13:05:22 #startmeeting NeuroFedora 2021-02-15 13:05:22 Meeting started Mon Feb 15 13:05:22 2021 UTC. 13:05:22 This meeting is logged and archived in a public location. 13:05:22 The chair is FranciscoD. Information about MeetBot at http://wiki.debian.org/MeetBot. 13:05:22 Useful Commands: #action #agreed #halp #info #idea #link #topic. 13:05:22 The meeting name has been set to 'neurofedora_2021-02-15' 13:05:27 #meetingname neurofedora 13:05:27 The meeting name has been set to 'neurofedora' 13:05:46 #chairs MeWjOr achilleas bt0 gicmo iztokf zbyszek omnidapps rachitt_shah[m] 13:05:51 #chair MeWjOr achilleas bt0 gicmo iztokf zbyszek omnidapps rachitt_shah[m] 13:05:51 Current chairs: FranciscoD MeWjOr achilleas bt0 gicmo iztokf omnidapps rachitt_shah[m] zbyszek 13:05:57 o/ 13:06:00 hello 13:06:03 anyone else here for the NeuroFedora meeting? :) 13:06:10 \o 13:06:15 we can only chair folks over IRC/Matrix unfortunately 13:06:25 omnidapps == Josh... right? 13:06:30 #topic Agenda 13:06:35 Today's agenda is: 13:06:40 Yes 13:06:43 #info New introductions and roll call. 13:06:48 #info Tasks from last week's meeting. 13:06:56 #info Open Pagure tickets. 13:07:04 #info Open bugs check. 13:07:10 #info Open package reviews check. 13:07:15 #info Koschei packages check. 13:07:21 #info CompNeuro lab compose status check 13:07:28 #info Neuroscience query of the week 13:07:33 #info Next meeting day, and chair. 13:07:38 #info Open Floor 13:07:45 did I miss anything? 13:08:00 * FranciscoD double checks 13:08:09 Looks OK. 13:08:10 lgtm 13:08:20 #topic New introductions and roll call 13:08:36 we usually go: FAS username, Full name (Timzeone), interests etc. 13:08:38 so: 13:09:16 #info ankursinha, Ankur Sinha (UTC), FranciscoD on IRC/Matrix and sanjay_ankur on Telegram. NeuroFedora/Fedora Join and wherever else I can jump in 13:09:33 if you're on IRC and were chaired, you can use the commands (like info) 13:09:47 if you're not yet chaired, please let me know and I'll chair you too 13:10:02 FranciscoD: I think achilleas is missing? 13:10:08 #chair achilleas 13:10:08 Current chairs: FranciscoD MeWjOr achilleas bt0 gicmo iztokf omnidapps rachitt_shah[m] zbyszek 13:10:18 #info nerdsville, Josh Santos (UTC+7), thatnerdjosh on Telegram, coding, learning, sharing, and helping out as much as I can 13:10:45 nerdsville++ 13:10:45 FranciscoD: Karma for nerdsville changed to 2 (for the current release cycle): https://badges.fedoraproject.org/tags/cookie/any 13:10:51 .thank nerdsville 13:10:52 FranciscoD thinks nerdsville is awesome and is happy they are helping! (Please also type nerdsville++ since that is what gives them a cookie) 13:10:58 haha! 13:11:02 haha 13:11:37 any other new folks here? :) 13:11:43 #info major/MeWjOr, Aniket Pradhan (UTC+5:30), random stuff related to Python, packaging, and somewhat related to imaging :D 13:11:50 omnidapps: you can see your badges when you log into badges.fp.o 13:11:54 Hey iztokf[m] 13:12:01 #chair iztokf[m] 13:12:01 Current chairs: FranciscoD MeWjOr achilleas bt0 gicmo iztokf iztokf[m] omnidapps rachitt_shah[m] zbyszek 13:12:05 Hello! 13:12:05 FranciscoD: didnt we normally do just .fas name? 13:12:25 gicmo: used to, but that doesn't show up in logs since it doesnt call the info command :/ 13:12:32 hey iztokf[m] 13:12:33 same with the hello commands 13:12:37 iztokf[m]: o/ 13:13:05 gicmo: anything is fine really: zodbot will record all the nicks that spoke 13:13:19 Let's go to the next topic then? 13:13:25 #info gicmo, Christian Kellner (CET), gicmo on IRC ;) 13:13:46 (Please continue introducing yourselves if you've just come: no issues) 13:13:55 #topic Tasks from last meeting 13:14:02 #info Last meeting minutes are here: https://meetbot.fedoraproject.org/teams/neurofedora/neurofedora.2021-02-01-13.00.html 13:14:22 1. MeWjOr Fix the deps for python-odml 13:14:26 MeWjOr: how is this going? 