Difference between revisions of "Development"

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== 2014 ==
See also the [https://github.com/VisTrails/VisTrails/wiki/Development Github wiki]
 
== 2017 ==
 
=== October 30, 2017 ===


=== November 19, 2014 ===
'''Updates'''
'''Updates'''
* [DK] PyQt5
* [RR] Running Python3 code


'''Items to Discuss'''
'''Items to Discuss'''
* [JF] Upgrade tree ([https://github.com/VisTrails/VisTrails/issues/949 #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 ([https://github.com/VisTrails/VisTrails/pull/27 #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 ===
* Installation:
** Use conda? (macOS hack to have .app bundle load conda-installed vistrails)
** Update conda recipe (pyqt4 restriction for now)
* Interpreter
* Release
* Integration
** hard to build same type of GUI in other apps that integrate core VisTrails (tend to use just the API)
** independent pieces of the GUI could be reused if they were more independent.
 
=== September 6, 2017 ===
 
'''Updates'''
'''Updates'''
* [RR] We moved to Github
 
* [RR] UV-CDAT moving to Github; UV-CDAT/VisTrails currently marked as fork
* [RR] Fixes for scikit-learn, tables, usagestats
** 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 [https://github.com/VisTrails/VisTrails/pull/956 #956])


'''Items to Discuss'''
'''Items to Discuss'''
* [RR] We are on Github!
** Please check [https://github.com/VisTrails/VisTrails/wiki/Development github-wiki/Development] for some guidelines on development
** Most importantly, be sure to check out tickets marked [https://github.com/VisTrails/VisTrails/labels/@question question] or [https://github.com/VisTrails/VisTrails/labels/@pending-review 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 [https://github.com/VisTrails/VisTrails/subscription 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 ([https://github.com/VisTrails/VisTrails/pull/27 #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 ===
* Stripped-down version of VisTrails to showcase new features?
** include meta-vistrail, bundles
** hide mashups, extra widgets, latex mode, etc.
* Interpreter
 
=== August 16, 2017 ===
 
'''Updates'''
'''Updates'''
* [TE] setting up buildbots to build the binaries
* [DK] meta-vistrail
** solved most of the issues
** Working actions: normal action in vistrail, pruning version tree, tagging operations, and change
** working on Windows buildbot
** Interface
 
'''Items to Discuss'''
'''Items to Discuss'''
* [RR] Job submission
* Notebook
** [https://docs.google.com/drawings/d/1NRHNwm48pgcAjMeat_zXNOLH-M4phPEkJ79TdyYaRKs/edit Flowchart]
* Interpreter
** JobMixin doesn't work for Rémi's use cases
* Web visualization packages (e.g. bokeh)
** Need to check on job more than once (based on signature, if server removed job, etc.)
** [https://github.com/VisTrails/VisTrails/pull/969 PR 969] has more details
** [TE] what if job failed or job has been submitted but isn't running?
* Pipeline templates
** Pull Request: [https://github.com/VisTrails/VisTrails/pull/27 #27]
 
* [RR] Github migration
=== August 2, 2017 ===
** 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'''
'''Updates'''
* [RR] Build scripts
* [DK] meta-vistrail work
** Tommy working on release scripts (updating version numbers in build scripts and splash screen)
** Extend Vistrail to MetaVistrail to support meta-actions
*** [TE] prepare_release.py updates version numbers, branch, hash, and splash (requires inkscape)
** Vistrail becomes less tied to workflows so it can also supporting versioning vistrails
** sdist and wheel ("PyPI" packages) fully automated, have [http://vistrails.poly.edu:9050/waterfall?show=pack-v2.1-sdist builder]
** conda too, [http://vistrails.poly.edu:9050/waterfall?show=pack-v2.1-conda 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'''
'''Items to Discuss'''
* [RR] Weird error in UV-CDAT has me baffled ([https://github.com/UV-CDAT/uvcdat/issues/843#issuecomment-60843062 #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 ===
* Interpreter
RR and TE meeting about job submission & RemoteQ status in VisTrails
** Using dask?
** Streaming an issue
* Notebooks
** What is an output of a module? (need to expose a specific output port or the entire module)
** Unifies some of the work from the script-workflow code


http://www.vistrails.org/index.php/JobSubmission
=== June 28, 2017 ===


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'''
'''Updates'''
* [DK] Testing UUID/SQLAlchemy branch
* [DK] Working on meta-versions
** would be nice to have pipeline and vistrail separate
** [RR] Then do we only have meta-actions, any change to the pipeline is a meta-action that adds a version that does the change?
** [DK] Yes?
* [RR] Notebook interface (Vizier) making good progress, figuring out cell outputs


'''Items to Discuss'''
'''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 ===
=== June 7, 2017 ===
 
'''Updates'''
'''Updates'''
* [TE] job-cache (merged)
* [DK] Merged UUID/SQLAlchemy branch with new bundle format branch, getting rid of the bugs
** 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'''
'''Items to Discuss'''
* (from last week)
* [RR] How to specify an "intermediate output" that should be presented to the user, from any module? (useful for notebook interface)
** Use Github and pull requests?
** Can designate in module description an output port
*** Have to find a way to import tickets from Trac
** Value has to be serializable
** Use a separate fork for UV-CDAT's vistrails?
** Should use the OutputModes work to handle multiple modes, configuration, selection, ...
** Check with Claudio
* [RR] Is VisTrails with SQL usable concurrently?
*** Claudio says yes
** [DK] Probably not, demo from [TE] exists
* VisTrails and ViDA?
* [http://i.imgur.com/nqjTolG.jpg 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
**** [http://mail.scipy.org/pipermail/ipython-dev/2014-October/thread.html#15145 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  [http://mail.scipy.org/mailman/listinfo/ipython-dev mailing-list] and [https://gitter.im/ipython/ipython gitter]


=== October 8, 2014 ===
=== May 10, 2017 ===
'''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'''
'''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? [https://github.com/UV-CDAT/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 [https://gist.github.com/remram44/978b23f2eac006d5a5bb 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 ===
* Identifiers
* Bundles & DB Code
* Interpreter
* Merge / Versioning Version Trees
* Python3
* Workings of List
* Packages: Wrappers + new Versions (VTK7)
* Script Conversion
* Intermediate Outputs: reuse output module work?
** would be useful for both workflows (run to a particular checkpoint)
** and useful for notebook interfaces
* SQL backend: does it allow for concurrent access?
** Yes, real-time collaboration work for concurrent single vistrail access
** Should be able to access different vistrails at once without issues
 
=== April 19, 2017 ===
 
'''Updates'''
'''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'''
'''Items to Discuss'''
* [RR] To review&merge: <tt>constant-classes</tt>, <tt>invalid-pipeline-hides-package-errors_/loops</tt> ([https://www.vistrails.org/ticket/901 #901]), <tt>version-flag</tt>
** 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 ([https://www.vistrails.org/changeset/968dede3c6bbe39aae9f37242af9cd2f0e61166e fix])
* [TC] have different namespaces with same modules
** using numpy docs to do most of the code generation


=== September 24, 2014 ===
=== April 5, 2017 ===
 
'''Updates'''
'''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'''
'''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 [http://build.remram.fr/builders/pylint/builds/1/steps/shell/logs/stdio/text 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 ===
=== March 8, 2017 ===
 
'''Updates'''
'''Updates'''
* [TE] Fixed database from command-line, server mode, command line flags
* [RR] Added a looping indicator on modules [https://github.com/VisTrails/VisTrails/pull/1217 #1217]
* [TE] Fixed slow view switching
** This makes it easier to understand what's looping, no need to follow edges and count
* [RR] Refactoring CLTools for integration in Docker package
* [RR] Will try to refactor autogenerated package logic next (need to update TensorFlow package for TF 1.0, should really be using this)


'''Items to Discuss'''
'''Items to Discuss'''
* [RR] unicode and python3 compatibility
* [RR] Problem with vtkRendererToSpreadsheet output mode: does it's own ModuleConnector handling, interfering with looping/streaming logic, to add the module ID on the renderers [https://github.com/VisTrails/VisTrails/issues/1216 #1216]
** [TC] <strike>Pull request doesn't change any behavior (text_type, or str)</strike>
** Can we move this up to the renderer modules?
** [TC] Many changes from py3 were backported to py2, no 2to3 conversion
** Thankfully RR couldn't find much of this madness in the rest of code (outside of controlflow and parallelflow)
*** 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)
=== February 24, 2017 ===
** 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'''
'''Updates'''
* [RR] Backported tabledata package: https://github.com/remram44/tabledata-backport
* [RR] Rich-text module documentation ([https://github.com/VisTrails/VisTrails/pull/1210 #1210])
* [TE] GUI Improvements
** Went over packages and fixed format; maybe we should have a test to validate RST?
** Added type checking in parameter view
* [RR] Single-instance shutdown with <tt>--remote-shutdown</tt> ([https://github.com/VisTrails/VisTrails/pull/1204 #1204])
** Switch to workflow info when no module selected
* [RR] Bundle installation not super reliable; probably need to go in and add checks for every usual environment
** 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'''
'''Items to Discuss'''
* Workflow longevity: mta example no longer works
* [RR] There are issues with list-depth
** Fernando suggested offering an option that saves the package (or a description of the package) together with the workflow
** Some VTK ports marked with depth=1 don't actually accept multiple inputs (vtkDataSetMapper)
** [DK] I agree, this had been talked about with the generic bundle support
** Issue with looping groups
** [TE] Everything stored in a zipped vt file, could also store to a directory
 
*** [DK] some support for this
=== January 25, 2017 ===
** [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'''
'''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'''
'''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 ===
* Scaling VisTrails
* sql-alchemy, uuid, bundle branches/merges
 
=== January 11, 2017 ===
 
'''Updates'''
'''Updates'''
* [TE] VisTrails 2.1.4 released
* [RR] New VisTrails version in Debian [https://packages.qa.debian.org/v/vistrails.html]
** [RR] Will update [https://pypi.python.org/pypi/vistrails PyPI] and [https://binstar.org/remram/vistrails Conda]. Note that this currently uses its own branch for 2.1.x (<tt>deployment/v2.1</tt>), will be easier in 2.2


'''Items to Discuss'''
'''Items to Discuss'''
* [https://github.com/UV-CDAT/uvcdat/issues/520 UV-CDAT Bug #520] and [https://github.com/UV-CDAT/uvcdat/issues/557 #557]: make sure we don't show errors for packages that don't load (put these at info level)
* [RR] Collaboration with school of medicine to port HiC-bench to VisTrails
** [RR] already created a branch with this name
** Have homemade workflow system based on R scripts and symlinks
* matplotlib and UV-CDAT: should be able to include freetype in binaries
*** Each steps has multiple sets of parameters
* [https://www.vistrails.org/ticket/886 Bug 886]:
*** Submits PBS jobs for each step with each set of parameters, using PBS job metadata to wait on previous step
** merge in this branch, perhaps not 100% ideal but still better than what we had
*** Gets all results in directory structure <code>step3-parameters/step2-parameters/step1-parameters/files</code>
** 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
** VisTrails improves provenance capture and makes editing pipelines easier
* [https://www.vistrails.org/ticket/892#comment:2 Bug 892]:
*** Need better support for aggregation (groupby operation might be good enough; pandas?)
** not pythonic to forceably squelch propagation
 
