February 2020 - Neurofedora - Fedora mailing-lists

List of ~40 current updates, FTBFS, and Py3.9 bugs
by Ankur Sinha 17 Feb '20

17 Feb '20

Hello folks, We have about 40 bugs related to (CSV attached): - updates (new version available), - FTBFS: fails to build from source - Py3.9: fails to build with Python 3.9 As discussed at the meeting yesterday, we need to prioritise these currently so that the packages we have already worked on are installable by our users. If you are working on a bug, please: - change the status to ASSIGNED, - "take" it so that it is assigned to you, - add upstream issues or pull requests as comments in the bugs, and as related links. (Basically, keep the team informed of your progress) Hopefully quite a few of them would be fixed upstream already, but if they are not, we've got to file upstream bugs, and if possible open pull requests. -- Thanks, Regards, Ankur Sinha "FranciscoD" (He / Him / His) | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

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Monitoring the CompNeuro Lab image builds: Compose Wrangler needed
by Ankur Sinha 16 Feb '20

16 Feb '20

Hello, We're getting closer to F32 release, and we must ensure that the CompNeuro ISO image keeps building correctly in each "compose" that the Fedora Release Engineering (releng) runs. Failed composes are now noted here with a new ticket: https://pagure.io/releng/failed-composes For example, in the latest compose, all images failed: https://pagure.io/releng/failed-composes/issue/989 Our image also failed because of an additional error: > - nothing provides python3-networkx-core needed by > python3-scikit-image-0.16.2-2.fc32.x86_64 I've filed a bug with the python-networkx maintainer here: https://bugzilla.redhat.com/show_bug.cgi?id=1802771 So, do we have someone who would like to be "Compose Wrangler" for us? The main responsibility is to monitor this repository on a daily basis to check if the ISO was created correctly. If it wasn't, to let the list here know why so that we can see what needs fixing. The time this task would require would be ~5/10 minutes per day (or every alternate day). Any volunteers? :) (If not, we can advertise for "Compose Wranger" as an open position on the blog etc., but it'll be good for one of us to start here for the time being.) -- Thanks, Regards, Ankur Sinha "FranciscoD" (He / Him / His) | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

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Estimating team resources: how much time can you give to NeuroFedora per week?
by Ankur Sinha 14 Feb '20

14 Feb '20

Hi everyone, We've got quite a lot of tasks, and we need to know what resources we have before we decide what to do next. So, can you please note how much time on average per week you can give to NeuroFedora? (It's only meant to be a rough estimation to help us plan better.) https://pagure.io/neuro-sig/NeuroFedora/issue/337 https://pagure.io/neuro-sig/NeuroFedora/issues -> ~200 open tickets -- Thanks, Regards, Ankur Sinha "FranciscoD" (He / Him / His) | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

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Open NeuroFedora meeting: 1600 UTC on Tuesday, 11th February
by Ankur Sinha 11 Feb '20

11 Feb '20

Hello everyone, You are invited to attend the next Open NeuroFedora team meeting this week on Tuesday at 1600UTC in #fedora-neuro on IRC (Freenode): https://webchat.freenode.net/?channels=#fedora-neuro You can convert the meeting time to your local time using: $ date --date='TZ="UTC" 1500 next Tue' or use this link: https://www.timeanddate.com/worldclock/fixedtime.html?msg=NeuroFedora+meeti… The meeting will be chaired by @ankursinha. The agenda for the meeting is: - Introductions and roll call. - Tasks from last week's meeting: NA - Pagure tickets: https://pagure.io/neuro-sig/NeuroFedora/issues?status=Open&tags=S%3A+Next+m… - Neuroscience query of the week. - Next meeting day, and chair. - Open floor. In the "Neuroscience query of the week" section, attendees can ask about/discuss a neuroscience topic that they are curious about. A few tickets on Pagure need comments. Please go through them beforehand and add your feedback. We hope to see you there! -- Thanks, Regards, Ankur Sinha "FranciscoD" (He / Him / His) | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

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Using Taiga (a Kanban board) on teams.fedoraproject.org for managing our packaging tasks
by Ankur Sinha 06 Feb '20

06 Feb '20

Hello everyone, Could you please check out teams.fedoraproject.org and see what you think of using a Kanban board there to manage our packaging tasks. It seems to be a better method of prioritising and visualising our work. Please comment here with your views: https://pagure.io/neuro-sig/NeuroFedora/issue/336: Issue #336: Use teams.fedoraproject.org (Taiga) kanban board for better planning I've set up a test kanban board with a user-story or two here: https://teams.fedoraproject.org/project/neurofedora-packaging/kanban Please ping me if you need me to give you permissions to play with etc. -- Thanks, Regards, Ankur Sinha "FranciscoD" (He / Him / His) | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

