Development

2015

January 7, 2015

Github: critical, question and pending-review labels

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

2014

December 17, 2014

Updates

Lots of progress on sklearn package on Monday (#955)
- AM ran into issues with port orders
  - any manually specified port order should always be left-to-right. perhaps don't change the default port order yet
- sklearn modules uses different port shapes for its different types: Estimators (diamond), data (circle), parameters (default, square)
  - [RR] Looks good; generalize this?
  - do this for types of ports rather than try to infer for any port
- Issue with Pipeline module: how to specify a variable number of inputs that need a specified order
  - DK wrote something with ConcatenateString for this
  - problem is you need a UI for ordering the connections (order-connections branch assumed order they were added)

Items to Discuss

scripting support
- how to go from one to another
crawler progress [TE]
- building a package to interact with the crawler
Two week break, Next Meeting is January 7

December 10, 2014

Updates

[TE] bundles
- Finished command-line and core API for handling bundle data
- controller has methods for adding data to bundle
- [DK] why command lines? [TE] allow other tools like reprozip to build bundles
- [DK] seems like could grow into a lot of command-line options
- [TE] can also add the files as a directory
- want to have call that allows user to specify what is saved in the bundle
- [TE] should the user have access to add other parts of the bundle besides data? Probably not.
- [TE] working on storing packages in bundle and loading them from bundle?
[TE] web crawler
- Using tej
  - Problems with closed sockets
  - No way to reconnect to queue
  - copy fails? TE to provide example to RR
- crawler works by submitting a job as a start and stop
- create a new completed job if it runs
- [RR] want to be able to get result even if not completed
[RR] web package for d3.js etc
- [DK] looks good, works for me, github comment on supporting more specific use cases
- RR working on code editor

Items to Discuss

Should source modules' code ports be control parameters? #973
- think about how to support the raw cases where the source is computed upstream
- static typing
unicode/string issue from BNL?
Remove Serializable: #966
- shuold we also remove the serialize calls in basic_modules.py
[TC] auto-wrapping all of numpy into VisTrails
- looks like matplotlib scraping
- ndarrays are labeled as lists, reason? no
- parameterized types? (have depth, could have Float with depth 2)
- do we convert the types? don't think so
- TC will add depth 0 ndarray
- override Module calls? potential issue with the depth computations?
- numpy has broadcasting to do internal parallel

December 3, 2014

Updates

[TE] bundles

Items to Discuss

[TE] bundle extensions
- jobs stored in 'jobs' file
- Data stored as file references in data/ directory
  - Add with gui/api or a method like 'add File data to bundle'
  - Have some way to browse by directory
- Packages stored in bundle
  - Add/delete package method
  - When loading, ask 'Do you want to import package in bundle' if not already existing.
  - [RR] need to fix reloading issues and conflicts with packages that already exist
  - [RR] Full name of a package can change (userpackages vs. vistrails.packages)
    - [DK] does this ever get saved anywhere? thought we only use "codename" which has no depth (dots)
- Package data (Like a Web Service wsdl stored in packagedata/my.package.identifier/
  - Packages can add/remove data as bundleobj file references
  - [JF] Do we need a package-specific directory?
  - decision to use the data directory for everything, no package-specific directory
Scripting support
- [RR] pipeline->python translation needs some tweaking/testing, PR #950
  - python->pipeline translation not done, we have some old code but might not be salvageable
- [RR] IPython notebooks integration still waiting for inputs/outputs definition in notebook format
  - we can probably use whatever metadata format in the meantime and reads theirs once it exists
  - send email to IPython folks
  - (the goal here is to wrap whole notebooks as VisTrails module, to string them together, still using IPython kernels to execute each notebook)
integrating web things in VisTrails
- [RR] wants to take a look at this but working through reprozip backlog

November 26, 2014

Updates

[TE] improve-vt-bundle
- .vt load/save is working
- incrementally writing to vistrail file?
[DK] add web inspector (merged)

Items to Discuss

[JF] scope of filenames
- [DK] what about copy-paste between vistrails? (hidden dependencies?)
  - [JF] shouldn't expect things to run here
  - need way for user to copy or extract from bundle
- other option: have toggle to say that name is local to bundle?
- determine API first
[TE] job-fixes
- RR working on improvements to job handling
- [TE] what still needs to be done here?
- [RR] bug where need to dedup jobs, two workflows with same job (same subworkflow signature) will store job twice in job monitor and will check for both separately, and when finished, assumes one is still running
- make job a first-class entity, work independently of workflow/vistrail
[DK] Move to a new version of Qt for improved well cell support?
[DK] Working with web frameworks/apps in VisTrails
- [RR] start a local web server for this to avoid some issues
- way to move files computed upstream to a resource that the web server can access

November 19, 2014

Updates

Items to Discuss

[JF] Upgrade tree (#949)
- list view
- every node is a new one
- [JF] most natural way is to have same tag
- [JF] cannot reselect the old version
- Upgrade a node and have that change propagate
- Meta-actions?
- Save and save as tag actions (save moves the tag, maintain the history of a tag)
- [RR] Suggest collapsing the upgraded node into the current node (hide the un-upgraded node)
[JF] Ability to refer to file names relative to the vt directory (related to packaging) -- this issue has arisen in the context of ReproZip
- flag in the File module to make things relative to the vt bundle?
- [TE] import data into vistrails?, truncate based on a map from file locations to bundle/local directory locations
[TE] job-fixes (#27) & tej
- we'll keep the job_id for now; tej exposes it
- changes to be merged in
- tej works, needs testing on actual clusters (NYU?), change name?
[TE] figured out how most of improve-vt-bundle is supposed to work
- bundle has method to get_db_object, get_db_objs

November 12, 2014

Updates

[RR] We moved to Github
[RR] UV-CDAT moving to Github; UV-CDAT/VisTrails currently marked as fork
- This means that opening a PR for a branch in that fork will target VisTrails/VisTrails by default
- People have to select UV-CDAT/VisTrails as base every time
- Unmark it as fork if accidents happen? (like #956)

Items to Discuss

[RR] We are on Github!
- Please check github-wiki/Development for some guidelines on development
- Most importantly, be sure to check out tickets marked question or pending-review
Email notifications from Github
- Right now vistrails-dev is watching the repository
- This means the list gets an email whenever anything happens (except from pushes)
- You can unsubscribe from issues, but you'll still get an email through the list
- You will receive everything twice, and receive notifications from your own actions, because of the list
- Is asking developers to watch the repo enough?
[RR] BuildBot/Github interaction status?
- [TE] buildbot is configured to use github with "git:" protocol.
- [TE] Web hook is not working, hook is using "https:", but repository is using "git:"?
- [TE] Binary nightly build working for 2.1, will soon be merged into master
[TE] Atomicity in Job Submission state graph (#27)
github shorthand? "fix" keywords close issues
feature branches move via pull requests
Different releases: windows (4x), github and sourceforge
Nightly releases? (should we push these to sourceforge?)