** should be a configuration option to do this
== 2016 ==
** add a filter to the root logger so that VisTrails messages can be controlled
=== December 14, 2016 ===
** 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 [https://www.vistrails.org/ticket/673 #673 (unicode)] and [https://www.vistrails.org/ticket/674 #674 (python3)]
* Relayout programmatically?
** [http://git.io/MR0hZw layout_modules()] in controller


=== August 20, 2014 ===
'''Updates'''
'''Updates'''
* [TE] Parameter Exploration bugfixes
* [RR] Single-instance code: over-engineered, but will work
** "Create Version" spreadsheet button fixed
** (Have to avoid race conditions on startup, and OSes offer very different locking primitives)
** Missing date attribute in xml caused errors
** Issue opening vtl links


'''Items to Discuss'''
'''Items to Discuss'''
* [RR] Pending branches:
* Email from Matt Dirks: combobox should work, ask for more code?
** pipeline-validation ([https://www.vistrails.org/ticket/886 #886])
* Email from marin.nl:
*** (dep for fix-open-workflow (loading a workflow keeps the locator, so saving will overwrite))
** looks like they would benefit from new interpreter
*** Ok, will merge
** how to store their consolidated provenance when they exchange .vt files around?
** logger-propagation ([https://www.vistrails.org/ticket/892 #892])
*** Might be a better way? Discuss this more?
** hide-missing-dependencies ([https://www.vistrails.org/ticket/895 #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 ([https://www.vistrails.org/ticket/898 #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 [https://www.vistrails.org/ticket/685 #685] then [https://www.vistrails.org/ticket/396 #396]


=== August 13, 2014 ===
=== November 30, 2016 ===
'''Items to Discuss'''
* [TE] FileOpen event on Mac ([https://www.vistrails.org/ticket/889 #889])
** We can pass argv to QApplication
* [TE] 1.0.3 schema differences ([https://www.vistrails.org/ticket/894 #894])
** We can restore schema 1.0.3 on master from branch v1.2


=== August 6, 2014 ===
'''Updates'''
'''Updates'''
* [DK] bug fixes, improve-vt-bundle, uvcdat


'''Items to Discuss'''
'''Items to Discuss'''
* [LB] LSU, instrument building, tomography, interferometry system
* [RR] Working on single instance code for MARIN ([https://github.com/VisTrails/VisTrails/pull/1205 #1205])
* [TC] image registration/processing, infrastructure at BNL
** Remote shutdown ready ([https://github.com/VisTrails/VisTrails/pull/1204 #1204])
* [ED] working on data analysis at BNL, hoping to leverage VT for data provenance, user activity
** Still improving it
* [LB] tomopy and VT integration
** Want to return something more structured to the client (success/fail code, stdout, stderr)
* [TC] how to integrate tomography software
** Should be usable without Qt
* [LB] goal to communicate with others, data security for crowdLabs?
* [DK] Shutting down VisTrails has issues: cleans up interpreter (to remove files) but also resets persistent pipeline for no reason
* [LB] improve parameter exploration
* [DK] Working on batch execution using console_mode
** [JF] different ways: whole workflows, loops inside workflows, multiple threads, implict looping
* [DK] Settings aliased parameters when using core.api?
** [TE] add new examples of saved parameter explorations, different versions
 
* [RR] Bug [https://www.vistrails.org/ticket/886 #886] ("from_root" parameter for <tt>change_selected_version()</tt>)
=== November 16, 2016 ===
* [RR] [[API Design|API redesign]], example: [http://nbviewer.ipython.org/gist/remram44/2a67e6269ba2f052a19d notebook], target: [http://nbviewer.ipython.org/gist/remram44/a59a6dbf2026a0433ede notebook]
** [DK] looks good, nicer string rep, improve access to and use of results is important
* Jeffrey Guenther - list handling


=== July 30, 2014 ===
'''Updates'''
'''Updates'''
* [DK] UV-CDAT animation, sql-alchemy branch update
 
* [RR] Issue [https://github.com/VisTrails/VisTrails/issues/1200 #1200] from @samtux: need to set PyQt to API version 2 before ever importing it; using require_pyqt_api2() does that (also can install bundle)
 
'''Items to Discuss'''
'''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 [[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 ===
* Email from Pieter: executing pipelines with parameters from command-line using single-instance
** Seems to work, main instance gets full command-line and alters configuration temporarily
** Not sure what his error is (VisTrails returns little information in a lot of cases); though execution error should return something more meaningful
** Actions:
*** Can add switch to kill main instance
*** Can improve single-instance code to return more meaningful errors + machine-readable output from "client" VisTrails
*** Add client/server code to <tt>core</tt> that doesn't use Qt? Also need a run.py-line entrypoint that doesn't use gui (calls console mode like <tt>gui.application.VistrailsApplicationSingleton#noninteractiveMode()</tt>)?
 
=== November 2, 2016 ===
 
'''Updates'''
'''Updates'''
* [DK] output-modules merge, uvcdat, improve-vt-bundle
 
* New version 2.2-2 of Debian package, still [https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=796994 wrong copyright], and [https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=748692 broken bundle installation]
** Finally replied, says copyright issue will be fixed soon, working on including VisTrails 2.2.4 for Debian Stretch
* Working on Docker package, low hanging fruit because we have CLTools, and useful for some workflow (also step towards CWL support)


'''Items to Discuss'''
'''Items to Discuss'''
* API design [[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 [https://github.com/Psycojoker/redbaron 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 ===
=== October 5, 2016 ===
'''Updates'''
* [TE] VisTrails 2.1.3 released
* [DK] UV-CDAT


'''Items to Discuss'''
'''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, [[API_Design|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 ===
* working toward a 3.0 release; [https://github.com/VisTrails/VisTrails/projects/1 project board]
** unique ids
** bundles
** GUI fixes
** wrapping updates
** python3
** interpreter?
 
* command-line input parameters to provenance
** [DK] we don't create a persisted workflow from those input params, i think
** [DK] these are already defined as aliases so we treat them differently form a normal input param
** [DK] still have the potential problem of allowing a user to view the workflow as it was run with a given set of aliases
** Do the vistrails variables values get stored in provenance? (what if values change?)
 
=== September 14, 2016 ===
 
'''Updates'''
'''Updates'''


'''Items to Discuss'''
'''Items to Discuss'''
* Claudio wants to make it easy to edit PythonSource without VisTrails
* [RR] [http://aosabook.org/en/vistrails.html VisTrails] in [http://aosabook.org/ The Architecture of Open Source Applications] Vol I (2012)
** [RR] Dropping url-encoding would allow you to edit them from XML? But they are also quoted because used in <parameter val="..."/>
** Did we know/contribute to this?
* Scripting support
*** [DK] Yes. We wrote the text for the VisTrails chapter
** Export workflow as standalone script:
** Drafted response
*** Modules could provide their own logic, or we can make something up from compute() ast in some cases
*** [DK] Looks good, will forward.
*** Also, add annotations to script to make it easy to reconstruct (and module IDs, so we can update)
 
** Read back script as workflow
=== August 31, 2016 ===
*** 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! (<code>app.new_vistrail(), ..., api.save_vistrails(f)</code> instead of <code>vt=Vistrail(), ..., vt.save(f)</code>)
** Should probably be in vistrails package directly


=== July 9, 2014 ===
'''Updates'''
'''Updates'''
* [TE] Added logging of parameter explorations
* [RR] Went over vgc.poly.edu/vistrails.org config:
** Added TLS certificate (vistrails.org, www.vistrails.org, lists.vistrails.org, vgc.poly.edu and a few others)
** Fixed usersguide scripts (won't disappear again)
** Moved some websites over to HTTPS
** [https://docs.google.com/document/d/18YZewjR2YY9cQ9pzdA-nU9jbu2L7jYcPlDi3iaPadwA/edit Websites]
* [RR] users' guide on readthedocs: doesn't seem like we can have both the internal docs ([http://vistrails.readthedocs.io/ currently there]) and users' guide under the same RTD "project"
* [DK] UUID support almost complete (use-uuid branch), bundle translation then fits more easily on top of that


'''Items to Discuss'''
'''Items to Discuss'''
* [TE] Crash when adding String module on Mac [https://www.vistrails.org/ticket/760 #760]
* [RR] Move www.vistrails.org (wiki) to HTTPS? There is a trac at https://www.vistrails.org/
** Updated binary to Qt 4.8.6
** Get rid of more services? (svn, trac, ...)
** Release 2.1 with Qt 4.8.6 to fix String module crash
* [RR] Notebook execution works. How do we support more languages (than Python)?
* [TE] Table cell - Use HTML cell and D3?
** Need: detection, metadata reader, code to input values
** Interactivity for free
* [RR] ALPS and VisTrails 2.1 issue: should be using 2.2?
** Can it work over multiple cells?
 
** Will work directly on web and crowdlabs
=== August 17, 2016 ===
* [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 [http://cycling74.com/products/max max] and [http://grasshopper3d.com grasshopper3d]
*** Claudio wants to test how parallellization works in VisTrails
*** How would scripting support work?
*** Meet on Friday


=== July 2, 2014 ===
'''Updates'''
'''Updates'''
* [TE] List handling improvements done
* [TE] Fixed [https://github.com/VisTrails/VisTrails/commit/2cd42d156243067a7663bb0bf0156e5d87188c2f parameter order upgrade bug] that breaks VTK examples.
** Now List ports can connect to anything
* [TE] Matplotlib and sklearn are exportable using module-to-script api
** Only exception is List<->Variant
* [TE] Need to add to_python_script to pythonfunction.py to get bokeh and numpy export working.


