13:00:40 <FranciscoD_> #startmeeting NeuroFedora 2023-06-05
13:00:40 <zodbot> Meeting started Mon Jun  5 13:00:40 2023 UTC.
13:00:40 <zodbot> This meeting is logged and archived in a public location.
13:00:40 <zodbot> The chair is FranciscoD_. Information about MeetBot at https://fedoraproject.org/wiki/Zodbot#Meeting_Functions.
13:00:40 <zodbot> Useful Commands: #action #agreed #halp #info #idea #link #topic.
13:00:40 <zodbot> The meeting name has been set to 'neurofedora_2023-06-05'
13:00:43 <FranciscoD_> #meetingname neurofedora
13:00:43 <zodbot> The meeting name has been set to 'neurofedora'
13:00:51 <FranciscoD_> #info bot commands: https://fedoraproject.org/wiki/Meeting:Guide#MeetBot_Commands
13:01:04 <FranciscoD_> #info agenda: https://neuroblog.fedoraproject.org/2023/06/05/next-open-neurofedora-meeting-05-June-1300-utc.html
13:01:11 <FranciscoD_> #topic Introductions and roll call
13:01:19 <FranciscoD_> .hello
13:01:22 <zodbot> FranciscoD_: (hello <an alias, 1 argument>) -- Alias for "hellomynameis $1".
13:01:36 <FranciscoD_> .hello ankursinha
13:01:40 <zodbot> FranciscoD_: ankursinha 'Ankur Sinha' <sanjay.ankur@gmail.com>
13:01:52 <FranciscoD_> we wait here for ~5 minutes
13:02:07 <FranciscoD_> @room : meeting just started, please join when convenient
13:02:19 <Penguinpee> .hello gui1ty
13:02:23 <zodbot> Penguinpee: gui1ty 'Sandro .' <gui1ty@penguinpee.nl>
13:02:44 <Penguinpee> .members neuro-sig
13:02:45 <zodbot> Penguinpee: Members of neuro-sig: sagitter, ignatenkobrain, bt0dotninja, zbyszek, sergiopr, blackfile, ankursinha, lbazan, ilgrad, gicmo, alciregi, nerdsville, mhough, music, major, fangq, anilbey, iztokf, aekoroglu, gui1ty, shaneallcroft, hardeborlaa, mairacanal, vanessakris
13:02:48 <Penguinpee> ^^
13:04:01 <Penguinpee> Matrix bridge seems to be working. Not a given these days...
13:06:19 <FranciscoD_> ah, I've stopped trying to use matrix from irc completely now
13:06:25 <FranciscoD_> let's proceed
13:06:38 <FranciscoD_> #topic Tasks from last meeting
13:06:52 <FranciscoD_> #info Last meeting logs are here: https://meetbot.fedoraproject.org/fedora-neuro/2023-05-22/neurofedora.2023-05-22-13.00.html
13:07:16 <FranciscoD_> #info FranciscoD_ update docs to mention the NeuroFedora hashtag for use on mastodon: DONE
13:07:53 <FranciscoD_> #info Docs updated: https://pagure.io/neuro-sig/documentation/c/80628998f923ddd71b38644460a77abea310394e?branch=main
13:08:21 <FranciscoD_> #info website also updated: https://github.com/neurofedora/neurofedora.github.io/commit/976602acfc138247b879c67735e10640d7955698
13:08:57 <FranciscoD_> #info FranciscoD_ open issue/PR in package maintainer docs about re-triggering CI on PRs: PENDING
13:09:00 <FranciscoD_> I forgot about that one
13:09:02 <FranciscoD_> re-assigning
13:09:07 <FranciscoD_> #action FranciscoD_ open issue/PR in package maintainer docs about re-triggering CI on PRs
13:09:45 <FranciscoD_> that's all, last one is about sending out logs etc, all done
13:10:36 <FranciscoD_> #topic Open Pagure tickets
13:10:49 <FranciscoD_> #info any tickets marked as "next meeting": https://pagure.io/neuro-sig/NeuroFedora/issues?status=Open&tags=S%3A+Next+meeting
13:10:54 <FranciscoD_> #info No tickets to discuss this week
13:11:14 <FranciscoD_> #topic Neuro-sig package health check
13:11:20 <FranciscoD_> #info Our packaging dashboard is at: https://packager-dashboard.fedoraproject.org/dashboard?groups=neuro-sig
13:12:46 <FranciscoD_> packages look pretty good, only a few FTBFS bugs
13:15:19 <Penguinpee> dashboard is still loading here...