November 5, 2014

Updates

[TE] setting up buildbots to build the binaries
- solved most of the issues
- working on Windows buildbot

Items to Discuss

[RR] Job submission
- Flowchart
- JobMixin doesn't work for Rémi's use cases
- Need to check on job more than once (based on signature, if server removed job, etc.)
- [TE] what if job failed or job has been submitted but isn't running?
- Pull Request: #27
[RR] Github migration
- Notification on the Github web page to let users know not to open new tickets for a couple of days
scikit-learn package:
- Jorge wrote a package about this in 2012 at ORNL, need to talk with him
[DK] Interaction provenance
- Current able to persist the state of a cell (e.g. Save Camera) if they align with parameters
- How would we capture interactions with the cells as they happen?
  - May not correspond to a compute-time parameter (e.g. mouse drags)
  - Capturing low-level user interactions may be problematic if we don't know how an interaction sequence translates to a meaningful action
- [JF] try to link back to parameters (otherwise, how do we have anything meaningful)
- [JF] Granularity issues
- Maya: hierarchy of actions, use geometry to try and infer this (analyze object and look for things that are separable)

October 29, 2014

Updates

[RR] Build scripts
- Tommy working on release scripts (updating version numbers in build scripts and splash screen)
  - [TE] prepare_release.py updates version numbers, branch, hash, and splash (requires inkscape)
- sdist and wheel ("PyPI" packages) fully automated, have builder
- conda too, builder
- Windows build script needs lots of binaries in fixed locations, e.g. C:\Python27, C:\Users\vistrails\src\vtk, ... build difficult to reproduce
  - could use conda here, but problems with the script
- Mac OS ???
  - [TE] Built with "make_app"
    - Needs installation of qt, vtk, etc., to build.
    - Building usersguide should be more contained
  - would py2app work on a condo-installed VisTrails?

Items to Discuss

[RR] Weird error in UV-CDAT has me baffled (#843)
- [DK] check on packages.uvcdat (generic name, could be overloaded) and/or the Variable name (also generic, could be overloaded)
[RR] JobSubmission and RemoteQ:
- some minor issues with the way things are stored, mostly because uuids and other items should be removed
- [RR] caching output values in the vistrails was not a good idea
- big issue is still that RemoteQ is not best solution
- keep mapping on server to map something in module (pipeline_signature) to job and output
- VT keeps track of which workflow submitted job
- start_job method just calls arbitrary line of code to start job
github migration
- [RR] to send github an email to ask what the best method might be
problems with terminator.vt example?
- potential interaction handler issue?
vt using temporary directory to store files
- disk cleaners can wipe these directories (USGS reported)
- question is whether disk cleaners *should* be doing that...

October 24, 2014

RR and TE meeting about job submission & RemoteQ status in VisTrails

http://www.vistrails.org/index.php/JobSubmission

Summary:

some details to be fixed in RemoteQ package
job result cache shouldn't be in vistrail
the RemoteQ library is a problem since Troels doesn't maintain it

October 22, 2014

Updates

Items to Discuss

[TE] improve-vt-bundle
- lack of documentation
- two layers of serializers
- serialize in more on-demand manner
- does auto-save save everything
- database bundles: try to tie into sqlalchemy
Github migration
- decide on how to move the open tickets
- 26 first issues are already used, can just add original ones
- Rémi needs access to the trac database (vistrails.org)
- if possible, move everything
[TE] New 2.1 release to fix examples?
- upgrades had a bug so could affect existing (older) vistrails
- changes to script commands
- remove tilde files in release
- [RR] is release process automated?
  - [TE] run scripts in the git repository
  - putting release note inside vistrails
- TE to look into which steps are more difficult to change
[TE] job-cache feedback?
- shareable jobs, but jobs are not persistent
[TE] update Web Services examples
- look into RESTful services?
- should we deprecate the old examples?
- check the user's guide and edit if necessary
[RR] VisTrails meant to written by developers and used by users
- writing packages is a bit hard
- developers want to use their own editors, specify which versions should be used
- still have to write your own wrappers
- if developers just want to integrate their tools, can be difficult
- get python program drag 'n drop into python source

October 15, 2014

Updates

[TE] job-cache (merged)
- Store jobs in vistrail
- Fixed jobs in automatic loops
- [RR] Probably shouldn't be in VisTrails
  - RemoteQ/BatchQ are nowhere to be found (except VisTrails's binaries), install procedure doesn't work, and unsupported
  - Not really used by anyone else ("proper" job submission, e.g. clusters, use PBS/...)
  - Sharing job status in vistrail is unsafe and WILL break if people make changes
  - Having that in the vistrail XML for the next release would force us to support it/provide upgrade paths
  - Suggest removing for now, while we think about this more

Items to Discuss

(from last week)
- Use Github and pull requests?
  - Have to find a way to import tickets from Trac
- Use a separate fork for UV-CDAT's vistrails?
- Check with Claudio
  - Claudio says yes
VisTrails and ViDA?
Notes from meeting with F. Perez
- Use whole notebook as modules in VisTrails (don't necessarily need to deconstruct cells)
  - IPython providing "kernels" (execution engine, behind notebooks) for 21 languages
  - connect notebooks that are of different languages
  - reduce serialization issues
  - implicit if two notebooks need to move outputs into inputs
  - They are discussing concepts of "notebook inputs" and "notebook outputs" right now
    - Kind of like our mashups
    - nbparameterise thread
  - Inter-notebook interactions probably not envisioned (but they'd like to be able to point to VisTrails for that)
  - [DK] interface workflow: how do users edit two different notebooks and connect in VisTrails (seems like a lot of windows)
  - restrictions on what can be serialized? notebooks need to be serialized properly
  - can you get a notebook without the stored outputs used by nbviewer?
- Using VisTrails workflows and capabilities from IPython
  - Generic Python API + some rich text augmentations for the notebook
  - Using VisTrails from notebooks using non-python kernels? IPC between kernels is not a goal for IPython folks
- Will try to follow their mailing-list and gitter

October 8, 2014

Updates

[TE] Store one job monitor per vistrail (almost done)
- Easier to share running jobs
- Jobs are shared between all workflows in a vistrail
- use new bundle structure
- what happens with local jobs?
  - doesn't really make sense to open a job started locally on another machine

Items to Discuss

[RR] Use Github and pull requests?
- BNL uses them, UV-CDAT switched to that to
- Development Branches is hard to keep updated and offers no categorization/sorting
  - create pull request when new feature is started, do not have to wait until branch is completed
- Also, use separate fork for UV-CDAT's vistrails? UV-CDAT/VisTrails is marked as fork but can have a different set of branches
  - vistrails.org might be the only UV-CDAT submodule that can't be served over https (see emails)
- user permissions?
- Juliana, thoughts on moving vistrails repository to github?
need to keep testing 2.2 features (e.g. automatic looping, new widget interface) so we can prepare that release
deprecation flag/error for old constant creation methods

October 1, 2014

Updates

[TE] Graphicsview font issues solved
- Preventing DPI changes on windows and using fixed values for module size calculations
- Windows fonts always look bad