'''Items to Discuss'''
'''Items to Discuss'''
* [DK] List/Variant bug: [https://www.vistrails.org/ticket/871 #871]
* Version checks: Please use a method instead of hard-coded `try: int(v) except ValueError: ...` logic!
** [TE] Fixed
* Mashups: why do they share the same id scope?? (see MashupsManager.createMashupController)
** [TE] Why is Map output a Variant?
* [TE] Wrap-up notes
** 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
=== August 10, 2016 ===
* [RR] added List.head as depth 1 port
** add documentation for this new functionality
* [DK] QPipelineScene.current_pipeline, controller refs [https://www.vistrails.org/ticket/869 #869]
* [DK] PythonSource crash? [https://www.vistrails.org/ticket/760 #760]
** update Qt for newer binaries?
** pyside support?
** Also, see [https://www.vistrails.org/ticket/737 #737]
* [TE] Log Parameter Exploration? [https://www.vistrails.org/ticket/870 #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'''
'''Updates'''
* [DK] master merged into output-modules


'''Items to Discuss'''
'''Items to Discuss'''
* [DK] Global configuration settings for output-modules when using inheritance:
* [TE] Python Wrapper and scripting
** Example: Allow different file.suffix='.dat', imageFile.suffix='.png'?
** All changes merged into python-wrapper branch
** 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?
*** Tests pass
** decided that overriding for specific subclases makes sense
*** Still need to update sub-branches
* [TE] automatic-looping
** Minor fixes
** get_input now merges all connections when depth>0
*** vtkPlot3DReader upgrade bug
** Typechecking now respects configuration flags - fix for float/int reverted
*** Added tuple exporting
** Issues with allowing List<->"Type of depth 1" conversions
** Most of vtk examples can be exported [https://gist.github.com/rexissimus/5ac7374cde8525d84f9443f019d234e2 example]
*** Treat list as Variant of depth 1
*** Sometimes connections are wrong, executing workflow sometimes works, otherwise copy/pasting is necessary
*** List->Variant need to be treated differently otherwise it would loop over the variant
**** Could be a bug in the old vistrail, but not sure
** wouldn't be able to do implicit looping over List/Variant because we don't know what the list depth of incoming list objects?
* [DK] Subworkflows and uuids
* [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 ===
=== August 3, 2016 ===


'''Updates'''
'''Updates'''
* [TE] Chris is using BatchQ
 


'''Items to Discuss'''
'''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
** [http://mpld3.github.io 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 ===
* [TE] Wrapper patches now stored as [https://github.com/VisTrails/VisTrails/blob/python-wrapper-script-patches/vistrails/packages/vtk/vtk_wrapper/vtk_patch.py python code]
** Connection variables now lowercase
** Can we use code as output variables?
*** E.g. "vtk_dataset_mapper.GetOutput(0)"
*** Could mutate output when output method is only supposed to be called once
*** Need to be able to rename output port as python code(e.g. when there are 2 "vtk_dataset_mapper"s)
 
=== July 27, 2016 ===


'''Updates'''
'''Updates'''
* [TE] RemoteQ jobs can now skip upstream
 
* [TE] Fixed zipfile bug corrupting vt files
* [DK] DB bundle serialization implemented
* [TE] Fixed ungrouping caused by
* [TE] Google maps binary available
** Updated for zipfile bug but not for ungrouping bug yet


'''Items to Discuss'''
'''Items to Discuss'''
* [TE] Finished using patch in script [https://github.com/VisTrails/VisTrails/tree/python-wrapper-script-patches python-wrapper-script-patches]
** locale?
** [https://gist.github.com/rexissimus/f0d6b026aa5a2a770847f3321744645d new patching example] vs [https://gist.github.com/rexissimus/b28d83ae516a519167f5751bb8ab3739 old patching example]
** [https://github.com/VisTrails/VisTrails/blob/python-wrapper-script-patches/vistrails/packages/vtk/vtk_wrapper/parse.py#L135-L273 Example of new patches]
** Legacy '.vtkInstance' is now added as a patch "self.vtkInstance=self" (see new patching example)
** [https://github.com/VisTrails/VisTrails/blob/python-wrapper-script-patches/vistrails/core/scripting/api.py New api for executing standalone modules]
*** Accessing module was disabled for core/api, but a different api for this is probably better anyway.
*** api.Package now gives [https://gist.github.com/rexissimus/f0d6b026aa5a2a770847f3321744645d#file-new_patching-py-L26 directly callable module compute functions]
*** Only works on modules not using interpreter functionality ('.interpreter', etc.)
**** for zip file modules and others that need temp files and use the interpreter for this, need to modify the module, but could work around with python libraries for managing temp files
** Fixed more renaming issues - [https://github.com/VisTrails/VisTrails/blob/python-wrapper-script-patches/vistrails/core/scripting/scripts.py#L63-L64 function argument names should not be replaced]
** Still need to do something nicer for the patch formatting
*** patch keys currently contain non-python-variable characters but this can be fixed
*** Need to replace string template with python variables that is replacable using RedBaron
**** Patches could then look like:


* [TE] File as parameter is confusing
    def vtkInstance():
** signature changes with mtime
        self.vtkInstance = self
** 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 ===
=== July 20, 2016 ===


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


'''Items to Discuss'''
'''Items to Discuss'''
* [TE] Test run.py [https://www.vistrails.org/ticket/863 #863]
* [TE] New patch method for python-wrapper [https://gist.github.com/rexissimus/009b303e4cadcd4b8f2fec6cf848cb2b example]
** Changes in run.py are currently not detected by test suite
** A patch is a string template with self/input/output variables for patching a class method
** Other changes in configuration also don't get tested
** Patches are stored in xml specification
** What about importing unittest2 in 2.6?
** Patches are assigned to methods in ClassSpec's
* [DK] userpackages/packages shadowing [https://www.vistrails.org/ticket/864 #864]
** Used both for execution in vistrails and when exporting as script
** add the directory
*** Executed with "exec" when run in vistrails
** being able to see both the package that exists in userpackages and packages
*** Turns patches into natural calls in script
** checking loading/unloading
** Wrapping VTK library no longer needed
* [DK] need to improve upgrade utility methods
*** Removes ".vtkInstance" (Automatically removed from PythonSources and vtkInteractionHandlers)
* [RR] Removing zip/unzip executables [https://www.vistrails.org/ticket/862 #862]
** Removed fix_classes.py (Subclassing of VTK classes to patch methods directly)
** check in the old commit logs and/or trac to figure out what the old problem was
** Also used for port translations (With patch names like "basic:Color#input") (No more ugly input_t method definitions)
* [RR] Rolling out conda packages: anyone has experience with Anaconda?
** TODO's
*** Add to export_as_script
*** Patch Modules that represent Python functions as well


=== May 28, 2014 ===
* [vistrails-users] Read data from SQL example?
 
=== July 13, 2016 ===


'''Updates'''
'''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
 
* [DK] bundles on sql-alchemy branch
** Bundle, BundleMapping, and BundleSerializer
** New BaseSerializers to deal with versions of directory, zip, db serializers
** Can register the BundleSerializers with the base serializers
** Translation between bundle versions
** Bundle.add_object "just works" if an appropriate mapping was registered


'''Items to Discuss'''
'''Items to Discuss'''
* [DK] extra_info on modules: is it really module-specific info?
* [TE] Simplified running module using API for scripting [https://gist.github.com/rexissimus/b28d83ae516a519167f5751bb8ab3739 example]
* [DK] programmatic package configuration settings without direct imports?
** API Module can be executed using '''compute''' method
* [TE] job-cache
*** Takes list of outputs to compute + inputs as keyword arguments
** New control parameter for caching module outputs to disk
* Status of general cell synchronization (vistrails-users)
** 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 ===
=== July 6, 2016 ===


'''Updates'''
'''Updates'''
* [DK] output-modules, MplFigureToFile
 
* [TE] VisTrails 2.1.2 Released (100 downloads so far)
* [DK] Working on bundles
 
'''Items to Discuss'''
'''Items to Discuss'''
* [DK] persistence across machines (USGS use case)
* [TE] Using vistrails API in scripting [https://gist.github.com/rexissimus/034d9c4dedc3299a079e84981dedd8c7 example 1 (API with VTK)] [https://gist.github.com/rexissimus/a4a9ca6c08d4058c64967d2b35415fd5 example 2 (DownloadFile only)]
* [TE] Merge automatic-loops-streaming into master?
** Call module in script using vistrails API
** Implicit looping
** Can be used when no export method is defined.
** Streaming
* [TE] [https://github.com/VisTrails/VisTrails/commit/c76c109349769fee1280f85c22678380a2f9cd39 Server news bug] Critical?
** ControlParameters
**[RR] No, unreleased
** New schema version 1.0.4
* [DK] New bundle organization
** Possible conflict with multithreaded-interpreter?
** BundleMapping contains individual mappings from raw objects to BundleObj
* control parameters can also be used for other things like caching?
** Must be separate in order to have in-memory, separate from serializer settings
* [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] [http://saga-project.github.io/saga-python/ 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 ===
=== June 29, 2016 ===


'''Updates'''
'''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'''
'''Items to Discuss'''
* vagrant for reproducibility
* [TE] Export VTK as python script
** simpler interface for exploring the experiments
** Works on Terminator (Isosurface, Volume Rendering, clipping plane, combined rendering) [https://gist.github.com/rexissimus/16caf5200802e150296f62a0c7844c5a example]
** [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
** Preludes (imports) still need improvements
** Works with vtkInteractionHandler (clipping plane)
** Resulting clipping plane is incorrect? (supposed to hide one side of the plane)
** vtkRendererOutput Uses VTKRenderWindow as output
*** Should support different output modes?
*** Does not work with multiple outputs (Next cell is displayed when current is closed)
*** Uses wrapped vtkInstance (as vvtk)
**** Create new patch system with code that can be used both in vistrails and in a python script?


=== May 7, 2014 ===
=== June 22, 2016 ===


'''Updates'''
'''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'''
'''Items to Discuss'''
* VTK 6
* [TE] Fix for upgraded analogies (PR [https://github.com/VisTrails/VisTrails/pull/1177 #1177])
* [DK] output-modules: target single module parameters?
** Uses module location to find module remap (The best we can do right now?)
** [RR] use labels to name specific modules, useful in command-line
** Also fixes remapped port names for connections to existing modules  
* scripting support
** May still fail on complex upgrades like adding a function on an upgraded module that has a different port name


=== Apr 30, 2014 ===
* [TE] Working on exporting wrapped libraries (VTK)
 
=== June 15, 2016 ===


'''Updates'''
'''Updates'''
* Does spreadsheet resizing work correctly? Is it too slow? ([https://www.vistrails.org/ticket/833 #833])
* [TE] Added depth logic to python script exporter ([https://github.com/VisTrails/VisTrails/commit/50f220e4f6abe5a7bb8689f73f456f43df2dbc12 full commit])
** looks like on downsize the image is smaller than it should be and then flickers to flll space (upsize is ok)
** Fully implements connection merging and list looping
* [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'''
'''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 ===
* [TE] Making analogy work on upgraded workflows ([https://github.com/VisTrails/VisTrails/issues/1175 #1175])
** Analogy only works We need to use the non-upgraded action chain
** But pipelines need to be valid (matcher uses module portspecs)
** Tried to get upgrade remap from upgrade action, but this seems impossible
** Use module location instead?
*** Location should be identical for one-to-one module upgrades
 
=== June 1, 2016 ===


'''Updates'''
'''Updates'''
* debugger
* VisTrails 2.2.4 announced (finally)
** have to enable the configuration option, starts python debugger in console
** 5 survey replies
** have similar flag for test suite
** 47 downloads last week
* 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'''
'''Items to Discuss'''
* output-specific modules (e.g. vtkInteractionHandler)
* [TE] Export VTK as script (python-wrapper)
** 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
** to_python_script
** not verify entire workflow?
*** needs the pipeline (or at least the connections)
** load module logic on-demand so we don't need dependencies?
**** Should not  generate code for any possible VTK method (exporter detects which ports is used in the source)
* reload packages
**** VTK needs to know connection order
** interactions with spreadsheet, stale controller objects
**** Adding functions directly to the script results in nicer code
** spreadsheet may need to get information about pipeline when copying cells (get from controller?)
** Add support for multiple input connections
* [TE] server mode
** Add support for list looping
** 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 ===
=== May 25, 2016 ===


'''Updates'''
'''Updates'''
* Branches to be merged in: readfile-module, save-module-moves ([https://www.vistrails.org/ticket/853 #853])
* Mailing-list fixed
* CrowdLabs needs update to VisTrails 2.1 with schema 1.0.3
* Getting stats from the "server news" mechanism (via [https://github.com/remram44/apache-log-info parser])
* [DK] OutputModules (FileOutput)


'''Items to Discuss'''
'''Items to Discuss'''
* LSU meetings
* [RR] Alexis doing writeup on VisTrails, curious about interesting streaming use-cases (and potential future users)
** Pausing workflow/confirmation module ([https://www.vistrails.org/ticket/854 #854])
* [TE] Union ports
*** Checking an intermediate result before carrying on with the workflow
** Show union ports in pipeline (DEMO)
*** 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 [http://www.kiwiviewer.org/ KiwiViewer]
** Wrapping SNARK09 (C++ code) as VisTrails modules
* eo4vistrails (Derek, Terence)
** Add FTP module?