13:14:43 The PR for the dep is still waiting on the maintainer 13:14:53 :/ 13:14:55 hrm :/ 13:14:57 Got a link? 13:14:58 hah, we have the python-odml upstream here, ... points to achilleas 13:15:06 O.O 13:15:10 :D 13:15:36 I can use my proven-packager powers, but I like to leave that as a last resort 13:15:50 MeWjOr: if you give me the link, I can comment there asking them if they need help etc. 13:16:02 #info akoutsou, Achilleas Koutsou (CET), achilleas on Freenode, achkts on Telegram 13:16:15 it;s all messed up in the deps for now (rdflib)... I'll ping the maintainer again, and if they don't reply by next meeting maybe we could do something else 13:16:20 FranciscoD, wait up 13:16:51 https://src.fedoraproject.org/rpms/python-rdflib/pull-request/2 <- here you go 13:17:11 thanks, looking now 13:17:19 OK, I'll drop a comment there after the meeting 13:17:38 :D 13:17:41 the package has 4 admins: someone should be able to work on it :D 13:17:55 #info MeWjOr Fix the deps for python-odml: WIP: waiting on https://src.fedoraproject.org/rpms/python-rdflib/pull-request/2 13:18:11 #action FranciscoD ping PR asking if any proven-packager help is needed 13:18:23 Next one is: 13:18:27 #info FranciscoD will chair the next meeting: DONE 13:18:32 Next: 13:18:37 #info bt0 send out the meeting logs and everything else: DONE 13:18:42 Next: 13:18:47 FranciscoD add info about compneuro container image to docs 13:19:03 also done: https://docs.fedoraproject.org/en-US/neurofedora/containers/ 13:19:12 #info FranciscoD add info about compneuro container image to docs: DONE: https://docs.fedoraproject.org/en-US/neurofedora/containers/ 13:19:37 so, folks can use the comp-neuro container, which includes all the stuff that the comp-neuro lab image includes 13:19:46 neat! that is so great 13:19:55 ++ 13:19:56 and of course, you can also use the fedora-minimal base container and add packages and stuff that you need 13:19:58 I have a question I'll ask after meeting about it 13:20:18 omnidapps: sure, or in the open floor if we have time :) 13:20:33 those were all the tasks from our last meeting, moving on 13:20:41 #topic Open Pagure tickets. 13:20:41 Congratulations for comp-neuro container. Nice stuffs. 13:21:20 iztokf[m]: we can create containers for each package also---similar review process: https://docs.fedoraproject.org/en-US/containers/introduction/index.html 13:21:36 they'll get added to registry.fedoraproject.org after review etc. 13:21:54 Yeah. I have already read about it. 13:22:00 #info Tickets marked for discussion: https://pagure.io/neuro-sig/NeuroFedora/issues?status=Open&tags=S%3A+Next+meeting 13:22:09 There's only the one really: 13:22:27 #info Issue #421: Use pluto instead of venus for planets? https://pagure.io/neuro-sig/NeuroFedora/issue/421 13:22:33 Any thoughts here? 13:22:40 "venus" does work, but it's unmaintained 13:22:59 These are the two "planets" by the way: 13:23:14 #info Planet neuroscience: (RSS feeds from journals): https://neuroblog.fedoraproject.org/planet-neuroscience/ 13:23:33 #info Planet Neuroscientists: (RSS feeds from neuroscience blogs etc.): https://neuroblog.fedoraproject.org/planet-neuroscientists/ 13:23:44 #agree wrt pluto 13:24:17 if we agree to move to pluto, the next question will be: any one want to take this up? 13:24:19 :P 13:24:48 * omnidapps raises hand half way haha 13:25:05 Also, for each planet, you can click on the "Feeds" link and get the full blog roll to import into your own RSS feed reader 13:25:09 omnidapps: :D 13:25:16 what do the others think? 