Difference between revisions of "Development"

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== Roadmap ==
<div class="nonumtoc toclimit-1">
__TOC__
</div>


See also the [https://github.com/VisTrails/VisTrails/wiki/Development Github wiki]


== Weekly Meetings ==
== 2017 ==


=== Nov 8, 2011 ===
=== October 30, 2017 ===


* Command-line flag fixes:
'''Updates'''
** detached history view done
** check multiheads for spreadsheet---spreadsheet not shown on startup now


* Merge core_no_gui branch with master
* [DK] PyQt5
** Check unit tests here
* [RR] Running Python3 code
** Can we merge this into master, or keep as a separate branch?


* UV-CDAT
'''Items to Discuss'''
** Call last Friday to talk about Variables
** Dave looking at Variables
** Tommy looking at workspace for UV-CDAT application
** Emanuele managing integration and gui development
** Keep track of things on new UV-CDAT Development page
** Examples: Tom's examples
** Avoid adding complications right now
** Persistence for variables: simplfy and have a checkbox to allow system to save those things
** Scenario from Jerry Potter?  Juliana working on
** Plot: graphics method, template, plot, variable (list)
** Templates for subworkflows?  Define all the subworkflows that must respect this interface
** Dave: write a Variable module
*** Emanuele: send Dave CDAT python examples, one vt in paraview package


=== Oct 18, 2011 ===
* Installation:
* We will focus on UV-CDAT and on completing the alpha version of the system. Please read the documents Emanuele emailed.
** 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.


* Using different servers with CrowdLabs
=== September 6, 2017 ===


* Closing tickets (Tommy)
'''Updates'''


=== Oct 11, 2011 ===
* [RR] Fixes for scikit-learn, tables, usagestats


* Bug reports:
'''Items to Discuss'''
** execute_cmdline issue: CLTools supports both


* 2.0 bug fixes: push new release soon (for change_selected_version bug fix)
* Stripped-down version of VisTrails to showcase new features?
** include meta-vistrail, bundles
** hide mashups, extra widgets, latex mode, etc.
* Interpreter


* Fix migrateTags issue and any other minor bugs, then release new version of 2.0
=== August 16, 2017 ===


* CLTools:
'''Updates'''
** latest is in repository
* [DK] meta-vistrail
** README in package directory
** Working actions: normal action in vistrail, pruning version tree, tagging operations, and change
** adding to online user's/developer's guide
** Interface


=== Oct 4, 2011 ===
'''Items to Discuss'''
* Notebook
* Interpreter
* Web visualization packages (e.g. bokeh)
** [https://github.com/VisTrails/VisTrails/pull/969 PR 969] has more details
* Pipeline templates


* We will discuss issues related to remote execution of VisTrails modules as well as multi-threaded and parallel execution of workflows
=== August 2, 2017 ===
* We will be joined by Matthias Troyer and Troels Frimodt Rønnow (ETH Zurich), Joel Daniels (NYU Poly), Marta Mattoso, Jonas Dias (UFRJ, Brazil)
* Terence Van Zyl and Derek Hohls (CSIR, South Africa) will not be able to make it today


We will develop a package that supports the ability to spawn a 'batch' job either on a local machine, a remote server, or a specialized cluster/supercomputer (with its own  batch submission system). The basic API will provide functions to:
'''Updates'''
* start jobs and obtain id (which will be saved in VisTrails and in UFRJ's database)
* [DK] meta-vistrail work
* poll the status of a job (if it is still running of it is completed)
** Extend Vistrail to MetaVistrail to support meta-actions
* copy files to and from the remote server
** Vistrail becomes less tied to workflows so it can also supporting versioning vistrails


Once a job is submitted by the 'remote module', the workflow stops. The user can poll the status through the UFRJ DB, or by running the workflow again on VisTrails. When the workflow is re-run, VisTrails will check the status of the job; if the job is still running, the workflow stops; if the job is complete, the files (if any) will be transferred and the execution of the workflow resumes.
'''Items to Discuss'''


Next steps:
* Interpreter
* Troels will work with Joel on extend Joel's package to implement the basic API; and with Dave on implementing the idea of  'persistent jobs'
** Using dask?
* Once the basic API is ready, we will work with Jonas to integrate his DB interface and the ability to access the provenance information about the remote jobs from multiple devices
** 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 ===


* Tommy gave an update on CLTools. He already has a GUI to create the wrappers. He will make some additional changes and we will get some people to try it out.
'''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


=== September 27, 2011 ===
'''Items to Discuss'''
* Stéphane Descorps-Declere and Loic Couderc from [http://www.pasteur.fr/ip/easysite/pasteur/en Institut Pasteur] will join us
** Show demo of their package
** Discuss their specific needs
** How to deal with tools that have a large number of parameters and help the users not get lost setting these parameters, some ideas:
*** Port documentation in tooltips so mouse-over shows the documentation---need to support the specification of port-level documentation in the wrapper
*** Defining in the wrapper required and dependent ports. For the latter, define the dependency graph among the different parameters, and then use this information in the GUI. For example, given parameters A, B, C and dependencies C->B, B->A, and if A is defined, the GUI should require that B and C be set
*** Define in the wrapper port cardinality, i.e., the number of connections supported by the port
*** Support HTML-style documentation, which would allow the inclusion of images---the problem here is that it isn't good for command-line based use of VisTrails, so we also need to support plain text
** Stephane and his group will take a stab at implementing these ideas in two steps: first, making the required changes to the registry; and then, updating the GUI to use the new information that will be available in the wrapper.


* Discuss CLTools features/design
=== June 7, 2017 ===
** Tommy has an initial function that parses man pages
** He will develop a GUI to help users wrap command-line tools---this will be a tool "separate" from VisTrails
** How to handle pre- and post-conditions? Could create scripts and wrap them using CLTools; or in VisTrails, use Python source
** reuse code from existing PythonSource GUI?  Maybe for pre/post-conditions, but the port list probably isn't a great interface for this.


* Issue with change_selected_version
'''Updates'''
** the graph is probably being corrupted by some version not being added to the version tree, could be a single action type
* [DK] Merged UUID/SQLAlchemy branch with new bundle format branch, getting rid of the bugs
** Asked Tom if he knows steps to reproduce


=== September 20, 2011 ===
'''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


* Tommy will give a demo of CLTools package for wrapping command line tools
=== May 10, 2017 ===
** Each tool creates a module, but modules cannot be versioned?
** Do you have specific tools/scripts I can try?
** Next step is to create more automatic wizards for tools and scripts.


=== September 13, 2011 ===
'''Items to Discuss'''


* Making it easier to wrap command line tools, motivated by the need to simplify the creation of executable papers
* Identifiers
** Goal: build a wizard that guides a user on the creation of a wrapper.
* Bundles & DB Code
** Assumption: the user has code that derived results for paper, and needs to package it in a way that reviewers can both reproduce and validate the results (e.g., try different parameter values)
* Interpreter
** Initially, require the user to manually provide the information---parameter names and optionally, types.
* Merge / Versioning Version Trees
** The output of the wizard should be a machine-readable specification which could be loaded as a module in VisTrails
* Python3
** Some desirable functionality:
* Workings of List
***ability to 'test' the wrapper; after the specification is input, show a vismashup-like interface for the user to set values, and allow him/her to execute the module
* Packages: Wrappers + new Versions (VTK7)
** provide 'smart' parsing to help in the wrapper construction, for example, extract the information from a python script
* 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


* We will create a separate branch for external developers, so that they can contribute patches to VisTrails
=== April 19, 2017 ===


* David has cleaned up most of the GUI dependencies, the only remaining ones are:
'''Updates'''
** Notes associated with versions  (they need Qt)
** Generation of PDF representation for workflows and trees
** Thumbnails


'''Items to Discuss'''


* Web services (EMBOSS example)
=== April 5, 2017 ===
** All now works except Prophet example (<choice> bug in SUDS). Should we remove it?


* Invalid modules (those in red) will not show parameters - Fixed
'''Updates'''


=== September 7, 2011 ===
'''Items to Discuss'''


* Query mode
=== March 8, 2017 ===
** need to finish this implementation


* Analogy parent() issue?
'''Updates'''
** check what this was (form August 16)
* [RR] Added a looping indicator on modules [https://github.com/VisTrails/VisTrails/pull/1217 #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)


* Web services (EMBOSS example)
'''Items to Discuss'''
** changes with SUDS (should be easier)
* [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]
** 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)


* VTK Examples:
=== February 24, 2017 ===
** check old examples (don't seem to work with new version)
** these were auto-generated from VTK python examples a while ago and may have issues with newer VTK versions


* Auto-updating tags: migrateTags option in preferences
'''Updates'''
** Document this
* [RR] Rich-text module documentation ([https://github.com/VisTrails/VisTrails/pull/1210 #1210])
** MIgrate notes as well so that the notes and tags are migrated
** Went over packages and fixed format; maybe we should have a test to validate RST?
* [RR] Single-instance shutdown with <tt>--remote-shutdown</tt> ([https://github.com/VisTrails/VisTrails/pull/1204 #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


=== August 31, 2011 ===
=== January 25, 2017 ===
* Diff tab has other view modes disabled.
** Opening a version or mashup from workspace, open in new tab instead of overwriting diff


* Binaries
'''Updates'''
** Matthias reported his tutorials were working with the current version
** Emanuele will start rebuilding the binaries more frequently again


* Mashup saving
** keep does not save
*** change the name keep to tag, to avoid confusion
** changes in workflows and mashups are reflected in the workspace now
*** still working on the executions


* Provenance browser
'''Items to Discuss'''
** instead of using version numbers for untagged versions, use the same convention used in pipeline view (eg., parent_tag + 1)


* Documentation
* Scaling VisTrails
** VTK?
* sql-alchemy, uuid, bundle branches/merges
** At least a section in the user's guide  that points the users to the right examples


* Examples
=== January 11, 2017 ===
** problem with examples that depend on 3rd-party packages
*** move them to the package folder?


