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 3, 2010 ===
=== October 30, 2017 ===


* Upgrading subworkflows (Dan)
'''Updates'''
** 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
* Any update on fixing VTK Package? It seems that the ParaView package has the same issues.
* Synchronizing VisTrails and ALPS releases (Emanuele)
** 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?
* Is a multi-touch interface to VisTrails possible now that it's supported by Qt? (Phillip)
** Yes, Qt 4.6+ supports multi-tocuh
** We still need to figure out what makes sense for multi-touch, however, do we have requirements from ETH-Zurich?
* 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-mac-10.5-intel-0.3-alpha-rev2219.dmg
** Do you mean iphone app? [Phillip: yes]
* Data Publishing with crowdLabs. (Phillip)
** Do we want data publishing capabilities in VisTrails and crowdLabs?
** 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]?


=== Oct 19, 2010 ===
* [DK] PyQt5
* [RR] Running Python3 code


* Update on Trac and Roadmap (Emanuele and David)
'''Items to Discuss'''
** 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 ====
* 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.


* Bug regarding userpackages at initial vistrails startup causing startup to fail.
=== September 6, 2017 ===
** 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.


'''Updates'''


=== Oct 12, 2010 ===
* [RR] Fixes for scikit-learn, tables, usagestats


* 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''.
'''Items to Discuss'''
** 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)
* Stripped-down version of VisTrails to showcase new features?
** ''Need to make sure that all messages are printed through debug.X, so that the debug level (verboseness in preferences) is correctly used''
** include meta-vistrail, bundles
** Can cut/copy/paste now
** hide mashups, extra widgets, latex mode, etc.
** Can we prevent the delete from happening?
* Interpreter
** 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)
=== August 16, 2017 ===
** 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.
'''Updates'''
** ''Erik will test this on Mac and Windows.''
* [DK] meta-vistrail
** Working actions: normal action in vistrail, pruning version tree, tagging operations, and change
** Interface


* Preparing a "Get Started" tutorial for SIGMOD repeatability
'''Items to Discuss'''
** Do we have instructions on how to use the latex package without crowdlabs?
* Notebook
*** links to actual workflows in latex
* Interpreter
*** have README and example for latex in the source
* Web visualization packages (e.g. bokeh)
** Metadata associated with VisTrails: should we have the ability to add vistrail-level metadata? e.g., who created the vistrail, its purpose, etc.
** [https://github.com/VisTrails/VisTrails/pull/969 PR 969] has more details
*** have pointers to paper to workflow and vistrails
* Pipeline templates
*** 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
=== August 2, 2017 ===
** 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)
'''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


=== Oct 5, 2010 ===
'''Items to Discuss'''


* Welcome Tommy!
* 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


* Update on subworkflow (Daniel)
=== June 28, 2017 ===


* Issues raised by Matthias:
'''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


- 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.
'''Items to Discuss'''


- explorations do not detect an MplFigureCell embedded in a subworkflow.
=== 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 [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)
 
'''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 [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)
 
=== February 24, 2017 ===
 
'''Updates'''
* [RR] Rich-text module documentation ([https://github.com/VisTrails/VisTrails/pull/1210 #1210])
** 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
 
=== 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 [https://packages.qa.debian.org/v/vistrails.html]
 
'''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 <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?)
 
== 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 ([https://github.com/VisTrails/VisTrails/pull/1205 #1205])
** 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?
 
=== November 16, 2016 ===
 
'''Updates'''
 
* [RR] Issue [https://github.com/VisTrails/VisTrails/issues/1200 #1200] from @samtux: need to set PyQt to API version 2 before ever importing it; using require_pyqt_api2() does that (also can install bundle)
 
'''Items to Discuss'''
 
* Email from Pieter: executing pipelines with parameters from command-line using single-instance
** Seems to work, main instance gets full command-line and alters configuration temporarily
** Not sure what his error is (VisTrails returns little information in a lot of cases); though execution error should return something more meaningful
** Actions:
*** Can add switch to kill main instance
*** Can improve single-instance code to return more meaningful errors + machine-readable output from "client" VisTrails
*** Add client/server code to <tt>core</tt> that doesn't use Qt? Also need a run.py-line entrypoint that doesn't use gui (calls console mode like <tt>gui.application.VistrailsApplicationSingleton#noninteractiveMode()</tt>)?
 