13:25:37 the planets are quite useful for quick views, for folks that still use RSS feeds 13:25:42 (like me XD) 13:25:57 I can also look around... but not sure whether I will be able to do it or not... I'll give Venus a try myself... and then if it works I'll ping you all on the ticket 13:25:59 If you see a source missing from there, open an issue/PR 13:26:06 OK, sounds god 13:26:09 s/god/good/ 13:26:26 omnidapps: MeWjOr : maybe start tinkering with Venus and see how different it is from Pluto? 13:26:39 if the template system etc. is similar, hopefully it won't be too much work to migrate then 13:26:52 If I may suggest, there is the option of using an RSS aggregator and then piping that to a static site generator, just an idea 13:27:05 separation of concerns 13:27:16 omnidapps: that's sort of what they do 13:27:50 omnidapps: got any examples where two separate tools have been connected? 13:28:02 i.e., an aggregator and a static site generator? 13:28:06 Ah, so Pluto uses a separate static site generator? I'll look into it... and not as of right now 13:28:42 omnidapps: not a separate tool, but it uses templates to generate the page from the rss feeds it gets using a feed parsing library 13:29:01 I haven't seen either pelican or jekyll used to generate feed pages 13:29:09 maybe venus does that, since it's written in Ruby like Jekyll 13:29:11 worth a look 13:29:29 #action omnidapps MeWjOr : look into Venus to ascertain how much work migration from Pluto would be 13:29:41 yeah this would be interesting to explore what is used in other places across fedora too 13:29:51 (for regular non-planet RSS templates) 13:29:59 omnidapps: planetfedora is still pluto 13:30:01 that's the one I know about 13:30:22 http://fedoraplanet.org/ 13:30:48 that looks nice 13:30:59 uh, I meant venus 13:31:02 venus is the old one, right? 13:31:11 yeah 13:31:23 yeh, so fedoraplanet is still on venus from what I know 13:31:53 they're also thinking of whether they should remain on venus (py2 only at this point) 13:32:08 I remember some discussion on the Fedora Infrastructure ML some time back 13:32:15 If Venus is already being used, then Pluto does seem to be a newer version of it... could compare them 13:32:41 +1 13:33:00 If you folks can collect your findings in the ticket, we can revisit it again in future meetings 13:33:13 sure 13:33:24 Next topic 13:33:26 #topic Open bugs check. 13:33:39 #info List of NeuroFedora bugs: https://tinyurl.com/neurofedora-bugs 13:34:20 Anyone notice any urgent bugs? 13:34:29 * MeWjOr looks 13:34:35 Most of them are low priority bugs about new versions being available from the looks of it 13:34:48 * omnidapps noticed but didn't document them yet 13:34:50 Some py3.10 bugs too 13:34:59 I'll try again and bring it into the IRC channel later 13:35:10 sounds good 13:35:31 I wouldn't say urgent though, just (I think) bugs in the compneuro lab 13:35:35 you can also comment on the bug saying you'd like to work on it: the maintainer will usually be very very happy to have your help :) 13:35:53 I'll try and reproduce then see if bug report already exists 13:35:57 +1 13:36:14 omnidapps: didnt you also want to go into package maintenance? 