genomicsdb, pilon, rockhopper, snpsift, sumaclust migrate to testing
- Bug triaging: #1088119, #1088129
- Fixing CVE in json-smart.
Sascha
- Finished work community talk up to ~80% completion.
- New upstream versions and bug fixes for python-filelock, python-codegen, and other Python libs.
- Fixed #1092702 in ruby-rgfa.
- Reviewed and discussed paper with Steffen.
- Many other discussions with Andreas, Michael about their plans and projects.
Maybe other things I missed
Étienne
dcmtk transition coordination in #1095266, the package was confirmed in a state of being migratable to unstable. Thanks to everyone involved!
Alas, I did not manage to focus on the newer Python modules that needed to be wrapped up.
- (Release Critical) Bugs tackling:
Bugs closed: #1095369, #1095396, #1095338, #1095798, #1092908 and #1091151
- Triage:
- #1094895: gathered debug information and forwarded upstream
- #1095090: related to upstream ticket
- #1091721: confirmed
- #1091257: severity reduced
- In addition to the initial agenda:
- Newer upstream version:
- castxml 0.6.11
- hyphy 2.5.68
- python-py2bit 0.3.3
- python-pyspoa: freshened copyright information; triggered a discussion upstream to check whether the choice of BSD-4-clause was an oversight due to the practical problems of the license
Did some keysigning
- Newer upstream version:
Andreas
- Fix autopkgtest in spades
- Fixing bug #1067271 in freebayes by also upgrading libvcslib
- Fixing bug #1088745 in htscodecs
- Fixing bug #1093231 in python-pbcommand
- Fixing bug #1078626 libbio-procedural-perl
- Report issues to qiime upstream
- New upstream version of sniffles
- Fixing bug #1094701 of pairtools
- Upload python-loky to new as a precondition for python-cogent
- Fixing bugs #1091516, #1063195 of vtk-dicom
- Reviewed and discussed paper with Steffen
- Report about DPL work
- Enjoy working together with team members
Acknowledgements
The sprint has been possible thanks to:
The venue is provided by DCSO GmbH.