Items to Discuss

[RR] To review&merge: constant-classes, invalid-pipeline-hides-package-errors_/loops (#901), version-flag
- constant-classes: get rid of dynamic generation, use metaclass for constant class
- version-flag: add --version flag back on argparse parser
- invalid-pipeline-hides-package-errors: switch to invalid pipeline and will try to fix it, handle upgrades
  - actual error is not showed
  - get into a deep recursion? upgrade to package and back
[RR] JobSubmission package status (does it work? is it useful?)
- should be able to remove it
- [TE] different things to control batch job
[TE] buidbot web interface got hung up
[TE] New features in 2.2 release (please extend/update)
- [RR] New features? Maybe we should maintain a CHANGELOG file in the repository
- Inline widgets ready? Need to test
- output modules
  - incremental change where we keep both cells and new output modules, then phase out output modules?
  - expose configuration keys as ports
Changes to interpreter
- Simplify/Have different interpreter
- Support different environments
- Move update method from Module to interpreter
- Merge multithreaded interpreter
  - Automatic loops/streaming should work during incremental transition
- Different modules will support different modes of execution
  - have documentation for the best practices
[TE] Error setting current_pipeline_view=None (fix)
[TC] have different namespaces with same modules
- using numpy docs to do most of the code generation

September 24, 2014

Updates

[TE] rewrite-startup integration finished
[TE] UV-CDAT bugfixes finished
- need to make sure that the Aashish and/or Charles are aware the changes have been made
- [TE] notification on github

Items to Discuss

[DK] parameterExploration flag: just run the latest of the selected version
- may be nice to have a way to set parameters directly from the command-line like we do with output variables
[RR] code issues found using pycharm
- there are a lot more issues than that, cf pylint
- use pycharm IDE or install pylint, pychecker to avoid committing basic mistakes
[TE] QGraphicsView size issues between Linux/Mac
- the text size is different even for the same fonts
- matplotlib ships with three fonts
- has logic with rules to determine what the closest fonts
- Qt has global configuration that can be hard to override
- terminator example has 15 parameters that are editable (adds 20+ pixels and messes up layout)
[RR] all tests pass on unicode branch
- will try to keep in sync
- [TC] lots of people with strange paths need to use
[JF] back and forth with scripts
- cloud execution
- have more rules for certain environment
- simplify the interpreter, have a different interpreter
- create a new direction for a restrictive environment
- have documentation for the best practices

September 17, 2014

Updates

[TE] Fixed database from command-line, server mode, command line flags
[TE] Fixed slow view switching

Items to Discuss

[RR] unicode and python3 compatibility
- [TC] ~~Pull request doesn't change any behavior (text_type, or str)~~
- [TC] Many changes from py3 were backported to py2, no 2to3 conversion
  - difference between text strings (always unicode) and byte strings (which are the default in py2)
  - six.text_type which on py2 aliases to str and on py3 aliases to str (runs through unicode object initializer)
- make sure to import unicode_literals from __future__
- [RR] more complicated than that. Let's convert everything to unicode in one go, and fix issues
  - [RR] issues with XML (de)serialization, locators, enum, configuration
- look at a 2.2 release before adding unicode support (unicode may need a while to work bugs out)
- [RR] don't move on Python 3 before unicode is supported. Probably no need to bring in six right now
[TE] Parameter Widgets (function-tooltip) ready to merge
- LOD error
[DK] improve-vt-bundle branch
- db/services/bundle.py exists on its own, need to link rest of code to use bundles
- sql-alchemy waiting, work on bundle first
[TE] adding command-line options to the documentation, update in one place now (used to have pdf and HTML)
[RR] Version flag missing in new startup, branch to add back, but argparse messes up the formatting
[RR] Trying to load the same package twice or different versions of the same package breaks VisTrails
[CS] Hire a couple of people for UV-CDAT, need someone to bring them up to date
- think about projects for them
- [DK] we are not sure the direction UV-CDAT will take after 2.0 release

September 10, 2014

Updates

[RR] Backported tabledata package: https://github.com/remram44/tabledata-backport
[TE] GUI Improvements
- Added type checking in parameter view
- Switch to workflow info when no module selected
- Improved fitToView (used a square setting?)
[TE] Edit widgets
- Hide when zooming out
- Improved proxied widgets
- Improved selection border
- Profiling
  - Nothing major for edit widgets
  - Fixed mark_list_depth calls when switching versions

Items to Discuss

Workflow longevity: mta example no longer works
- Fernando suggested offering an option that saves the package (or a description of the package) together with the workflow
- [DK] I agree, this had been talked about with the generic bundle support
- [TE] Everything stored in a zipped vt file, could also store to a directory
  - [DK] some support for this
- [DK] to look over old code and point out what needs to be done for bundle support
[RR] maybe work to distribute packages independent of VisTrails (or at least make moving between versions of packages easier)
[RR] VisTrails integration with ReproUnzip: https://github.com/ViDA-NYU/reprozip/issues/69
- [DK] possible to do python install using smarter package installers?

September 3, 2014

Updates

[TE] Fixed 1.0.3 schema and log upgrades
- [TE] Make sure that 1.0.3 has the right items across versions
- Keep startup only in master since it is only needed for upgrades

Items to Discuss

[TE] Edit widgets demo
- don't show name of port for constants
- boolean widget doesn't look great (still native widget)
- different layout on Linux than Mac/Windows due to font?
[DK] UV-CDAT build:
- Linux build and check for scipy issue (#590)
python3?
[TC] Good way to wrap up userpackages?
- using conda package manager (environment has directory and hard-linked into, need to be able to hard link into environment)
- [RR] is working to do a standard python package to recognize these automatically
- For userpackages, can configure userPackageDirectory to point to a hard-linked environment
- Preferences -> Paths & URLs -> Local Packages Directory
- everything to be in a "bubble" at BNL
[ED] Parameter exploration:
- one variable that I care about but plot as 5x3 not 15x1 or 1x15, enhancement request
[ED] Series of Qt widgets wrapped into VisTrails modules
- subclass SpreadsheetCell, Qt widgets use matplotlib
- [ED] to provide a demo on what is going on trac

August 27, 2014

Updates

[TE] VisTrails 2.1.4 released
- [RR] Will update PyPI and Conda. Note that this currently uses its own branch for 2.1.x (deployment/v2.1), will be easier in 2.2

Items to Discuss

UV-CDAT Bug #520 and #557: make sure we don't show errors for packages that don't load (put these at info level)
- [RR] already created a branch with this name
matplotlib and UV-CDAT: should be able to include freetype in binaries
Bug 886:
- merge in this branch, perhaps not 100% ideal but still better than what we had
- problem is that you sort of want to be able to do a bunch of actions and then raise InvalidPipeline so you don't have to do multiple try-catch
Bug 892:
- not pythonic to forceably squelch propagation
- should be a configuration option to do this
- add a filter to the root logger so that VisTrails messages can be controlled
- will think about this more
[TC] blocker on python3 compatibility?
- [RR] unicode support should probably be done first: unicode from all the files, weird casts everywhere in the code because we used Qt before api v2
- from future unicode literals and str type makes the right thing happen on 2 and 3?
- BNL really wants 3 support, willing to work on
- Issues are #673 (unicode) and #674 (python3)
Relayout programmatically?
- layout_modules() in controller

August 20, 2014

Updates

[TE] Parameter Exploration bugfixes
- "Create Version" spreadsheet button fixed
- Missing date attribute in xml caused errors
- Issue opening vtl links

