2013-12-03 Tuesday Team Meeting
Attending: Dundee: Kenny, Emil, Petr, Ola, Mark, Blazej, Jean-Marie, Chris, Will, Andrew, Roger, June, Gus, Helen, Jason Remote: Douglas, Melissa, Carlos, Josh M, Josh B, Mark H, Sebastien S, Sebastien B
Accepting minutes from last meeting
- accepted
Project Status/Testing Update - 14:34 UK
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Jean-Marie: around 40 tickets for beta2
- 2 or 3 per person
- some PRs open
- Josh: nice not to add further tickets to beta2
- Josh: continuing Hudson issues, not fully diagnosed
- Petr: prepared nightshade questionnaire, for users to check their data on upgraded staging server
- Jean-Marie, Will: tiles not loading is main beta2 blocker now
- Sebastien B: release process is in good shape, once Hudson is back
- Jean-Marie: still not reviewing dev_4_4 code PRs
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Jean-Marie: around 40 tickets for beta2
Glencoe Update (Chris) - 14:42 UK
- continuing work reported last week
- various PRs have come into mainline, more coming
- working on new JCB screen
- Carlos has done some IE8 work, no more this year
- working on ROIs in webclient, including drawing
Upcoming meetings/conferences/outreach visits 14:45 UK
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OMERO Demos (Gus)
- mostly new users, some existing users with specific questions
- referred a few people to Michael re. his Matlab tools
- Andrew: interest in finding and counting spots, so interest in Alex’s scripts
- Andrew: figure creation was received well
- Jason: we are planning to visit elsewhere in UK to show OMERO to users and help them with it
- Petr: should make Michael’s stuff more available
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OMERO Demos (Gus)
Die, die, die “public static final” (Chris, Josh; <5 mins) - 14:49 UK
- need custom Bio-Formats versions and specific importers
- builds use specific versions and downstream importers can pick which to use
- importer was logging incorrect Bio-Formats version
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value of public static final variables is copied by compiler into code that uses them
- if JARs with such constants are changed, code previously compiled using those JARs does not get the updated values
- specifically concerns native and String types expected to change for different builds
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Curtis: can make public static final values not evaluable at compile time
- Chris: also, properties files
Schema and Data Model: The way forward - Andrew's presentation (20 mins) - 15:01 UK
- various changes in how schema versions, folders, publications, etc. are done
- hoping to avoid further monolithic PRs
- was an InProgress version, now a -dev-# on next version
- InProgress folder was at top level of Specification, new -dev-# folder is inside released-schema
- -dev-# schemas are available for validation but not included on HTML index pages
- publication scripts adjusted accordingly, Jenkins will soon be able to publish schema on request
- PRs now split into initial new-schema PR with actual model changes following in multiple subsequent per-change PRs
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initial new-schema PR made only if previous dev release content is finalized
- model change PRs not included in that previous release are rebased into new version
- don’t want to break API for minor schema tidyup
- for start of beta3 need work on timestamp, annotation points, map
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beta3 topics: lightsource, color, wavelength, units, rendering settings (saving into OME-TIFF)
- Bio-Formats could possibly read rendering settings from proprietary formats
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new data: light sheet (various), phase contrast, combinations (e.g., 3D EM with correlative light)
- researching, talking to users
- http://www.xnpig2014.de/
- OpenSPIM: Pavel Tomancak can provide data
- improve adoption of OME-TIFF by helping others to write it
- Jason: for model changes, propose to light sheet community as soon as possible
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Josh: allow dev versions to change frequently to encapsulate breaking changes
- Andrew: could be an issue if there are many long-running change PRs
- Chris: a dev version’s change PRs must be mutually independent, not possible for substantial PRs
- Jean-Marie: make model changes sequentially, one open PR at a time
- Jason: order of changes is worth getting right, e.g., interaction with optical tomography
- Jason: speak up soon if anything to add to model changes already suggested: planning is happening imminently
- Chris: don’t need transforms between unreleased versions
Any other business (<5 mins) - 16:06 UK
- Jean-Marie: Sebastien B will present next month on CI, build system, etc.
- Jean-Marie: report about Paul Felts / Ninewells, etc. would be useful
Done 16:08 UK