=== August 16, 2011 ===
'''Updates'''
* [RR] New VisTrails version in Debian [https://packages.qa.debian.org/v/vistrails.html]


* Diff tab should have other view modes disabled.
'''Items to Discuss'''
** Tab doesn't make sense to switch back to history
* [RR] Collaboration with school of medicine to port HiC-bench to VisTrails
** Could either try to make mode buttons work or just disable the modes
** Have homemade workflow system based on R scripts and symlinks
** Easier to disable the other modes
*** Each steps has multiple sets of parameters
** If open a version or mashup from workspace, open in new tab instead of overwriting diff
*** Submits PBS jobs for each step with each set of parameters, using PBS job metadata to wait on previous step
** this way, a diff view is only closed by a user explicitly closing it
*** Gets all results in directory structure <code>step3-parameters/step2-parameters/step1-parameters/files</code>
** VisTrails improves provenance capture and makes editing pipelines easier
*** Need better support for aggregation (groupby operation might be good enough; pandas?)


* Binaries for Mac
== 2016 ==
** Can build 64-bit binary and not 32-bit
=== December 14, 2016 ===
** Emanuele will try to build 32-bit again
** ALPS has separate 32-bit and 64-bit versions
** Have two DLLs and registry for 2008 and 2010 Visual Studio
** Problem is that VisTrails may not run if the registry does not have the updates from Visual Studio
** 64-bit support allows more than 4GB of memory


* Should Mashups or Workflows be children if the vistrail in the workspace?
'''Updates'''
** Expand them automatically
* [RR] Single-instance code: over-engineered, but will work
** Mashups are meant to be shortcuts
** (Have to avoid race conditions on startup, and OSes offer very different locking primitives)


* Mashup saving
'''Items to Discuss'''
** keep does not save (workspace is not updated)
* Email from Matt Dirks: combobox should work, ask for more code?
** can we emit signal to workspace so it is updated
* Email from marin.nl:
** can we put things in memory for the workspace?
** looks like they would benefit from new interpreter
** set_changed is called so we should update the workspace when a vistrail to be changed
** how to store their consolidated provenance when they exchange .vt files around?


* Subworkflows
=== November 30, 2016 ===
** new changes to infrastructure to address distributed version control
** issue where multiple versions of the same subworkflow are listed
** multiple edits still an issue


* Analogies
'''Updates'''
** issue with parent() bug, Dave needs to file this


* Databases
'''Items to Discuss'''
** no direct database access currently allowed at NYU
* [RR] Working on single instance code for MARIN ([https://github.com/VisTrails/VisTrails/pull/1205 #1205])
** either create localhost database or use via crowdlabs
** Remote shutdown ready ([https://github.com/VisTrails/VisTrails/pull/1204 #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?


=== August 9, 2011 ===
=== November 16, 2016 ===


* Ticket #459
'''Updates'''
** for an empty pipeline, the exploration is not resetting correctly


* Dave looking into query issues
* [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)


* Issue with views not being set up correctly and handling callbacks (#469) amy also play a role in #473.
'''Items to Discuss'''


* Ticket #472.  Setting values in the user-defined list or any other type of window
* Email from Pieter: executing pipelines with parameters from command-line using single-instance
** Going to any other window causes everything to reset, after executing, focus out event causes things to reset
** 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>)?


* Subworkflows: edit bugs, Claurissa
=== November 2, 2016 ===


* Groups inside of groups: currently cannot view them, Claurissa was looking at this
'''Updates'''


* Cmd-Q when the spreadsheet is on top seems to cause problems, need to force quit on the Mac.
* 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)


* Enhancement: spreadsheet camera reset button?
'''Items to Discuss'''


* Cmd-E for configuring ports, Ticket #443 fix the old configuration windows or do away with, maybe keep this
=== October 5, 2016 ===


* Parameter exploration: link spreadsheet to the parameter explorations, or display the parameters used with each cell, way to write
'''Items to Discuss'''


* Missing example for vtk.vt for cell locations and sheet references.
* working toward a 3.0 release; [https://github.com/VisTrails/VisTrails/projects/1 project board]
** unique ids
** bundles
** GUI fixes
** wrapping updates
** python3
** interpreter?


* Diff when upgraded doesn't work
* 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?)


* Upgrade entire version tree? How do we preserve tree structure?
=== September 14, 2016 ===


* Mashups: display with pipelines? having both expanded to solve the extra click
'''Updates'''
** add this as a preference, other ways to view, add a button


* Opening a lot of vistrail files, closing them without saving, have "Yes to All", "No to All" buttons.
'''Items to Discuss'''
* [RR] [http://aosabook.org/en/vistrails.html VisTrails] in [http://aosabook.org/ The Architecture of Open Source Applications] Vol I (2012)
** Did we know/contribute to this?
*** [DK] Yes. We wrote the text for the VisTrails chapter
** Drafted response
*** [DK] Looks good, will forward.


=== August 2, 2011 ===
=== August 31, 2016 ===
* Ticket [https://www.vistrails.org/ticket/459 #459] (Tommy)
** Pipeline inspector may not get updated correctly when pipeline is empty


=== July 26, 2011 ===
'''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
** [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


* Zoom level in the first vistrail bug
'''Items to Discuss'''
** file on trac
* [RR] Move www.vistrails.org (wiki) to HTTPS? There is a trac at https://www.vistrails.org/
** start vistrails and go to version view, history tree is not there, Cmd+R shows root node
** Get rid of more services? (svn, trac, ...)
** all vistrails after work fine
* [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?


* Subworkflows
=== August 17, 2016 ===
** issue with adding input ports and naming
** separate issue with editing a subworkflow more than once


* Analogies
'''Updates'''
** how to update the algorithm so the terminator with HTTPFile works correctly
* [TE] Fixed [https://github.com/VisTrails/VisTrails/commit/2cd42d156243067a7663bb0bf0156e5d87188c2f 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.


* LaTeX Assistant
'''Items to Discuss'''
** Dave's new changes (read tex file and find \vistrails tags) moved to 2.1, remove from 2.0 for now
* Version checks: Please use a method instead of hard-coded `try: int(v) except ValueError: ...` logic!
** Add back as a new feature for 2.1
* Mashups: why do they share the same id scope?? (see MashupsManager.createMashupController)
* [TE] Wrap-up notes


* ungrabMouse in setModuleLabel
=== August 10, 2016 ===
** probably happens on any module


* query issue: want to get back to original query from the search results and modify the query, currently just removes the query and resets everything
'''Updates'''


* keep triangle menu initially in 2.0, may remove in later versions if we can maintain access to all features
'''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 [https://gist.github.com/rexissimus/5ac7374cde8525d84f9443f019d234e2 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


=== July 19, 2011 ===
=== August 3, 2016 ===
* Features added
** Display mashups in the workspace
** Detach configuration window, rename, in a read-only, non-changing state (allow copy)
*** Improve button layout?
*** move read-only to left side and other buttons to be right side
* Status of 2.0
** subworkflows bug, claurissa
* [Dave] Need to fIx bug with retagging


=== July <del>12</del> 13, 2011 ===
'''Updates'''


* Features added
** Display mashups in the workspace
*** Tommy added the support for the workspace, items need to be added
** Detach configuration window, rename, in a read-only, non-changing state (allow copy)
* Menu/Key shortcuts issues
** QBaseView window with menubar, add parts of menu
** QVistrailView inherits so we can reuse part of menus
** Need to show menus on Windows and Linux for other windows
** PythonSource has no menubar by default, can create its own menu
* Show Pipeline for a group
** delegate the creation of this window to QVistrailView?
** windows are set on show_group_function
** don't create a separate window
** eventually we should make groups logical not physical (so everything doesn't change each time to modify a group)
** just capture new pipeline


* spreadsheet editing and analogies
'''Items to Discuss'''
** add static methods to controller to allow general access to create methods
** need to factor code so virtual_cell can work with this code, too


* look into the issue when seeing a workflow for the first time; might be linked to upgrades and indexing
* [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]
** Tommy should check that the exceptions are propograted
** 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 5, 2011 ===
=== July 27, 2016 ===
* Server migration is almost completed
** GIT/Wiki/Trac working fine. Machine will be relocated to get better bandwidth
** <del>Still need to update vistrails.org to point to new location</del>


* Some bugs from last week were fixed, still a few more to go (see trac tickets)
'''Updates'''
* Minor issues raised at the meeting
** Add shortcut key for executing a pipeline
*** [ES] Ctrl+Return (Command+Return on a Mac) should work. The problem is that the shortcut does not show up on the Menu on a Mac. I've tested on QtDesigner and it doesn't show up there either. So it seems an issue with Macs.
** Being able to execute the selected node in Version View (having to open a pipeline just to execute it involve too many steps)
* Features to be implemented, then VisTrails will be feature frozen
** Display mashups in the workspace
** Detach configuration window, rename, in a read-only, non-changing state (allow copy)


