13:02:35 <FranciscoD> #startmeeting NeuroFedora 2021-05-24
13:02:36 <zodbot> Meeting started Mon May 24 13:02:35 2021 UTC.
13:02:36 <zodbot> This meeting is logged and archived in a public location.
13:02:36 <zodbot> The chair is FranciscoD. Information about MeetBot at http://wiki.debian.org/MeetBot.
13:02:36 <zodbot> Useful Commands: #action #agreed #halp #info #idea #link #topic.
13:02:36 <zodbot> The meeting name has been set to 'neurofedora_2021-05-24'
13:02:41 <FranciscoD> #meetingname neurofedora
13:02:41 <zodbot> The meeting name has been set to 'neurofedora'
13:03:01 <FranciscoD> #chair omnidapps osezer achilleas alciregi bt0 gicmo music iztokf[m] jnsamyak
13:03:01 <zodbot> Current chairs: FranciscoD achilleas alciregi bt0 gicmo iztokf[m] jnsamyak music omnidapps osezer
13:03:15 <FranciscoD> if I've missed anyone, please let me know
13:03:30 <FranciscoD> #topic Agenda for today
13:03:41 <FranciscoD> #info New introductions and roll call.
13:03:49 <FranciscoD> #info Task from last meeting
13:03:55 <FranciscoD> #info Open Pagure tickets.
13:04:00 <FranciscoD> #info Package health check.
13:04:07 <FranciscoD> #info Open package reviews check.
13:04:13 <FranciscoD> #info CompNeuro lab compose status check for Fedora 35.
13:04:18 <FranciscoD> #info Neuroscience query of the week
13:04:25 <FranciscoD> #info Next meeting day, and chair.
13:04:32 <FranciscoD> #info Open floor.
13:04:40 <FranciscoD> #topic New introductions and roll call
13:04:50 <FranciscoD> .hello ankursinha
13:04:50 <zodbot> FranciscoD: ankursinha 'Ankur Sinha' <sanjay.ankur@gmail.com>
13:05:38 * FranciscoD will wait 5 minutes before proceeding
13:05:56 <jnsamyak> .hello jnsamyak
13:05:57 <zodbot> jnsamyak: jnsamyak 'Samyak Jain' <samyak.jn11@gmail.com>
13:06:03 <FranciscoD> hey jnsamyak
13:06:19 <tg-fedneuro> <s​anjay_ankur> @MeWjOr here?
13:06:38 <jnsamyak> Hi this is my first time here! I look forward to get involved more in future. Thanks FranciscoD to your ping, I could make it in time.
13:06:49 <FranciscoD> awesome, good to have you here :)
13:07:01 <FranciscoD> we'll see how many we are today, otherwise I may just do quick checks and close the meeting
13:07:20 <tg-fedneuro> <b​ittin1> sadly busy today will attend for real in two weeks
13:07:59 <FranciscoD> @bittin1: no worries, necessary tasks come before our volunteering duties :)
13:08:42 <FranciscoD> OK, let's quickly do the basic checks, and then close up
13:08:46 <FranciscoD> #topic Tasks from last meeting
13:08:50 <FranciscoD> #info https://meetbot.fedoraproject.org/teams/neurofedora/neurofedora.2021-05-10-13.02.html
13:09:24 <FranciscoD> #info FranciscoD ask Troels Arvin on https://bugzilla.redhat.com/show_bug.cgi?id=1956962 to maintain the EPEL7 port of dcmtk since they requested it: DONE
13:09:34 <FranciscoD> I've sponsored them now, they should be maintaining dcmtk for EPEL
13:09:52 <FranciscoD> #info MeWjOr to ask for a review swap for PuLP on -devel: DONE
13:09:55 <FranciscoD> the package was approved too
13:10:11 <hugh-osborne[m]> Hi, I'm Hugh. I'd like to introduce some neural simulation software which you might be interested in including in Neurofedora. Let me know if its appropriate to talk about it here
13:10:19 <FranciscoD> #action MeWjOr add new packages to docs + neuro-sig + koschei
13:10:52 <FranciscoD> hugh-osborne[m]: welcome, yes of course. Could you let me finish with this topic in 2 minutes, and then we can discuss more? (Just to keep the logs somewhat organized)
13:11:09 <hugh-osborne[m]> <FranciscoD "hugh-osborne: welcome, yes of co"> no problem
13:11:18 <FranciscoD> awesome, I have a couple of tasks left to check only
13:11:24 <FranciscoD> #info MeWjOr continue with snakemake package: WIP
13:11:31 <FranciscoD> #action MeWjOr continue with snakemake package
13:11:41 <FranciscoD> that's all for tasks from the last meeting
13:11:55 <FranciscoD> I'll skip to Open floor now and come back to other topics after
13:11:58 <FranciscoD> #topic Open Floor
13:12:09 <FranciscoD> hugh-osborne[m]: all yours---could you tell us about this tool etc please? :)
13:12:35 <FranciscoD> #chair hugh-osborne[m]
13:12:35 <zodbot> Current chairs: FranciscoD achilleas alciregi bt0 gicmo hugh-osborne[m] iztokf[m] jnsamyak music omnidapps osezer
13:12:39 <hugh-osborne[m]> no worries, I'm a PhD student at University of Leeds in the UK building our simulation software, MIIND
13:12:47 <hugh-osborne[m]> https://github.com/dekamps/miind here is the github link
13:13:31 <hugh-osborne[m]> the software uses a population density technique to simulate the behaviour of populations of neurons based on an udnerlying neuron model which can be in 1D or 2D (3D coming soon!)]