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Re: 13 packages still requiring Python 3.7 in Fedora 32
by Ankur Sinha 05 Feb '20

05 Feb '20

On Wed, Feb 05, 2020 12:32:57 +0100, Miro Hrončok wrote: > In Fedora 32, we have updated Python to 3.8: > > https://fedoraproject.org/wiki/Changes/Python3.8 > > There are last 13 packages that were still not successfully rebuilt with > Python 3.8 and they require Python 3.7 at run-time, causing broken > dependencies. The packages are not installable. I don't think the bugzillas > are moving anywhere. > > > Technically, such noninstallable packages should be retired one week before > the beta freeze. I'm writing this e-mail to raise awareness about the > problem. Some of the packages are awaiting upstream fixes. > > <snip> > python-nineml https://bugzilla.redhat.com/show_bug.cgi?id=1746850 > <snip> > > > Maintainers by package: > <snip> > python-nineml ankursinha > <snip> Upstream has been informed, but they're just too busy to fix it at the moment. It isn't a simple enough issue for me to fix either, unfortunately. I'll have another look this week. I think nineml is a leaf package that isn't affecting other packages. So, could we please leave it with the hope that upstream will be able to look at it sometime soon? Otherwise, we'll have just retire and un-retire it when upstream does eventually get to it. -- Thanks, Regards, Ankur Sinha "FranciscoD" (He / Him / His) | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

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URGENT: NeuroFedora at the INCF Congress, Seattle, Aug 20-21, 2020: Submission deadline 10th Feb
by Ankur Sinha 04 Feb '20

04 Feb '20

On Mon, Feb 03, 2020 11:20:08 -0500, Danny Lee wrote: > Yes, next week works for me as well. Just briefly, bootcamp was great, still > have a lot of work to do but it was a great jumping off point. Im really > looking forward to getting back into groove and get some work done! :) > Great. We're looking forward to having you back! Is anyone in or around North America around August? Would you be interested in presenting NeuroFedora at the INCF congress in Seattle in August? The abstract submission closes on the 10th, so this is now urgent. We can request funds from the Fedora community budget. https://www.incf.org/blog/call-investigator-presentations-neuroinformatics-… I'm asking for folks around NA because that will reduce the travel etc. costs. If someone flies from EU or APAC, the flights will be far too expensive. (Personally, I'll be in Australia in early August presenting NeuroFedora at CNS*2020, so it'll be very hard for me to fly to Seattle immediately after even if we get the financial support.) https://www.cnsorg.org/cns-2020 -- Thanks, Regards, Ankur Sinha (He / Him / His) | https://ankursinha.in Time zone: Europe/London

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Fwd: Invitation to speak on eLife Innovation Leaders
by Aniket Pradhan 04 Feb '20

04 Feb '20

Hello Team! Please have a look at the below e-mail and then we can discuss what can we do for the same... :D ---------- Forwarded message --------- From: Emmy Tsang <e.tsang(a)elifesciences.org> Date: Mon, Feb 3, 2020 at 9:13 PM Subject: Invitation to speak on eLife Innovation Leaders To: Aniket Pradhan <aniketpradhan1999(a)gmail.com> Hi Aniket, My name is Emmy– I work for eLife <http://elifesciences.org>, and I was at your presentation at the FOSDEM open research tools devroom on Saturday! I really liked it (: We're currently running eLife Innovation Leaders <http://elifesci.org/innovationleaders>, a mentorship and open leadership training programme for innovators developing open tools for research, and I'm wondering if you would like to present NeuroFedora on one of our cohort calls during the programme. We have quite a few participants who are neuroscientists on the programme (myself included ;)), so it's a good opportunity to reach out to a wider potential user/contributor community too. The call is scheduled on *Feb 19, 2pm GMT*. The topic for discussion is *roadmapping for an open project*, so it will be interesting to hear your experience with developing a roadmap for NeuroFedora! The talk is 10-15 mins + 5 mins Q&A. This speakers' guide <https://docs.google.com/document/d/1cD3M19d7U8LLP2c52xwC08ZG0p0WyZ5HoZeFL3p…> will provide more information. Please let me know your thoughts and questions – I look forward to hearing from you! Many thanks, Emmy -- Emmy Tsang Innovation Community Manager elifesciences.org/labs | @eLifeInnovation <http://twitter.com/eLifeInnovation> eLife Sciences Publications, Ltd is a limited liability non-profit non-stock corporation incorporated in the State of Delaware, USA, with company number 5030732, and is registered in the UK with company number FC030576 and branch number BR015634 at the address Westbrook Centre, Milton Road, Cambridge, CB4 1YG. -- *ThanksRegardsAniket Pradhanhttp://home.iiitd.edu.in/~aniket17133/ <http://home.iiitd.edu.in/~aniket17133/>Aliases: MeWjOr/major() ascii ribbon campaign - against html e-mail/\ www.asciiribbon.org <http://www.asciiribbon.org> - against proprietary attachments*

