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2012-07-31 Tuesday meeting

Attending: Elwood (notes), Will, Roger, Colin, Gus, Scott, Chris, Scott, Jason, Andrew, Carlos, Douglas, Liza, Mark, Melissa, Sebastien, Stick (14:39)

Attending: Elwood (notes), Will, Roger, Colin, Gus, Scott, Chris, Scott, Jason, Andrew, Carlos, Douglas, Liza, Mark, Melissa, Sebastien, Stick (14:39)

Agenda - 2:30pm Start

  1. Accepting minutes from last meeting

    • Colin: Fine
  2. Sprint Tickets/bugs

    • Chris: 9359 - importer jar signing issue, don’t not how to fix it, jar signing fails sporadically, dependant on environment
      • Colin: rebuilding can fix it, on a build have to check the cli importer
    • Chris: 6732 file annotation without original file, don’t know yet, same applies to
    • Chris: 8888, should be fixed, call render no channels active, dirty exception, error or blank image?
    • Chris: 7780 cleanup stuff
    • Melissa: 9375, 9376, 9389 - in progress this week
  3. Whiteboard

    • CLS repository
      • Colin: updating tickets once deployed
    • Scott: FS plans, notes done, show to Gus & Colin
      • Colin: work so far, gather bigger ideas
  4. Minigroup Updates (points for Sprint page)

    • Model

    • Web

    • Insight

    • FS

    • Usability

    • Bio-Formats

    • Chgrp

    • Docs

      • Sphinx Docs @ squig:/ome/team/sphinx/html/index.html (also at

        • Roger: set of pages based on plone, version 4 hierarchy. Taken markdown and html, used pandoc to convert to rst (reStructuredTest) cleaned up and fixed links, converted syntax, internal / extranal links, some sphinx features. Still quite a bit to do, organised in to chapters. Blazej, Sebastien, Roger
        • Roger: overall impression, sphinx doc is relatively felxible, equivalent to markdown, can be extended in python, citation in text could be used to generate bibliography, doi cross reference number. Could gernerate pdf manual from, epidoc to use sphinx, can reference using table of contents. Could cross link with other docs such as bioformats
        • Sebastien: pros and cons of sphinx, should we move, do we know what should be tricky, couple fo things to think about, learning curve, more tedious for non-dev people, trickier than plone. Refactoring to do at some point, sphinx creating something more similar to a manual. Decide what should be moved, how we allocate parts to people, trac / plone. Took a sprint (60 pages) to convert, trac 200ish pages, customization of themes/rendering. not urgent, 4.4.2 milestone, candidates for conversion, what resources we allocate for that?
        • Jason: does sphinx cause nightmares?
        • Roger: learning curve to syntax in sphinx, we have experience to do it faster. Wording and structure is page orientated, sphinx is manual based. Highlights inconsistencies and holes we are missing in documentation, some incomplete and outdated. No web tutorial. Doing conversion will force improvement in docs
        • Will: being forced to be more organised is better
        • Roger: per-page duplication, system requirements, limitations pages, single sections to be cross referenced.
        • Jason: conversion (learning curve) at some point will go to creation and improvements.
        • Roger: readme file, pointers to ome specific stuff we’ve done, free-form syntax. sub-sections, sections standards
        • Will: github, edit online don’t have to have entire thing.
        • Scott: accessible for training material edits, institutions might be able to tailor and contribute back, barrier low enough for people to pick up and do it.
        • Chris: not a CMS! not a click and edit
        • Roger: trac site? delete
        • Will: spreadsheet (gdoc, 10% delete, 90% update)
        • Chris/Jason: pick a section and try it
        • Roger: manually importing plone pages as they change, ongoing maintainence, for 4.4.2, dropping plone would remove this cost.
        • Roger: make edits, run make html, builds entire site, have to build everytime, only rebuilds changes, commit to git and gets updated live?
        • Chris: that would be the idea yes.
        • Will: versioning?
        • Roger: cross reference with other things, something to look at
        • Roger: we have branches for release process
        • Sebastien: how to integrate with the work flow, open PR for code change and PR for docs, how to co-ordinate them, multiple PRs
        • Chris: not convinced that submodules is the way to go
        • Roger: images directory, 100 or more, screenshots, will balloon the repository size
        • Andrew: lots of images in schema doc already
      • Movies

        • Major topics coming from feedback
        • Essential Movies
        • User focussed vs Dev focussed
          • Elwood: into to trello, burden, is it value
          • Jason: Burden of creating movies, is it the right content for tutition? install omero, a number of steps, is that suitable for movies. Download stats probably click and hit back, only knew by url. When are movies powerful? see tha latest stuff. How to movies. End of sprint functionality, dev focussed
          • Chris: Tutorial and ref manuals, used movis as ref manuals, one feature change rebuild tutorial movies. At Galaxy team as same problems, trying to showcase videos, wiki updated by everyone (incl. community)
          • Chris: Quality of them as time goes on,
          • Will: overview movie... What is OMERO? What is bioformats? ome-tiff? What can omero do for you?
          • Jason: im a dev how do I work with ome tools?
          • Scott: more abstract away from feature driven
          • Roger: movies should be backed by movie documentation
          • Elwood: Movies show stuff you can’t do in user docs, z-section showcase, performance, rendering settings
          • Douglas: not keen on the videos
          • Douglas: for users sure but not for sys-admins
          • Sebastien: only side to explain what I wanted to do and why connect to omero, to explain the satellite, more for poeple working on similar things, not directly omero what they do is connected to omero.
    • Big images / learning

    • Matlab runner #1410

      • Sebastien: need to eventually have a system on a system at some point and start running the test jobs, a couple of ones for bioformats, so I can write more, which machine? buy it / locations? Jean-marie, list of toolbox to install, unit testing framework for matlab, some xp with hudson, when do we do that? Then I can start writing tasks and tests.
  5. Next OME Dev Mtg

    • Sept 13/14?
      • Jason: do we need to have one?
      • Melissa: Sept is fine, but short notice for some people.
      • Jason: decide the meeting adgenda / topics, looking for input / feedback
      • Sebastien: 4.4.2 milestone, same time.
    • Josh & Melissa visit Dundee w/c 20 Aug
  6. 4.4.2 release

    • #9417
    • #9411
    • #9344 (new XSLT for inclusion in bio-formats and insight)
    • #9405
    • #9423
      • Chris: wait at least until end of next week, to give Jean-Marie a chance to look voer things. HCS in web was missed in testing. Several bugs in web viewer, may be always there.
      • Jason: fix through to mig august and a batch of testing.
      • Chris: get away from branches being away from develop a long time.
      • Elwood: working on a number of small insight fixes.
      • Colin: When Melissa & Josh are here aim for FS scoping and not on releasing.
      • Jason: 4.4.2 release Sept 1st, work 2-3 weeks then testing.
      • Melissa: fine as long as nothing interupts
  7. Recruitment Update

    • Positions (Needing Filled, Advertised, Interviewed)
  8. Glencoe Update

  9. Any other business (<5 mins)

    • Scott: define a satellite
      • Jason: how do we become a satellite?
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