Items to Discuss

[RR] Pending branches:
- pipeline-validation (#886)
  - (dep for fix-open-workflow (loading a workflow keeps the locator, so saving will overwrite))
  - Ok, will merge
- logger-propagation (#892)
  - Might be a better way? Discuss this more?
- hide-missing-dependencies (#895)
  - Ok, will merge
[TE] New bugfix release? - Parameter Explorations and wrong usersguide in Mac binary
[TE] Module edit widgets demo
- start with tooltips for type names rather than showing them right now
- give warnings on input validation -- add to trac (#898)
[Thomas] matplotlib is meant to be used the other way
- [RR] problem: this is not the way our other plotting packages work (including VTK: data -> data -> renderer -> cell)
- [RR] we've already released a matplotlib package (data -> plots -> figure -> cell) and can't really turn it around
- [RR] we all agree that current code is hacky (but works), see #685 then #396

August 13, 2014

Items to Discuss

[TE] FileOpen event on Mac (#889)
- We can pass argv to QApplication
[TE] 1.0.3 schema differences (#894)
- We can restore schema 1.0.3 on master from branch v1.2

August 6, 2014

Updates

[DK] bug fixes, improve-vt-bundle, uvcdat

Items to Discuss

[LB] LSU, instrument building, tomography, interferometry system
[TC] image registration/processing, infrastructure at BNL
[ED] working on data analysis at BNL, hoping to leverage VT for data provenance, user activity
[LB] tomopy and VT integration
[TC] how to integrate tomography software
[LB] goal to communicate with others, data security for crowdLabs?
[LB] improve parameter exploration
- [JF] different ways: whole workflows, loops inside workflows, multiple threads, implict looping
- [TE] add new examples of saved parameter explorations, different versions
[RR] Bug #886 ("from_root" parameter for change_selected_version())
[RR] API redesign, example: notebook, target: notebook
- [DK] looks good, nicer string rep, improve access to and use of results is important
Jeffrey Guenther - list handling

July 30, 2014

Updates

[DK] UV-CDAT animation, sql-alchemy branch update

Items to Discuss

[TE] parameters in workflow - demo
- show functions on mouse_over
- move set functions to the top
- inline parameter widgets
  - show/hide all
  - toggle in ports list to show/hide these widgets
API design wiki page
- vistrails.api versus vistrails.core.api
- API is currently stateful, would like to change
- API calls using module names, parameter names instead of ids
- tighter integration with iPython (what were ideas from meeting last year with iPython devs)?
argparse mutually_exclusive_group bug
provenance viewer: make panel wider
parameter views: combo box with different parameter viewing types
change parameter not updating GUI
installing python packages into binary
modules that dynamically configure their ports

July 23, 2014

Updates

[DK] output-modules merge, uvcdat, improve-vt-bundle

Items to Discuss

API design wiki page
[TE] output-modules feedback
- Can we have 'Output' module that uses input value to determine output?
  - [DK] Unsure what this means, we could have more than one input port, seems like the mode of output is independent of what the value is
  - [RR] Infer from python types would take a lot of work, explicit easier to understand
  - Usability vs. issues for developers
- Hide all but value port for outputmodules
  - Unsure here
- Make output mode be an enumeration rather than text entry (actually need to allow own entry)
- Should vtkRendererOutput replace VTKCell?
  - [DK] Need to see if display views are involved, interaction handler, etc.
- Use module name as base name?
  - Also naming for parameters on command-line here
  - if you name module "flower", default base name is "flower"
- Also consider possibly only generating one output based on this type of naming
- Global imageFile format setting not working?
  - Put on trac
- Created WebGL output for vtkRenderer (As empty package)
- Matplotlib WebAgg and MBAgg backends better for web
- Clash between mode identifiers
  - Register this on trac
- [RR] how to load a specific mode if it isn't loaded? How do we find it?
[TE] other ideas
- See other workflow systems: http://imgur.com/a/xY37B
- Add icons to modules (graphical representation)
- Add module by double-clicking in the pipeline view and writing module name
- Edit parameters directly on the module
  - First step: move set parameters to top of list (or make more visible)
  - Second step: mine to find commonly used parameters
- Better use of hovering to provide module information
  - Show parameters on right
- [JF] Inspect workflows in the same window
[DK] matplotlib feedback from Thomas Caswell
- figure top-down?
- see Tom's github fork of matplotlib of pyplot changes
- declarative syntax (MEP 25), goal for 1.5
- create artists in modules
[RR] export-as-script
- It's mainly about renaming variables, to connect module and avoid collisions
- Currently gets code for script using package-provided to_python_script methods
- Using the redbaron library for this (under early development)
- Need to handle the different types of input corresponding to different calls (get_input, get_input_list, force_get_input, ...)
[BNL] Adding new palette tool
- search box with many fields to format query, send back dictionaries
[BNL] Use numpy docstring format? yes
[BNL] PEP whitespace? yes
[BNL] python3 compatibility? no a big priority right now
[BNL] PyQt new style connections: yes
[BNL] Access to vistrails.org repository? yes

July 16, 2014

Updates

[TE] VisTrails 2.1.3 released
[DK] UV-CDAT

Items to Discuss

Integrate patches from github
- we push from vistrails.org to github

git fetch git@github.com:VisTrails/VisTrails.git +refs/pull/17/head:refs/heads/pull17
git checkout master
git merge pull17
git push origin master

- Synchrotron needs tools for computational pipelines
Discussion on scripting support
- we are going to have to support a set of restricted operations
- readability versus parsing
- blocks vs. functions
layered API:
- scripting api is base, interactive api has convenience methods that use state
- design document on API, wiki page?
Other requirements for scripting
- higher-level operations to find results linked to certain provenance
vt bundles
- should we look into improve-vt-bundle and sql-alchemy branches?
- design this (configurable bundles)
- have some hooks to add files to the vt bundle already
move-dist-directory branch
- conflicts with python build directories
- does this affect build machines?

July 11, 2014

Updates

Items to Discuss

Claudio wants to make it easy to edit PythonSource without VisTrails
- [RR] Dropping url-encoding would allow you to edit them from XML? But they are also quoted because used in <parameter val="..."/>
Scripting support
- Export workflow as standalone script:
  - Modules could provide their own logic, or we can make something up from compute() ast in some cases
  - Also, add annotations to script to make it easy to reconstruct (and module IDs, so we can update)
- Read back script as workflow
  - General case is hard
  - Building PythonSources from blocks might be doable
  - First step: simply reading some parameters from some modules in annotated script (i.e. has module ids)
IPython notebook integration
- Wait on output-modules branch; then we can show visualizations in notebook
API needs work
- API calls need to return things (to put them in notebook)
- Make initialization easier (shouldn't need to create application, etc)
- Currently stateful! (app.new_vistrail(), ..., api.save_vistrails(f) instead of vt=Vistrail(), ..., vt.save(f))
- Should probably be in vistrails package directly