13:13:54 <FranciscoD> that looks great!
13:14:09 <FranciscoD> I don't think we have it in our queue yet: https://pagure.io/neuro-sig/NeuroFedora/issues
13:14:23 <FranciscoD> I'll file us a ticket now
13:14:25 <hugh-osborne[m]> the simulator is competetive speed wise with NEST but uses significantly less memory
13:14:33 <jnsamyak> I have a lesser background about it, but seems interesting! hugh-osborne
13:14:58 <FranciscoD> hugh-osborne[m]: are its dependencies limited to what pyproject.toml says here? https://github.com/dekamps/miind/blob/master/pyproject.toml
13:15:00 <hugh-osborne[m]> and is designed to be completely agnostic to the underlying neuron model to allow users to try out new models and see how that affects the population level behaviour
13:15:16 <FranciscoD> (if yes, this should be simple enough to package and include in Fedora/NeuroFedora)
13:16:04 <hugh-osborne[m]> I've built MIIND like "python setup.py install" you need further dependencies
13:16:19 <FranciscoD> yeh, looking at the CMakeLists file now
13:16:25 <hugh-osborne[m]> but the version on pypi (pip install miind) has the dependencies included
13:16:30 <hugh-osborne[m]> (using buildwheel)
13:16:57 <FranciscoD> OK, that sounds good. We need to build packages from source, and as far as possible, we need to package the deps independently
13:17:10 <FranciscoD> so that there's one copy of a library/software in the Fedora repos that all packages use
13:17:52 <hugh-osborne[m]> let me link the readthedocs which has more infor on dependencies
13:18:06 <hugh-osborne[m]> https://miind.readthedocs.io/en/latest/installation.html
13:18:48 * hugh-osborne[m] < https://matrix.org/_matrix/media/r0/download/matrix.org/PcDRKvbTXmTdzGDpQOoPzSFE/message.txt >
13:18:52 <FranciscoD> ah, awesome, thanks
13:19:16 * hugh-osborne[m] < https://matrix.org/_matrix/media/r0/download/matrix.org/ZaskxDYoBMDGDabMnlwZWuAH/message.txt >
13:19:27 <FranciscoD> We have them all
13:19:36 <hugh-osborne[m]> do you support cuda?
13:19:38 <jnsamyak> FranciscoD: Do we have all of them?
13:19:38 <FranciscoD> and we have mpich/openmpi too, so we can build mpi enabled versions too
13:19:42 <jnsamyak> oh you answered
13:19:51 <FranciscoD> hugh-osborne[m]: not cuda, unfortunately since it isn't FOSS
13:20:05 <hugh-osborne[m]> no problem, it's not required
13:20:13 <FranciscoD> RPMFusion provides CUDA to users, but since it isn't in the Fedora repos we can't build CUDA compatible versions
13:20:26 <FranciscoD> hugh-osborne[m]: https://rpmfusion.org/Howto/CUDA
13:20:52 <FranciscoD> what we do is provide mpi builds etc. in Fedora, and in our documentation we link to RPMFusion. But yes, users will have to do the CUDA build themselves
13:22:04 <hugh-osborne[m]> here is a paper covering the theory behind the technique
13:22:05 <hugh-osborne[m]> https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006729
13:22:30 <music> a caveat that python-descartes upstream is dead—the bitbucket went away—and the package is at risk of being retired in Fedora (https://bugzilla.redhat.com/show_bug.cgi?id=1907389)
13:22:32 <hugh-osborne[m]> and i've used it recently to model populations of neurons in the spinal cord
13:22:32 <hugh-osborne[m]> https://www.biorxiv.org/content/10.1101/802736v1.abstract
13:23:02 <music> so long-term it would be helpful to find an alternative to that dependency, or ensure it can be optional
13:23:35 <hugh-osborne[m]> <music "a caveat that python-descartes u"> Interesting, it's something I can look at removing  (replacing with something more up to date) on our end if required.