13:15:31 <FranciscoD_> #info FTBFS: python-pyswarms: https://bugzilla.redhat.com/show_bug.cgi?id=2210608 -> issue and PR already filed upstream
13:15:39 <FranciscoD_> oo, that's slow---loaded here fine
13:15:55 <FranciscoD_> let me refresh too, just to make sure I'm not seeing a cached copy
13:17:00 <Penguinpee> It's loaded now.
13:17:59 <FranciscoD_> cool!
13:18:13 <Penguinpee> Quite a few FTBFS
13:19:16 <FranciscoD_> a lot of them are on s390x, which we exclude, so don't look at those
13:19:26 <Penguinpee> Quite a few specific to only certain branches. Smells like some update broke stuff.
13:20:34 <FranciscoD_> yeh---how does stuff start to go FTBFS in F37? :(
13:20:54 <Penguinpee> Outages? Aka red herrings?
13:20:58 <FranciscoD_> hopefully the versions in the repos are still functional---no FTIs
13:21:09 <FranciscoD_> could be, or  dep breakage, but that would cause an FTI
13:21:17 <FranciscoD_> it's hard to tell without trying a test build
13:21:40 <Penguinpee> I've seen one FTBFS without any dep changes. That must have been a failed builder.
13:22:07 <FranciscoD_> (or looking at logs)
13:22:57 <Penguinpee> Yeah. Normally I would offer to go through them, trying to determine a common cause, but I'll be on the road starting Thursday.
13:23:26 <FranciscoD_> I think as long as they're functional, that's fine, espcially for already released branches
13:23:34 <FranciscoD_> we won't be rebuilding them unless they get a new version etc
13:23:58 <FranciscoD_> and in some cases, we won't update them because it'll be a major update
13:24:17 <FranciscoD_> python-nibabel is one example---FTBFS for F37, but that's still on 3.x, and F38+ is on 5.x
13:24:27 <FranciscoD_> we won't push a 5.x update to F37 now
13:24:27 <Penguinpee> "BuildrootError: could not init mock buildroot, mock exited with status 1; see build.log or root.log for more information" <-- That's a failing builder.
13:24:46 <FranciscoD_> ah, yeh, that's clearly an infra issue
13:25:00 <FranciscoD_> https://bugzilla.redhat.com/show_bug.cgi?id=2171714 -> non responsive maintainer from the looks of it
13:25:27 <Penguinpee> Maybe just leave as is and look again in two weeks time. Provided there aren't any more planned or unplanned outages.
13:25:36 <FranciscoD_> +1
13:26:26 <Penguinpee> .bug 2171714
13:26:28 <zodbot> Penguinpee: 2171714 – rubygem-nifti: FTBFS in Fedora rawhide/f38 - https://bugzilla.redhat.com/2171714
13:26:40 <Penguinpee> ^^ Are you going to take over or retire?
13:27:22 <FranciscoD_> let me see what's up with upstream, if it's still maintained, we could keep it I guess
13:27:51 <Penguinpee> Unless it's a leave package. Depends also on how many people are using it.
13:27:54 <FranciscoD_> https://rubygems.org/gems/nifti -> last release was 2014?
13:28:05 <Penguinpee> s/leave/leaf/
13:28:48 <FranciscoD_> looks unmaintained/inactive: https://github.com/brainmap/nifti
13:28:54 <FranciscoD_> last commit is also on 2014
13:28:57 <FranciscoD_> s/on/in/
13:28:58 <Penguinpee> 2014 - that's the stone age in software development cycles. 🦣
13:29:31 <Penguinpee> Drop it like it's hot...
13:29:39 <FranciscoD_> yeh
13:29:48 <FranciscoD_> we can't orphan it, I don't think---we only have commit access
13:30:09 <FranciscoD_> I may be able to do it as a provenpackager though?
13:30:11 <FranciscoD_> let me try
13:30:25 <Penguinpee> It will get orphaned eventually, if that bug stays open.
13:30:40 <FranciscoD_> yeh, I guess we let it get automatically orphaned
13:30:50 <FranciscoD_> no way to remove neuro-sig from commit access, is there?