July 9, 2014

Updates

[TE] Added logging of parameter explorations

Items to Discuss

[TE] Crash when adding String module on Mac #760
- Updated binary to Qt 4.8.6
- Release 2.1 with Qt 4.8.6 to fix String module crash
[TE] Table cell - Use HTML cell and D3?
- Interactivity for free
- Can it work over multiple cells?
- Will work directly on web and crowdlabs
[Claudio] Scripting support
- VisTrails is general but does not interact well with other systems
- What is not working, how can we make it easier?
- Need ability to work without the GUI
  - Construct workflows using utility functions that does not use the VisTrails GUI
- Convert python script to/from vistrails workflow
  - Show PythonSource contents in script
  - Start with workflow that do not show stuff at spreadsheet
- TODO:
  - Design a better mechanism to integrate VisTrails with other tools, starting with Python
    - Provide the ability to save a workflow in a format that can be edited using a text editor -- for example, save a workflow and use an editor to change the contents of the Python Source boxes in the workflow
  - Provide functionality similar to what was implemented in UV-CDAT, where workflows can be used as black-boxes from Python. See slide 41 in http://uvcdat.llnl.gov/media/pdf/VisTrails_UV-CDAT_course.pdf
  - For which applications would scripting support be useful?
  - Look at max and grasshopper3d
  - Claudio wants to test how parallellization works in VisTrails
  - How would scripting support work?
  - Meet on Friday

July 2, 2014

Updates

[TE] List handling improvements done
- Now List ports can connect to anything
- Only exception is List<->Variant

Items to Discuss

[DK] List/Variant bug: #871
- [TE] Fixed
- [TE] Why is Map output a Variant?
- looks like this was done because Fold produces a Variant (makes sense since fold can be a sum), but Map should always be a list)
- this will allow depth 1 input ports to connect
[RR] added List.head as depth 1 port
- add documentation for this new functionality
[DK] QPipelineScene.current_pipeline, controller refs #869
[DK] PythonSource crash? #760
- update Qt for newer binaries?
- pyside support?
- Also, see #737
[TE] Log Parameter Exploration? #870
- Very simple to enable, but we should annotate cell info
[DK] tabledata pandas support?
- investigate on best way to make this available (data types, scripts, modules)?
[JF] SIGMOD: python is becoming lingua franca for data analysis, munging

June 25, 2014

Updates

[DK] master merged into output-modules

Items to Discuss

[DK] Global configuration settings for output-modules when using inheritance:
- Example: Allow different file.suffix='.dat', imageFile.suffix='.png'?
- For an individual output module, we only have one setting since imageFile derives from file, but how should this work if we a global setting for moduleA=vtkRendererOutput and moduleB=FileOutput?
- decided that overriding for specific subclases makes sense
[TE] automatic-looping
- get_input now merges all connections when depth>0
- Typechecking now respects configuration flags - fix for float/int reverted
- Issues with allowing List<->"Type of depth 1" conversions
  - Treat list as Variant of depth 1
  - List->Variant need to be treated differently otherwise it would loop over the variant
- wouldn't be able to do implicit looping over List/Variant because we don't know what the list depth of incoming list objects?
[RR] matplotlib issue: log doesn't reflect the actual execution
- can we update logging provenance here?
- other packages (VTK) have similar issues since the renderer actually causes some of the upstream internal modules to do computations.

June 18, 2014

Updates

[TE] Chris is using BatchQ

Items to Discuss

[TE] automatic-loops-changes
- Mixing 0 and 1 depth types now works
- Removed use of moduleInfo
- transfer_attrs copies specs and control parameters
- Use get_input_list to support multiple connections
[RR] matplotlib issues
- pushed branch to create a function that does this
- mpld3 -- do they use same matplotlib model where figure must exist?
[DK] list of depth 1, can we pass a list here
- exception of List input port type?
- will this work? allows only
[TE] numpy types in matplotlib?
- e.g. different float types
- workaround for numpy for List types already
- what about adding other types later? how would a package developer do this?
- Converter modules could work here but add more modules? hide the extra modules?
- Unify type checking that occurs over connections (controlled by settings) and Loop/depth type checking method (now in vistrails.core.modules.vistrails_module)
[RR] depth 1 port going to List head port
[TE] variant for (float, integer) tuple
[RR] multiple connections into a depth-1 port only use one of the values
- should we have a self.get_input_list(flatten=True) option?
[DK] output-modules: should work on so we can merge

June 11, 2014

Updates

[TE] RemoteQ jobs can now skip upstream
[TE] Fixed zipfile bug corrupting vt files
[TE] Fixed ungrouping caused by
[TE] Google maps binary available
- Updated for zipfile bug but not for ungrouping bug yet

Items to Discuss

[TE] File as parameter is confusing
- signature changes with mtime
- Make File non-constant and use Path instead
[TE] Talked with Chris at LSU
- PBS Jobs 20 min to a few hours
- VisTrails does most of what they need
  - Suggest we focus on bug-fixing and documentation
- Want interactivity
  - Fetch and visualize files while PBS Job is running
- May use Hadoop in the future

June 4, 2014

Updates

[TE] Added skip upstream for RemoteQ jobs
[DK] tabledata/gmaps updates

Items to Discuss

[TE] Test run.py #863
- Changes in run.py are currently not detected by test suite
- Other changes in configuration also don't get tested
- What about importing unittest2 in 2.6?
[DK] userpackages/packages shadowing #864
- add the directory
- being able to see both the package that exists in userpackages and packages
- checking loading/unloading
[DK] need to improve upgrade utility methods
[RR] Removing zip/unzip executables #862
- check in the old commit logs and/or trac to figure out what the old problem was
[RR] Rolling out conda packages: anyone has experience with Anaconda?

May 28, 2014

Updates

[DK] rewrite-startup close to stable, fixed issue with going back and forth from v2.1 (trying to resolve package config settings issue), means output-modules is close, too

Items to Discuss

[DK] extra_info on modules: is it really module-specific info?
[DK] programmatic package configuration settings without direct imports?
[TE] job-cache
- New control parameter for caching module outputs to disk
- checks for Constant modules, so any Constant module can be cached
- used for any module to save state of, not necessarily jobs
- is_serializable flag?
- will this be package-specific?
- have an is_pickeable decorator and allow more complex is_serializable interface code
[TE] LSU feedback (Jinghua and Chris)
- Have used PBS with VisTrails (by running commands over SSH)
- Want to use distributed workflows with vistrails (more than one machine) Could use IPython?
- Using MOAB (Meta scheduler) Module would be useful
- Interested in moving files back and forth
- Have experience with SAGA (Could likely make use of it)

May 21, 2014

Updates

[DK] output-modules, MplFigureToFile
[TE] VisTrails 2.1.2 Released (100 downloads so far)

Items to Discuss

[DK] persistence across machines (USGS use case)
[TE] Merge automatic-loops-streaming into master?
- Implicit looping
- Streaming
- ControlParameters
- New schema version 1.0.4
- Possible conflict with multithreaded-interpreter?
control parameters can also be used for other things like caching?
[TE] job-cache
- Make module jobs independent of workflow
- Ability to cache jobs for all modules with constant outputs. Set in module/PythonSource/ControlParameter
- Needs branches: controlflow-fake-signatures, jobs-use-signature_/connect-folded-module
[TE] [vistrails-users] Michele: VisTrails on remote machine
[TE] SAGA-Python: A Light-Weight Access Layer for Distributed Computing Infrastructure
- Alternative to support distributed computing in VisTrails?
- Support for most job schedulers
- Could replace BatchQ/SSH/PBS/LSF/HTTP modules
- No Hadoop support
- Open Grid standard
- Compatibility with VisTrails/ModuleSuspended?
[RR] Debian vistrails package

