13:00:42 <FranciscoD_> #startmeeting NeuroFedora - 2022-08-15
13:00:42 <zodbot> Meeting started Mon Aug 15 13:00:42 2022 UTC.
13:00:42 <zodbot> This meeting is logged and archived in a public location.
13:00:42 <zodbot> The chair is FranciscoD_. Information about MeetBot at https://fedoraproject.org/wiki/Zodbot#Meeting_Functions.
13:00:42 <zodbot> Useful Commands: #action #agreed #halp #info #idea #link #topic.
13:00:42 <zodbot> The meeting name has been set to 'neurofedora_-_2022-08-15'
13:00:47 <FranciscoD_> #meetingname neurofedora
13:00:47 <zodbot> The meeting name has been set to 'neurofedora'
13:01:14 <digua> hello?
13:01:19 <FranciscoD_> #topic Agenda
13:01:25 <FranciscoD_> #info New introductions and roll call
13:01:32 <FranciscoD_> hi digua !
13:01:42 <FranciscoD_> #info Tasks from last meeting.
13:01:51 <tg-fedneuro> <t​hemasch> Hello!
13:01:59 <FranciscoD_> #info Open Pagure tickets
13:02:05 <FranciscoD_> #info Package health check
13:02:15 <FranciscoD_> #info Open package reviews check
13:02:24 <FranciscoD_> #info CompNeuro lab compose status check for Fedora 36/37
13:02:36 <FranciscoD_> #info Neuroscience query of the week
13:02:49 <FranciscoD_> #info Next meeting day, and chair
13:02:50 <FranciscoD_> #info Open floor
13:03:01 <FranciscoD_> Let's start with the first item
13:03:17 <FranciscoD_> #topic New introductions and roll call
13:03:18 <FranciscoD_> hi @themasch!
13:03:18 <FranciscoD_> sorry, I can't chair folks over the bridge
13:03:34 <FranciscoD_> :(
13:03:35 <FranciscoD_> #chair digua
13:03:35 <zodbot> Current chairs: FranciscoD_ digua
13:03:59 <FranciscoD_> #chair digua
13:03:59 <zodbot> Current chairs: FranciscoD_ digua
13:04:03 <FranciscoD_> #chair music
13:04:03 <zodbot> Current chairs: FranciscoD_ digua music
13:04:03 <music[m]> .hello music
13:04:05 <zodbot> music[m]: music 'Benjamin Beasley' <code@musicinmybrain.net>
13:04:06 <FranciscoD_> .hello ankursinha
13:04:08 <zodbot> FranciscoD_: ankursinha 'Ankur Sinha' <sanjay.ankur@gmail.com>
13:04:42 * FranciscoD_ thinks the bot may be slightly slow
13:04:56 <FranciscoD_> if there's anyone here that I haven't chaired, please let me know too
13:05:21 <FranciscoD_> you can use the bot commands when you are chaired, that's all
13:06:16 <FranciscoD_> I'll wait another few minutes for folks to join us, and then proceed with the agenda
13:06:24 <FranciscoD_> please feel free to introduce yourselves in the meantime :)
13:06:43 <FranciscoD_> (especially if this is your first meeting :))
13:07:01 <tg-fedneuro> <t​hemasch> This is my first time on the meeting, so I don´t know what should I do. So,  I'm going to stay here to learn what you do
13:07:20 <FranciscoD_> sounds good @themasch :)
13:07:41 <FranciscoD_> would you like to tell us a little about yourself so the community can get to know you a little better ?
13:08:52 <NitochondriaC[m]> I’m a biology student with an interest in neuroscience, so I’m here with a friend to see how computer science and neuroscience can collaborate
13:08:55 <acyanbird[m]> Hi I'm just a computer student come with my friend Nitochondria C , I' familiar with Linux and open source
13:09:27 <FranciscoD_> That's awesome, welcome to the community Nitochondria C acyanbird
13:09:42 <FranciscoD_> we have a few new folks, so maybe i'll give a short summary of what we do
13:10:03 <tg-fedneuro> <t​hemasch> I'm a software developer, I've been using Fedora for almost 15 years and I would love to know more about Neuro Fedora. I love to learn about Neuroscience and Conscience.