=== November 2, 2016 ===
 
'''Updates'''
 
* New version 2.2-2 of Debian package, still [https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=796994 wrong copyright], and [https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=748692 broken bundle installation]
** Finally replied, says copyright issue will be fixed soon, working on including VisTrails 2.2.4 for Debian Stretch
* Working on Docker package, low hanging fruit because we have CLTools, and useful for some workflow (also step towards CWL support)
 
'''Items to Discuss'''
 
=== October 5, 2016 ===
 
'''Items to Discuss'''
 
* working toward a 3.0 release; [https://github.com/VisTrails/VisTrails/projects/1 project board]
** unique ids
** bundles
** GUI fixes
** wrapping updates
** python3
** interpreter?
 
* command-line input parameters to provenance
** [DK] we don't create a persisted workflow from those input params, i think
** [DK] these are already defined as aliases so we treat them differently form a normal input param
** [DK] still have the potential problem of allowing a user to view the workflow as it was run with a given set of aliases
** Do the vistrails variables values get stored in provenance? (what if values change?)
 
=== September 14, 2016 ===
 
'''Updates'''
 
'''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 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
** [https://docs.google.com/document/d/18YZewjR2YY9cQ9pzdA-nU9jbu2L7jYcPlDi3iaPadwA/edit Websites]
* [RR] users' guide on readthedocs: doesn't seem like we can have both the internal docs ([http://vistrails.readthedocs.io/ currently there]) and users' guide under the same RTD "project"
* [DK] UUID support almost complete (use-uuid branch), bundle translation then fits more easily on top of that
 
'''Items to Discuss'''
* [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 [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.
 
'''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 [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
 
=== August 3, 2016 ===
 
'''Updates'''
 
 
'''Items to Discuss'''
 
* [TE] Wrapper patches now stored as [https://github.com/VisTrails/VisTrails/blob/python-wrapper-script-patches/vistrails/packages/vtk/vtk_wrapper/vtk_patch.py python code]
** Connection variables now lowercase
** Can we use code as output variables?
*** E.g. "vtk_dataset_mapper.GetOutput(0)"
*** Could mutate output when output method is only supposed to be called once
*** Need to be able to rename output port as python code(e.g. when there are 2 "vtk_dataset_mapper"s)
 
=== July 27, 2016 ===
 
'''Updates'''
 
* [DK] DB bundle serialization implemented
 
'''Items to Discuss'''
* [TE] Finished using patch in script [https://github.com/VisTrails/VisTrails/tree/python-wrapper-script-patches python-wrapper-script-patches]
** locale?
** [https://gist.github.com/rexissimus/f0d6b026aa5a2a770847f3321744645d new patching example] vs [https://gist.github.com/rexissimus/b28d83ae516a519167f5751bb8ab3739 old patching example]
** [https://github.com/VisTrails/VisTrails/blob/python-wrapper-script-patches/vistrails/packages/vtk/vtk_wrapper/parse.py#L135-L273 Example of new patches]
** Legacy '.vtkInstance' is now added as a patch "self.vtkInstance=self" (see new patching example)
** [https://github.com/VisTrails/VisTrails/blob/python-wrapper-script-patches/vistrails/core/scripting/api.py New api for executing standalone modules]
*** Accessing module was disabled for core/api, but a different api for this is probably better anyway.
*** api.Package now gives [https://gist.github.com/rexissimus/f0d6b026aa5a2a770847f3321744645d#file-new_patching-py-L26 directly callable module compute functions]
*** Only works on modules not using interpreter functionality ('.interpreter', etc.)
**** for zip file modules and others that need temp files and use the interpreter for this, need to modify the module, but could work around with python libraries for managing temp files
** Fixed more renaming issues - [https://github.com/VisTrails/VisTrails/blob/python-wrapper-script-patches/vistrails/core/scripting/scripts.py#L63-L64 function argument names should not be replaced]
** Still need to do something nicer for the patch formatting
*** patch keys currently contain non-python-variable characters but this can be fixed
*** Need to replace string template with python variables that is replacable using RedBaron
**** Patches could then look like:
 
    def vtkInstance():
        self.vtkInstance = self
 
=== July 20, 2016 ===
 
'''Updates'''
 