13:23:48 <fm-neuro> pagure.issue.new -- ankursinha opened a new ticket neuro-sig/NeuroFedora#449: "Package MIIND" https://pagure.io/neuro-sig/NeuroFedora/issue/449
13:24:31 <FranciscoD> uh, thanks for catching that music
13:24:33 <FranciscoD> music++
13:24:35 <zodbot> FranciscoD: Karma for music changed to 1 (for the current release cycle):  https://badges.fedoraproject.org/tags/cookie/any
13:25:10 <fm-neuro> pagure.issue.comment.added -- ankursinha commented on ticket neuro-sig/NeuroFedora#449: "Package MIIND" https://pagure.io/neuro-sig/NeuroFedora/issue/449#comment-734129
13:25:24 <FranciscoD> hugh-osborne[m]: I've filed us a ticket so it's on our radar now
13:25:34 <hugh-osborne[m]> lovely. Thanks very much
13:26:11 <hugh-osborne[m]> i'm the best person to contact for now if there are any questions. can I give my email address here or is it better to pass it on some other way?
13:26:21 <FranciscoD> music: would you know if there are any alternatives to descartes by any chance?
13:26:36 <FranciscoD> hugh-osborne[m]: I'm filing a bug on your GitHub about the descartes issue now
13:26:37 <music> not that i know of
13:26:53 <music> i co-maintain python-shapely in Fedora, and it still uses descartes to build its documentation
13:27:07 <FranciscoD> we tend to communicate over open channels, so either this here, or our public ticketing chanel, or the mailing list are best to keep in touch
13:27:22 <FranciscoD> (it also ensures that we're all aware of what's going on so there isn't a single point of contact/failure)
13:27:30 <music> i think it is abandoned but still on PyPI and still working for most users, so people are just still using it
13:27:55 <FranciscoD> music: I guess that's where we package maintainers come in to prod other devs to drop abandoned deps :D
13:28:28 <FranciscoD> hugh-osborne[m]: would someone from the dev team also be open to maintaining the package in Fedora?
13:28:59 <FranciscoD> All of us will help---we share responsibilities, but it's always good to have someone who actively uses the tool and even better if they keep an eye on development
13:29:48 <hugh-osborne[m]> I guess that would involve fixing issues when they come up? Is there a regular time requirement?
13:30:19 <hugh-osborne[m]> so I can pass it along to my supervisor
13:30:19 <FranciscoD> yes, or reporting them to the upstream tracker
13:30:34 <FranciscoD> sort of as a middleperson between users and the dev team
13:30:47 <FranciscoD> we're all volunteers, I guess we spend a few hours a week on NeuroFedora
13:30:53 <FranciscoD> sometimes less depending on jobs etc
13:30:57 * FranciscoD is a postdoc at UCL
13:31:32 <hugh-osborne[m]> OK, i'll be happy to take on that role
13:32:29 <FranciscoD> hugh-osborne[m]: that's great. I can add you as a co-maintainer once I've packaged and included it in Fedora
13:32:43 <FranciscoD> would you have a Fedora account yet? It gives you access to all the infra etc.
13:32:58 <FranciscoD> You can create one here: https://accounts.fedoraproject.org/
13:33:35 <hugh-osborne[m]> two secs
13:34:15 <hugh-osborne[m]> right, i'm registered as hugh-osborne
13:35:08 <FranciscoD> can you login to pagure.io?
13:35:23 <FranciscoD> I'll then cc you to our ticket, so you'll get updates etc. and can communicate with us there
13:36:38 <hugh-osborne[m]> hmm, it won't allow me to do that with the credentials I just created
13:37:04 <hugh-osborne[m]> oh never ming
13:37:08 <hugh-osborne[m]> mind*. it worked it out
13:37:09 <hugh-osborne[m]> I'm in
13:37:19 <FranciscoD> thanks
13:37:36 <hugh-osborne[m]> I hit approve
13:38:09 <fm-neuro> pagure.issue.comment.added -- ankursinha commented on ticket neuro-sig/NeuroFedora#449: "Package MIIND" https://pagure.io/neuro-sig/NeuroFedora/issue/449#comment-734133
13:38:41 <FranciscoD> hugh-osborne[m]: ^
13:39:07 <FranciscoD> oddly enough I think we may have found a bug in pagure. it doesn't format FAS usernames with hyphens correctly
13:39:12 * FranciscoD will file a bug on this later
13:39:27 <FranciscoD> hugh-osborne[m]: here is the upstream issue: https://github.com/dekamps/miind/issues/48
13:39:47 <fm-neuro> pagure.issue.edit -- ankursinha edited the close_status and status fields of ticket neuro-sig/NeuroFedora#424 https://pagure.io/neuro-sig/NeuroFedora/issue/424
13:39:48 <fm-neuro> pagure.issue.comment.added -- ankursinha commented on ticket neuro-sig/NeuroFedora#424: "Package PuLP: A python Linear Programming API" https://pagure.io/neuro-sig/NeuroFedora/issue/424#comment-734134
13:39:52 <hugh-osborne[m]> <FranciscoD "oddly enough I think we may have"> hah, glad to be of service!
