Development

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2015

February 11, 2015

Updates

  • Update from Friday's meeting
    • discussed VisTrails internals
    • discussed wrapping
      • xml discussion, hard to modify because tied to db code
      • TE has made it possible to add the schema-defined attributes to the intermediate representation
      • higher-level operations on the port specs

Items to Discuss

  • [TE] VTK wrapping
    • Dynamic loading works
    • Reading XML is fast enough, but serializing data is slow)
    • Working on patterns for patching
    • Matplotlib has many advanced patterns like argument ordering, nested arguments, alternateSpecs, output types.
      • Having all this in a general wrapper might confuse users?

February 4, 2015

Updates

Items to Discuss

  • Wrapping
    • Format to use? Currently XML (like current matplotlib)
      • JSON and YAML have simple "to python dictionary" methods
      • But don't stream
      • YAML a lot easier for humans
    • [DK] vtk-new-package also changes parameter names, creates enumerations
      • intermediate schema needs to be extensible
      • packages will want to store there specific infos for compute() method generation
      • also might have specs-altering info, like matplotlib's alternateSpec
    • representation to code , registry already has schema for some aspects
    • [RR] We might want to see if Module subclasses can be created lazily
      • no need to create all the classes just to register them in the registry and never actually use most of them
      • future effort
  • [RR] Where should VisTrails packages live?
    • tej installs as 'vistrailspkg.tej', TE installed it as 'userpackages.tej'
    • Currently, standard packages are 'vistrails.packages.', user packages are 'userpackages.' and packages loaded through pkg_resources might be anything
    • [RR] Use 'vistrailspkg.' everywhere?
    • Long-term effort to simplify package distribution/installation (and have VisTrails get them automatically?)

January 28, 2015

Updates

  • T. Caswell to come visit on Fri 6 to discuss wrapping work

Items to Discuss

  • [TE] New VTK wrapping
    • Current code by DK seems a good deal faster
    • Generates XML that can be patched/tweaked, generates Python code from it, VisTrails only loads generated Python code
    • RR would rather have VisTrails load intermediate representation (= XML) directly, wants to make sure this is not slower
    • The goal is to turn the intermediate step into something generic that would be used for every wrapped package (vtk, numpy, matplotlib, sklearn, java) instead of each having its own
    • TC has its own code at github:VTTools which parses numpy docstrings and generates modules, doesn't yet handle classes or persist anything
  • Web crawler
    • Right now, TE starts jobs for "start crawler", "stop crawler", "install classifier"
    • RR would rather have the crawling be a job as far as VisTrails and tej are concerned
    • The whole thing would be one pipeline: load examples, train classifier, start crawler [check for job, kill previous one, upload model, start processes], get snapshot, visualize
      • Need some support in tej and job submission system: long-running jobs, stop a job (wait for it to finish?), restart a job even though results are cached

January 21, 2015

Updates

Items to Discuss

  • [RR] Unified wrapping method discussion #991
    • TE to work on reusable method with intermediate representation, starting with VTK
  • [RR] Examples for scikit-learn: JF has an old example using Weka with parameter exploration (not currently in source tree)
    • AM's examples are enough
  • [AM] scikit-learn package is done, merge it in? #955
    • RR will merge
  • [RR] What should copyright headers say? #994
    • Let's keep everything in there: Utah/Poly/NYU

January 14, 2015

Updates

  • [TE] Working on classifier
  • [RR] Scripting integration, work in progress

Items to Discuss

  • [RR] Unified wrapping method discussion (#991)
    • Let's talk next week, [AM] and [DK] are not here

January 7, 2015

Updates

Items to Discuss

  • make sure that we address critical issues, questions, and pending review branches in a timely manner
  • scripting support
    • [RR] no issues if we want to just keep annotations in the generated code to allow the link back to a workflow
    • [RR] can translate from workflow to script, working on script to workflow
    • will work for parameter value changes, structural changes require changes to the annotations
    • need to publish best practices here
    • would be cool to do looping in scripts (easier interface than with workflows)
  • notebook support (convert form notebook to workflow)
    • RR will sync with FC on this
  • Issue with console in built-from-scratch
    • [TC] iPython rearranged some of the completion stuff in 2.2 and 2.3
    • binary has old version of iPython -> 1.0.0, should we update?
  • [TC] automated wrapping of numpy and scipy
    • discovered a bunch of malformed documentation in numpy and scipy
    • has github repo for vistrails tools
    • example modules wrap a bunch of R stuff (not baked in, just how things are)
    • will be pushing wrapping logic up
    • port names forbidden (window and domain)
    • have an import hook to get from yaml directly to VisTrails Modules
    • should work for any python modules with well-formed numpy docstrings.
  • [Action] should make it clear in documentation that Constant now means serializable not that the value doesn't change (e.g. List)
  • [TC] might be interesting to try to build components of matplotlib and accumulate in figure (long-term project, but thinking about how this might work)
  • [TE] build and build scripts
    • completely automatic, buildbot
    • need to set the build machines for the environment we want for the binary
    • would virtualenv work here?
    • [TC] anaconda can pin versions, potential path to test different configurations
    • Q: upload nightly binary builds? A: makes sense, make sure they are well-labeled
  • sourceforge stats: e.g. http://sourceforge.net/projects/vistrails/files/vistrails/nightly/vistrails-src-nightly.tar.gz/stats/timeline?dates=2014-01-01+to+2015-01-07
  • package issues (see Remi's message)
  • [TE] Scope of tej
    • Support single ssh commands?
    • Queue can be used as a remote machine (crawler is using queue.call*)
  • SourceForge stats: http://sourceforge.net/projects/vistrails/files/vistrails/nightly/vistrails-src-nightly.tar.gz/stats/timeline?dates=2014-01-01+to+2015-01-07

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