13:10:05 <FranciscoD_> We're a sub-team in the Fedora Linux community that is interested in Neuroscience
13:11:49 <FranciscoD_> There's a lot of software out there that neuroscience heavily relies on---from use in experiments (calcium imaging/fMRI/electrophysiology etc. etc. ), to data analysis (lots of ML and statistics), to modelling (theoretical modelling at different levels---from high level behavioural models all the way to biophysically detailed neuron modelling and even lower---sub-cellular scales)
13:12:24 <FranciscoD_> And of course, there's just a lot of general FOSS (Free/Open Source Software) out there
13:13:20 <FranciscoD_> What the Fedora community does is take a lot of this software and build a Linux "distribution"---which is just a whole operating system (OS) with all its components---the kernel, different hardware support, and lots of applications for users (and all the underlying libraries/APIs that are required for them to work)
13:13:34 <FranciscoD_> so the Fedora community doen't develop all the software that's included in a Fedora Linux release
13:14:00 <FranciscoD_> we are "downstream"---so we take software that "upstream" developers create and build + package it for use in Fedora
13:14:05 <FranciscoD_> The Neuro-sig does the same thing, only, we focus on software that's neuroscience related
13:14:28 <FranciscoD_> An example is our "comp-neuro" OS image---it's just a Fedora Linux workstation image with lots of neuroscience related software packed in
13:15:01 <FranciscoD_> so, you can download our comp-neuro OS image, install it on your computer, and you have lots of software for computational modelling already available to you
13:15:09 <FranciscoD_> https://labs.fedoraproject.org/en/comp-neuro/
13:15:47 <FranciscoD_> we want to also have similar Fedora Linux "flavours" for other aspects of neuroscience, like data analysis, experiments, and so on. So as we get more and more software included in Fedora, we'll make more "all inclusive" OS images too
13:16:09 <FranciscoD_> I think that's a short summary---any questions/feedback is always welcome ;)
13:16:17 <acyanbird[m]> oh that's great, I'm thinking about making my own distribution too
13:16:24 <FranciscoD_> music: would you have anything else to add? did I miss anything?
13:17:08 <music[m]> Sounds pretty good to me.
13:17:12 <FranciscoD_> awesome :)
13:17:34 <FranciscoD_> that's great acyanbird : if it's all FOSS, then we can work with you and get all your software included in Fedora---and then create a new Fedora flavour :)
13:18:04 <FranciscoD_> that's our one strict rule---we're strongly pro FOSS, and all software that we package in Fedora must be FOSS
13:18:18 <acyanbird[m]> www i'm just a beginner to it, so i will look at that later. it's base on centos because i'm part of centos community
13:18:30 <FranciscoD_> nice!
13:19:03 <FranciscoD_> Fedora and CentOS are quite strongly related---so if something is included in Fedora, it's usually quite easy to include it in CentOS too
13:19:33 <FranciscoD_> I think most people consider Fedora "upstream" to CentOS and Enterprise Linux (although I don't know what the latest status of this is)
13:19:35 <acyanbird[m]> yes that's true
13:19:56 <acyanbird[m]> so i'm coming for fedora meeting here, hope i can learn more~
13:20:54 <FranciscoD_> sounds good. We'll go through our agenda, and that should give you an idea of how things work
13:20:59 <acyanbird[m]> www
13:21:18 <FranciscoD_> #topic Tasks from last meeting
13:21:38 <FranciscoD_> #info Logs from meeting on Aug 1, 2022 are here: https://meetbot.fedoraproject.org/fedora-neuro/2022-08-01/neurofedora.2022-08-01-13.00.html
13:21:51 <FranciscoD_> if you scroll down, you should see an "Action items" section
13:22:01 <FranciscoD_> #info omnidapps to follow up on Pluto migration from Venus: WIP
13:22:11 <tg-fedneuro> <t​hemasch> Thanks for the resume @FranciscoD_
13:22:30 <FranciscoD_> A little bit of context here
13:22:46 <FranciscoD_> The Fedora community maintains a "planet" instance, which is just a tool that collects lots of RSS feeds in one place
13:23:07 <FranciscoD_> http://fedoraplanet.org/
13:23:08 <FranciscoD_> We, the NeuroFedora team, also maintain two planets
13:23:56 <FranciscoD_> #info Collecting lots of neuroscience blog/web site feeds is planet neuroscientists: https://neuroblog.fedoraproject.org/planet-neuroscientists/
13:24:19 <FranciscoD_> #info Collecting lots of RSS feeds from journals (peer-reviewed and pre-prints) is planet neuroscience: https://neuroblog.fedoraproject.org/planet-neuroscience/
13:24:40 <FranciscoD_> the tool that the Fedora community uses is called "venus", but it's no longer maintained
13:24:52 <FranciscoD_> we use a newer tool called "pluto", and we're helping the Fedora infrastructure team migrate from venus to pluto too
13:25:04 <FranciscoD_> https://github.com/rubys/venus
13:25:06 <FranciscoD_> https://github.com/feedreader/pluto/
13:25:33 <FranciscoD_> #info You can follow the Fedora infrastructure team's progress in this thread on their mailing list: https://lists.fedoraproject.org/archives/list/infrastructure@lists.fedoraproject.org/thread/OKKBJFPZCZHW664NNPWWKKHCDEJIQHFJ/#ZERC37LOEP5X2SJ5MMNOS7DY5V6LJQSQ
13:26:02 <FranciscoD_> I'll reassign the task to omnidapps for the moment
13:26:03 <FranciscoD_> #action omnidapps to follow up on Pluto migration from Venus
13:26:21 <FranciscoD_> #info FranciscoD fix arbor and genesis FTBFS bugs -> WIP
13:26:34 <FranciscoD_> I've got genesis fixed, but I need to check to see that I haven't missed anything. Should have it done this week or the next
13:26:34 <FranciscoD_> #action FranciscoD fix arbor and genesis FTBFS bugs
13:26:54 <digua> oh venus last commit was 11 years ago!