May 14, 2014

Updates

CrowdLabs mashups done
v2.1.2 release ready
[DK] work on rewrite-startup, make sure preferences work in new style; output-modules

Items to Discuss

vagrant for reproducibility
- simpler interface for exploring the experiments
- [RR] generating a VisTrails workflow from reprozip was planned, but not integration of the tracer in VisTrails, to trace VisTrails workflows -- it probably makes sense. See https://github.com/remram44/reprozip-ptrace/issues/8

May 7, 2014

Updates

CrowdLabs mashups
- Uploading works
- HTML looping works
- Flash removed (actually hidden)
[DK] output-modules
- Running in batch mode switches to file mode
- Allows parameters to be specified on command-line
- Work on GUI for parameters

Items to Discuss

VTK 6
[DK] output-modules: target single module parameters?
- [RR] use labels to name specific modules, useful in command-line
scripting support

Apr 30, 2014

Updates

Does spreadsheet resizing work correctly? Is it too slow? (#833)
- looks like on downsize the image is smaller than it should be and then flickers to flll space (upsize is ok)
[TE] Mashups on Crowdlabs
- HTML mashups is now rendered in the crowdlabs template
- Added embedding html mashups (using jsonp)
- Fixed uploading mashups with a vistrail
- Investigating issue with saving mashups to DB
[DK] rewrite-startup, output-modules
- working on command-line and global parameters

Items to Discuss

2.1.2 release
- some major bugs a
VTK 6
iPython integration
- how to migrate from scripts to workflows
Introducing vistrails as a normal python package
- check on anaconda support for Qt, VTK support?
output-modules
- make sure that filenames can be set
- output directory
- interpreter should return a dictionary with python objects produced (what is input to the output modules?)
- unify OutputPort and OutputModule? Right now, act differently, but function in similar ways
directions: scripting support, large-scale data analysis, reproducibility

Apr 23, 2014

Updates

debugger
- have to enable the configuration option, starts python debugger in console
- have similar flag for test suite
Branches to be merged in: new-url-package
- API calls don't go through upgrades currently, can we support this so we don't break scripts?
- added HTTPS certificate verification
- new dependencies for binaries?
dont-use-modules-as-data?
- branch is ready?
- changes a lot of packages,

Items to Discuss

output-specific modules (e.g. vtkInteractionHandler)
- only need to be enabled when spreadsheet is active, but if we create a workflow with such a module, it would be nice to still be able to run that workflow in batch mode
- not verify entire workflow?
- load module logic on-demand so we don't need dependencies?
reload packages
- interactions with spreadsheet, stale controller objects
- spreadsheet may need to get information about pipeline when copying cells (get from controller?)
[TE] server mode
- Changed to non-interactive
- Pass debug messages back?
- Auto-load packages security?
  - startup.xml file gets corrupted?
  - using same xml file for multiple instances
- Locale errors
  - crowdlabs defaults to english, but vistrails server does not.
  - set LANGUAGE will fix it
  - should we set this environment variable in VisTrails
  - decided to chose English for now, can reevaluate when unicode branch is ready
- Default to HTML5 interface?
  - Flash interface as backup
  - look at animations for mashups in HTML5
module descriptor weakrefs
VTK6
continue-dialog branch
- changes SpreadsheetCell modules
- merge into 2.1 for the LSU folks
output modules: where should the output module live? only one package?

Apr 16, 2014

Updates

Branches to be merged in: readfile-module, save-module-moves (#853)
CrowdLabs needs update to VisTrails 2.1 with schema 1.0.3
[DK] OutputModules (FileOutput)

Items to Discuss

LSU meetings
- Pausing workflow/confirmation module (#854)
  - Checking an intermediate result before carrying on with the workflow
  - Their problems: Qt event loop, sinks ordering
- CLTools problem
- crowdLabs usage? (they have 100+GB files)
  - Parameter exploration
- Running mathematica on a cluster (JobSubmission, RemoteQ?)
- Exporting VTK visualization (vti/vtp?) for Kitware's KiwiViewer
- Wrapping SNARK09 (C++ code) as VisTrails modules
eo4vistrails (Derek, Terence)
- Add FTP module?

Apr 9, 2014

Updates

Branches to be merged in: export-cells, reset-cell-sizes-button (-> v2.1; icon?), export-versiontree-dot & custom-colors, input-module-no-subclass
[DK] UV-CDAT release, OutputModules (see below)

Items to Discuss

In-place spreadsheet updates: #847
- need to be able to replacement mode toggle on and off
- Colin has a working solution, is there a need to do this globally?
Autosave for existing vistrails not working ~~#849~~
Other tickets from USGS
- Reason for pipeline scroll area being 100 times greater than pipeline?
- File Selection Dialog ~~#846~~
- Copy/paste with retained connections #851
- Auto-connect ports when moving modules #852
  - Also think about fixing some of the port-snapping for selecting a port on the same module when there are multiples of the same type
Unicode support
- question on mailing list
- [RR} dates is something else, should be able to put on v2.1
- fix for LC on master, port to v2.1?
- should try to persist dates in numeric formats, but GUI level can be language-specific.
VTK 6 support #739
[TE] Analogies does not delete annotations #848
- Code never worked as intended
[TE] Add eo4vistrails features to vistrails? https://github.com/ict4eo/eo4vistrails
- Look at these and try to determine what may be appropriate
- data types are probably most important, doesn't look like anything there
[DK] OutputModules

Apr 2, 2014

Updates

[TE] Added annotations and control parameters to visual diff
- three tabs
- TODO: analogies
  - just work on making sure the actions execute, don't worry about the matching
[TE] Build documentation using buildbot
- makefile is run directly so no need to patch (no merges)
- the nightly build still generates the pages, and the cron job now pulls the built pages
- cron job is set to pull built pages after nightly build
[TE] Updated code coverage tester (currently 33%)
- coverage is done manually, it is not done nightly
- takes 15-minutes to run, on vis-7.
[DK] Output modules

Items to Discuss

Unicode support
- question on mailing list
- fix for LC on master, port to v2.1?
Output modules
- outputs, modes, mode configurations
- spreadsheet as a package
- output mode configuration dependencies
VTK 6 support #739
- trying to complete output modules before new VTK package

Mar 26, 2014

Updates

Branches to be merged in: application-no-default-argv, export-cells, testsuite-module-imports, reset-cell-sizes-button (icon?), export-versiontree-dot, custom-colors
[TE] Added branch control-parameters (used by list handling)
- For setting hashed control options on modules (How to combine lists, while looping, caching)
- Missing: Include in diff/merges/analogies?

Items to Discuss

iPython
- script to workflow bridge
- access to VisTrails commands in iPython
- changes to the API
Multi-faceted output
[RR] Documentation buildbot
- [TE] currently here
- problem is that we don't get a message when the documentation failed to build
- what about copying the output from a build machine to vistrails.org?
[RR] Last(?) migration issue: #837
- [DK] to look at
VTK 6 support #739
spreadsheet export button in UV-CDAT
Develop menu?