'''Items to Discuss'''
* [TE] New patch method for python-wrapper [https://gist.github.com/rexissimus/009b303e4cadcd4b8f2fec6cf848cb2b 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 [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)
 
=== July 6, 2016 ===
 
'''Updates'''
 
* [DK] Working on bundles
 
'''Items to Discuss'''
* [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)]
** Call module in script using vistrails API
** Can be used when no export method is defined.
* [TE] [https://github.com/VisTrails/VisTrails/commit/c76c109349769fee1280f85c22678380a2f9cd39 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) [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?
 
=== June 22, 2016 ===
 
'''Updates'''
 
'''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
 
* [TE] Working on exporting wrapped libraries (VTK)
 
=== June 15, 2016 ===
 
'''Updates'''
* [TE] Added depth logic to python script exporter ([https://github.com/VisTrails/VisTrails/commit/50f220e4f6abe5a7bb8689f73f456f43df2dbc12 full commit])
** Fully implements connection merging and list looping
 
'''Items to Discuss'''
 
* [TE] Making analogy work on upgraded workflows ([https://github.com/VisTrails/VisTrails/issues/1175 #1175])
** Analogy only works We need to use the non-upgraded action chain
** But pipelines need to be valid (matcher uses module portspecs)
** Tried to get upgrade remap from upgrade action, but this seems impossible
** Use module location instead?
*** Location should be identical for one-to-one module upgrades
 
=== June 1, 2016 ===
 
'''Updates'''
* 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 [https://github.com/remram44/apache-log-info 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 [https://github.com/VisTrails/VisTrails/issues/1173 #1173]
 
=== May 11, 2016 ===
 
'''Items to Discuss'''
* [TE] Union type [https://github.com/VisTrails/VisTrails/issues/1172 #1172]
** 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)
 
* [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'''
* [TE] Union type [https://github.com/VisTrails/VisTrails/issues/1172 #1172]
 
=== 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: [https://github.com/VisTrails/VisTrails/issues/1168 #1168])
 
'''Items to Discuss'''
* New bugfix release
** Merge usagestats
** Need to finalize survey
 
=== April 13, 2016 ===
'''Updates'''
 
'''Items to Discuss'''
* [TE] Chaining upgrades done ([https://github.com/VisTrails/VisTrails/pull/1164 #1164])
** Replace "Upgrade" description annotation with "upgraded_from" annotation to identify which tags to hide?
 
* [TE] Iterating handle_invalid_pipeline ([https://github.com/VisTrails/VisTrails/pull/1165 #1165])
** Not based on [https://github.com/VisTrails/VisTrails/tree/chain-upgrades-loop chain-upgrades-loop]
** Cherry-pick test to preserve source?
** Need maxPipelineFixAttempts option?
*** The code is now smarter about recursion, so max attempts will "probably" never be reached.
** Need [https://github.com/VisTrails/VisTrails/commit/0ef0667426937eddb1d1c1e397f0657ffec039a9 debug messages]?
*** Would need to be moved into handle_invalid_pipeline
 
=== April 6, 2016 ===
'''Updates'''
* [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 ([https://github.com/VisTrails/VisTrails/pull/1164 #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: [https://github.com/VisTrails/VisTrails/pull/1092 #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? [https://github.com/VisTrails/VisTrails/issues/1146 #1146]
 