=== June 28, 2011 ===
* [DK] DB bundle serialization implemented


* svn offline this weekend to migrate servers (Huy)
'''Items to Discuss'''
** send an email to vistrails-dev
* [TE] Finished using patch in script [https://github.com/VisTrails/VisTrails/tree/python-wrapper-script-patches python-wrapper-script-patches]
* fix bugs from demo
** locale?
** fix zoom on open, change view
** [https://gist.github.com/rexissimus/f0d6b026aa5a2a770847f3321744645d new patching example] vs [https://gist.github.com/rexissimus/b28d83ae516a519167f5751bb8ab3739 old patching example]
** detach configuration window, rename, in a read-only, non-changing state (allow copy)
** [https://github.com/VisTrails/VisTrails/blob/python-wrapper-script-patches/vistrails/packages/vtk/vtk_wrapper/parse.py#L135-L273 Example of new patches]
** read-only controller for diff view, or use Emanuele's read-only view flag
** Legacy '.vtkInstance' is now added as a patch "self.vtkInstance=self" (see new patching example)
** check for pruned versions in "(latest)" version
** [https://github.com/VisTrails/VisTrails/blob/python-wrapper-script-patches/vistrails/core/scripting/api.py New api for executing standalone modules]
** failed to index error on open (possibly old version of vistrail--with filenames)
*** 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:


* releases?
    def vtkInstance():
** waiting for ALPS build for Mac OS X 10.5
        self.vtkInstance = self
** allow 2.0 vt files to open in 1.7 (e.g. those with mashups)


=== June 21, 2011 ===
=== July 20, 2016 ===


* Querying
'''Updates'''
** need ability to better navigate results
** show query results in side panel?
** search all open vistrails (change label on the search)


* Updated workspace window
'''Items to Discuss'''
** Separate open and recent files
* [TE] New patch method for python-wrapper [https://gist.github.com/rexissimus/009b303e4cadcd4b8f2fec6cf848cb2b example]
** Delete closes an open vistrail or removes a closed one from recent file list
** A patch is a string template with self/input/output variables for patching a class method
** Also has an "open in new open window" option for right-click, suggested "open in new window", "open in new tab" for workflows
** Patches are stored in xml specification
** Want to be able to show this palette at all times?  This allows better navigation, but problem is the screen space
** Patches are assigned to methods in ClassSpec's
** Try showing the workspace window in the upper left and "normal" left palettes in the lower-left.
** 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


* Module Palette
* [vistrails-users] Read data from SQL example?
** Searching should expand things automatically, especially for searches that have only a few search results
** What about searching a particular package? Could auto-expand on begin search, user collapses and then expands the package they are intereseted in


* Global variables
=== July 13, 2016 ===
** one bug on disconnecting variables


* Spreadsheet and analogy issue on re-executing pipelines? Dave will look at
'''Updates'''


* Diff
* [DK] bundles on sql-alchemy branch
** Diff properties not showing up automatically, Emanuele will check
** Bundle, BundleMapping, and BundleSerializer
** Implement a diff in workspace window so you can do cross-vistrail diff
** New BaseSerializers to deal with versions of directory, zip, db serializers
** Diff uses version tree for efficiency, but we can use analogy match or heuristic even when no actions are shared
** Can register the BundleSerializers with the base serializers
** Translation between bundle versions
** Bundle.add_object "just works" if an appropriate mapping was registered


* Inspector window: would be nice to keep this window smaller (certain tabs keep it large)
'''Items to Discuss'''
* [TE] Simplified running module using API for scripting [https://gist.github.com/rexissimus/b28d83ae516a519167f5751bb8ab3739 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)


=== June 14, 2011 ===
=== July 6, 2016 ===


* Detach windows
'''Updates'''
** notifications?
** creating secondary windows
** don't duplicate the entire vistrails window, just individual views
** detach icon not displaying correctly in Windows


* Global Variables
* [DK] Working on bundles
** How to add to modules?
** Drag constant modules to the vistrails variables panel
** Set the value by editing the constant in the vistrals variables panel
** Connect the value by dragging the constant from the vistrails variables panel to a port in the pipeline
** Update default text to "Drag constants from Modules panel to create variables"
** Fix bugs with connecting globals and deleting them (versionTab issue, etc.)


* Query tab in vistrail
'''Items to Discuss'''
** Can we use normal version/pipeline views as result views?
* [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)]
*** Which view to start with? history/pipeline
** Call module in script using vistrails API
*** Show the workspace panel instead of history view
** Can be used when no export method is defined.
*** Show results in the query panel (as pipeline or workspace as appropriate)
* [TE] [https://github.com/VisTrails/VisTrails/commit/c76c109349769fee1280f85c22678380a2f9cd39 Server news bug] Critical?
** Should we always combine "keyword" and "visual" queries?
**[RR] No, unreleased
*** try to combine queries when possible, but allow user to search just text if there is no pipeline or just pipeline if there is no text
* [DK] New bundle organization
*** get back to the search window after seeing results (need a button here)
** BundleMapping contains individual mappings from raw objects to BundleObj
** What interactivity do we want? Open pipeline when matching version is double-clicked?
** Must be separate in order to have in-memory, separate from serializer settings
*** yes, single-click shows in results view, double-click opens as normal vistrail
** Dave will look at query view


* Add read-only PythonSource
=== June 29, 2016 ===


* Workspace: keep closed vistrails here too
'''Updates'''
** try to order so that open vistrails are on top (highlighted in bold?)
** also show different views here (full tree view)
** show current workflow (ie latest version in the panel), too


=== June 7, 2011 ===
'''Items to Discuss'''
* [TE] Export VTK as python script
** Works on Terminator (Isosurface, Volume Rendering, clipping plane, combined rendering) [https://gist.github.com/rexissimus/16caf5200802e150296f62a0c7844c5a 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?


* Status of 2.0
=== June 22, 2016 ===


=== May 31, 2011 ===
'''Updates'''


* Go over bugs and new features for 2.0
'''Items to Discuss'''
* [TE] Fix for upgraded analogies (PR [https://github.com/VisTrails/VisTrails/pull/1177 #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


=== May 17, 2011 ===
* [TE] Working on exporting wrapped libraries (VTK)


* Add comments, bugs, critiques, etc. about the 2.0 changes [[Version 2 | here]]
=== June 15, 2016 ===


* Global variables
'''Updates'''
** Check issue on MacOS
* [TE] Added depth logic to python script exporter ([https://github.com/VisTrails/VisTrails/commit/50f220e4f6abe5a7bb8689f73f456f43df2dbc12 full commit])
** Add documentation
** Fully implements connection merging and list looping


* Mashups [Emanuele]
'''Items to Discuss'''
** on track, separate feedback
** switching vistrails issue
** execute button move --- move to right side (and make it possible to disable)
** how does execute work
** close builder window doesn't trigger quit?


* Provenance view [Tommy]
* [TE] Making analogy work on upgraded workflows ([https://github.com/VisTrails/VisTrails/issues/1175 #1175])
** read all provenance right now
** Analogy only works We need to use the non-upgraded action chain
** create an index file in the vt to load pieces of provenance on demand
** But pipelines need to be valid (matcher uses module portspecs)
** enhancement idea: highlight errors in the list view of Log Details
** Tried to get upgrade remap from upgrade action, but this seems impossible
** tooltips in the browser view show large icons
** Use module location instead?
** search for provenance browser
*** Location should be identical for one-to-one module upgrades
** fix issues with the left box
** number of search boxes...


* Update splash screen [Juliana will talk to Nathan]
=== June 1, 2016 ===


* Go over Jan's feedback on the PythonSource editor
'''Updates'''
* VisTrails 2.2.4 announced (finally)
** 5 survey replies
** 47 downloads last week


''A slight UI glitch is that I couldn't access the undo/redo functionality with the usual Cmd+[Shift+]Z shortcuts (neither via the menu or toolbars) but only via the right mouse button. One additional feature that might be nice in the future would be some minimal indentation assistance, like when pressing [Return] the current indentation is kept for the new line.''
'''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 2, 2011 ===
=== May 25, 2016 ===


* Demos of new 2.0 functionality:
'''Updates'''
** Mashup
* Mailing-list fixed
*** log issue: break the link between vistrail.log and controller.log...
* Getting stats from the "server news" mechanism (via [https://github.com/remram44/apache-log-info parser])
*** experimental version so we can play with it and see if there are issues, what improvements
** Provenance browser
*** waiting to merge
** PythonSource editor
*** compile for windows, check how it works on Mac
*** issue with multiple windows?
** Global variables
*** expressions with variable, wait on this
*** set parameters on vistrail
*** click on ports to associate with globals


* Bug fixes
'''Items to Discuss'''
** Web services
* [RR] Alexis doing writeup on VisTrails, curious about interesting streaming use-cases (and potential future users)
*** upgrades are working
* [TE] Union ports
*** Upgrades are in a separate package
** Show union ports in pipeline (DEMO)
*** hooks in vistrails to allow detection when a package is not loaded


=== Apr 26, 2011 ===
=== May 18, 2016 ===


* Updates:
'''Items to Discuss'''
** Mashup
* [TE] mailing list still down - Julio working on it
*** easier ways to generate package wrappers
* [TE] Improved union port
*** working on merging code
** New schema 1.0.5 adds portitem.union string attribute
** Provenance browser
** Works with pipeline view, parameter exploration view, and mashup view
*** fixed thumbnails to show larger thumbnails
** Should work well for matplotlib
*** via tooltip?
** Use with VTK ports?
*** keeping separate branch right now, detailed commit message on merge
*** It uses [item_1,item_2] style ports usually with different tuple length.
** Persistence Package
* [TE] Remove emacs dependency from db generate [https://github.com/VisTrails/VisTrails/issues/1173 #1173]
*** stand-alone browser for writing and deleting files
*** writing annotations for execution provenance
*** find where version is not being written as an execution annotation
** bug: upgrade and Web services
*** last modified header not in all http transfers (e.g. for wsdl)
*** how to track versions of web services
*** one package per wsdl? see if this will work
*** seems to be an issue with network and that server (have to lookup twice)
** Global variables
*** next week demo
** new GUI


** v2.0 branch
=== May 11, 2016 ===
*** keep mashups off master
*** merging is pretty good using git
*** changing to a single-window interface, adding menus back


* Decide:
'''Items to Discuss'''
** PythonSource editor
* [TE] Union type [https://github.com/VisTrails/VisTrails/issues/1172 #1172]
*** try Eric or some QScintilla-based approach
** GUI-based solution [https://github.com/VisTrails/VisTrails/tree/union-port 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)


=== Apr 18, 2011 ===
* [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.