=== Apr 9, 2014 ===
=== May 18, 2016 ===


'''Updates'''
'''Items to Discuss'''
* Branches to be merged in: export-cells, reset-cell-sizes-button (-> v2.1; icon?), export-versiontree-dot & custom-colors, input-module-no-subclass
* [TE] mailing list still down - Julio working on it
* [DK] UV-CDAT release, OutputModules (see below)
* [TE] Improved union port
** New schema 1.0.5 adds portitem.union string attribute
** Works with pipeline view, parameter exploration view, and mashup view
** Should work well for matplotlib
** Use with VTK ports?
*** It uses [item_1,item_2] style ports usually with different tuple length.
* [TE] Remove emacs dependency from db generate [https://github.com/VisTrails/VisTrails/issues/1173 #1173]
 
=== May 11, 2016 ===


'''Items to Discuss'''
'''Items to Discuss'''
* In-place spreadsheet updates: [https://www.vistrails.org/ticket/847 #847]
* [TE] Union type [https://github.com/VisTrails/VisTrails/issues/1172 #1172]
** need to be able to replacement mode toggle on and off
** GUI-based solution [https://github.com/VisTrails/VisTrails/tree/union-port Branch union-port] Demo?
** Colin has a working solution, is there a need to do this globally?
*** Shows single port for all ports with same sort_key
* Autosave for existing vistrails not working <strike>[https://www.vistrails.org/ticket/849 #849]</strike>
*** Select specific type when adding/showing
* Other tickets from USGS
*** Only one type should be visible on the module at any time
** Reason for pipeline scroll area being 100 times greater than pipeline?
*** Making tuple parameters union types is probably too complicated
** File Selection Dialog <strike>[https://www.vistrails.org/ticket/846 #846]</strike>
*** Should work with alternate specs like matplotlib (if sort_key is defined correctly)
** Copy/paste with retained connections [https://www.vistrails.org/ticket/851 #851]
 
** Auto-connect ports when moving modules [https://www.vistrails.org/ticket/852 #852]
* [TE] Feature suggestion: Let connections connect to functions/parameters
*** 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
** Show functions and parameters as ports and toggle port visibility directly for functions and parameters
* Unicode support
** Use separate views for ports and functions (like before)
** question on mailing list
*** Allow rearranging of functions
** [RR} dates is something else, should be able to put on v2.1
** Pros:
** fix for LC on master, port to v2.1?
*** Supports ordered connections. Create 2 functions, make them visible as ports, make connections to them.
** should try to persist dates in numeric formats, but GUI level can be language-specific.
**** We can also have, e.g., a line joining the ports on the module to indicate they are part of a list.
* VTK 6 support [https://www.vistrails.org/ticket/739 #739]
**** Makes List module simpler
* [TE] Analogies does not delete annotations [https://www.vistrails.org/ticket/848 #848]
*** Connect to parameter in tuple
** Code never worked as intended
*** Functions that are visible on the module can connect to an actual function, and not just to the first one it finds.  
* [TE] Add eo4vistrails features to vistrails? https://github.com/ict4eo/eo4vistrails
*** Can replace operation modules (in python-wrapper) in some cases for, e.g., numpy.
** Look at these and try to determine what may be appropriate
** Cons:
** data types are probably most important, doesn't look like anything there
*** Interface more complicated and crowded
* [DK] [[OutputModules]]
*** More difficult for users to grasp?
*** No immediate use case
*** Makes no union type for tuple parameters a bigger problem.


=== Apr 2, 2014 ===
* [TE] Publish user survey?
** No response from vistrails release yet
** Not announced on vistrails-users yet.


=== May 4, 2016 ===
'''Updates'''
'''Updates'''
* [TE] Added annotations and control parameters to visual diff
* VisTrails 2.2.4 released
** three tabs
** TODO: analogies
*** just work on making sure the actions execute, don't worry about the matching
* [TE] Build documentation using [http://128.238.102.101:9050/builders/usersguide-master 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 [http://128.238.102.101:9050/builders/coverage 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'''
'''Items to Discuss'''
* Unicode support
* [TE] Union type [https://github.com/VisTrails/VisTrails/issues/1172 #1172]
** 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 [https://www.vistrails.org/ticket/739 #739]
** trying to complete output modules before new VTK package
 
=== Mar 26, 2014 ===


=== April 27, 2016 ===
'''Updates'''
'''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'''
'''Items to Discuss'''
* iPython
* [TE] Wrapping Bokeh
** script to workflow bridge
** New method type "operation"
** access to VisTrails commands in iPython
*** Transforms Figure->Glyph->Output into Glyph->Figure->Output
** changes to the API
**** Glyph sets function name and arguments as output
* Multi-faceted output
***** Not serializable, but should always be computed together with the subject of the operation.
* [RR] Documentation buildbot
**** Figure applies Glyph operation on itself
** [TE] currently [https://www.vistrails.org/#Testing here]
*** Useful for matplotlib?
** problem is that we don't get a message when the documentation failed to build
**** matplotlib currently find actors by searching upstream?
** what about copying the output from a build machine to vistrails.org?
**** But this is more difficult since matplotlib is not function-based.
* [RR] Last(?) migration issue: [https://www.vistrails.org/ticket/837 #837]
** New "union" port type
** [DK] to look at
*** Turns "x(float), x(list)" into "x (float, list)" and uses first set value
* VTK 6 support [https://www.vistrails.org/ticket/739 #739]
**** Uses only first value in tuple
* spreadsheet export button in UV-CDAT
**** Bokeh have many properties that support (list, string, Float)
* Develop menu?
*** Does not work with depth=1 types (e.g. Float of depth 1)
**** Turn Depth 1 types with known type into lists?


=== Mar 19, 2014 ===
* [TE] New bugfix release
** Finalize survey


=== April 20, 2016 ===
'''Updates'''
'''Updates'''
* [DK] UV-CDAT #407 fix, version tree rewrites
* Merged upgrade fixes
** Now has infinite loop test
** loop test now correctly loops 5 times
*** remap_module used wrong (current) package version when creating ModuleDescriptor
* Fixed multi-step group upgrades (PR: [https://github.com/VisTrails/VisTrails/issues/1168 #1168])


'''Items to Discuss'''
'''Items to Discuss'''
* [TE] Cleaning up test suite log
* New bugfix release
** Deprecated core.modules.constant_configuration imports
** Merge usagestats
*** check whether the deprecations for vistrails.core.vistrails_module.VistrailsModule camel-case are similar
** Need to finalize survey
** KeyError (Ticket [https://www.vistrails.org/ticket/837 #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 [https://www.vistrails.org/ticket/739 #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 ===


=== April 13, 2016 ===
'''Updates'''
'''Updates'''
* [RR] Package dependency ordering issue ([https://www.vistrails.org/ticket/829 #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 ([https://www.vistrails.org/ticket/373#comment:7 #373], [https://www.vistrails.org/ticket/779 779]); 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'''
'''Items to Discuss'''
* [RR] Do not run modules upstream of submitted job
* [TE] Chaining upgrades done ([https://github.com/VisTrails/VisTrails/pull/1164 #1164])
** jobs-use-signatures: Uses the subpipeline signature to identify jobs
** Replace "Upgrade" description annotation with "upgraded_from" annotation to identify which tags to hide?
** 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: [https://github.com/UV-CDAT/uvcdat/issues/407 #407] and [https://github.com/UV-CDAT/uvcdat/issues/408 #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 [https://www.vistrails.org/ticket/831 #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 ===
* [TE] Iterating handle_invalid_pipeline ([https://github.com/VisTrails/VisTrails/pull/1165 #1165])
** Not based on [https://github.com/VisTrails/VisTrails/tree/chain-upgrades-loop chain-upgrades-loop]
** Cherry-pick test to preserve source?
** Need maxPipelineFixAttempts option?
*** The code is now smarter about recursion, so max attempts will "probably" never be reached.
** Need [https://github.com/VisTrails/VisTrails/commit/0ef0667426937eddb1d1c1e397f0657ffec039a9 debug messages]?
*** Would need to be moved into handle_invalid_pipeline


=== April 6, 2016 ===
'''Updates'''
'''Updates'''
* [TE] Query View improvements
** Done except for displaying "Version Info" and #1164
* [RR] Working on finishing new interpreter (finally!)


'''Items to Discuss'''
'''Items to Discuss'''
* [RR] New SQL package, using tabledata and sqlalchemy
* [TE] Chaining upgrades ([https://github.com/VisTrails/VisTrails/pull/1164 #1164])
** No upgrade possible? (output changed from List (of rows) to Table)
** Try latest upgrade first, then previous.
*** Should we make it a new package?
** If all fail, select latest upgrade?
*** Will try to make backwards compatible
* [TE] Change pinning to always show pinned panels? ([https://www.vistrails.org/ticket/828 #828])
** Yes, it is a better behavior
* [RR] Package dependency ordering issue ([https://www.vistrails.org/ticket/829 #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 ===


=== March 30, 2016 ===
'''Updates'''
'''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'''
'''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 ===
* [TE] Query View improvements
** Unified do_version_switch and get_upgrades as validate_version()
** Problems with query view using its own controller
*** Fixed module info not being displayed for query results
*** Still no version info for query results
*** Still an issue with version query view not being updated


=== March 23, 2016 ===
'''Updates'''
'''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'''
'''Items to Discuss'''
* [TE] automatic-loops-streaming
* [RR] Usage reporting almost ready to go
** Add documentation
** Need to record whether specific features are used: paramexpore, mashup, query
** Perhaps a matplotlib example where the plot updates as more data streams
*** [DK] Record if LaTeX extension is used? But hard to distinguish from direct batch invocation
** Do we want to add additional controlflow features?
** How to record size of vistrail?
*** Implemented while module, but this needs to be improved because of annotations
*** [DK] IdScope already walks over vistrail, use that
*** annotations don't invalidate cache
*** but total number of modules and versions doesn't give an idea of average size of individual pipelines
*** 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 ===
=== March 16, 2016 ===
'''Updates'''