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Re: Happy new year: when should we restart meetings?
by Ankur Sinha 03 Feb '20

03 Feb '20

On Mon, Jan 27, 2020 12:25:09 -0500, Danny Lee wrote: > Hi all! Hi Danny! (I think your reply only went to me, so I quote it below for everyone) > > Ive finished my bootcamp and am currently job hunting, but I'm available > again. Yay! 😀 Yay! Welcome back! I hope the bootcamp went well! > > The time works for me! I'm excited to see what 2020 has for Neurofedora. > > Is there anything that has been on table and that is something > prioritized for 2020? Not much yet. The first meeting would be used to make a plan for 2020, so we'll wait for that. Here's a quick update on what's currently going on for everyone (Would anyone like to convert this to a blog post for us?): - We're monitoring the comp-neuro lab image that should release with F32. We have a few tasks pending here: * https://fedoraproject.org/wiki/Changes/Comp_Neuro_Lab * https://pagure.io/neuro-sig/NeuroFedora/issue/331 * https://pagure.io/neuro-sig/NeuroFedora/issue/330 * https://pagure.io/neuro-sig/NeuroFedora/issue/329 * https://pagure.io/neuro-sig/NeuroFedora/issue/328 * https://pagure.io/neuro-sig/NeuroFedora/issue/327 - And then we've got to submit an abstract to CNS*2020 to show this off to the community: * https://pagure.io/neuro-sig/NeuroFedora/issue/332 - Folks are at devconf.cz now, but we don't have a NeuroFedora talk there. - @major is presenting NeuroFedora at FOSDEM on 1st of February: * https://fosdem.org/2020/schedule/track/open_research_tools_and_technologies/ - We're continuing to add and maintain our packages in the meantime: * https://tinyurl.com/neurofedora-bugs I think you're the only NeuroFedora member in North America at the moment. So, would you like to attend the INCF conference in Seattle in August to present NeuroFedora, by the way? NeuroFedora would fit in the "Modern ways of doing and sharing science" track. The deadline is Feb 10, so I'm sure we can whip up an abstract in time :) https://www.incf.org/blog/call-investigator-presentations-neuroinformatics-… Lastly, as we complete the CompNeuro deliverable, we'll begin focussing on NeuroImaging. However, it'll be good to have some folks that work in NeuroImaging there---domain knowledge would very important. So, I expect we'll have to work more on outreach and increasing the team (which we'll be doing anyway). If I've missed anything, please add to the list. -- Thanks, Regards, Ankur Sinha (He / Him / His) | https://ankursinha.in Time zone: Europe/London

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Updating hdfview requires netcdf-java, which requires gradle: ideas?
by Ankur Sinha 02 Feb '20

02 Feb '20

Hello, I was looking at fixing/updating hdfview[1], but the situation isn't straightforward: - it requires netcdf-java, which used to be provided by thredds, but thredds was retired[2], - the latest version of netcdf-java is now released separately[3], so I think packaging it up as a new package would be the easiest thing to do, - but, netcdf-java uses the Gradle build system which was retired as "out of date, broken, fails to build, basically unmaintainable"[4]. - and I can't find a way of using maven to build gradle projects in a straightforward way. So, to update hdfview, we need to package and maintain both Gradle and netcdf-java. Now, the state of java packages in Fedora is not too good---the Stewardship SIG[5] is keeping a lot of them afloat. Thoughts? Do we have any folks proficient who may want to work on this? [1] https://bugzilla.redhat.com/show_bug.cgi?id=1797361 [2] https://src.fedoraproject.org/rpms/thredds [3] https://github.com/Unidata/netcdf-java [4] https://src.fedoraproject.org/rpms/gradle [5] https://fedoraproject.org/wiki/SIGs/Stewardship -- Thanks, Regards, Ankur Sinha "FranciscoD" (He / Him / His) | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

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Neurofedora February 2020