Mar 19, 2014

Updates

[DK] UV-CDAT #407 fix, version tree rewrites

Items to Discuss

[TE] Cleaning up test suite log
- Deprecated core.modules.constant_configuration imports
  - check whether the deprecations for vistrails.core.vistrails_module.VistrailsModule camel-case are similar
- KeyError (Ticket #837), one of [DK]'s commits
  - [DK] to look at
- Skip modules not to be imported (or fix/remove)
- Python invalid drawable (Probably from mashups)
- Missing version 0.8 of package org.vistrails.vistrails.tests.upgrade (bug?)
[TE] Add annotations to signature? (hash-annotations)
- for the streaming/automatic looping for new values on the modules
- could be any module
- label doesn't affect caching
- prefix, flag involved, add fields to module about looping
- schema change? problem is that don't want to have to recreate module each time
- backward compatibility
- new type of "control parameter"
VTK 6?
- See Ticket #739
UV-CDAT #408: [RR] has worked on this
- support adding more formats to export
- decided to have single menu item, and put all available formats in the dialog
Spreadsheet resizing bug
- if you resized the sheet, would reset to equal-size cells
- spreadsheet-resizing branch changed this to allow non-equal-size cells on resize
- has some math issues because doing this dynamically difficult
- button to resize to equal-size on branch
- updating the documentation
- [TE] can we store the locations more precisely? (problem might be if a header column is also resized)

Mar 13, 2014

Updates

[RR] Package dependency ordering issue (#829); fixed(?), merge?
- [DK] Yes, merge
[RR] Will merge in tabledata additions
[RR] New SQL package, using tabledata and sqlalchemy. Should be fully backward compatible(?)
- Check if Fernando has anything here from the Oracle workflow and database provenance
[RR] Searching in vistrail and regex (#373, 779); fixed?
- Error was hidden (entering '?' searched for '.*?.*' which was a valid regex but still didn't do what was expected)
[TE] IPython console now shows <STANDARD OUTPUT> before printing from stdout/stderr
[TE] Vistrail variables fixed
- Deleting a module with a variable did not remove the variable from the workflow
- Copying modules with variables now works

Items to Discuss

[RR] Do not run modules upstream of submitted job
- jobs-use-signatures: Uses the subpipeline signature to identify jobs
- works: if job is submitted, check it without running upstream (we don't need the parameters this time(?))
- doesn't work in Map
- jobs-use-signatures_/connect-folded-module
  - create a connection from folded module to InputList upstream
  - looped module can run upstream if it needs, else we don't
  - problem: the Map still needs the list, for length and type-checking
- Could we rearchitect the looping behavior? Basically, just copy the pipelines and run them with each entry from the loop
  - Provenance could expand
[RR] module-upgrade-recursion status? (not yet merged)
- [DK] to look at and merge (should be done)
[DK] UV-CDAT Issues: #407 and #408
[RR] Thumbnail comparison bug: different references are selected on master and dont-use-modules-as-data! (pipeline results are identical) Problem with upgrade code?
- using different reference images
- [TE] to look at
- look at the console_mode, how it gets back the upgraded version id
- filed as #831
[TE] Vistrail variables
- Normally only one hidden module exist for each vistrail variable, but pasting a module with a vistrail variable will create a new hidden module. This does not break anything, but should be taken into account when modifying the code.
- When a vistrail variable module is created, an input named "value" is created. A bug with default values gave it the value "None". This is fixed. To make validation of existing vistrail variables work we need to check if the value is "None", but this would not allow "None" as a string.
- [DK] to look into this, we cannot have "None" there.
[JF] NSF Big Data proposals (due in June)
uuid status
- need to check tests and features outside of normal execution

Mar 5, 2014

Updates

Items to Discuss

[RR] New SQL package, using tabledata and sqlalchemy
- No upgrade possible? (output changed from List (of rows) to Table)
  - Should we make it a new package?
  - Will try to make backwards compatible
[TE] Change pinning to always show pinned panels? (#828)
- Yes, it is a better behavior
[RR] Package dependency ordering issue (#829)
- Will try to fix
[RR] Merging multithreaded-interpreter and JobManager
- Need examples of JobSubmission
[TE] Merging automatic-loops-streaming
- Try to merge with multithreaded-interpreter
Wiki menu looks strange in Chrome
- [TE] Will try to fix

Feb 26, 2014

Updates

Branch to be merged in: hidden-port-icon (v2.1)
[RR] tabledata-merge-tabdata: added tests, fixed issues (todo: json)
[TE] Added package RemoteQ (BatchQ/PBS/Hadoop)
- new Mac binary that includes everything here
[DK] gmaps, climate proposal

Items to Discuss

Climate proposal
- recommendation and best practices
- automatically segmenting the version tree, better modes of interaction
[RR] tabledata
- selections, projections, joins
- writing out table as csv?
- much improved bugs
- [DK] should merge aggregate module int
- [RR] working on different json representations
[TE] Hadoop configuration
- has package configuration now
- still have machine module to hardcode a configuration for a workflow
- http://www.vistrails.org/index.php/Hadoop_Package
Data cleaning/repo:
- always need the vistrails engine to run things
- scripting interface

Feb 19, 2014

Updates

[TE] automatic-loops-streaming works
[TE] Hadoop package:
- Merged BatchQ-PBS and hadoop into RemoteQ
[DK] improvements to tabledata, gmaps
[RR] java-pkg is done

Items to Discuss

[TE] automatic-loops-streaming
- Add documentation
- Perhaps a matplotlib example where the plot updates as more data streams
- Do we want to add additional controlflow features?
  - Implemented while module, but this needs to be improved because of annotations
  - annotations don't invalidate cache
  - could include annotations in hasher for cache updates
  - how does if module work?
- [RR] pairwise for three ports?
  - the list modules do this, but we may need an interface for this
- http://dev.mygrid.org.uk/wiki/display/taverna/List+handlings
[TE] Hadoop package:
- Best way to separate task and configuration parameters?
- URI is different for different clusters
- use package configuration variables
- move from checkbox to allow more general configuration?
- use configuration file for this?
[RR] working to merge multithreading code with job-monitor, look at streaming
[RR] java-pkg
- works for some classes (call constructors, setters, getters)
- cannot call any methods from VisTrails, don't want to mutate
- can call these methods from your own modules, also insert code in Python into these packages
- may add in an interface for loading jar files and wrapping them

Feb 11, 2014

Updates

[TE] automatic-loops-streaming - partially works
- Using a python generator for each streaming module
- TODO: Streaming Sinks
  - last module collecting values
- Logging/Feedback performance
- Demo?
[DK] vtk-new-package
[RR] java package: conflicts with dlls and jpype, going to work

Items to Discuss

[TE] Hadoop package:
- a few installation issues, vistrails-hadoop pkg on git but was not accessible to public
- same package for local cluster and aws? Yes, but need to change two lines, path to configuration files on server
- could config files be set in a module instead or in the preferences?
- directories are hardcoded in hadoop package, need to be parameters
- anything that can change in different installations should be parameters
- can be hard to figure out what does change
[DK] merge tabledata-merge-tabdata, matplotlib-add-helpers?
- examples are not very useful, no example with multiple plotline modules?
- Update matplotlib examples to better show off capabilities
[DK] package loading speed, kwargs
- kwargs can be significantly slower
java issues:
- [RR] should work, just a few installation issues
- machine learning in python: scikit-learn (http://scikit-learn.org/stable/)