'''Items to Discuss'''
* [TE] Upgrades in Query Mode
** Now using code similar to do_version_switch
*** Uses handle_invalid_pipeline
*** Differences: Not using current_pipeline, flushes changes
*** New controller method get_pipeline optimized using cached pipelines (but not current_pipeline)
*** Integrate to avoid repeated code?
*** Use this for query mode?
* [TE] VisTrails 2.2.4 ready for release?
** tej package updated. Others?
* [JF] upgrades and the version tree
* [JF] provenance in Jupyter
* [DK] bundles: [https://github.com/VisTrails/VisTrails/pull/1092 #1092]
=== March 9, 2016 ===
'''Updates'''
'''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'''
'''Items to Discuss'''
* [TE] Hadoop package:
* [TE] Fixing search mode
** a few installation issues, vistrails-hadoop pkg on git but was not accessible to public
** String query now matches all by default
** same package for local cluster and aws? Yes, but need to change two lines, path to configuration files on server
*** This caused pipeline queries to never match
** could config files be set in a module instead or in the preferences?
** String query can search: User/Notes/Tagname/Time/Module name
** directories are hardcoded in hadoop package, need to be parameters
*** Should we search module names by default? (Disabled by default because it is expensive)
** anything that can change in different installations should be parameters
*** Fixed notes search
** can be hard to figure out what does change
** '>' parameter queries in documentation but has been removed
* [DK] merge tabledata-merge-tabdata, matplotlib-add-helpers?
** Fixed module matches for upgraded pipelines (By not upgrading pipeline)
** examples are not very useful, no example with multiple plotline modules?
*** Upgrades still a problem
** Update matplotlib examples to better show off capabilities
*** Add "Upgrade all menu option?" (Or upgrade all on open when `hideUpgrades`)
* [DK] package loading speed, kwargs
*** [JF] Allow search on past tags
** 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 ===
* [TE] Create new bugfix release
** Finish querying
** Path issue on windows


* [DK] Look into sqlalchemy and new bundle branches
=== March 2, 2016 ===
'''Updates'''
'''Updates'''
* [TE] automatic-loops
* [TE] Fixed cache bug with port specs
** PortSpec-based version now works
* [TE] VisTrails Next
*** Connections show how modules will be iterated
** Most packages now work
** Streaming is tricky
** No qgis for Python 3
* [DK] Examples, merging tabledata


'''Items to Discuss'''
'''Items to Discuss'''
* mailing list question
** Always dereference symlinks? [https://github.com/VisTrails/VisTrails/issues/1146 #1146]
** 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 ===
=== February 23, 2016 ===
'''Updates'''
* [TE] Fixed PythonSource 100% CPU bug
* [TE] VisTrails Next
** Updated [http://opendap.co-ops.nos.noaa.gov/axis/webservices/wind/ NOAA Web Service] examples
*** Now uses REST service, tabledata, and Google Maps
*** Web Service replaced with DownloadFile
 
'''Items to Discuss'''
* [RR] Couple of fixes are in for API, and tej&reprounzip on the Mac binary. Also new release of tej, and working on anonymous usage reports.
** New 2.2 release soon?
* [RR] Anonymous usage reports
** Sends out info like number of modules & versions, packages used, Python & libs versions, execution time, specific features [https://github.com/VisTrails/VisTrails/pull/1154 #1154]
* [JF] Bring in noWorkflow to track variable dependencies, for the considered Jupyter integration?
* noWorkflow - provenance for python scripts
** Recent work on tracking dependencies
* Also integrates ReproZip with Jupyter
** [http://mybinder.org mybinder]
*** Use with ReproZip to automatically build Jupyter notebook interfaces
* Daves comments on Jupyter integration
** It is possible to identify cell order on the server side
** Not trivial to track order of cells on client side
* How does Galaxy workflows relate to VisTrails?
** Packaging in Galaxy is hard
** Galaxy for biomedical workflows, difficulty making it general
* Action items
** How difficult to track cell dependencies in Jupyter notebooks?
** Use noWorkflow to track cell dependencies?
** How difficult to modify mybinder to use ReproZip packages?


=== February 17, 2016 ===
'''Updates'''
'''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'''
'''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
* [TE] Fixed Group memory usage
** [DK] watch out for dynamically created format strings, could cause inconsistency at compute time if the format string doesn't match the ports
** Modules in groups are supposed to be freed when done executing
** Go ahead to merge since similar problem with PythonSource
*** Prevented by logger that stored references to the modules (fixed, now using id(module))
** What about using number of connections to enforce this? (set to 0 for config-style ports?)
*** Prevented by list iterator bug that stored list of modules on the 'self' port bug (fixed)
* Streaming in VisTrails
* [TE] VisTrails Next
** Q: how is parallelism working in VisTrails? A: both theading and multiprocessing, but separate branch
** Removed deprecated code
** for streaming, order of input and outut must be preserved
*** Core imports that should be gui imports
** module can generate a number of pieces, a module that collects needs to know when the stream ends
*** GetInputFromPort etc.
** need to preserve order of map operations and
**** PythonSources will be upgraded
** 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
*** Fixes for Python < 3
** hyperflow needs to know when a stream starts and when it ends: start and end token, hyperflow wraps data in a token
*** fixes for VTK < 6
** Huy advises getting rid of the list and using tokens instead?
** TODOs
** interpreter can call compute-upstream and just tell interpreter to go upstream
*** Remove RemoteQ
** VTK streaming interpreter: might be in svn
**** Port Hadoop to tej (Already have pbs)
** 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)
*** Merge package wrapper
*** where do we call get-next? module in the collector calls
*** Finish SQLAlchemy branch
** main advantage of streaming is being able to do aggregation during the compute (otherwise, we're doing map-reduce)
*** Finish new bundle branch
** the iterator encapsulates the calls to the module's compute
** [JF] Will contact Jeff and Matthias about moving to Python 3
** issue with logging? already rewritten for parallel, should work here
* [JF] Query by Example is broken
** Examples: triangle_area, image histograms
* [JF] VisTrails Data Cleaning Project
** Slowdown caused by lists? colors? logging?
** Use VisTrails to process and explore task-specific data while keeping provenance.
** Schema changes: need to record depth, what type of semantics for combining port values
** Remi's Idea
** Also probably means that we don't pass just raw values, need to wrap with depth and iterator
*** Use VisTrails as the backend in a Jupyter notebook
** Issues Huy raised:
*** Overcome problems with executing cells in random order
*** issue with multithreading and streaming both enabled
**** Interesting research topic, but little interest has yet been noted
*** triangle with modules: need to be careful about order with items coming from two different modules (e.g. BuildTable in Rémi's example)
*** Interesting to study how such a notebook would be used (Is there notebook usage data available?)
* UV-CDAT
*** Impose restrictions to notebook cell boundaries
*** It will only work for functional operations
*** Can we fix, or detect, non-functional (mutating) operations?
*** Analyse code and data flow and see if it mutates data in unexpected ways?
*** Mutable operations can be created in many ways in Python
* Next meeting Tuesday 11:30
 
=== February 10, 2016 ===
'''Updates'''


=== Jan 22, 2014 ===
'''Items to Discuss'''
* VisTrails Next
** Test suite passes
*** Python 3 less deterministic, module upgrade order random.
** [RR] updating packages: Reprounzip (pushed), tej, persistent_archive, ...
** All of our packages should run fine :)
** VTK thumbnail comparison works
*** Rendering bug on some systems
**** QVTKCell now inherits QGLWidget
*** Old thumbnails had wrong height due to spreadsheetwindow being too small
**** Fixed by regenerating thumbnails
*** Silenced deprecation messages when generating modules
*** Many new classes in VTK 7
** Remove deprecated code
*** Core imports that should be gui imports
*** GetInputFromPort etc.
**** Will break existing PythonSources
**** Try to upgrade?
*** Old-style packages
**** Or only allow a new style, like __init__.py renamed to info.py? (merge with identifiers.py?)
***** Read info.py without importing package?
*** Fixes for Python < 3
*** Fixes for Qt < 5
*** fixes for VTK < 7
*** Remove self port?


=== February 3, 2016 ===
'''Updates'''
'''Updates'''
* [RR] Branches to be merged in: reload-disabled-package ([https://www.vistrails.org/ticket/714 #714]), ungroup-keep-disconnected-ports_/hybrid
* [TE] VisTrails 2.1.1 released
* [DK] matplotlib, uuid work


'''Items to Discuss'''
'''Items to Discuss'''
* [TE] Automatic Looping
* [vistrails-users] [http://lists.vistrails.org/pipermail/vistrails-users/2016-January/000402.html Rendering a .pvd (ParaView) file?]
** 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 [https://www.vistrails.org/report/18 issues for the 2.0 milestone] and [https://www.vistrails.org/report/17 issues that affect released versions]. Tickets assigned to 2.1 are [https://www.vistrails.org/report/19 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 ===
* VisTrails Next
** All tests but thumbnail comparison passes
** Still issues with gui and more packages needs to be tested
** PythonSource and MplSource upgraded with lib2to3
** Keep contrib packages? Update?
** [https://blog.kitware.com/vtk-7-0-0/ VTK 7 is released]
*** Supports Python 3
*** Will hopefully get into conda and others soon
*** Deprecates a bunch of modules


* [https://travis-ci.org/VisTrails/VisTrails/builds/106743348 Travis builder] for VisTrails Next
** Runs!
** Uses conda
*** Many levels of requirements
**** apt packages
**** conda packages
**** python packages in requirements.txt
**** python packages in setup.py
*** Can probably drop conda. Default builder does not have Qt5, but beta builder do!
*** But useful if we want to use conda in our own build process.
** Lots of errors I do not get locally?
* [http://goo.gl/forms/Z4HBrwaBWL User Survey]
** Have you used any alternatives to vistrails?
*** Relevant? More options?
** How often do you use any of these particular features in VisTrails?
*** Add/Remove alternatives?
** How important would you rank the following potential improvements to VisTrails?
*** Add alternatives?
=== January 27, 2016 ===
'''Updates'''
'''Updates'''
* [RR] improves-logging:
* New interpreter
** Pass exceptions to it directly for single line, or traceback.format_exc() for traceback
** Working prototype soon
** WARNING level now printed in the console by default, -V 1: INFO (log() calls), -V 2: DEBUG (debug() calls)
** Looping not completely done (and port combination mode: pairwise/cartesian...)
** Messages view now shows whatever is selected, no matter the console log level
** Need to integrate with VisTrails
** Python warnings get captured
*** Compatibility with existing modules
** Use warnings.warn(..., category=VistrailsWarning|VistrailsDeprecation) to warn once
*** Use log controller
** Backport to v2.1? (so deprecation warnings actually show up)
*** Want to cache at multiple levels (whole stream/single element of stream)
*** -> Yes, include in v2.1.1
*** Non-runtime attributes of modules (cache check, automatic conversion check, constant from/to string)
* [TE] Hadoop package documented here: http://www.vistrails.org/index.php/Hadoop_Package
* [DK] UV-CDAT, LSU


'''Items to Discuss'''
'''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...
* User Survey
** 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 ===
* ZMQ failing on windows (vistrails-users)