13:27:03 <FranciscoD_> #info vanessa_kris update python-pyABF as noted in review (apply patch to fix failing tests etc.) -> WIP
13:27:14 <FranciscoD_> vanessa isn't here today, so I'll reassign this and we can discuss it at the next meeting
13:27:15 <FranciscoD_> #action vanessa_kris update python-pyABF as noted in review (apply patch to fix failing tests etc.)
13:27:59 <FranciscoD_> #info vanessa_kris add neuro-sig to python-ephyviewer, python-astor, python-neatdend -> DONE
13:28:18 <FranciscoD_> for example: https://src.fedoraproject.org/rpms/python-neatdend
13:28:36 <FranciscoD_> if you click on "members", you should see that the neuro-sig has admin rights there
13:29:02 <FranciscoD_> src.fedoraproject.org is where all the source files for our packages are kept---the "spec" files mostly, that are required to build rpms
13:29:14 <FranciscoD_> #info FranciscoD make python-mne base package archful and sub-package noarch to ensure it's built + tested on all arches and conditional BR on python-pyedflib is taken into account -> DONE
13:29:48 <FranciscoD_> music completed this one, you can see the commit history here: https://src.fedoraproject.org/rpms/python-mne/commits/rawhide
13:30:09 <FranciscoD_> #info FranciscoD backport commits fixing CVEs to dcmtk and push update -> WIP
13:30:37 <FranciscoD_> Context: the dcmtk package had a few security bugs (CVEs) reported against the 3.6.6 version. A new version 3.6.7 has been released that includes these fixes. So we want to update to it
13:31:23 <FranciscoD_> This has been done in "rawhide", but for stable Fedora releases, we need to request permission from FESCo because 3.6.7 includes a "soname bump" (that is, the library versions have changed and all software that uses dcmtk needs to also be rebuilt)
13:31:38 <FranciscoD_> So we have a ticket here, that I expect will be processed this week: https://pagure.io/fesco/issue/2848
13:31:54 <FranciscoD_> and then we can also update dcmtk in Fedora 35/36/37 and rebuild the dependent software packages
13:32:18 <FranciscoD_> #action FranciscoD update dcmtk after FESCo decision
13:32:35 <FranciscoD_> OK, those are all the action items from the last meeting. Moving on to the next topic
13:33:00 <FranciscoD_> If there are any comments at any time, please just make them
13:33:09 <FranciscoD_> (I tend to go quite swiftly over the agenda to ensure we finish on time)
13:33:15 <FranciscoD_> #topic Open Pagure tickets
13:33:38 <FranciscoD_> #info Tickets that need to be discussed in meetings can be opened on our Pagure project and tagged with "next meeting": https://pagure.io/neuro-sig/NeuroFedora/issues?status=Open&tags=S%3A+Next+meeting
13:34:08 <FranciscoD_> #info No tickets to discuss (reading list ticket is discussed in the neuroscience query of the week topic)
13:34:18 <FranciscoD_> #topic Package health check
13:34:31 <FranciscoD_> #info We take a quick look at all our packages to see if any of them need urgent attention
13:34:47 <FranciscoD_> #info The neuro-sig's package dashboard is here: https://packager-dashboard.fedoraproject.org/neuro-sig
13:35:01 <FranciscoD_> hrm, says no packages..