* 2.0 Release: new features to be included and bug fixes
* [TE] Publish user survey?
** Mashup
** No response from vistrails release yet
*** if already have alias, carry these over
** Not announced on vistrails-users yet.
*** have ability to choose GUI elements
*** storing provenance
*** allow users to import aliases, but don't write back to vistrail unless users wants to
*** provide user
*** create new palette for showing information about subworkflows and mashups (and tagged workflows) that shows on the left side [Dave]
** Provenance browser
*** Index for provenance information
*** Showing this in a separate tab, linking to a existing workflow
** Global variables
*** create a separate window
*** have underlying code for this
** control-flow assistant
*** Dan send documentation to Juliana and Claurissa
** Updated documentation
*** especially for executable paper
*** mashups
** Feature 'executable publications' more prominently
** FIX: upgrade and Web services
** Python editor
*** indentation and coloring
*** modeless window


* Updates
=== May 4, 2016 ===
** Workflow search [Tommy]
'''Updates'''
*** can now save multiple objects to the database in two round trips (modulo number of groups)
* VisTrails 2.2.4 released
*** create bigger thumbnails using tooltip in Ubuntu
*** view pipeline execution with groups
*** qbe. indexing high-level overview to Tommy
** Global variables [Daniel]
** Mashup integration [Emanuele]
** Python source editor [Emanuele]
** Web services update [Dan]
*** don't have upgrades
*** version numbers for web services modules, detect via some type of hashing
*** use last modified date + hash


=== Apr 12, 2011 ===
'''Items to Discuss'''
* [TE] Union type [https://github.com/VisTrails/VisTrails/issues/1172 #1172]


* Workflow search [Tommy]
=== April 27, 2016 ===
** Thumbnails in search
'''Updates'''
** Workflow search for individual workflows
** Materialize workflows: user-controlled for now, button in search interface to materialize workflows
** 2.0: log search for sure, possibly workflow/execution search
** Show groups in the execution view, add navigation bar at top of view (like Illustrator group navigation)
** Dave look at code for QBE & Indexing
** Also try to work with data


* Groups/Subworkflows
'''Items to Discuss'''
** need more documentation
* [TE] Wrapping Bokeh
** better ways to view and navigate still needed
** 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?


* Documentation [Claurissa]
* [TE] New bugfix release
** Persistence
** Finalize survey
** Could use ListToDirectory to take a list of files and convert to Directory (use for example)
** Delete/modify persistent data
** Persistent data provenance [Dave]


* Mashups in VisTrails [Emanuele, In Two Weeks]
=== 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: [https://github.com/VisTrails/VisTrails/issues/1168 #1168])


* Interface changes [Dave]
'''Items to Discuss'''
* New bugfix release
** Merge usagestats
** Need to finalize survey


* PythonSource updates [Emanuele]
=== April 13, 2016 ===
** DeVide, Eric4
'''Updates'''


* HTTPDirectory
'''Items to Discuss'''
** create a manifest file that can be used for HTTP directory
* [TE] Chaining upgrades done ([https://github.com/VisTrails/VisTrails/pull/1164 #1164])
** check with Matthias for how this works, not supported by HTTP
** Replace "Upgrade" description annotation with "upgraded_from" annotation to identify which tags to hide?


===Apr 1, 2011===
* [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


* Meeting time change suggestion to 10AM (Tommy) -- sorry Tommy, only now I saw this item...
=== April 6, 2016 ===
** Next week: meet if need be
'''Updates'''
** Move future meetings to 10am if room is possible (Juliana checking with Deb)
* [TE] Query View improvements
* Workflow Execution Explorer demo (Tommy)
** Done except for displaying "Version Info" and #1164
** search interface for workflow executions
* [RR] Working on finishing new interpreter (finally!)
** thumbnails?  problem is size
** can open a result and view the execution provenance
** querying vistrails
** materialize tagged versions in the database (so we can query workflows directly)
** extensions to allow query-by-example to work?
* 1.6.2 release (mainly with bug fixes) (Emanuele)
** integrate changes to module configuration?  on master, wait for 2.0 to put in release
** investigate different options for Python editors
** users guide? change to use sphinx for this release, add new features for 2.0
* VisMashup support in VisTrails discussion (Emanuele, Wendel)
* Wendel will give a demo of his work on supporting interactive visualizations in Web browsers; and of his simplified version of VisMashup
** generate 3D view and parameter interaction just from aliases
** suggested parameters: can associate parameters from workflows from other vistrails to labels, also order according to prevalence
** data: allow user to select other datasets from crowdlabs
** how to identify parameters that occur in different modules
** identify aliases in the web interface
** creating workflow view
** how to store the provenance of such views
** save dictionary of values from the mashup with the executions
** workflow to mashup bridge
** also allow a mashup mode to start from
** assistant interface
* Executable Pubs
** shell-escape not as well supported
** change the latex extension to be a preprocessing step (and make a vt_pdflatex cmd or something like that)
** Microsoft and MacOS X for publishing plugins--no Active X, known issue
** add better annotations to pdfs after the fact so that users can annotate papers
** meta-presenting
* Manual
** packages: difference between wiki page and users guide
** split users and developers guide, may have to do this for chapters like ControlFlow
** keep list of questions, write emails, talk to people


===Mar 22, 2011===
'''Items to Discuss'''
* [TE] Chaining upgrades ([https://github.com/VisTrails/VisTrails/pull/1164 #1164])
** Try latest upgrade first, then previous.
** If all fail, select latest upgrade?


* support a subset of VisMashup within VisTrails: re-use subworkflow infrastructure, and add the functions which create the application. Similar to subworkflows, mashups could live inside a vistrail
=== March 30, 2016 ===
** [DK] Note that mashups are higher-level objects than workflows.  It would seem that mashups should include vistrails.
'''Updates'''
** [JF] My idea is really simple: when we create a subworkflow we are essentially creating a 'view' that hides away the details of the underlying modules and only exposes a subset of the parameters. What I would like to have is the component of VisMashup that takes a subworkflow specification and generates the app.  This would greatly simplify the publication of *interactive* results. And I believe, it would be simple to implement since it would re-use the existing infrastructure we have for subworkflows.


* support for global variables: maybe, an initial approach could be to have such variables associated with a vistrail. This would greatly simplify packaging of workflows, in particular, to deal with file locations in different systems
'''Items to Discuss'''
** [DK] We have discussed this before as having '''workflow'''-global parameters and have proposed a method for accomplishing this---namely modify the interface to hide global parameters.  It may be possible to have them for entire vistrails, but note that this poses problems. Suppose a user that creates a workflow identifying 'x' (a Float) as a global variable, and then changes the workflow and identifies a new parameter as 'x' but its type is now a String.  A per-workflow definition of the global 'x' is fine, but a per-vistrail definition is not.  I agree that we should try to support some style of alias-like behavior so that a user can set parameters more globally, but it is important that these settings are saved as provenance as many of these might be per-session...
** [JF] I want global variables to simplify packaging of results. Having them on a per workflow basis would not solve the problem I had: In the WikiQuery case study I have a series of related workflows that all rely on the same set of input files; so in this case, I would need global variables at the VisTrails level.
** [JF] As for the issue DK raised, I think we could have a very simple solution: we check for conflicts with global variables and prevent the used from making mistakes


* SubWorkflows in the database (Tommy)
* [TE] Query View improvements
** abstractions==subworkflows? Some error messages still refer to abstractions
** Unified do_version_switch and get_upgrades as validate_version()
** Logic for merging subworkflows from different sources? (Upgrading issues?)
** Problems with query view using its own controller
* Control Flow Assistant feedback (Tommy)
*** Fixed module info not being displayed for query results
* From Matthias:
*** Still no version info for query results
** Remote execution: make it easier to move executions to clusters, starting them from VisTrails, waiting for the results.  Can we make Joel's code for the wildfire simulations more flexible?
*** Still an issue with version query view not being updated
** Using VisTrails for validation: make it possible to take results of a workflow, and compare them with a previous result to validate that changes in code or VisTrails have not affected the results.
** Make it easier to select a persistent repository (test, release, etc.) so that the same workflow can be run against different repositories
** Better support for querying hundreds of data files (ie create a database of metadata that a user can use to filter the set of files to locate specific files quickly)
** Along with this, allow this to work over existing (non-persistent) repositories.
** A better python editor for PythonSource


===Mar 15, 2011===
=== March 23, 2016 ===
'''Updates'''