13:40:08 <fm-neuro> pagure.issue.edit -- ankursinha edited the close_status and status fields of ticket neuro-sig/NeuroFedora#424 https://pagure.io/neuro-sig/NeuroFedora/issue/424
13:40:10 <fm-neuro> pagure.issue.comment.added -- ankursinha commented on ticket neuro-sig/NeuroFedora#424: "Package PuLP: A python Linear Programming API" https://pagure.io/neuro-sig/NeuroFedora/issue/424#comment-734135
13:40:17 <FranciscoD> hugh-osborne++
13:40:35 <FranciscoD> zodbot hasn't picked up your account yet, it'll sync in a bit
13:40:52 <FranciscoD> hugh-osborne[m]: thanks very much---I'll work on the package and get in touch if I run into any issues.
13:41:08 <FranciscoD> It looks like a relatively straightforward cmake build, so should be easy to do
13:42:13 <hugh-osborne[m]> brilliant, thanks very much, is there any material for beginners I can read with regard to maintaining fedora?
13:42:47 <FranciscoD> hugh-osborne[m]: sure, this is general info on Fedora (most of which you probably already know) https://docs.fedoraproject.org/en-US/project/
13:43:00 <FranciscoD> NeuroFedora related docs are here: https://neuro.fedoraproject.org
13:43:13 <hugh-osborne[m]> <FranciscoD "hugh-osborne: sure, this is gene"> thanks
13:43:19 <FranciscoD> to join the package collection maintainers, these are the steps: https://fedoraproject.org/wiki/Join_the_package_collection_maintainers
13:43:31 <FranciscoD> but I'll sponsor you as a co-maintainer, so you don't need to go through all of these
13:43:49 <FranciscoD> you can pick it all up while co-maintaining miind with the neuro sig folks
13:44:00 <FranciscoD> https://fedoraproject.org/wiki/How_to_get_sponsored_into_the_packager_group
13:44:46 <hugh-osborne[m]> ok, i'll have a read.
13:45:31 <FranciscoD> awesome, if you have any questions about packaging etc. you can always e-mail me at ankursinha@fedoraproject.org
13:45:43 <FranciscoD> or use the mailing list: neurofedora@lists.fedoraproject.org
13:45:49 <hugh-osborne[m]> <FranciscoD "awesome, if you have any questio"> great will do
13:46:01 <FranciscoD> thanks very much
13:46:39 <FranciscoD> I'll quickly go over the rest of the agenda now
13:46:50 <FranciscoD> #topic Open pagure tickets
13:46:53 <FranciscoD> #info https://pagure.io/neuro-sig/NeuroFedora/issues?status=Open&tags=S%3A+Next+meeting
13:47:02 <FranciscoD> #info Nothing new here.
13:47:18 <FranciscoD> #info Package health check
13:47:21 <FranciscoD> #undo
13:47:21 <zodbot> Removing item from minutes: INFO by FranciscoD at 13:47:18 : Package health check
13:47:24 <FranciscoD> #topic Package health check
13:47:42 <FranciscoD> #info Packager dashboard for neuro-sig: https://packager-dashboard.fedoraproject.org/neuro-sig
13:49:05 <FranciscoD> #info a few package updates and FTBFS bugs, but nothing urgent/new this week
13:49:13 <FranciscoD> #nick neuro-sig
13:49:30 <FranciscoD> #action neuro-sig go over open bugs and update packages etc.