* [TE] [https://github.com/VisTrails/VisTrails/pull/1143 Python 3 branch]
** Testsuite almost passes
*** Failing are unicode filenames, some users guide examples, and thumbnail comparisons.
** Fixed issues
*** Signatures are now bytes (convert to string to show in widget)
*** Cannot compare different types, e.g.,  (None < 1)
**** PortSpec.depth and min/maxConn could be None. (Backport!)
**** cell.row could be None
*** Lots of unicode/bytes fixes to serializations
**** We have encryption implementations in the code! (keychain)
*** Lots of small fixes to package method differences
** Current issues
*** logging widget empty?
*** version tree signals messed up
*** provenance view legend icons black
*** Text do not fit in some widgets
*** VTK thumbnail comparison fails
**** VTK Cells have some faces in wrong direction?
****  Because running in VM?
** Installing on Ubuntu LTS/Latest Mint
*** Install latest matplotlib from pip
*** Install VTK 7.0.0rc2 from source
*** No QtWebEngine binary (controversial) (Must install sip/PyQt5/Qt5 from source)
=== January 20, 2016 ===
'''Updates'''
'''Updates'''
* [TE] Hadoop package: Added -combine option for [http://www.vistrails.org/index.php/Cs9223_Mapreduce_Assignment 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 ([https://docs.google.com/uc?id=0B3ucPz7GSthBZG5TS2pXUVdUWEk&export=download 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'''
'''Items to Discuss'''
* Colin's feedback on loops is that it has taken some time to wrap his head around what is going on
* [TE] Backporting features from Python 3 + PyQt5 + Qt5
** what does Taverna do? automatically determines when a collection is being input and does iteration over the input and determines what output looks like
** Merged unicode with master ([https://github.com/VisTrails/VisTrails/tree/unicode unicode])
** look at what this would take, figure out what the best way to attack this ([[Automatic loops]])
*** One unicode test failing
* Colin also asked about use of persistence in another module
*** Problem saving to xml
** Used [http://python-future.org/ python-future] to run futurize stage 1 to update legacy (pre 2.6) code ([https://github.com/VisTrails/VisTrails/tree/unicode-futurized unicode-futurized])
*** Updates print to functions 'from __future__ import print_function'
*** Updates exception calls to use 'as'
*** removes most usages of 'long' (mostly used unnecessarily)
**** Only needed for 32-bit support
*** Fixes relative imports (from __future__ import absolute_import)
** Fixing code that is deprecated in Qt 4.8 and removed in Qt 5 ([https://github.com/VisTrails/VisTrails/tree/unicode-futurized-qt5 unicode-futurized-qt5])
*** Updated all signals to new-style
* If we go 2 to 3, this could break packages
** means we should schedule any package format changes for the same time
** e.g., imports should be unrelated to code path (function to load module from package identifier?) (take them out of vistrails.* [https://github.com/VisTrails/VisTrails/pull/1002 #1002])
** any structural changes (e.g. the __init__ versus init thing) (RR thinks it makes sense, though having both named "init" is unfortunate)
** putting package identifier as xml?
*** Python not so bad, plus some stuff in there is Python code (checking dependencies)
** version the APIs?
*** RR planning on versioning vistrails_module.Module, no point versioning the whole package?
* file formats on 2 to 3:
** no real translation/upgrade, but non-ascii values that work on 3 won't load in 2


=== Jan 3, 2014 ===
=== January 13, 2016 ===
'''Updates'''
 
'''Items to Discuss'''
* [TE] [https://gist.github.com/rexissimus/dfd27e466427529c385c Porting to Python 3 / PyQt5]
** Basic GUI and execution works
** Minimal work to support 2to3
** Hard to support both PyQt4 and PyQt5


=== January 6, 2016 ===
'''Updates'''
'''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'''
'''Items to Discuss'''
* Updating VisTrails dependencies
** Successfully built [https://gist.github.com/rexissimus/f1a1aada7de1c00a57c7 Win7-64/Python3/PyQt5/Qt5/WebEngine/VTK7]
*** VTK 7 is the first supporting Python 3 but is only in release candidate phase.
**** Next version of VTK 6 is rumored to support Python 3
**** There is a development branch of VTK 6 supporting Python 3
*** Can travis build this?
**** We can skip tests for WebEngine and VTK if needed
** Python 3 [https://python3wos.appspot.com/ showstoppers]
*** No MySQL-python (sqlalchemy supports mysql through other drivers)
*** No suds (there are active forks but we could also drop support?)
* Options for python2/3 support:
** Interpreter could be python2/python3 based on packages
** six layer works but not the easiest to maintain (e.g. in reprozip)
* Drop support for win-64
* Update copyright headers to 2016


== Older meetings ==
== Older meetings ==
* [[Development/2015]]
* [[Development/2014]]
* [[Development/2013]]
* [[Development/2013]]
* [[Development/2012]]
* [[Development/2012]]
* [[Development/2011]]
* [[Development/2011]]
* [[Development/2010]]
* [[Development/2010]]

Latest revision as of 15:34, 30 October 2017

See also the Github wiki

2017

October 30, 2017

Updates

  • [DK] PyQt5
  • [RR] Running Python3 code

Items to Discuss

  • Installation:
    • Use conda? (macOS hack to have .app bundle load conda-installed vistrails)
    • Update conda recipe (pyqt4 restriction for now)
  • Interpreter
  • Release
  • Integration
    • hard to build same type of GUI in other apps that integrate core VisTrails (tend to use just the API)
    • independent pieces of the GUI could be reused if they were more independent.

September 6, 2017

Updates

  • [RR] Fixes for scikit-learn, tables, usagestats

Items to Discuss

  • Stripped-down version of VisTrails to showcase new features?
    • include meta-vistrail, bundles
    • hide mashups, extra widgets, latex mode, etc.
  • Interpreter

August 16, 2017

Updates

  • [DK] meta-vistrail
    • Working actions: normal action in vistrail, pruning version tree, tagging operations, and change
    • Interface

Items to Discuss

  • Notebook
  • Interpreter
  • Web visualization packages (e.g. bokeh)
  • Pipeline templates

August 2, 2017

Updates

  • [DK] meta-vistrail work
    • Extend Vistrail to MetaVistrail to support meta-actions
    • Vistrail becomes less tied to workflows so it can also supporting versioning vistrails

Items to Discuss

  • Interpreter
    • Using dask?
    • Streaming an issue
  • Notebooks
    • What is an output of a module? (need to expose a specific output port or the entire module)
    • Unifies some of the work from the script-workflow code

June 28, 2017

Updates

  • [DK] Testing UUID/SQLAlchemy branch
  • [DK] Working on meta-versions
    • would be nice to have pipeline and vistrail separate
    • [RR] Then do we only have meta-actions, any change to the pipeline is a meta-action that adds a version that does the change?
    • [DK] Yes?
  • [RR] Notebook interface (Vizier) making good progress, figuring out cell outputs

Items to Discuss

June 7, 2017

Updates

  • [DK] Merged UUID/SQLAlchemy branch with new bundle format branch, getting rid of the bugs

Items to Discuss

  • [RR] How to specify an "intermediate output" that should be presented to the user, from any module? (useful for notebook interface)
    • Can designate in module description an output port
    • Value has to be serializable
    • Should use the OutputModes work to handle multiple modes, configuration, selection, ...
  • [RR] Is VisTrails with SQL usable concurrently?
    • [DK] Probably not, demo from [TE] exists

May 10, 2017

Items to Discuss

  • Identifiers
  • Bundles & DB Code
  • Interpreter
  • Merge / Versioning Version Trees
  • Python3
  • Workings of List
  • Packages: Wrappers + new Versions (VTK7)
  • Script Conversion
  • Intermediate Outputs: reuse output module work?
    • would be useful for both workflows (run to a particular checkpoint)
    • and useful for notebook interfaces
  • SQL backend: does it allow for concurrent access?
    • Yes, real-time collaboration work for concurrent single vistrail access
    • Should be able to access different vistrails at once without issues

April 19, 2017

Updates

Items to Discuss

April 5, 2017

Updates

Items to Discuss

March 8, 2017

Updates

  • [RR] Added a looping indicator on modules #1217
    • This makes it easier to understand what's looping, no need to follow edges and count
  • [RR] Refactoring CLTools for integration in Docker package
  • [RR] Will try to refactor autogenerated package logic next (need to update TensorFlow package for TF 1.0, should really be using this)

Items to Discuss

  • [RR] Problem with vtkRendererToSpreadsheet output mode: does it's own ModuleConnector handling, interfering with looping/streaming logic, to add the module ID on the renderers #1216
    • Can we move this up to the renderer modules?
    • Thankfully RR couldn't find much of this madness in the rest of code (outside of controlflow and parallelflow)

February 24, 2017

Updates

  • [RR] Rich-text module documentation (#1210)
    • Went over packages and fixed format; maybe we should have a test to validate RST?
  • [RR] Single-instance shutdown with --remote-shutdown (#1204)
  • [RR] Bundle installation not super reliable; probably need to go in and add checks for every usual environment

Items to Discuss

  • [RR] There are issues with list-depth
    • Some VTK ports marked with depth=1 don't actually accept multiple inputs (vtkDataSetMapper)
    • Issue with looping groups

January 25, 2017

Updates


Items to Discuss

  • Scaling VisTrails
  • sql-alchemy, uuid, bundle branches/merges

January 11, 2017

Updates

  • [RR] New VisTrails version in Debian [1]

Items to Discuss

  • [RR] Collaboration with school of medicine to port HiC-bench to VisTrails
    • Have homemade workflow system based on R scripts and symlinks
      • Each steps has multiple sets of parameters
      • Submits PBS jobs for each step with each set of parameters, using PBS job metadata to wait on previous step
      • Gets all results in directory structure step3-parameters/step2-parameters/step1-parameters/files
    • VisTrails improves provenance capture and makes editing pipelines easier
      • Need better support for aggregation (groupby operation might be good enough; pandas?)

2016

December 14, 2016

Updates

  • [RR] Single-instance code: over-engineered, but will work
    • (Have to avoid race conditions on startup, and OSes offer very different locking primitives)

Items to Discuss

  • Email from Matt Dirks: combobox should work, ask for more code?
  • Email from marin.nl:
    • looks like they would benefit from new interpreter
    • how to store their consolidated provenance when they exchange .vt files around?

November 30, 2016

Updates

Items to Discuss

  • [RR] Working on single instance code for MARIN (#1205)
    • Remote shutdown ready (#1204)
    • Still improving it
    • Want to return something more structured to the client (success/fail code, stdout, stderr)
    • Should be usable without Qt
  • [DK] Shutting down VisTrails has issues: cleans up interpreter (to remove files) but also resets persistent pipeline for no reason
  • [DK] Working on batch execution using console_mode
  • [DK] Settings aliased parameters when using core.api?

November 16, 2016

Updates

  • [RR] Issue #1200 from @samtux: need to set PyQt to API version 2 before ever importing it; using require_pyqt_api2() does that (also can install bundle)

Items to Discuss

  • Email from Pieter: executing pipelines with parameters from command-line using single-instance
    • Seems to work, main instance gets full command-line and alters configuration temporarily
    • Not sure what his error is (VisTrails returns little information in a lot of cases); though execution error should return something more meaningful
    • Actions:
      • Can add switch to kill main instance
      • Can improve single-instance code to return more meaningful errors + machine-readable output from "client" VisTrails
      • Add client/server code to core that doesn't use Qt? Also need a run.py-line entrypoint that doesn't use gui (calls console mode like gui.application.VistrailsApplicationSingleton#noninteractiveMode())?