* database to file: works for log now
'''Items to Discuss'''
* database: save subworkflows to the database
* [RR] Usage reporting almost ready to go
* add uuids for vistrails, subworkflows, merges
** Need to record whether specific features are used: paramexpore, mashup, query
* merging: same uuid and data changed
*** [DK] Record if LaTeX extension is used? But hard to distinguish from direct batch invocation
* look into distributed algorithm
** How to record size of vistrail?
* merge should possibly include logs
*** [DK] IdScope already walks over vistrail, use that
* allow additional metadata to be controlled, possible to have a 1-1 correspondence
*** but total number of modules and versions doesn't give an idea of average size of individual pipelines


* speedup on database queries to speed up joins over entities, combine different attributes
=== March 16, 2016 ===
* loops on module executions
'''Updates'''
* traversing module executions
* build transitive closure
* build table to link the workflow_exec with module_exec


* fix for users-list problem with Embed GUI issue
'''Items to Discuss'''
* how to handle users that want to contribute code or examples
* [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]


* [Dan] committing control flow assistant soon, issue with database version (see trac commit from today)
=== March 9, 2016 ===
'''Updates'''


===Mar 8, 2011===
'''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


* DB speedup finished? [Tommy]
* [TE] Create new bugfix release
** Speedup done.
** Finish querying
** Looking into issues with saving log
** Path issue on windows
** Execution Provenance API


* Control flow [Dan]
* [DK] Look into sqlalchemy and new bundle branches
** Fixed issues
** Input List Override working
** Cartesian product now working
** Error message with version tree
** Weird issue with the group executing before the map starts


* Documentation [Claurissa]
=== March 2, 2016 ===
** check in guide to git
'''Updates'''
* [TE] Fixed cache bug with port specs
* [TE] VisTrails Next
** Most packages now work
** No qgis for Python 3


===Mar 1, 2011===
'''Items to Discuss'''
** Always dereference symlinks? [https://github.com/VisTrails/VisTrails/issues/1146 #1146]


* [[Documentation Log]]
=== 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


* Updating the relational DB (Tommy)
'''Items to Discuss'''
** Import vistrail from DB is now very fast.
* [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.
** Mostly done with export vistrail to DB. Still a few issues.
** 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?


=== Feb 22, 2011 ===
=== February 17, 2016 ===
'''Updates'''


* Python Source widget (Emanuele)
'''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


* News: Claurissa will help us with documentation. She will start by translating the existing user guide into Sphynx, and then move on to updating the content as well as documenting the many features that are currently not described in the manual.
=== February 10, 2016 ===
** Please add any undocumented features as well any (informal/incomplete) descriptions you might have to the following page: [[Undocumented Features]]
'''Updates'''


** focus issue (will ask Huy if he knows a good solution for this)
'''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?


* Browser updates (Tommy)
=== February 3, 2016 ===
** project browser, workspace
'''Updates'''


* Updating the relational DB (Tommy)
'''Items to Discuss'''
** insert size: Tommy tested with 60,000 inserts
* [vistrails-users] [http://lists.vistrails.org/pipermail/vistrails-users/2016-January/000402.html Rendering a .pvd (ParaView) file?]
** loading: multiple selects and retrieve them all at once
** incremental updates, is_dirty, is_new
** no need to bump the schema version
** start thinking about better ways to do queries
** can prepare statements via low level mysql commands


* Loop Assistant (Dan)
* VisTrails Next
** add tutorial for this loop
** 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


* mailing list emails
* [https://travis-ci.org/VisTrails/VisTrails/builds/106743348 Travis builder] for VisTrails Next
** Dan: keep track of which emails and update the FAQ with answers
** Runs!
** Could think about putting this into a system eventually, but for now it's low-traffic enough
** 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?


=== Feb 8, 2011 ===
* [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?


* LaTex extension demo (Emanuele)
=== 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)


** New embed dialog
'''Items to Discuss'''
* User Survey


* Non-modal PythonSource windows ([https://vistrails.sci.utah.edu/ticket/408 link to discussion])
* ZMQ failing on windows (vistrails-users)


** make it non-modal, single window
* [TE] [https://github.com/VisTrails/VisTrails/pull/1143 Python 3 branch]
** update selection on click
** Testsuite almost passes
 
*** Failing are unicode filenames, some users guide examples, and thumbnail comparisons.
* Where to keep User's guide and other documentation
** Fixed issues
 
*** Signatures are now bytes (convert to string to show in widget)
** Sphinx, commit to doc directory
*** Cannot compare different types, e.g., (None < 1)
 
**** PortSpec.depth and min/maxConn could be None. (Backport!)
* Log Explorer demo (Tommy)
**** cell.row could be None
 
*** Lots of unicode/bytes fixes to serializations
* [[Log_API]] RFC (Tommy)
**** We have encryption implementations in the code! (keychain)
 
*** Lots of small fixes to package method differences
* Control Flow Assistant (Daniel)
** Current issues
 
*** logging widget empty?
=== Feb 1, 2011 ===
*** version tree signals messed up
 
*** provenance view legend icons black
* Execution Provenance View (Tommy)
*** Text do not fit in some widgets
 
*** VTK thumbnail comparison fails
* Control flow assistant (Daniel)
**** VTK Cells have some faces in wrong direction?
 
****  Because running in VM?
* Script Interaction (Emanuele)
** Installing on Ubuntu LTS/Latest Mint
** CDAT feature that might be useful in other settings
*** Install latest matplotlib from pip
 
*** Install VTK 7.0.0rc2 from source
* Port/parameter management (Dave)
*** No QtWebEngine binary (controversial) (Must install sip/PyQt5/Qt5 from source)
** moved close button
** what about NULL parameters?
** global parameters
 
=== Jan 18, 2011 ===
 
* VisTrails browser (Tommy)
** demo
** can import files and directories to the list of files
** can see and open vistrails, workflows
**  need to think about how to show execution information
 
* Control flow assistant (Daniel)
** integration with parameter exploration
** can re-use infrastructure with parameter exploration
** can keep provenance for parameter explorations for free if we use the looping constructs
 
* New port/parameter management (Dave)
** demo
** ordering?
** ability to filter, sort parameters
** documentation
** required ports
** update modules to show when parameters are set on ports
** talk to Matthias
 
* 1.6.1 Release
** tomorrow, bug fixes + executable papers
** create tickets
 
*
 
=== Jan 11, 2011 ===
 
* Release (Emanuele)
** 1.6 released 1/7/2011
** there is a branch on git
** nightly builds
** bundling ALPS python support into releases
 
* Control flow assistant (Dan)
** focus on supporting the Map module
 
* VisTrails browser/repository (Tommy)
** open a vistrail get included in an index
** index includes vistrails, workflows, and executions
** use thumbnails for showing the workflows
** in the future, sort by projects
 
* Port and parameter updates (Dave)
** Colin Talbert at USGS-Fort Collins requests the same global parameters feature that Matthias has already mentioned.  We should start working on this functionality.
** Colin also asked about highlighting required ports
** Changes to schema: add required flag, cardinality flag, and global parameters
** Changes to execution: way to add global parameters and connections to workflow before execution begins (not display visually)
** Changes to interface: method to select ports and tie them to global parameters, global parameter display, highlight for ports to show required (red?), do we need to show cardinality?
 
* Executable paper tasks
 
=== Dec 21, 2010 ===
 
* saving parameters in a module (email from Tom Maxwell, from NASA)
* explorations still do not detect MplFigureCell modules inside groups or subworkflows
 
=== Dec 14, 2010 ===
 
* [ES] Unit tests
** Ran unit tests last week
** Errors with old versions of pipelines, need to fix pipelines
** console_mode_test can't be enabled
 
* Data publishing with CrowdLabs
** using persistent files and directories?
** couldn't think about how to synch user directories with server directories
** look into how to push data files across with git
** how to organize data (ie persistent files) from a specific workflow or all workflows with specific parameters
 
* [DR] Subworkflow upgrades: update--is it a wrap?
** functionality are completed
** one cosmetic issue -- disabling a package
** subworkflows move from top to bottom of the list
** [DR] Add documentation to wiki on subworkflow upgrade paths
 
* [DR] control flow assistant
** started looking into this
 
* [TE] [[Data/provenance browser]]: update
** looking at the old code
** some problems with the logs
** cannot find parent workflow
** adding project annotations to sort VisTrails into different projects, different vistrails in different project, need to have gui to do this
** synchronize when vistrail changes, especially with execution logs, create index schema for these files (vistrail and workflow exec)
** persistent data index, need to integrate eventually, scan through actions to generate list of files used
 
* PythonSource editor
** seeing which PythonSource editor is open
** need to be able to have "save now" button or automatically save when someone presses "execute"
** generate id tag automatically, close the other window immediately
** highlight module being edited/configured, keep window open (like console, messages)
 
* Lack of global variables and bookmarks
** don't need to reconfigure executions to do this
** just don't display the "global" modules and connections
 
* [CS] look into 3 items for [MT]'s group: ports display, python source, global vars and bookmarks (and persistent files dump)
 
* [PM] Merging master and crowdlabs git branches. How should we merge the crowdlabs branch into the master branch?
** problem is that there are changes in crowdlabs that can't go in the master branch (i.e. HTTPFile)
** [ES] just merge both so we don't have the crowdlabs branch
** [PM] change RepoSync to have a server config preference that is set to True for server, False for client, and RepoSync has an if in the compute that does one thing if server is true, another if server is false
** have a branch for workflow indexing so that patch lives in another place
 
* Box input ports should be colored (e.g. black) if they are already set by an internal method. Another color (e.g. red) could be used to indicate mandatory input ports.
** Currently, non-optional ports are square, shown. Optionals are circles and must be enabled
** Add a third category for mandatory, problem is backward compat.
** [ES] Colors are already overloaded, not for ports, use shading instead?
** Also needs to be with global settings, etc.
 