Feb 5, 2014

Updates

[TE] automatic-loops
- PortSpec-based version now works
  - Connections show how modules will be iterated
- Streaming is tricky
[DK] Examples, merging tabledata

Items to Discuss

mailing list question
- no resopnse yet
UV-CDAT: warnings when downsizing spreadsheet
- problem: warnings will pop up a lot
- keep offscreen cache of (x,y) locations in spreadsheet?
- cache pipeline instead of full rendered pipeline
[TE] streaming with branches becomes interesting
- only want to update upstream branches once
- Taverna has streaming-style (pipelining)
PythonSource deleting port?
[RR] Java: possibly considering the matplotlib-style port creation versus java-style ports

Jan 29, 2014

Updates

[TE] automatic-loops - Groups and Multi-level looping now works
[DK] matplotlib-add-helpers: Rework the semi-automatic generators
[RR] java-pkg: bringing in old code, spreadsheet still works, probably going for dynamic generation of packages
- looking at jpype versus pyjnius

Items to Discuss

[RR] str-format-module: in master. Merge in v2.1? Having to open the configuration window and click on a button is awkward
- [DK] watch out for dynamically created format strings, could cause inconsistency at compute time if the format string doesn't match the ports
- Go ahead to merge since similar problem with PythonSource
- What about using number of connections to enforce this? (set to 0 for config-style ports?)
Streaming in VisTrails
- Q: how is parallelism working in VisTrails? A: both theading and multiprocessing, but separate branch
- for streaming, order of input and outut must be preserved
- module can generate a number of pieces, a module that collects needs to know when the stream ends
- need to preserve order of map operations and
- goal is to reduce the storage costs, want to make sure that we don't keep entire data in memory, don't generate the entire list at beginning
- hyperflow needs to know when a stream starts and when it ends: start and end token, hyperflow wraps data in a token
- Huy advises getting rid of the list and using tokens instead?
- interpreter can call compute-upstream and just tell interpreter to go upstream
- VTK streaming interpreter: might be in svn
- Remi: just be able to pass an object on the conection that knows the shape of the data and how to get next element (basically an iterator)
  - where do we call get-next? module in the collector calls
- main advantage of streaming is being able to do aggregation during the compute (otherwise, we're doing map-reduce)
- the iterator encapsulates the calls to the module's compute
- issue with logging? already rewritten for parallel, should work here
- Examples: triangle_area, image histograms
- Slowdown caused by lists? colors? logging?
- Schema changes: need to record depth, what type of semantics for combining port values
- Also probably means that we don't pass just raw values, need to wrap with depth and iterator
- Issues Huy raised:
  - issue with multithreading and streaming both enabled
  - triangle with modules: need to be careful about order with items coming from two different modules (e.g. BuildTable in Rémi's example)
UV-CDAT

Jan 22, 2014

Updates

[RR] Branches to be merged in: reload-disabled-package (#714), ungroup-keep-disconnected-ports_/hybrid
[TE] VisTrails 2.1.1 released
[DK] matplotlib, uuid work

Items to Discuss

[TE] Automatic Looping
- Using ListOf module as input will trigger the looping
  - Runtime type checking because we don't have a ListOfT class for each type.
  - [DK] USGS interested in working with this
  - Add a merge module to make it clear where the iteration stops and ends
  - Have different type of ports
  - Remi to talk to Huy about streaming ideas
  - can we detect the iteration and draw those modules differently
  - decided that some fold/merge module would be useful, even if we don't always need to use it explicitly
[RR] Ticking in matplotlib
- formatters, locators, tick scale
[RR] Sort tickets? There are issues for the 2.0 milestone and issues that affect released versions. Tickets assigned to 2.1 are here.
[DK] To contact USGS about the new persistence package and get feedback
[DK] Merge weather and subway examples to use new tabledata package
Look into pandas http://pandas.pydata.org/
- could be helpful to support some of the table operations
- in the future, we may want to support it for data analysis and stats (but for this, additional dependencies are required)

Jan 15, 2014

Updates

[RR] improves-logging:
- Pass exceptions to it directly for single line, or traceback.format_exc() for traceback
- WARNING level now printed in the console by default, -V 1: INFO (log() calls), -V 2: DEBUG (debug() calls)
- Messages view now shows whatever is selected, no matter the console log level
- Python warnings get captured
- Use warnings.warn(..., category=VistrailsWarning|VistrailsDeprecation) to warn once
- Backport to v2.1? (so deprecation warnings actually show up)
  - -> Yes, include in v2.1.1
[TE] Hadoop package documented here: http://www.vistrails.org/index.php/Hadoop_Package
[DK] UV-CDAT, LSU

Items to Discuss

[RR] input-module-no-subclass: input ports of type 'Module' shouldn't accept any output? These are used for 'self'->controlflow module connections...
- controlflow modules have a function port that accepts a module
- check for modules that might use Module for something else
- suggestion is to use Variant for any type being supported (StandardOutput, List, others)
- warns for now (doesn't actually disallow the connection until next version)
- -> David wants to look at this more
[RR] ungroup-keep-disconnected-ports: alternative ungrouping, keeps pipeline disconnected and preserves InputPort/OutputPort modules
- ideally, want to edit in place, could try to emulate the edit subworkflow code here, just have to save things back to the original vistrail
- -> hybrid approach, materialize the unconnected ports
Bugfix release? Would solve issues with server and parameter exploration. (also, logging improvement?)
- [TE] Also fixes to workspace
[DK] font issue for OS X 10.9
Look at Java support in Java?
- can we leverage Rémi's past work here? on Weka
- pyjnius: cannot subclass a Java class in Python, should be able to create and call out to java classes
- issue with Jython is the interface
- also had java-based spreadsheet
also look at moving VTK to a matplotlib style generation

Jan 8, 2014

Updates

[TE] Hadoop package: Added -combine option for Cs9223_Mapreduce_Assignment
- tricky to set up the package still, need documentation to understand how to assemble workflows from scratch
[RR] Logging improvements underway (branch 'improves-logging')
- Fixes some logging gotchas
- Better exception printing (pass them directly to critical|warning|log)
- WARNING is now the default level for the console (only CRITICAL displays a popup)
[RR] Alternative Mac .app (example dmg)
- Standard build of Python (currently as a Mac .framework)
- Have to relink libraries with install_name_tool
- Seems to work
- Advantages: standard, full build of Python; pip will work
- Last problem: if Qt is installed, it gets loaded and conflicts with bundled Qt (I missed a dylib link)
[DK] Work with USGS, refactoring version trees

Items to Discuss

Colin's feedback on loops is that it has taken some time to wrap his head around what is going on
- what does Taverna do? automatically determines when a collection is being input and does iteration over the input and determines what output looks like
- look at what this would take, figure out what the best way to attack this (Automatic loops)
Colin also asked about use of persistence in another module

Jan 3, 2014

Updates

[TE] VisTrails 2.1 released
[DK] UUID branch, USGS work, upgrade recursion
- van Wijk on tree vis, and Buneman on XML Updates

Items to Discuss

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