November 2, 2016

Updates

  • New version 2.2-2 of Debian package, still wrong copyright, and broken bundle installation
    • Finally replied, says copyright issue will be fixed soon, working on including VisTrails 2.2.4 for Debian Stretch
  • Working on Docker package, low hanging fruit because we have CLTools, and useful for some workflow (also step towards CWL support)

Items to Discuss

October 5, 2016

Items to Discuss

  • working toward a 3.0 release; project board
    • unique ids
    • bundles
    • GUI fixes
    • wrapping updates
    • python3
    • interpreter?
  • command-line input parameters to provenance
    • [DK] we don't create a persisted workflow from those input params, i think
    • [DK] these are already defined as aliases so we treat them differently form a normal input param
    • [DK] still have the potential problem of allowing a user to view the workflow as it was run with a given set of aliases
    • Do the vistrails variables values get stored in provenance? (what if values change?)

September 14, 2016

Updates

Items to Discuss

August 31, 2016

Updates

  • [RR] Went over vgc.poly.edu/vistrails.org config:
    • Added TLS certificate (vistrails.org, www.vistrails.org, lists.vistrails.org, vgc.poly.edu and a few others)
    • Fixed usersguide scripts (won't disappear again)
    • Moved some websites over to HTTPS
    • Websites
  • [RR] users' guide on readthedocs: doesn't seem like we can have both the internal docs (currently there) and users' guide under the same RTD "project"
  • [DK] UUID support almost complete (use-uuid branch), bundle translation then fits more easily on top of that

Items to Discuss

  • [RR] Move www.vistrails.org (wiki) to HTTPS? There is a trac at https://www.vistrails.org/
    • Get rid of more services? (svn, trac, ...)
  • [RR] Notebook execution works. How do we support more languages (than Python)?
    • Need: detection, metadata reader, code to input values
  • [RR] ALPS and VisTrails 2.1 issue: should be using 2.2?

August 17, 2016

Updates

  • [TE] Fixed parameter order upgrade bug that breaks VTK examples.
  • [TE] Matplotlib and sklearn are exportable using module-to-script api
  • [TE] Need to add to_python_script to pythonfunction.py to get bokeh and numpy export working.

Items to Discuss

  • Version checks: Please use a method instead of hard-coded `try: int(v) except ValueError: ...` logic!
  • Mashups: why do they share the same id scope?? (see MashupsManager.createMashupController)
  • [TE] Wrap-up notes

August 10, 2016

Updates

Items to Discuss

  • [TE] Python Wrapper and scripting
    • All changes merged into python-wrapper branch
      • Tests pass
      • Still need to update sub-branches
    • Minor fixes
      • vtkPlot3DReader upgrade bug
      • Added tuple exporting
    • Most of vtk examples can be exported example
      • Sometimes connections are wrong, executing workflow sometimes works, otherwise copy/pasting is necessary
        • Could be a bug in the old vistrail, but not sure
  • [DK] Subworkflows and uuids

August 3, 2016

Updates


Items to Discuss

  • [TE] Wrapper patches now stored as python code
    • Connection variables now lowercase
    • Can we use code as output variables?
      • E.g. "vtk_dataset_mapper.GetOutput(0)"
      • Could mutate output when output method is only supposed to be called once
      • Need to be able to rename output port as python code(e.g. when there are 2 "vtk_dataset_mapper"s)

July 27, 2016

Updates

  • [DK] DB bundle serialization implemented

Items to Discuss 

   def vtkInstance():
       self.vtkInstance = self

July 20, 2016

Updates

Items to Discuss

  • [TE] New patch method for python-wrapper example
    • A patch is a string template with self/input/output variables for patching a class method
    • Patches are stored in xml specification
    • Patches are assigned to methods in ClassSpec's
    • Used both for execution in vistrails and when exporting as script
      • Executed with "exec" when run in vistrails
      • Turns patches into natural calls in script
    • Wrapping VTK library no longer needed
      • Removes ".vtkInstance" (Automatically removed from PythonSources and vtkInteractionHandlers)
    • Removed fix_classes.py (Subclassing of VTK classes to patch methods directly)
    • Also used for port translations (With patch names like "basic:Color#input") (No more ugly input_t method definitions)
    • TODO's
      • Add to export_as_script
      • Patch Modules that represent Python functions as well
  • [vistrails-users] Read data from SQL example?

July 13, 2016

Updates

  • [DK] bundles on sql-alchemy branch
    • Bundle, BundleMapping, and BundleSerializer
    • New BaseSerializers to deal with versions of directory, zip, db serializers
    • Can register the BundleSerializers with the base serializers
    • Translation between bundle versions
    • Bundle.add_object "just works" if an appropriate mapping was registered

Items to Discuss

  • [TE] Simplified running module using API for scripting example
    • API Module can be executed using compute method
      • Takes list of outputs to compute + inputs as keyword arguments
  • Status of general cell synchronization (vistrails-users)

July 6, 2016

Updates

  • [DK] Working on bundles

Items to Discuss

  • [TE] Using vistrails API in scripting example 1 (API with VTK) example 2 (DownloadFile only)
    • Call module in script using vistrails API
    • Can be used when no export method is defined.
  • [TE] Server news bug Critical?
    • [RR] No, unreleased
  • [DK] New bundle organization
    • BundleMapping contains individual mappings from raw objects to BundleObj
    • Must be separate in order to have in-memory, separate from serializer settings

June 29, 2016

Updates

Items to Discuss

  • [TE] Export VTK as python script
    • Works on Terminator (Isosurface, Volume Rendering, clipping plane, combined rendering) example
    • Preludes (imports) still need improvements
    • Works with vtkInteractionHandler (clipping plane)
    • Resulting clipping plane is incorrect? (supposed to hide one side of the plane)
    • vtkRendererOutput Uses VTKRenderWindow as output
      • Should support different output modes?
      • Does not work with multiple outputs (Next cell is displayed when current is closed)
      • Uses wrapped vtkInstance (as vvtk)
        • Create new patch system with code that can be used both in vistrails and in a python script?

June 22, 2016

Updates

Items to Discuss

  • [TE] Fix for upgraded analogies (PR #1177)
    • Uses module location to find module remap (The best we can do right now?)
    • Also fixes remapped port names for connections to existing modules
    • May still fail on complex upgrades like adding a function on an upgraded module that has a different port name
  • [TE] Working on exporting wrapped libraries (VTK)

June 15, 2016

Updates

  • [TE] Added depth logic to python script exporter (full commit)
    • Fully implements connection merging and list looping

Items to Discuss

  • [TE] Making analogy work on upgraded workflows (#1175)
    • Analogy only works We need to use the non-upgraded action chain
    • But pipelines need to be valid (matcher uses module portspecs)
    • Tried to get upgrade remap from upgrade action, but this seems impossible
    • Use module location instead?
      • Location should be identical for one-to-one module upgrades

June 1, 2016

Updates

  • VisTrails 2.2.4 announced (finally)
    • 5 survey replies
    • 47 downloads last week

Items to Discuss

  • [TE] Export VTK as script (python-wrapper)
    • to_python_script
      • needs the pipeline (or at least the connections)
        • Should not generate code for any possible VTK method (exporter detects which ports is used in the source)
        • VTK needs to know connection order
        • Adding functions directly to the script results in nicer code
    • Add support for multiple input connections
    • Add support for list looping

May 25, 2016

Updates

  • Mailing-list fixed
  • Getting stats from the "server news" mechanism (via parser)

Items to Discuss

  • [RR] Alexis doing writeup on VisTrails, curious about interesting streaming use-cases (and potential future users)
  • [TE] Union ports
    • Show union ports in pipeline (DEMO)

May 18, 2016

Items to Discuss

  • [TE] mailing list still down - Julio working on it
  • [TE] Improved union port
    • New schema 1.0.5 adds portitem.union string attribute
    • Works with pipeline view, parameter exploration view, and mashup view
    • Should work well for matplotlib
    • Use with VTK ports?
      • It uses [item_1,item_2] style ports usually with different tuple length.
  • [TE] Remove emacs dependency from db generate #1173

May 11, 2016

Items to Discuss

  • [TE] Union type #1172
    • GUI-based solution Branch union-port Demo?
      • Shows single port for all ports with same sort_key
      • Select specific type when adding/showing
      • Only one type should be visible on the module at any time
      • Making tuple parameters union types is probably too complicated
      • Should work with alternate specs like matplotlib (if sort_key is defined correctly)
  • [TE] Feature suggestion: Let connections connect to functions/parameters
    • Show functions and parameters as ports and toggle port visibility directly for functions and parameters
    • Use separate views for ports and functions (like before)
      • Allow rearranging of functions
    • Pros:
      • Supports ordered connections. Create 2 functions, make them visible as ports, make connections to them.
        • We can also have, e.g., a line joining the ports on the module to indicate they are part of a list.
        • Makes List module simpler
      • Connect to parameter in tuple
      • Functions that are visible on the module can connect to an actual function, and not just to the first one it finds.
      • Can replace operation modules (in python-wrapper) in some cases for, e.g., numpy.
    • Cons:
      • Interface more complicated and crowded
      • More difficult for users to grasp?
      • No immediate use case
      • Makes no union type for tuple parameters a bigger problem.
  • [TE] Publish user survey?
    • No response from vistrails release yet
    • Not announced on vistrails-users yet.

May 4, 2016

Updates

  • VisTrails 2.2.4 released

Items to Discuss

April 27, 2016

Updates

Items to Discuss

  • [TE] Wrapping Bokeh
    • New method type "operation"
      • Transforms Figure->Glyph->Output into Glyph->Figure->Output
        • Glyph sets function name and arguments as output
          • Not serializable, but should always be computed together with the subject of the operation.
        • Figure applies Glyph operation on itself
      • Useful for matplotlib?
        • matplotlib currently find actors by searching upstream?
        • But this is more difficult since matplotlib is not function-based.
    • New "union" port type
      • Turns "x(float), x(list)" into "x (float, list)" and uses first set value
        • Uses only first value in tuple
        • Bokeh have many properties that support (list, string, Float)
      • Does not work with depth=1 types (e.g. Float of depth 1)
        • Turn Depth 1 types with known type into lists?
  • [TE] New bugfix release
    • Finalize survey

April 20, 2016

Updates

  • Merged upgrade fixes
    • Now has infinite loop test
    • loop test now correctly loops 5 times
      • remap_module used wrong (current) package version when creating ModuleDescriptor
  • Fixed multi-step group upgrades (PR: #1168)

Items to Discuss

  • New bugfix release
    • Merge usagestats
    • Need to finalize survey

April 13, 2016

Updates

Items to Discuss

  • [TE] Chaining upgrades done (#1164)
    • Replace "Upgrade" description annotation with "upgraded_from" annotation to identify which tags to hide?
  • [TE] Iterating handle_invalid_pipeline (#1165)
    • Not based on chain-upgrades-loop
    • Cherry-pick test to preserve source?
    • Need maxPipelineFixAttempts option?
      • The code is now smarter about recursion, so max attempts will "probably" never be reached.
    • Need debug messages?
      • Would need to be moved into handle_invalid_pipeline

April 6, 2016

Updates

  • [TE] Query View improvements
    • Done except for displaying "Version Info" and #1164
  • [RR] Working on finishing new interpreter (finally!)