* 1.6 release: [ES] already has 1.6 candidate
** don't include the new gui features yet
** freeze 1.6, just bug fixes
** merge crowdlabs branch
 
* [DK] persistent files on the server
** [MT] has problems with files on server, issue with /tmp/, running older python (2.5)
** stress test, test on [DR]'s machine
 
=== Dec 7, 2010 ===
 
* [DR] Subworkflow upgrades
** Made sure that we don't rewrite actions but create new actions that show where subworkflows are upgraded
** Document what is implemented and how it works (at high level), also what isn't yet implemented
 
* [TE] Errors and web services
** allow user to decide to only display errors to messages window instead of also showing popup windows
** Allow add/delete of web services from GUI without going to preferences
** Qt dependencies for error messages gone
 
* [PM] Some specific questions
** Question: Should v1_0_1 MySql schemas be upgraded to v1_0_2?
** db_connection.begin() being removed, stale results
** memory size is too big for the field size
** [DK] check on schema changes, see what is important for changes
 
* Question: do we display 'warnings' or only errors?
** Need to write ModuleErrors (maybe make ModuleWarnings) to the messages (debug) as well as adding as tool tips
 
* Some suggestions/requests by Matthias:
** Support the grouping of vistrails and files into projects
*** Annotation here?
** Ability to set global parameters/bookmarks=workflows (e.g., a filename or path)
** Archive results -- create a big tar/zip file with all vt and results
** Ability to add a vt: if a node is deleted, all data associated with that should also be deleted
** Create a test suite: run a workflow, save and archive results (user could specify which results should be saved)
 
* [[Data/provenance browser]]
** We need a better mechanism that allows users to search/query for workflows and provenance, for example search by project, parameter names and values
** One way to view this is to allow the creation of mappings between the vistrails/projects into different structures---like "smart folders", e.g., /projectN/vt1/wf3/exec23/O1....
** Support editing and synchronization in both ways (if edit smart folder, should update vt)
** Should be able to script the use of the browser, e.g., to test a new version of a workflow against a saved test suite
** Scientists like a directory structure and can go browse there like they browse files with finder/explorer
** Keep mappings from our datatypes to file structures
** Need an exportable archive (to send with a paper, allow browsing outside of VisTrails)
 
* On merging master and crowdlabs git branches
** some updates on the crowdlabs branch need to be merged/patched into the master branch
** how should this be done?
 
* PythonSource editor
** modal or multiple window editors?
 
* Lack of global variables and bookmarks
** Problem is that aliases don't change workflow specification
** Need to store these values in the execution log
** Keep alias dictionary for everything
** [PM] Not a need for global variables above the single workflow level
** This already exists at the conceptual level---one module with connections to other modules, this just is cluttered
 
* Unit tests
** [ES]: I ran the test suite on current master branch and 207 tests are executed of which 11 fail. Some of the tests are failing because console_mode_test package can be imported anymore (this is a package created specific to run console_mode tests).
** Most of the other problems are issues with
 
  InvalidPipeline: Pipeline cannot be instantiated:
  Missing version 0 of package <package>
 
* Data publishing with CrowdLabs
** Using git to manage data between local and server data stores might be too messy.
*** Does one create a new git repository for each vistrail on crowdlabs?
*** The local persistent git repo holds all persistent data used on that machine. How does one push/publish just one data product using git?
*** Can anybody think of a plausible git workflow to do this?
** Perhaps we should just look into adding directory support for RepoSync module along with a better data management UI.
** Are there OS independent file transfer protocols better than HTTP? Something like rsync might work nicely, but windows support is limited.
 
=== Nov 30, 2010 ===
 
* Subworkflow Upgrades (Daniel)
** Should be completed finished tonight
** Local subworkflow upgrades should be working now
** Need to test these after the checkin
** Using a dummy controller
 
* Assistant for control package (Daniel)
** Look at examples
** Try to make an assistant to modify workflow using currently selected modules as looping group
 
* [[Improve error handling/reporting]]
** Tons of message boxes pop up when a workflow has a bunch of errors, UI response is bad after this...
** Update existing error messages
** Show Details rendering on Mac
** What to do when multiple errors occur in a single event?
** New dialog that shows "next message" but allows user to dismiss messages or view all in the messages window
** Color coding for messages: use gui/theme.py to configure: maybe try black for warning, gray for log level messages
 
* Data and workflow browser (Nivan will give a status update)
 
* Saving Explorations (Feature Request from ALPS)
** We already save parameter explorations with the workflow in the version tree. As is, we save only the last exploration that was done for a given workflow.  If you ship the vistrail, the saved parameter explorations will be there.  Is this sufficient?
** [MT] Yes, that takes us a long way. Could one add a button in the explorations to save a certain set of explorations as a new version, like you do with the camera angle in the spreadsheet? That way one could store more than one set of exploration parameters without forcing a new version to be created with every change?
** Eventually we should provide a selector in parameter exploration
** Fastest to just allow a null action new version (a bit clunky) but wouldn't require too many changes
 
* Clean up/prune persistent directory
** What are the concrete use cases for this?
** [MT] Here are two concrete use cases that appeared over the last week:
*** a project is done, the important results copied to an archive and I want to get rid of all its intermediate files, etc., to save space - but not those files associated with other projects. Or, similarly, I'm done testing some workflows, want to remove all (partially buggy or irrelevant) files, and then start with production runs.
*** there was a problem in a workflow(e.g. a bug in HTTPFile module with binary files or a bug in some user code). I want to force a certain persisted directory to be "forgotten", so that I can repair the wrong files. Bumping the version number of the ALPS package would be one way, but that is overkill since it would immediately invalidate all persisted files. Removing the whole persistence directory is just as radical.
** just testing simple tutorials with small files leaves me with 2 GB of persistent data after 10 days, in 142 persistent directories or files. I need some way to clean this up that is less radical then removing all persistent directories and files. This could be done, by e.g. removing all those which do not occur in tagged or leaf workflows in a certain set of vistrails. Or marking those which occur in certain vistrails with certain labels, and then being able to prune all those with or without some label/tag. Another option might be having the ability to choose from various repositories.
** [DK] follow up on this
 
* Improvements to VisTrails server communication with clients to better handle errors/crashes (Phillip)
** work in progress
 
* Data Publishing with crowdLabs. (Phillip) 
** Do we want data publishing capabilities in VisTrails and crowdLabs?  '''YES!!!'''
** If so...
*** Currently limited data provenance for data. HTTPFile module lacks meta data, RepoSync module has poor usability.
*** Persistent Data works for experimental data. Can we use it for publishing data?
**** Publishing data or storing data on the server and pushing back and forth?
**** What is the current scheme for identifying data on the server?
**** Do we need to do better than the ids, versions, hashes that the peristence package provides?
*** Do we want to utilize data publishing software like [http://thedata.org/home The Dataverse Network] or maybe [http://www.fedora-commons.org/ Fedora Commons]?
** [ES] Feature request: Can RepoSync support a directory of files?
*** [PM] It can't, and I'm not sure how add it. I also don't really like the current RepoSync interface. It's not obvious how your data is being handled, hence me bring up data publishing, so hopefully we can come up with something more usable/robust.
** persistence used more for exploratory
** want to focus on more archive
** move from exploratory data to published
** Dataverse: essentially a site to curate data, archive data, host their own site, each university has their own server, linked together
** persistent store integration: maybe use git to do this, can add to local repositories to move to git
** use some of the dataverse: standard hash schemes, etc.
** privacy: can users push workflows without exposing data
** permissions for who can check things out: download permissions, upload permissions
** look into setting up persistent store on
 
* DisplayWall (Wendel)
** new version of vistrails receives rotate/scale messages much more slowly
** using the vtk version that is already there
** comparing VisTrails 1.2 with nightly src
** test when the messages are received on the clients
** [ES] Changed something in the VTKCell, using the Qt interactor from vtk now, just uncomment this (vtkcell.py file)
** some commands are missed; check why this is happening
** preferences switch? 2x2 not 2x3
** check what modifications exist in the client code that's not exactly 1.2?
** new version of vtk package changed some things
** update vtk upgrade: resetcamera and addrgbpoint => _# versions
** Demos on displaywall: Wendel has to keep both VisTrails running and stop work when visitors stop by unannounced
 
* Relative paths in workflows, how to deal with them? (Emanuele)
** [ES] Updated all examples to use HTTPFile for these
** some of these had to change completely (color widget), kept tree the same format
 
=== Nov 16, 2010 ===
 
* Data and workflow browser (Nivan)
** Check into git branch (Dave)
** Add data support to the vistrails, workflows, and execs already exposed in the browser
** Add thumbnails to the browser
** Bittorrent support?
 
* Upgrade issues -- a wrap? (Daniel)
** Fixing some issues with namespaces
** Upgrades for subworkflows that are included with packages, need to save these upgrades with the vt file as a "local abstraction" to ensure provenance.  May be able to tie these back to the package versions once the package is upgraded.
 