13:31:58 <FranciscoD_> removed us from the bug in the meantime
13:32:30 <FranciscoD_> #info rubygem-nifti is unmaintained upstream, last commit from 2014---neuro-sig will not carry it any more, nor fix FTBFS. Let is get automatically retired.
13:32:43 <Penguinpee> Nope. Only the main-admin can do that. Can we deprecate, though?
13:33:08 <Penguinpee> Orphaning in the Web UI didn't work (lack of permissions).
13:33:14 <FranciscoD_> yeh, same here
13:33:24 <FranciscoD_> I don't think we can do anything without Ilya's help
13:33:34 <FranciscoD_> .fasinfo ilgrad
13:33:36 <zodbot> FranciscoD_: User: ilgrad, Name: Ilya Gradina, Email: ilya.gradina@gmail.com, Creation: 2015-01-09T23:15:42, IRC Nicks: None, Timezone: Europe/Moscow, Locale: en, GPG Key IDs: None, Status: None
13:33:39 <zodbot> FranciscoD_: Groups: fedora-contributor, fedorabugs, neuro-sig, packager
13:33:41 <FranciscoD_> I don't think they've been active in ages, though
13:33:52 <FranciscoD_> I can e-mail them and ask I guess
13:34:16 <Penguinpee> Maybe initiate unresponsive maintainer procedure? It's a PITA, I know.
13:34:26 <FranciscoD_> Yeh, I think we should
13:34:34 <FranciscoD_> I'll do the checks and get it started
13:34:55 <FranciscoD_> #action FranciscoD_ start non-responsive maintainer checks for Ilya (FAS: ilgrad)
13:36:01 <FranciscoD_> Should Koschei not also file bugs for packages? is there some config that we haven't turned on?
13:36:30 <Penguinpee> I'm not sure how that is meant to work.
13:36:52 <Penguinpee> I can ask around, read.
13:36:56 <FranciscoD_> I know one can go to koschei and file bugs manually, not sure I understand why it doesn't file bugs automatically
13:37:53 <FranciscoD_> I think it's not meant to file bugs, just notify
13:37:54 <FranciscoD_> https://docs.fedoraproject.org/en-US/infra/sysadmin_guide/koschei/ etc.
13:38:24 <Penguinpee> Could we have these notifications send to the list for awareness?
13:38:56 <FranciscoD_> I'm not sure. I think one can enable notifications personally: https://fedoraproject.org/wiki/Koschei#Reporting_FTBFS_bugs_through_Koschei
13:39:04 <FranciscoD_> as in for themselves, not sure if it can be done to the ML
13:39:45 <Penguinpee> I'll ask in #admin. Please actiion to me.
13:39:55 <FranciscoD_> awesome
13:40:17 <FranciscoD_> #action Penguinpee ask around if Koschei can be made to send notifications to the ML or automatically file bugs
13:41:04 <FranciscoD_> #info Few FTBFS bugs but lots of FTBFS reports from Koschei: please take a look at the dashboard and fix packages if you have a minute
13:44:22 <FranciscoD_> #info packages with FTBFS reports: COPASI, python-mne, arbor, bionetgen, python-neatdend, python-neo, ctk, python-nibabel, python-nilearn, python-nipy, genesis-simulator, python-pandas, getdp, highfive, libsonata, python-pynn, python-pynetdicom, mcpanel, morphio, munge, neuron, octave-dicom, python-pyswarms, python-astor, python-bluepyopt, python-pyunicorn, python-chaospy, python-shapely, pyton-cyipopt, python-deap, python-dipy,
13:44:23 <FranciscoD_> python-tabulate, python-toposort...
13:44:28 <FranciscoD_> that's quite a few
13:45:12 <FranciscoD_> #info FTBFS reports for packages on s390x may be spurious---the packages may exclude s390x as a buildarch
13:45:49 <FranciscoD_> #info about 10 packages have new versions available: please update and open PRs if you can
13:46:04 <FranciscoD_> I think that's all for packages
13:46:48 <FranciscoD_> Penguinpee: did we decide to close the CVEs on tiff? I see loads of them still open
13:47:32 <Penguinpee> The earlier one, yes. But there was another one after that. I didn't dig into it. Just scratched the surface.