Items to Discuss

  • [TE] Chaining upgrades (#1164)
    • Try latest upgrade first, then previous.
    • If all fail, select latest upgrade?

March 30, 2016

Updates

Items to Discuss

  • [TE] Query View improvements
    • Unified do_version_switch and get_upgrades as validate_version()
    • Problems with query view using its own controller
      • Fixed module info not being displayed for query results
      • Still no version info for query results
      • Still an issue with version query view not being updated

March 23, 2016

Updates

Items to Discuss

  • [RR] Usage reporting almost ready to go
    • Need to record whether specific features are used: paramexpore, mashup, query
      • [DK] Record if LaTeX extension is used? But hard to distinguish from direct batch invocation
    • How to record size of vistrail?
      • [DK] IdScope already walks over vistrail, use that
      • but total number of modules and versions doesn't give an idea of average size of individual pipelines

March 16, 2016

Updates

Items to Discuss

  • [TE] Upgrades in Query Mode
    • Now using code similar to do_version_switch
      • Uses handle_invalid_pipeline
      • Differences: Not using current_pipeline, flushes changes
      • New controller method get_pipeline optimized using cached pipelines (but not current_pipeline)
      • Integrate to avoid repeated code?
      • Use this for query mode?
  • [TE] VisTrails 2.2.4 ready for release?
    • tej package updated. Others?
  • [JF] upgrades and the version tree
  • [JF] provenance in Jupyter
  • [DK] bundles: #1092

March 9, 2016

Updates

Items to Discuss

  • [TE] Fixing search mode
    • String query now matches all by default
      • This caused pipeline queries to never match
    • String query can search: User/Notes/Tagname/Time/Module name
      • Should we search module names by default? (Disabled by default because it is expensive)
      • Fixed notes search
    • '>' parameter queries in documentation but has been removed
    • Fixed module matches for upgraded pipelines (By not upgrading pipeline)
      • Upgrades still a problem
      • Add "Upgrade all menu option?" (Or upgrade all on open when `hideUpgrades`)
      • [JF] Allow search on past tags
  • [TE] Create new bugfix release
    • Finish querying
    • Path issue on windows
  • [DK] Look into sqlalchemy and new bundle branches

March 2, 2016

Updates

  • [TE] Fixed cache bug with port specs
  • [TE] VisTrails Next
    • Most packages now work
    • No qgis for Python 3

Items to Discuss

    • Always dereference symlinks? #1146

February 23, 2016

Updates

  • [TE] Fixed PythonSource 100% CPU bug
  • [TE] VisTrails Next
    • Updated NOAA Web Service examples
      • Now uses REST service, tabledata, and Google Maps
      • Web Service replaced with DownloadFile

Items to Discuss

  • [RR] Couple of fixes are in for API, and tej&reprounzip on the Mac binary. Also new release of tej, and working on anonymous usage reports.
    • New 2.2 release soon?
  • [RR] Anonymous usage reports
    • Sends out info like number of modules & versions, packages used, Python & libs versions, execution time, specific features #1154
  • [JF] Bring in noWorkflow to track variable dependencies, for the considered Jupyter integration?
  • noWorkflow - provenance for python scripts
    • Recent work on tracking dependencies
  • Also integrates ReproZip with Jupyter
    • mybinder
      • Use with ReproZip to automatically build Jupyter notebook interfaces
  • Daves comments on Jupyter integration
    • It is possible to identify cell order on the server side
    • Not trivial to track order of cells on client side
  • How does Galaxy workflows relate to VisTrails?
    • Packaging in Galaxy is hard
    • Galaxy for biomedical workflows, difficulty making it general
  • Action items
    • How difficult to track cell dependencies in Jupyter notebooks?
    • Use noWorkflow to track cell dependencies?
    • How difficult to modify mybinder to use ReproZip packages?

February 17, 2016

Updates

Items to Discuss

  • [TE] Fixed Group memory usage
    • Modules in groups are supposed to be freed when done executing
      • Prevented by logger that stored references to the modules (fixed, now using id(module))
      • Prevented by list iterator bug that stored list of modules on the 'self' port bug (fixed)
  • [TE] VisTrails Next
    • Removed deprecated code
      • Core imports that should be gui imports
      • GetInputFromPort etc.
        • PythonSources will be upgraded
      • Fixes for Python < 3
      • fixes for VTK < 6
    • TODOs
      • Remove RemoteQ
        • Port Hadoop to tej (Already have pbs)
      • Merge package wrapper
      • Finish SQLAlchemy branch
      • Finish new bundle branch
    • [JF] Will contact Jeff and Matthias about moving to Python 3
  • [JF] Query by Example is broken
  • [JF] VisTrails Data Cleaning Project
    • Use VisTrails to process and explore task-specific data while keeping provenance.
    • Remi's Idea
      • Use VisTrails as the backend in a Jupyter notebook
      • Overcome problems with executing cells in random order
        • Interesting research topic, but little interest has yet been noted
      • Interesting to study how such a notebook would be used (Is there notebook usage data available?)
      • Impose restrictions to notebook cell boundaries
      • It will only work for functional operations
      • Can we fix, or detect, non-functional (mutating) operations?
      • Analyse code and data flow and see if it mutates data in unexpected ways?
      • Mutable operations can be created in many ways in Python
  • Next meeting Tuesday 11:30

February 10, 2016

Updates

Items to Discuss

  • VisTrails Next
    • Test suite passes
      • Python 3 less deterministic, module upgrade order random.
    • [RR] updating packages: Reprounzip (pushed), tej, persistent_archive, ...
    • All of our packages should run fine :)
    • VTK thumbnail comparison works
      • Rendering bug on some systems
        • QVTKCell now inherits QGLWidget
      • Old thumbnails had wrong height due to spreadsheetwindow being too small
        • Fixed by regenerating thumbnails
      • Silenced deprecation messages when generating modules
      • Many new classes in VTK 7
    • Remove deprecated code
      • Core imports that should be gui imports
      • GetInputFromPort etc.
        • Will break existing PythonSources
        • Try to upgrade?
      • Old-style packages
        • Or only allow a new style, like __init__.py renamed to info.py? (merge with identifiers.py?)
          • Read info.py without importing package?
      • Fixes for Python < 3
      • Fixes for Qt < 5
      • fixes for VTK < 7
      • Remove self port?

February 3, 2016

Updates

Items to Discuss

  • VisTrails Next
    • All tests but thumbnail comparison passes
    • Still issues with gui and more packages needs to be tested
    • PythonSource and MplSource upgraded with lib2to3
    • Keep contrib packages? Update?
    • VTK 7 is released
      • Supports Python 3
      • Will hopefully get into conda and others soon
      • Deprecates a bunch of modules
  • Travis builder for VisTrails Next
    • Runs!
    • Uses conda
      • Many levels of requirements
        • apt packages
        • conda packages
        • python packages in requirements.txt
        • python packages in setup.py
      • Can probably drop conda. Default builder does not have Qt5, but beta builder do!
      • But useful if we want to use conda in our own build process.
    • Lots of errors I do not get locally?
  • User Survey
    • Have you used any alternatives to vistrails?
      • Relevant? More options?
    • How often do you use any of these particular features in VisTrails?
      • Add/Remove alternatives?
    • How important would you rank the following potential improvements to VisTrails?
      • Add alternatives?

January 27, 2016

Updates

  • New interpreter
    • Working prototype soon
    • Looping not completely done (and port combination mode: pairwise/cartesian...)
    • Need to integrate with VisTrails
      • Compatibility with existing modules
      • Use log controller
      • Want to cache at multiple levels (whole stream/single element of stream)
      • Non-runtime attributes of modules (cache check, automatic conversion check, constant from/to string)

Items to Discuss

  • User Survey
  • ZMQ failing on windows (vistrails-users)
  • [TE] Python 3 branch
    • Testsuite almost passes
      • Failing are unicode filenames, some users guide examples, and thumbnail comparisons.
    • Fixed issues
      • Signatures are now bytes (convert to string to show in widget)
      • Cannot compare different types, e.g., (None < 1)
        • PortSpec.depth and min/maxConn could be None. (Backport!)
        • cell.row could be None
      • Lots of unicode/bytes fixes to serializations
        • We have encryption implementations in the code! (keychain)
      • Lots of small fixes to package method differences
    • Current issues
      • logging widget empty?
      • version tree signals messed up
      • provenance view legend icons black
      • Text do not fit in some widgets
      • VTK thumbnail comparison fails
        • VTK Cells have some faces in wrong direction?
        • Because running in VM?
    • Installing on Ubuntu LTS/Latest Mint
      • Install latest matplotlib from pip
      • Install VTK 7.0.0rc2 from source
      • No QtWebEngine binary (controversial) (Must install sip/PyQt5/Qt5 from source)

January 20, 2016

Updates

Items to Discuss

  • [TE] Backporting features from Python 3 + PyQt5 + Qt5
    • Merged unicode with master (unicode)
      • One unicode test failing
      • Problem saving to xml
    • Used python-future to run futurize stage 1 to update legacy (pre 2.6) code (unicode-futurized)
      • Updates print to functions 'from __future__ import print_function'
      • Updates exception calls to use 'as'
      • removes most usages of 'long' (mostly used unnecessarily)
        • Only needed for 32-bit support
      • Fixes relative imports (from __future__ import absolute_import)
    • Fixing code that is deprecated in Qt 4.8 and removed in Qt 5 (unicode-futurized-qt5)
      • Updated all signals to new-style
  • If we go 2 to 3, this could break packages
    • means we should schedule any package format changes for the same time
    • e.g., imports should be unrelated to code path (function to load module from package identifier?) (take them out of vistrails.* #1002)
    • any structural changes (e.g. the __init__ versus init thing) (RR thinks it makes sense, though having both named "init" is unfortunate)
    • putting package identifier as xml?
      • Python not so bad, plus some stuff in there is Python code (checking dependencies)
    • version the APIs?
      • RR planning on versioning vistrails_module.Module, no point versioning the whole package?
  • file formats on 2 to 3:
    • no real translation/upgrade, but non-ascii values that work on 3 won't load in 2

January 13, 2016

Updates

Items to Discuss

January 6, 2016

Updates Items to Discuss

  • Updating VisTrails dependencies
    • Successfully built Win7-64/Python3/PyQt5/Qt5/WebEngine/VTK7
      • VTK 7 is the first supporting Python 3 but is only in release candidate phase.
        • Next version of VTK 6 is rumored to support Python 3
        • There is a development branch of VTK 6 supporting Python 3
      • Can travis build this?
        • We can skip tests for WebEngine and VTK if needed
    • Python 3 showstoppers
      • No MySQL-python (sqlalchemy supports mysql through other drivers)
      • No suds (there are active forks but we could also drop support?)
  • Options for python2/3 support:
    • Interpreter could be python2/python3 based on packages
    • six layer works but not the easiest to maintain (e.g. in reprozip)
  • Drop support for win-64
  • Update copyright headers to 2016

Older meetings

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