* Test Suite
** Matthias has his own test suite now
** We should make sure that our tests are up-to-date and run them before releases
 
* Web services on users' guide (Tommy)
** Users' guide needs only a few changes.  One of the changes should be a note making it explicit that we are using a new library and the old one was deprecated.
** Do we want to update the 39-page guide as well?  For now, just update the users' guide.  Don't distribute this guide.  Just include it in a zip file that includes the old version.
 
* [[Improve error handling/reporting]] (Tommy)
** print statements, has a new window
** add a menu item to view message window and also keep all messages from the session
** look into writing QMessageBox errors and warning to message window
** write all messages to a single window, write critical messages in red?
** have a utility method that encapsulates the gui error display and the core.debug display (if not running gui, only write to core.debug)
** don't display stack trace in a qmessagebox?  -- try to emulate the invalid pipeline with "Show Details" button.
** make it easier for users to report errors by having a "copy" or "send to developers" button to report the details of an error.
 
* DisplayWall (Wendel)
** What examples should be in the SVN? If we decide to keep some examples in the svn, some of them use data that should be along.
*** Indicate progress of HTTPFile
*** Had to upgrade examples to work with new examples of VisTrails
*** VisTrails can send progress information with another thread like crowdlabs can do
*** Each machine has a .vistrails and needs to download own version of data, make a single .vistrails for all machines?
*** All slave machines can use the server as a cache?
** DisplayWall Client on the Apple Store? I dont like the idea of sharing the client source code. And putting the app without login/password will allow anyone to access our displaywall.
*** Add a password for this
*** Do user management?
 
* VTK package:
** Have two ResetCamera modules now
** Need to write upgrade code
** Only with vtk 5.7 right now
** Encode library version in the package version?
** For reproducibility, we probably want to stick to specific versions
** We still need some ability to run new versions of vtk for testing, new features, etc., too...
 
* Relative paths in workflows, how to deal with them? (Emanuele)
** Should we use dataDirectory?
** Change examples to not use hard-coded files?
** Problem with workflows, not data files
** On Windows, use ../examples
** On Mac, use ../../../examples
** dataDirectory not used, I think
** create "$VT_EXAMPLES"?
** problem is using new versions of VisTrails, data may change so referencing old location will fail
** don't allow users to change this variable
** convert to use HTTPFile
 
* Data files and the GIT Repository (Emanuele)
** make a separate repository or use the submodule git functionality
** go with submodule
 
* Next release: What still needs to be done?
** high priority from ALPS list
** Dan's fixes to the upgrade workflow
** Date for release?  Official release in beginning of December for ALPS
** All developers should run test suite on push
** Could make this somewhat automatic, run with nightly release script and email -dev list
** Could have different classes of tests, make sure that critical ones pass
** Tests have a bunch of errors currently
 
* Saving explorations:
** Keeps track of the latest exploration for each version
** Check with Matthias what the requirements for this are
** Have way to send just specification to a server (run this workflow with this parameter exploration)?
** Can we have an xml spec that specifies the parameter exploration (export parameter exploration)
** Currently persisting via xml and then converting to string so we already have an xml serialization
** Dan wrote API that takes xml string and populates the param_exp gui with the appropriate values
** Need to back the GUI state with core state to enable short-circuiting the gui
 
 
* Box input ports should be colored (e.g. black) if they are already set by an internal method. Another color (e.g. red) could be used to indicate mandatory input ports.
** Currently, non-optional ports are square, shown.  Optionals are circles and must be enabled
** Add a third category for mandatory, problem is backward compat.
** [ES] Colors are already overloaded, not for ports, use shading instead?
 
=== Nov 9, 2010 ===
 
* FAQ
** As we reply to users queries, let's add the question and answer to the FAQ!
** Just a reminder
 
* Caching of File module
** There was a message from a user who got confused because this module is cached by default (and silently). And in his application, since the file actually changed in between runs, he did not see the 'expected' result.
** Should we keep a hash for files and check whether they changed?
** Should we no cache File by default?
** [DK] File is supposed to have a special signature computation that detects changes in the file contents so this may be a bug instead.  It does work, it seems to be an issue with the create_file
** [ES] In this particular case, the file was empty. He deleted the file outside VisTrails and executed it again. As he set create_file to True, he was expecting the file to be created again.
** [DK] Add random salt to hash signature when the file doesn't exist and create_file is True
** [JF: DONE] Juliana will edit the FAQ to note that the signatures are dependent on modification times
 
* Claurissa will demo different ways to visualize the version tree
** weighting on various criteria for displaying nodes (importance from session, user, tags, etc.)
** other modes for viewing the versions (lists or timelines)
** often see only linear trees, teaching or thinking other than tree?
 
 
 
* Upgrade issues (Dan)
** Vanilla upgrades should be in today's commit
** Added code so when doing upgrade to check whether the latest code is upgraded
** Two types of upgrades: (1) User changes the subworkflow, (2) Modules are out-of-date and need to be upgraded.
** Add higher-level features like "Upgrade All" for (1), "Import Changes to My Subworkflows", etc.
** Want a 1-1 mapping between unique subworkflow id and a subworkflow file (even if we copy the same subworkflow to different vistrails)
 
* Offscreen bug  (update from Huy)
** Mac issue when switching to Cocoa
** Huy added a QWidget for each of the render windows that is created, so should be fixed.
 
* Gesture support
** Someone on Windows check the pinch gesture support; it doesn't work for Matthias under Parallels
** VTKCell is working now
** Cell dependent, panning now maps to middle button, pinch on the base widget
** What are Matthias's requirements here? Does touch gestures in the cells matter or only in the vt/wf views
 
* Thumbnails: [JF: this needs to go to trac, for 2.0?] [ES: 2 tickets were created for 2.0]
** Resolution? -- [ES] problem is the size of the vistrail, but this can be configured
** Can we export to PDF instead of PNG? [ES] cannot display the thumbnail as a PDF in Qt?
** Can we have the option to save higher-res or PDF versions of the thumbnails
** Can we have preferences that allow users to save a higher-res or PDF version, maybe a checkbox
** Maybe associate a high-res version with a spreadsheet cell so that we can save a high-res version on demand
** high-res version associated with a version but allow user to initiate action from spreadsheet
** can we have thumbnails dependent on camera position [ES] doesn't like, user won't see exactly that image upon re-executing
** compact vistrail option by removing thumbnails
 
* Tommy has rewritten the Web services module as well as updated all of the examples
** Server for one of the examples seems to be down
** Need to update the manual
 
* [[Improve error handling/reporting]] (Tommy)
** Maybe display the intialization messages with the splash screen?
** Debugging levels have no way to access debug level
** Tommy takes first cut at trying to determine how to map print statements, notes those he is unsure of
** Developer guidelines for debug usage, use them instead of print statements in the futur
 
* Merge functionality (Tommy) [JF: Cool!]
** Can now merge an existing vistrail into your own vistrail using menu item
 
* Improvements to VisTrails server communication with clients to better handle errors/crashes (Phillip)
** [PM] I haven't had a chance to implement anything yet.
 
* Data Publishing with crowdLabs. (Phillip) 
** Do we want data publishing capabilities in VisTrails and crowdLabs?  '''YES!!!'''
** If so...
*** Currently limited data provenance for data. HTTPFile module lacks meta data, RepoSync module has poor usability.
*** Persistent Data works for experimental data. Can we use it for publishing data?
**** Publishing data or storing data on the server and pushing back and forth?
**** What is the current scheme for identifying data on the server?
**** Do we need to do better than the ids, versions, hashes that the peristence package provides?
*** Do we want to utilize data publishing software like [http://thedata.org/home The Dataverse Network] or maybe [http://www.fedora-commons.org/ Fedora Commons]?
** [ES] Feature request: Can RepoSync support a directory of files?
*** [PM] It can't, and I'm not sure how add it. I also don't really like the current RepoSync interface. It's not obvious how your data is being handled, hence me bring up data publishing, so hopefully we can come up with something more usable/robust.
 
=== Nov 3, 2010 ===
 
* Upgrading subworkflows (Dan)
** add updated versions to subworkflow vistrail and push to registry
** fixed bug with version/descriptor redirects
** key remaining task is to replace the box representing the subworkflow in the top-level workflow to reflect the change to the upgraded version of the subworkflow
** many corner cases, but we should get the vanilla upgrade (working) to git
** need to ensure that each subworkflow file has its own uuid; if a subworkflow exists in two different vistrails, it should have a different uuid (namespace).
** otherwise, we can get crosstalk where one vt can update the subworkflow from another vt (we can propgate changes to other vts via merges, but this should be a user choice...)
** enhancements:
*** allow users to merge subworkflows from a file into their own subworkflow (to incorporate outside changes)
*** latest version is the most recent non-upgraded version; if that version has an upgrade, use the upgrade
***'''Next step: work on usability for controlflow package; explore Dave's idea of an assistant'''
 
* Offscreen bug
** Huy is looking into this
 
* Crash due to issues in loaded user packages (Tommy has fixed this)
 
* Web services (Tommy)
** Package is completed, and all but one of our examples are working
** '''Tommy will test if the Web services will work when there is a proxy'''
 
* Improve error handling/reporting (Tommy)
** we should have a single point for all error messages to pass through that is linked to both core.debug and GUI elements that display error messages.
** the goal is to implement a function that will be the single point for error messages, and that work without emitting GUI signals in core. As Huy suggested, we should have a GUI-wrapper which will be a no-op when the GUI is not instantiated---this will get rid of some of the pyqt dependencies (at least for the error messages).
 