13:35:10 <FranciscoD_> maybe the link changed, let me get a fresh one
13:35:41 <FranciscoD_> hrm, no, not getting anything
13:35:50 <FranciscoD_> anyone else seeing "no packages"?
13:36:09 <NitochondriaC[m]> No packages on my side
13:36:32 <music[m]> try https://packager-dashboard.fedoraproject.org/dashboard?groups=neuro-sig
13:37:13 <music[m]> shrug
13:37:29 <FranciscoD_> ah, that works
13:37:39 <FranciscoD_> very odd, I went back to the home page and searched for `neuro-sig` there..
13:37:55 <FranciscoD_> #action FranciscoD file ticket against packager-dashboard
13:38:39 <music[m]> Yeah, I constructed that URL manually following the pattern in the URL for my FAS account. Not exactly discoverable.
13:38:59 <FranciscoD_> Yeh, must be an update or something. I'll report the issue
13:39:08 <FranciscoD_> Some terminology for the dashboard:
13:39:38 <FranciscoD_> FTBFS -> fails to build from source: the package does not build currently (happens when things like underlying libraries the package depends on change API/ABI)
13:40:01 <FranciscoD_> FTI -> fails to install: the package does build, but cannot be installed using `dnf` (happens because runtime dependencies may have changed)
13:40:19 <FranciscoD_> we prioritise FTI/FTBFS bugs because they basically mean that users aren't able to use the software packages
13:40:59 <FranciscoD_> there's also a policy in place where if a software package remains FTBFS/FTI for too long, it gets removed (retired) from Fedora: https://docs.fedoraproject.org/en-US/fesco/Fails_to_build_from_source_Fails_to_install/#_package_removal_for_long_standing_ftbfs_and_fti_bugs
13:41:40 <acyanbird[m]> yeah i want to learn how to package actually
13:41:40 <FranciscoD_> Note that the dashboard tells us about these issue beforehand, but we tend to wait until a bug if filed to work on the package
13:41:41 <acyanbird[m]> i will have a try
13:42:19 <FranciscoD_> I'll be happy to help with that acyanbird . I'm a sponsor, so I can also sponsor you to the packager group when you're ready. Your starting point would be this doc: https://docs.fedoraproject.org/en-US/package-maintainers/Joining_the_Package_Maintainers/
13:42:38 <FranciscoD_> (that goes for everyone that would like to learn packaging---we're happy to help you learn and to sponsor you to the packager team)
13:42:54 <acyanbird[m]> thank you so much
13:43:15 <NitochondriaC[m]> I would love to learn as well. That's wonderful！
13:43:24 <music[m]> I’m also a packager sponsor.
13:43:55 <FranciscoD_> acyanbird: Nitochondria C please feel free to ping us whenever. There's also the Fedora devel channel where lots of package maintainers etc. hang out
13:44:20 <FranciscoD_> https://matrix.to/#/%23devel:fedoraproject.org
13:44:34 <FranciscoD_> I see only a few FTBFS/FTI bugs, so that's good
13:44:48 <FranciscoD_> Lots of new versions for packages have been released, though, so we can work on those
13:45:30 <FranciscoD_> #info Packages in good health, not a lot of FTI/FTBFS bugs---please work on updating to new versions
13:46:14 <acyanbird[m]> yeah
13:46:48 <FranciscoD_> I'll look at owl_rl and pynwb---they should only require quick rebuilds (it's a fall out from the magic number for python pyc files changing recently)
13:47:00 <FranciscoD_> https://bugzilla.redhat.com/show_bug.cgi?id=2113640
13:47:00 <FranciscoD_> https://bugzilla.redhat.com/show_bug.cgi?id=2113648
13:47:13 <FranciscoD_> but yeh, please feel free to take up bugs and work on them :)
13:47:56 <FranciscoD_> #topic Open package reviews check
13:48:15 <FranciscoD_> When a new package is to be included in Fedora, it must go through a review process to see that it follows the Fedora packaging guidelines
13:48:24 <FranciscoD_> For our new packages, we "block" this "tracker" bug:
13:48:24 <FranciscoD_> https://bugzilla.redhat.com/show_bug.cgi?id=fedora-neuro
13:48:50 <FranciscoD_> so if you click on "show advanced fields" on the right side, and then see what bugs this one "depends on", you'll see all our package reviews
13:49:29 * FranciscoD_ uploaded an image: (255KiB) < https://libera.ems.host/_matrix/media/r0/download/fedora.im/81d7b8b42d61da05c9ee768b741247254ad8c34e/neuro-reviews.png >
13:49:37 <FranciscoD_> should look like this ^
13:49:58 <FranciscoD_> the package review process is explained here:
13:49:58 <FranciscoD_> https://docs.fedoraproject.org/en-US/package-maintainers/Package_Review_Process/
13:50:17 <FranciscoD_> #info Only python-pyABF review is in progress
13:50:32 <FranciscoD_> vanessa is working on this, but she isn't here today, so we'll leave it for next meeting
13:51:09 <FranciscoD_> #topic CompNeuro lab compose status check for Fedora 36/37
13:51:26 <FranciscoD_> in this topic, we check the status of the comp-neuro OS image
13:51:42 <FranciscoD_> #info the task on our "Koji" builder is here: https://koji.fedoraproject.org/koji/packageinfo?packageID=30691
13:51:52 <FranciscoD_> a green tick means it's built correctly
13:52:18 <FranciscoD_> #info Comp neuro build is fine for rawhide and f37
13:52:26 <FranciscoD_> I need to update the topic to say f37/f38 now..