13:49:44 <FranciscoD> #topic Open package reviews
13:49:58 <FranciscoD> #info Neuro-SIG package review tracker: https://bugzilla.redhat.com/show_bug.cgi?id=fedora-neuro
13:50:36 <FranciscoD> #info spikeextractors still blocked by hdmf: https://bugzilla.redhat.com/show_bug.cgi?id=1931183
13:50:43 <FranciscoD> #
13:50:55 <FranciscoD> #info snakemake now WIP, deps all packaged: https://bugzilla.redhat.com/show_bug.cgi?id=1821189
13:51:14 <FranciscoD> #info sumatra is probably an inactive project: https://bugzilla.redhat.com/show_bug.cgi?id=1809405
13:51:35 <FranciscoD> #topic F34 CompNeuro compose check
13:51:43 <FranciscoD> #info Compose task on Koji: CompNeuro lab compose status check for Fedora 35.
13:51:45 <FranciscoD> #undo
13:51:45 <zodbot> Removing item from minutes: INFO by FranciscoD at 13:51:43 : Compose task on Koji: CompNeuro lab compose status check for Fedora 35.
13:51:51 <FranciscoD> #info Compose task on koji: https://koji.fedoraproject.org/koji/packageinfo?packageID=30691
13:52:12 <FranciscoD> #info F35 compose building nicely, last build on 2021-05-24 (today)
13:52:26 <FranciscoD> #info skipping query of the week topic
13:52:36 <FranciscoD> #topic Next meeting: day and chair
13:53:06 <jnsamyak> FranciscoD: Is there any packages that I can take care of that is not urgent so that I can work on packaging knowledge from scratch by following documentation?
13:53:12 <FranciscoD> #info next meeting in two weeks, same time
13:53:48 <FranciscoD> jnsamyak: i think its best to look at some of the package update bugs---that way you don't have to write the spec from scratch but you still get to go through the full build pipeline
13:53:51 <FranciscoD> How does that sound?
13:54:14 <jnsamyak> good enough, I'll let you know if stuck, thanks!
13:54:40 <jnsamyak> I'll check the issues page once.
13:54:45 <FranciscoD> jnsamyak: should I find you a bug to work on?
13:54:55 <jnsamyak> FranciscoD: it would be great!
13:55:08 <FranciscoD> great, one sec
13:55:23 <FranciscoD> jnsamyak: maybe try this one: https://bugzilla.redhat.com/show_bug.cgi?id=1921493
13:55:38 * jnsamyak is sorry for interrupting the meeting :)
13:55:47 <FranciscoD> should be a simple update, you can open a PR with the updated spec and we can review and merge it?
13:55:51 <jnsamyak> FranciscoD: I'll take a look at it, thanks for the link!
13:55:53 <FranciscoD> jnsamyak: no, not at all---that's what open meetings are for
13:56:07 <FranciscoD> jnsamyak: what's your FAS?
13:56:16 <jnsamyak> jnsamyak
13:56:22 <FranciscoD> .fasinfo jnsamyak
13:56:23 <zodbot> FranciscoD: User: jnsamyak, Name: Samyak Jain, email: samyak.jn11@gmail.com, Creation: 2020-01-12, IRC Nick: None, Timezone: UTC, Locale: en, GPG key ID: None, Status: active
13:56:26 <zodbot> FranciscoD: Approved Groups: cla_fpca cla_done
13:57:36 <jnsamyak> I need to ask someone to add me to the infra group as well, I opened a PR there (Just to be sure is it necessary to be in the approved groups to open a PR or something)?
13:58:19 <FranciscoD> jnsamyak: the infra group, because it's security sensitive, has its own onboarding process
13:58:51 <FranciscoD> jnsamyak: take a look at this, and follow the steps: https://fedoraproject.org/wiki/Infrastructure#Contribute_to_Fedora_Infrastructure
13:59:30 <jnsamyak> oh okayy, I created the account last year with gsoc and college stuff never got time to get back. I finally got time last month to become actively involved!
13:59:42 <jnsamyak> <FranciscoD "jnsamyak: take a look at this, a"> Will take a look at it thanks!
13:59:48 <FranciscoD> that sounds good, take your time
14:00:02 <FranciscoD> jnsamyak: I've assigned the bug to you now, you can comment there if you have issues etc.
14:00:07 <FranciscoD> or ping us here in the channel if needed
14:00:27 <jnsamyak> Thank you once again FranciscoD !
14:00:37 <jnsamyak> FranciscoD++
14:00:37 <zodbot> jnsamyak: Karma for ankursinha changed to 6 (for the current release cycle):  https://badges.fedoraproject.org/tags/cookie/any
14:00:56 <FranciscoD> #action bittin to chair next meeting
14:01:03 <FranciscoD> jnsamyak: no worries, thanks for volunteering :)
14:01:14 <FranciscoD> oo, we're past the hour mark
14:01:22 <FranciscoD> #action FranciscoD send out logs
14:01:27 <FranciscoD> #endmeeting