* Improvements to VisTrails server communication with clients to better handle errors/crashes (Phillip)
** Currently the VisTrails servers consists of: a single-threaded instance with GUI; multiple GUI-less threads
** We will extend the server API to allow clients to check the server status. The server will provide a separate socket and the client will be able to 'ping' the server; if the server is working properly, it will respond; if it does not respond, the client will have a time out
** The API will also support the ability to kill both the GUI-less threads and the single-threaded GUI instance. We can then restart the server components using Emanuele's new script.
** We should also allow users to set a per-workflow time-out; if the workflow execution takes longer than the pre-defined threshold, VisTrails will abort the execution
 
 
* Update on fixing VTK Package (Wendel)
 
** It seems that the ParaView package has the same issues.
** '''Wendel has already checked in the new wrapper into the trunk; Emanuele will test it'''
 
* Synchronizing VisTrails and ALPS releases (Emanuele)
** VisTrails latex package was extended so that python is no longer required. If python is not present in the system, instead of issuing a request to execute the workflow and retrieve the image from the Web, a local, previously saved image will be used.  It is now also possible to embed the images of workflows into the latex file. Documentation about these and other features are currently in the README file and examples (example.tex) provided with the latex package.
** Windows and Mac beta binaries already include ALPS
** Are we distributing ALPS as part of VisTrails then?  This seems backwards.  ALPS should VisTrails as part of their stuff, no?
*** '''We will have separate binary distributions: one with and one without ALPS'''
 
* Is a multi-touch interface to VisTrails possible now that it's supported by Qt? (Phillip)
** Yes, Qt 4.6+ supports multi-tocuh --- '''Huy will look into this; the goal is to make this work both for the workflow builder/tree view and the spreadsheet'''
** We still need to figure out what makes sense for multi-touch, however, do we have requirements from ETH-Zurich?
*** We want to map the zoom, pan, click, etc to multi-touch, so that VisTrails can be intractable on a multi-touch screen without a mouse
 
* What is the status of the Vismashup i{Phone|Pad|Touch} app? (Phillip)
** If you mean mac binary, there's an alpha version here: http://www.sci.utah.edu/~emanuele/files/vismashup
** Do you mean iphone app? [Phillip: yes]
** '''Wendel will look into this'''
*** One of the issues is how to effectively handle images that are larger than the memory on the iPods and iPads---we need to process these on the server or use a model that allows the image to be manipulated on the client
*** We also need to connect the app with the crowdlabs server, so that the app can get the list of mashups
*** Phillip will investigate the feasibility of working directly with JavaScript and bypass flash
 
 
 
=== Oct 19, 2010 ===
 
* Update on Trac and Roadmap (Emanuele and David)
** Trac is now linked to git repository
** Roadmap on Trac has been cleaned up so we can hide completed milestones
** Tickets are being reassigned/revisited. Many tickets (24) are not associated with a milestone yet https://vistrails.sci.utah.edu/report/3
* Synchronizing VisTrails and ALPS releases
* Web services support (Tommy)
** discuss the interaction between the Web Services package and upgrades
* Subworkflows update (Daniel)
* Testing of new module drawing (Erik)
* Aliases
** Currently, an alias is stored on a parameter.  We need aliases to be stored at a higher level so that changing an alias is not a change to a parameter.  The one issue is that there is a link between parmaeters and aliases in that an alias can only exist for versions that have the specified parameter.  We might also have two versions where the alias points to different parameters.  We could just store aliases as a root-level workflow element so that the set of aliases is versioned corrected.
** In the current implementation, the aliases parsed from the parameters are stored in a dictionary in the workflow, so storing aliases as a root-level workflows element might be the way to go --[[User:Emanuele|Emanuele]] 19:50, 15 October 2010 (MDT)
* Error logging
** Suggest that we have a single point for all error messages to pass through that is linked to both core.debug and GUI elements that display error messages.  This should improve our error handling significantly
* PyQt dependencies in core
** Can we get rid of PyQt dependencies in core (and db)?  This would probably require moving the signals/slots that we currently use to a similar Python implementation which shouldn't be too difficult.  This would also require the specification of configuration widgets not as classes but rather some text that can be used to import the GUI elements only when using the GUI code.  However, what would happen with workflows that run in command-line mode but require some graphical output?
* Ports
** One annoying part of the current VisTrails model is that users are not given any visual indication that a port value is already set by a function or vice versa by a connection.  In addition, we have no way to specify or enforce cardinality on ports at design time.  It seems like we could allow developers to specify when a port should not be connected to more than one value (via a function or a connection), and give some visual feedback when a port has already been specified in one manner.
 
==== Meeting Notes ====
 
* Bug regarding userpackages at initial vistrails startup causing startup to fail.
** Still an issue, ticket still open as a 1.6 milestone
* Copy-paste bug
** Shortcut not working on Mac. Focus makes shortcut try to copy pipeline.
** Current fix appends to clipboard as users type - this is not a good fix.
* Synchronizing ALPS and VisTrails releases
** 1.6 scheduled for Dec. 1
* Webservices
** New library being used, but it's very low level.
** Simple types may cause problems with some web-services using complex or XML-based types.
** Need to make sure that this library can handle at least MOST of the web-services out there.
* Sub-workflows
** Daniel's changes seem functional and very slick.
** A little more work on it seems necessary.
** Need some easy GUI mechanism to delete a subworkflow.
** Is the exclamation point in the module draw the best way to handle this? Make a tool-tip to explain it.
* VTK Wrapping
** Changes to VTK Python wrapping is causing headaches - particularly in backwards compatibility.
** Method typing has changed to expect things like "List" or "Vector" - makes things hard on the user when defining these inputs.
** Removing List and Vector types and replacing them with dynamically generated versions from Tuples.
* Aliases - Agenda pushed until after Vis.
* Error Logging - Unify some error handling to improve how exceptions are dealt with.  More on this after Vis.
* Refactoring out PyQt dependencies from Core/Db/etc - Need to move all the signals/slots into GUI elements.  Questions come when a workflow uses GUI elements as inputs.  - More after vis.
* Ports - We need a way of showing how a port is specified - function vs. input port.  Cardinality must be established in these cases.  Ordering on multiple connections should be handled in some way - whether it's just a documentation issue or a more fundamental one.
** Should we have a tutorial mode that bring up tooltips when someone does something new as if it were a live tutorial.
 
 
=== Oct 12, 2010 ===
 
* Trac and Roadmap (Emanuele): Emanuele suggested we should create a development roadmap and make it a permanent item on the agenda. The idea is to go through the Trac tickets and use them to build the roadmap that would be made ''public''.
** go through trac and sort by priority
** add other suggestions to roadmap as well
** admins can add milestones via the admin tab
** ''David will assign tasks on list; those assigned need to follow up and check and fix them''
 
* Update on [[PythonSource error reporting and logging]] (Tommy)
** ''Need to make sure that all messages are printed through debug.X, so that the debug level (verboseness in preferences) is correctly used''
** Can cut/copy/paste now
** Can we prevent the delete from happening?
** Phillip noted the spyder project has an interactive python console: http://packages.python.org/spyder/
** Can press enter to get to the end
** Need to check if this works or if we need to change
** Now have ability to see stack trace from the GUI (triangle menu)
** ''Suggest using a dialog to display trace when this item is selected instead of printing to console''
** Also saving stack trace to the execution log
** Also printing debug information to vistrails log
** ''Add trac item to fix prints to use debug''
** ''Try to fix core.debug to have gui.debug to eliminate Qt dependency''
 
* Update on subworkflow (Daniel)
** Notification when subworkflow is outdated triggered
** new_abstraction signal from registry in addition to new_module signal so that we can check if we need subworkflows to update
** How to display the possible upgrades (can be upgraded, can be upgraded but may break, etc.)
 
* New utility added by Carlos (currently at scripts/module_appearance) to draw fringes visually, which generates output that can be pasted directly into the add_module call.
** ''Erik will test this on Mac and Windows.''
 
* Preparing a "Get Started" tutorial for SIGMOD repeatability
** Do we have instructions on how to use the latex package without crowdlabs?
*** links to actual workflows in latex
*** have README and example for latex in the source
** Metadata associated with VisTrails: should we have the ability to add vistrail-level metadata? e.g., who created the vistrail, its purpose, etc.
*** have pointers to paper to workflow and vistrails
*** add pointers to papers
*** allow access to add/edit annotations at the vistrail level
*** ''add GUI element to allow people to edit/add annotations''
 
* Maintaining VTK package
** have four classes that don't wrap, have error even in python level
** works well with VisTrails otherwise
** haven't checked the new changes from the wrapping
** ''Wendel will check on the new version''
 
* [[Web services package]] (Tommy)


=== Oct 5, 2010 ===
=== January 20, 2016 ===
'''Updates'''


* Welcome Tommy!
'''Items to Discuss'''
* [TE] Backporting features from Python 3 + PyQt5 + Qt5
** Merged unicode with master ([https://github.com/VisTrails/VisTrails/tree/unicode unicode])
*** One unicode test failing
*** 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


* Update on subworkflow (Daniel)
=== January 13, 2016 ===
'''Updates'''


* Issues raised by Matthias:
'''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


- need to automatically upgrade subworkflows. Currently it is necessary to manually upgrade a subworkflow whenever the version of one of the modules inside them changes.
=== January 6, 2016 ===
'''Updates'''
'''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


- explorations do not detect an MplFigureCell embedded in a subworkflow.
== Older meetings ==
* [[Development/2015]]
* [[Development/2014]]
* [[Development/2013]]
* [[Development/2012]]
* [[Development/2011]]
* [[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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