13:36:48 I can help where it is needed, I would be coming in green on package maintenance... but I like to learn 13:37:16 Some of these update bugs are simple ones: the package is already in Fedora. You need to make minor tweaks to the spec and open a PR 13:37:24 omnidapps: maybe try this? https://bugzilla.redhat.com/show_bug.cgi?id=1922612 13:37:35 looking 13:38:13 ah yeah that should be easy, update patch version 13:38:16 I'll try it 13:38:33 great 13:38:46 Is your account on bugzilla the same? I'll see if I can assign it to you 13:38:57 #action FranciscoD assign https://bugzilla.redhat.com/show_bug.cgi?id=1922612 to omnidapps 13:39:12 I don't have a bugzilla account yet, I don't think... making one now 13:39:14 #action omnidapps work on updating matplotlib-scalebar: https://bugzilla.redhat.com/show_bug.cgi?id=1922612 13:39:23 omnidapps: cool, you should be able to sign in with your FAS 13:39:25 Should it match my FAS username? 13:39:53 omnidapps: if you use your FAS to login, it'll pick up your e-mail from FAS 13:40:02 k 13:40:12 if you use an e-mail/password combination, you need to use the same e-mail as you've used in FAS 13:40:19 so that it can link the two accounts + their ACLs etc 13:40:25 lol Proxy Error on login... trying to go direct to link 13:40:32 uhoh XD 13:40:51 omnidapps: this link is worth looking at too: https://fedoraproject.org/wiki/Package_update_HOWTO 13:41:07 there we go, making an acct now... and thx for link 13:41:13 OK, so no urgent bugs then. Folks, please update your packages when you have time 13:41:18 if you need help, please ping others 13:41:35 remember: we're maintaining these packages as a team, that's the point of having the neuro-sig packager group :) 13:41:56 #info neuro-sig package group has commit access to all neurofedora packages: https://src.fedoraproject.org/group/neuro-sig 13:42:17 #topic Open package reviews check. 13:42:54 #info Look at the open bugs in the "Depends on" field here: https://bugzilla.redhat.com/show_bug.cgi?id=fedora-neuro 13:43:25 #info https://bugzilla.redhat.com/show_bug.cgi?id=1727506: spike-extractors is a dead review. Andy has said they'll package it up. 13:43:42 #info https://bugzilla.redhat.com/show_bug.cgi?id=1809405: sumatra: also inactive 13:43:54 #action FranciscoD ping https://bugzilla.redhat.com/show_bug.cgi?id=1809405 for updates 13:44:18 MeWjOr: https://bugzilla.redhat.com/show_bug.cgi?id=1821189 -> snakemake. What's the status here? 13:44:20 more deps? 13:45:11 oooh... completely forgot about that... if I recall correctly the deps had been fixed and I just need to update the snakemake version 13:45:19 OK, cool 13:45:40 #action MeWjOr complete https://bugzilla.redhat.com/show_bug.cgi?id=1821189 : snakemake 13:46:11 #info https://bugzilla.redhat.com/show_bug.cgi?id=1849706: bluepyopt: needed some work and is stalled. I'll open a new ticket and get this included 13:46:22 #action FranciscoD follow up on https://bugzilla.redhat.com/show_bug.cgi?id=1849706 13:46:51 #info https://bugzilla.redhat.com/show_bug.cgi?id=1926700: batalgorithm approved, iztokf[m] is working on importing etc. 13:47:03 those are all the open reviews 13:47:33 please do remember to block the "fedora-neuro" tracker bug when you create a new one: that way all neuro-sig package maintainers get a notification 13:48:07 #topic Koschei packages check. 13:48:20 #info Neuro-sig packages on Koschei: https://koschei.fedoraproject.org/groups/neuro-sig 13:48:40 Koschei is a CI system that tries to rebuild packages if some deps etc. change to see if they're still building 13:48:56 uh 13:48:58 wait 13:49:03 why are only 19 packages being shown as tracked? 