13:52:29 <music[m]> On package reviews, since there are some new folks in the meeting: any Fedora packager can review packages, and there is a huge backlog (less so in packages specific to this group) because there aren’t enough people doing it, so this is a great and underappreciated way to help out.
13:52:32 <music[m]> Prospective packagers can do unofficial reviews, which is a nice way to get some experience with diverse packages, to get familiar with Fedora packaging policies, and to build a track record for sponsorship as a packager.
13:52:43 <FranciscoD_> #action FranciscoD update meeting topic to say F37/F38
13:52:52 <FranciscoD_> @music +1
13:52:59 <acyanbird[m]> music[m]: thks
13:53:20 <FranciscoD_> More links:
13:53:21 <FranciscoD_> Search all reviews: https://fedoraproject.org/PackageReviewStatus/
13:53:45 <music[m]> Plus, pointing out issues helps reduce the workload for the official reviewer.
13:53:50 <FranciscoD_> +1
13:53:55 <FranciscoD_> all additional reviews are welcome
13:54:12 <FranciscoD_> and reviewing others packages is a great way of practising + learning the process
13:54:12 <music[m]> Also, reviews miss stuff, so extra eyes help.
13:54:33 <FranciscoD_> #topic Neuroscience query of the week
13:54:50 <FranciscoD_> (sorry, we've got 6 minutes left so I want to make sure we complete the agenda---we can keep talking after that :))
13:55:30 <FranciscoD_> if you have anything interesting to share related to neuroscience, you can share it in this topic
13:55:38 <FranciscoD_> we also collect bits in this ticket: https://pagure.io/neuro-sig/NeuroFedora/issue/318
13:55:55 <FranciscoD_> I don't have anything at the moment, lots of detailed papers, but nothing general that's new
13:56:17 <FranciscoD_> haven't been through the planet recently, though---so I'll put stuff on the ticket when I do go through it
13:56:30 <FranciscoD_> #topic Next meeting day, and chair
13:56:49 <FranciscoD_> Next meeting in 2 weeks at the same time (1300 UTC, 29th Aug)?
13:57:15 <FranciscoD_> if that works for you, you can go "+1"
13:57:16 <FranciscoD_> +1
13:57:25 <NitochondriaC[m]> +1
13:57:30 <acyanbird[m]> +1
13:58:15 <music[m]> +1 (although I don’t always make it to these)
13:58:59 <FranciscoD_> thanks all
13:59:09 <acyanbird[m]> thank you so much!
13:59:16 <FranciscoD_> yeh, if anyone cannot make it, please go through the logs later and ping us etc.
13:59:18 <NitochondriaC[m]> Thanks
13:59:29 <FranciscoD_> #agreed Next meeting on 29th August at 1300 UTC
13:59:36 <FranciscoD_> would someone like to chair it? :P
14:00:03 <FranciscoD_> it's just about going through the script
14:00:14 <acyanbird[m]> we are so new to this so...
14:00:18 <FranciscoD_> (I usually keep the last meeting logs open and copy paste lots of stuff :P)
14:00:38 <FranciscoD_> ok, I'll do it again, and then we can volunteer you folks when you've been around for a bit ;)
14:00:40 <FranciscoD_> #action FranciscoD to chair next meeting
14:01:08 <FranciscoD_> we've hit the hour mark, so let me close the meeting, and then we can keep talking etc
14:01:10 <FranciscoD_> #topic Open floor
14:01:25 <FranciscoD_> #info skipping because we're out of time
14:01:26 <FranciscoD_> #endmeeting