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  • 05:33
    heavywatal opened #3061
  • 05:33
    heavywatal labeled #3061
  • 03:31

    cmdcolin on main

    Use older testing-library/react… (compare)

  • 01:07
    cmdcolin synchronize #3043
  • 00:03
    cmdcolin commented #3027
  • 00:03
    cmdcolin closed #3027
  • 00:03
    github-actions[bot] labeled #3060
  • 00:02
    cmdcolin opened #3060
  • 00:02

    cmdcolin on v1.8.0_release_announce

    [skip ci] Add release announce (compare)

  • Jun 27 23:59

    cmdcolin on v1.8.0_release_announce

    [skip ci] Add release announce (compare)

  • Jun 27 23:53

    cmdcolin on main

    [skip ci] Update docs on embedd… (compare)

  • Jun 27 23:51

    cmdcolin on npm_and_yarn

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  • Jun 27 23:51

    cmdcolin on main

    Bump next in /demos/jbrowse-rea… (compare)

  • Jun 27 23:51
    cmdcolin closed #3034
  • Jun 27 23:50

    cmdcolin on fix_floating_labels

    (compare)

  • Jun 27 23:50

    cmdcolin on main

    Fix feature labels being choppy… (compare)

  • Jun 27 23:50
    cmdcolin closed #3059
  • Jun 27 23:50
    cmdcolin unlabeled #3059
  • Jun 27 23:49
    github-actions[bot] labeled #3059
  • Jun 27 23:49
    cmdcolin unlabeled #3059
Teresa Martinez
@teresam856
For anyone interested, here is a link to the jbrowse-jupyter https://github.com/GMOD/jbrowse-jupyter/tree/docs. All feedback is welcomed.
Junjun Zhang
@junjun-zhang
nice!
Robin Haw
@hawrobin
@scottcain @rbuels - do we want to do an ISMB 2022 tutorial? The deadline is monday.
Colin Diesh
@cmdcolin
rob is out on vacay right now just fyi
also, the tutorial for ismb says it's not generally used for presenting a specific software https://www.iscb.org/ismb2022-submissions/tutorials
Robin Haw
@hawrobin
opps, thx @cmdcolin. You are correct, it would be from a data viz or workflow persective. I was just looking over the tutorials from last year and they did not reflect a software demo style.
i was also surprised too see a relatively shortlist of tutorials! In previous years, their had been more.
Colin Diesh
@cmdcolin
i suppose if we want to focus more on jbrowse, probably go for a technology track like the link says
1 reply
Junjun Zhang
@junjun-zhang
anyone knows why we use a particular version of the mst library: "mobx-state-tree": "3.14.1", latest release is 5.1.0
Garrett Stevens
@garrettjstevens
I think it's because we use mobx v5, and mobx-state-tree >=v4 requires mobx v6. There are some breaking changes in mobx v6 and we haven't made it a priority to get things working with that version.
Also, we re-export mobx, mobx-state-tree, react, material-ui, and others for plugins to use, so if we upgrade them we risk breaking plugins. Those breaking changes may have to happen someday, but we'll have to plan for it.
Junjun Zhang
@junjun-zhang
thanks @garrettjstevens in terms of plugin, in the isoform inspector I am trying to use the same major versions of the main libraries as you listed, but still try to make sure it works with newer ones
Colin Diesh
@cmdcolin
docs for the d4 format now say it has some support for static http requests https://github.com/38/d4-format#reading-d4-file-served-by-static-http-server
Robin Haw
@hawrobin
@scottcain @cmdcolin - in view of rob being away, are we still meeting at 1?
Colin Diesh
@cmdcolin
hmm
i do want to try to make more progress on the pag workshop if possible. i dunno
Scott Cain
@scottcain
I’ve had no time this week to work on it unfortunately. AGR and WormBase releases have soaked up all my time, so I’d vote for putting it off
bbimber
@bbimber
Hey - I wanted to re-ask a question from earlier: does anyone have suggestions on coaxing an embedded LGV to make itself full page height? This would both be aesthetically preferable to us (otherwise we just have this white space), and at least in our hands it doesnt reliably auto-expand itself. The user can manually drag to open it, but that's not ideal here. Thanks for any ideas.
Colin Diesh
@cmdcolin
@scottcain @hawrobin ok. i suppose we can skip