13:49:51 something is broken somewhere :( 13:50:16 o.O? 13:50:43 looks like the sync broke 13:50:52 they're showing up in my list, but not marked as "neuro-sig" packages: https://koschei.fedoraproject.org/user/ankursinha 13:51:24 I'll file a bug with Infra 13:51:39 #action FranciscoD file a bug with infra about neuro-sig packages not marked in Koschei 13:51:59 Good news is that I don't see any new packages broken 13:52:05 #topic CompNeuro lab compose status check 13:52:19 #info The comp neuro lab image task on Koji: https://koji.fedoraproject.org/koji/packageinfo?packageID=30691 13:52:21 Maybe the format of something changed? 13:52:45 omnidapps: yeh, most likey the branch name change broke the script that syncs src.fp.o with koschei 13:52:52 Ah 13:52:57 (we went from master to main/rawhide on src.fp.o) 13:53:19 #info CompNeuro lab image broke for rawhide this morning: julia has broken deps 13:53:32 Nothing to worry about though, that'll get fixed as soon as the maintainer notices it 13:53:51 the F34 image is building fine 13:53:56 (which is the important bit right now) 13:54:04 #info F34 comp neuro image is building correctly 13:54:14 Hrm, have I added pynn to it yet? 13:54:47 Hrm, nope 13:54:58 #action FranciscoD add python3-pynn to f34+ kickstarts 13:55:38 the kickstarts used to generate all the installer live images are here: https://pagure.io/fedora-kickstarts/blob/f34/f/fedora-comp-neuro-common.ks 13:56:25 #topic Neuroscience query of the week 13:57:06 I'd only found this review/consensus paper on Cerebellar organistation if anyone is interested: https://link.springer.com/article/10.1007/s12311-018-0952-3 13:57:27 #info If you find anything interesting, add it to this ticket here: https://pagure.io/neuro-sig/NeuroFedora/issue/318 13:57:37 it could be a question too, and we'll try and see if we can answer it 13:57:54 Any other interesting neuro tid-bits? :D 13:58:04 that link is neat, I'll check it out 13:58:52 The OCNS talk is tomorrow, right? 13:59:00 MeWjOr: yeh, I'll mention that in open floor 13:59:07 ooookay 13:59:07 #topic Next meeting: time/day/chair 13:59:17 I can chair :D 13:59:19 Next meeting in 2 weeks at the same time? Does that work for everyone? 13:59:20 dibs 13:59:21 awesome 13:59:28 Can I post a question? 13:59:30 #action MeWjOr chair next meeting 13:59:34 one sec 13:59:47 everyone good with meeting at the same time in 2 weeks? 13:59:49 same time is fine for me 14:00:01 ie. 1300 UTC on 1 March (Monday)? 14:00:06 sure 14:00:15 #info Next meeting: same time in 2 weeks 14:00:20 #topic Open floor 14:00:22 iztokf[m]: go :) 14:01:16 What do I need to do if I would like to include python-niapy in live image? Just edit this file: https://pagure.io/fedora-kickstarts/blob/f34/f/fedora-comp-neuro-common.ks 14:01:43 iztokf[m]: is it relevant for computational modelling? 14:02:01 since the live image is the "comp-neuro" image and focusses on modelling 14:02:04 Many optimization tasks can be found also in neuroscience. 14:02:24 yeh, but the question is whether it should go into the comp-neuro image 14:02:27 It is just a question. 14:02:32 or if a different image for optimisation is warranted 14:03:18 random q: Is there an image that includes all the neuroscience packages? 14:03:25 omnidapps: no, that'll be far too large 14:03:31 the comp-neuro image is already 2 gigs 14:03:31 ok lol 14:03:35 yea 14:03:53 No problem. We can leave it out. 14:04:12 about the container image for comp-neuro... does it support GPU usage? 