13:48:00 <FranciscoD_> ah, cool, no worries. I'd expect it to be the same given the very very old tiff that neuron bundles
13:48:06 <Penguinpee> Shall I take a look and open tickets in Pagure or ask on the ML?
13:48:46 <Penguinpee> Yeah, the bundled TIFF is way behind and all the CVEs appeared to be on recently added features.
13:49:21 <Penguinpee> But I'm not a developer. So, it's a bit like shooting in the dark for me...
13:50:55 <FranciscoD_> for tiff?
13:51:07 <FranciscoD_> maybe we start with a ticket on our tracker and let folks chime in
13:51:33 <FranciscoD_> neuron is such a niche piece of software that CVEs in it aren't really as important as something that's more generally used
13:52:07 <FranciscoD_> #topic Open package reviews check
13:52:24 <FranciscoD_> #info Our review ticket tracker is here: https://bugzilla.redhat.com/show_bug.cgi?id=fedora-neuro (all new review should block this bug)
13:52:59 <FranciscoD_> #info No new review tickets needing reviews
13:53:13 <FranciscoD_> #topic CompNeuro lab compose status check for Fedora 39/rawhide.
13:53:13 <FranciscoD_> #info Compose is ticking along nicely: https://koji.fedoraproject.org/koji/packageinfo?packageID=30691
13:53:16 <FranciscoD_> #info Neuroscience query of the week
13:53:21 <FranciscoD_> #undo
13:53:21 <zodbot> Removing item from minutes: INFO by FranciscoD_ at 13:53:16 : Neuroscience query of the week
13:53:28 <FranciscoD_> #topic Neuroscience query of the week
13:54:45 <FranciscoD_> there was this paper in Science, which (as I understand it) claimed to have been able to record/detect membrane voltages in neurons using fMRI: https://www.science.org/doi/10.1126/science.abh4340
13:55:21 <FranciscoD_> that's a massive breakthrough because at the moment, to record neuronal voltages, one has to use very complex techniques like calcium imaging with expensive/complex microscopes
13:56:02 <FranciscoD_> recently though, a group posted a pre-print noting that they were unable to replicate these results: https://pubpeer.com/publications/0EF432E4E7D84352E9B582CEC6DF07
13:57:19 <FranciscoD_> so that's interesting---shows how important replication of scientific results is
13:57:50 <FranciscoD_> #info https://www.science.org/doi/10.1126/science.abh4340 + https://www.biorxiv.org/content/10.1101/2023.05.26.542419v1
13:58:08 <FranciscoD_> #topic next meeting
13:58:14 <FranciscoD_> 2 weeks, same time I gues
13:58:36 <Penguinpee> What voltages are we talking about? mV or even 𝛍V?
13:59:02 <Penguinpee> In two weeks I'll be back from vacation. Should be able to make it.
13:59:58 <FranciscoD_> membrane potentials are usually in mV
14:00:46 <FranciscoD_> https://en.wikipedia.org/wiki/Action_potential#Process_in_a_typical_neuron -> got a graph there
14:01:27 <Penguinpee> Nice. I'll take a look.
14:01:48 <FranciscoD_> here's an interactive tutorial with a general "hodgkin-huxley" neuron: https://www.opensourcebrain.org/projects/hodgkin-huxley-tutorial?explorer=https%3A%2F%2Fraw.githubusercontent.com%2Fopensourcebrain%2Ftutorials%2Fdevelopment%2Fmodels%2FhodgkinHuxley%2FGEPPETTO.json
14:02:07 <FranciscoD_> sources here: https://github.com/openworm/hodgkin_huxley_tutorial
14:02:20 <Penguinpee> I like the domain name...
14:02:39 <FranciscoD_> :D
14:02:45 <Penguinpee> Does it differ from a proprietary brain?
14:02:47 <FranciscoD_> the lab I work at maintains it
14:02:50 <FranciscoD_> XD
14:03:06 <FranciscoD_> it's intended to push open neurocience
14:03:14 <FranciscoD_> so that folks share their data/models etc
14:03:30 <FranciscoD_> https://docs.opensourcebrain.org/Landing.html etc.
14:04:00 <FranciscoD_> #info Next meeting in 2 weeks at same time
14:04:14 <FranciscoD_> let's close the meeting, we're a few minutes over today
14:04:16 <FranciscoD_> #endmeeting