@bbimber if you have a link that shows what you mean by not autoexpanding it may be useful
11 replies
bbimber
@bbimber
image.png
That screenshot is related to the thread above about autoexpanding LGV
Robin Haw
@hawrobin
@cmdcolin @scottcain can we meet sometime later next week?
Colin Diesh
@cmdcolin
@hawrobin we have a meeting scheduled again dec 17 if that helps
Colin Diesh
@cmdcolin
since christmas and new years will basically prevent us from meeting for awhile, would be good if we can flesh out that google doc before that dec 17 meeting
@scottcain @hawrobin maybe we can assign ourselves to one or more of the todo items here https://docs.google.com/document/d/11sEGtgM3pUjJJz0te_IhijbdVjHK_KWVOK2-z9eAMZk/edit#heading=h.7vukgf527z6j
Robin Haw
@hawrobin
sounds good!
Garrett Stevens
@garrettjstevens
image.png
Really wish you could put images in threads. This belongs in the view height thread above
2 replies
Colin Diesh
@cmdcolin
any thoughts on a jbrowse 2 release this week?
Garrett Stevens
@garrettjstevens
I think it would be a good idea
Colin Diesh
@cmdcolin
any blockers?
Garrett Stevens
@garrettjstevens
not that I can think of
Caroline Bridge
@carolinebridge-oicr
Colin Diesh
@cmdcolin
that is a baddy of a bug. i tried to evaluate our apollo codebase for the vuln but i think it dodged a bullet by using an older version of log4j
log4j 1.x which still has a vuln but it is a non default configuration
bbimber
@bbimber
I'm trying to follow an example from one of the plugins, in a .ts rather than js file. Is the following the best solution for typing track.configuration? Without that cast on getContainingTrack(), npm build fails:
      .views(self => {
         const { renderProps: superRenderProps } = self
         const filterMenu = {
            label: 'Filter By Attributes',
            icon: FilterListIcon,
            onClick: () => {
               const session = getSession(self)
               const track = getContainingTrack(self) as IAnyStateTreeNode & { configuration: AnyConfigurationModel }
               const widgetId = 'Variant-' + getConf(track, 'trackId');
               const filterWidget = session.addWidget(
                  'InfoFilterWidget',
                  widgetId,
                  { track: track.configuration }
               )
               session.showWidget(filterWidget)
            }
         }
Colin Diesh
@cmdcolin
that is probably a reasonable thing right now. we could possibly improve the typescript on the function itself to return that
there are cases in the typescript related to configs, getting parent things, etc. that are not perfectly typescripted so just doing best effort and casts is generally ok
Teresa Martinez
@teresam856
Just released the first version of JBrowse Jupyter. https://pypi.org/project/jbrowse-jupyter/ https://github.com/GMOD/jbrowse-jupyter . If anyone in the team would like to be added to both Dash JBrowse and JBrowse Jupyter, let me know and I can add you to the repos on Pypi. :)
Robin Haw
@hawrobin
Wonderful. I will send out a tweet if that’s OK
Teresa Martinez
@teresam856
Awesome, sounds good to me!
Ian Holmes
@ihh
Awesome @hawrobin @teresam856 - please let me know when the tweet is tweeted and I will retweet the tweeted tweet
Elliot Hershberg
@elliothershberg
I will also retweet the tweeted tweet when said tweet is tweeted (just saying)
Teresa Martinez
@teresam856
😂 that's a tongue twister
bbimber
@bbimber
Do features support a tooltip in JBrowse2, like JBrowse 1? i'm specifically interested in SvgRenderer, like VCF tracks.
Ian Holmes
@ihh
@hawrobin just checking in about the tweet from yesterday
Robin Haw
@hawrobin
It just went out
1 reply
bbimber
@bbimber
@cmdcolin you asked above if i could give a live instance of the lack of height expansion we see from LGV. This should be accessible: https://prime-seq.ohsu.edu/home/jbrowse-jbrowse.view?session=mgap. It's loading a fairly small dummy VCF dataset, but it has high feature depth over a very small region. You'll see the track immediately gives a scroll bar, rather than having the overall LGV expand.
Colin Diesh
@cmdcolin
thanks for the example