14:04:18 iztokf[m]: no, really: any package that is comp modelling related should go in to the live image 14:04:33 i don't know enough about niapy to make that decision :) 14:04:41 :) 14:04:49 pagure.pull-request.comment.added -- music commented on PR #1 on rpms/python-graph-tool https://src.fedoraproject.org/rpms/python-graph-tool/pull-request/1#comment-67449 14:04:50 pagure.pull-request.comment.added -- music commented on PR #1 on rpms/python-graph-tool https://src.fedoraproject.org/rpms/python-graph-tool/pull-request/1#comment-67449 14:05:17 omnidapps: well, packages in fedora can't be built with cuda etc support, because all of it is proprietary (non FOSS) 14:05:40 if they don't need to be built with cuda support, they should probably work on GPUs 14:06:00 ok cool 14:06:42 iztokf[m]: since you're the niapy maintainer: if you think it is modelling related and should be in the image with NEST/NEURON etc., you need to open a PR in the kickstart repo to include it there 14:07:02 I need to open a PR to include PyNN, so I can also add niapy. Please do let me know 14:07:34 the intention is to have images for specific "domains". So if we get enough neuro-imaging packages in Fedora, we'd like to have another installer image for neuro-imaging tools 14:08:18 but it won't quite make sense to add all packages to one large image 14:08:50 (given that most people can easily install additional bits from repos) 14:09:05 omnidapps: did you have anything to ask in open floor? 14:09:06 Is there a neuroscience section on the store? 14:09:12 omnidapps: what store? 14:09:18 fedora app store 14:09:25 gnome-software etc? 14:09:27 yea 14:09:30 Thanks! 14:10:00 omnidapps: No, there's an "education and science" section where stuff will probably end up 14:10:08 sounds good 14:10:16 only GUI tools are shown in Gnome-software, though 14:10:19 Is there some label to identify these packages? 14:10:32 probably can dnf search against specific repo? 14:10:34 so a majority of our packages, which are libraries and command line tools, won't show up 14:10:41 omnidapps: just dnf search should do it 14:10:45 k 14:10:55 and we list the important tools in our docs 14:11:02 great 14:11:20 that's all for me :D 14:11:21 look at the pages under the "Software" section: https://docs.fedoraproject.org/en-US/neurofedora/software/ 14:11:39 Sorry. I have to go now. Thanks for great discussion. 14:11:59 iztokf[m]: thanks for coming 14:12:02 please let me know about niapy 14:12:13 We're over our time now, let's close the meeting 14:12:14 Yeah. Will send you an email soon. 14:12:26 iztokf++ 14:12:26 FranciscoD: Karma for iztokf changed to 1 (for the current release cycle): https://badges.fedoraproject.org/tags/cookie/any 14:12:33 .thank iztokf 14:12:33 FranciscoD thinks iztokf is awesome and is happy they are helping! (Please also type iztokf++ since that is what gives them a cookie) 14:12:45 Okay, closing in 1 minute 14:12:58 if there's anything we missed out on, this is the time to bring it up :D 14:13:02 #action FranciscoD send out logs 14:13:11 Ah, well, there is actually 14:13:17 MeWjOr: I almost forgot XD 14:13:28 o.o 14:13:34 We're doing a session on how NeuroFedora is developed tomorrow 14:13:45 at the INCF/OCNS Software working group's dev session 14:13:53 #info Software WG dev session: https://ocns.github.io/SoftwareWG/2021/02/07/dev-session-ankur-sinha-neurofedora.html 14:14:02 1700 UTC, 16th Feb 14:14:09 It'll be really cool if folks can join in 14:14:18 I'd like to show how our community based volunteer project works :) 14:14:46 I'll be there :D 14:14:51 that's midnight for me, may not be able to 14:14:52 Thanks MeWjOr 14:15:01 I'll start 15 minutes early so I can make you host etc 14:15:11 omnidapps: no worries, the recordings will be made available later too 14:15:17 k 14:15:41 OK, closing now, at 15 past the hour 14:15:50 thanks for coming everyone, see you in 2 weeks! 14:15:52 thanks all :) good meeting 14:15:52 #endmeeting