Update reproiner from bookworm to trixie

[yarikoptic]

I would like to update reproiner to newer Debian release, we have a few components which might be affected

reprostim-videocapture "service" - should switch to use the reprostim container

@vmdocua , ATM I think we still have our video grabbers running there not from the containers:

yoh@reproiner:~$ ps auxw -H | grep reprostim
reprost+    1005  0.0  0.0   6932  3416 ?        Ss   Mar20   0:00     /bin/bash /home/reprostim/reprostim/Events/dev_run_loop
reprost+    1006  0.0  0.0   6932  3348 ?        Ss   Mar20   0:00     /bin/bash /data/reprostim/code/reprostim-videocapture-cron
reprost+    1015  0.0  0.0   5460  1044 ?        S    Mar20   0:00       flock -E 0 -e -n /data/reprostim/reprostim-videocapture.lck reprostim-videocapture -d /data/reprostim -f /data/reprostim/logs/2026-03-20T08:55-04:00.log
reprost+    1017  0.8  0.0 395956 14740 ?        Sl   Mar20 574:57         reprostim-videocapture -d /data/reprostim -f /data/reprostim/logs/2026-03-20T08:55-04:00.log
reprost+ 1827812  0.0  0.0   2576   904 ?        S    10:36   0:00           sh -c duct -l NONE -p /data/reprostim/Videos/2026/05/2026.05.05-10.36.50.910--.mkv.duct_ -c none --sample-interval 10 --report-interval 60 ffmpeg -f alsa -ac 2 -thread_queue_size 4096 -i hw:1,0 -f v4l2 -input_format yuyv422 -framerate 60 -video_size 1920x1080 -thread_queue_size 4096 -i /dev/video0 -vaapi_device /dev/dri/renderD128 -vf 'format=nv12,hwupload,setpts=PTS-STARTPTS' -c:v h264_vaapi   -acodec aac -af asetpts=PTS-STARTPTS -metadata comment=7da7c65a-ede8554d-5fa04f78 /data/reprostim/Videos/2026/05/2026.05.05-10.36.50.910--.mkv 2>&1
reprost+ 1827813  0.0  0.0 169416 17544 ?        Sl   10:36   0:00             /usr/bin/python3 /usr/bin/duct -l NONE -p /data/reprostim/Videos/2026/05/2026.05.05-10.36.50.910--.mkv.duct_ -c none --sample-interval 10 --report-interval 60 ffmpeg -f alsa -ac 2 -thread_queue_size 4096 -i hw:1,0 -f v4l2 -input_format yuyv422 -framerate 60 -video_size 1920x1080 -thread_queue_size 4096 -i /dev/video0 -vaapi_device /dev/dri/renderD128 -vf format=nv12,hwupload,setpts=PTS-STARTPTS -c:v h264_vaapi -acodec aac -af asetpts=PTS-STARTPTS -metadata comment=7da7c65a-ede8554d-5fa04f78 /data/reprostim/Videos/2026/05/2026.05.05-10.36.50.910--.mkv
reprost+ 1827814 80.8  0.6 1215356 222544 ?      RLsl 10:36  94:23               ffmpeg -f alsa -ac 2 -thread_queue_size 4096 -i hw:1,0 -f v4l2 -input_format yuyv422 -framerate 60 -video_size 1920x1080 -thread_queue_size 4096 -i /dev/video0 -vaapi_device /dev/dri/renderD128 -vf format=nv12,hwupload,setpts=PTS-STARTPTS -c:v h264_vaapi -acodec aac -af asetpts=PTS-STARTPTS -metadata comment=7da7c65a-ede8554d-5fa04f78 /data/reprostim/Videos/2026/05/2026.05.05-10.36.50.910--.mkv

what do you think it would take to finally start using reprostim-videocapture from the container -- any gotchas? we already have ///repronim/containers there under /data/reprostim/code/containers/ .

/home/reprostim/reprostim/Events/dev_run_loop -- need to be added to container (I think)

auxililary recorder @TheChymera created for curdes. Uses venv ATM. Ideally IMHO we should just include it within reprostim container and use from there and within the same python env (if compatible, I do not think we would run into conflicts)

/data/reprostim/code/manual-annex-sync -- datalad/git-annex

We use (I think uv produced) .venv with git-annex and datalad in it, and that one relies on system /usr/bin/python so we would need to recreate -- I am not sure we would want to run datalad/git-annex from container, but I immediately do not recall "why not" as far system is not too outdated

... anything else @vmdocua which comes to mind?

[vmdocua]

Yes, we have issue to run reprostim-videocapture tool from container rather than using system-wide local installation:

• Adjust code/reprostim-videocapture-cron to use container #237

Events is not included in reprostim package, but exists in GitHub aside, as obsolete code. We need to understand what to do with it - keep as is, or refactor and include somewhere inside reprostim under src. It will have problems with linters, shellcheck, and structure. It need to be reworked and cleaned, provided with tests, update and include into existing RTD docs etc.

Regarding git-annex - we have only git there inside, but may be would be good to install there git-annex and datalad as soon as it heavily used in reprostim runtime environment and configuration.

Maybe other neuroimaging tools and BIDS related software will be necessary to be installed with time if missed to work with NIfTI, DICOMS, BIDS datasets in command line mode.