=== February 23, 2016 ===
'''Updates'''
* [TE] Fixed PythonSource 100% CPU bug
* [TE] VisTrails Next
** Updated [http://opendap.co-ops.nos.noaa.gov/axis/webservices/wind/ NOAA Web Service] examples
*** Now uses REST service, tabledata, and Google Maps
*** Web Service replaced with DownloadFile
 
'''Items to Discuss'''
* [RR] Couple of fixes are in for API, and tej&reprounzip on the Mac binary. Also new release of tej, and working on anonymous usage reports.
** New 2.2 release soon?
* [RR] Anonymous usage reports
** Sends out info like number of modules & versions, packages used, Python & libs versions, execution time, specific features [https://github.com/VisTrails/VisTrails/pull/1154 #1154]
* [JF] Bring in noWorkflow to track variable dependencies, for the considered Jupyter integration?
* noWorkflow - provenance for python scripts
** Recent work on tracking dependencies
* Also integrates ReproZip with Jupyter
** [http://mybinder.org mybinder]
*** Use with ReproZip to automatically build Jupyter notebook interfaces
* Daves comments on Jupyter integration
** It is possible to identify cell order on the server side
** Not trivial to track order of cells on client side
* How does Galaxy workflows relate to VisTrails?
** Packaging in Galaxy is hard
** Galaxy for biomedical workflows, difficulty making it general
* Action items
** How difficult to track cell dependencies in Jupyter notebooks?
** Use noWorkflow to track cell dependencies?
** How difficult to modify mybinder to use ReproZip packages?
 
=== February 17, 2016 ===
'''Updates'''
 
'''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-users] [http://lists.vistrails.org/pipermail/vistrails-users/2016-January/000402.html Rendering a .pvd (ParaView) file?]
 
* VisTrails Next
** All tests but thumbnail comparison passes
** Still issues with gui and more packages needs to be tested
** PythonSource and MplSource upgraded with lib2to3
** Keep contrib packages? Update?
** [https://blog.kitware.com/vtk-7-0-0/ VTK 7 is released]
*** Supports Python 3
*** Will hopefully get into conda and others soon
*** Deprecates a bunch of modules
 
* [https://travis-ci.org/VisTrails/VisTrails/builds/106743348 Travis builder] for VisTrails Next
** Runs!
** Uses conda
*** Many levels of requirements
**** apt packages
**** conda packages
**** python packages in requirements.txt
**** python packages in setup.py
*** Can probably drop conda. Default builder does not have Qt5, but beta builder do!
*** But useful if we want to use conda in our own build process.
** Lots of errors I do not get locally?
 
* [http://goo.gl/forms/Z4HBrwaBWL User Survey]
** Have you used any alternatives to vistrails?
*** Relevant? More options?
** How often do you use any of these particular features in VisTrails?
*** Add/Remove alternatives?
** How important would you rank the following potential improvements to VisTrails?
*** Add alternatives?
 
=== January 27, 2016 ===
'''Updates'''
* 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] [https://github.com/VisTrails/VisTrails/pull/1143 Python 3 branch]
** Testsuite almost passes
*** Failing are unicode filenames, some users guide examples, and thumbnail comparisons.
** Fixed issues
*** Signatures are now bytes (convert to string to show in widget)
*** Cannot compare different types, e.g.,  (None < 1)
**** PortSpec.depth and min/maxConn could be None. (Backport!)
**** cell.row could be None
*** Lots of unicode/bytes fixes to serializations
**** We have encryption implementations in the code! (keychain)
*** Lots of small fixes to package method differences
** Current issues
*** logging widget empty?
*** version tree signals messed up
*** provenance view legend icons black
*** Text do not fit in some widgets
*** VTK thumbnail comparison fails
**** VTK Cells have some faces in wrong direction?
****  Because running in VM?
** Installing on Ubuntu LTS/Latest Mint
*** Install latest matplotlib from pip
*** Install VTK 7.0.0rc2 from source
*** No QtWebEngine binary (controversial) (Must install sip/PyQt5/Qt5 from source)
 
=== January 20, 2016 ===
'''Updates'''
 
'''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
 
=== January 13, 2016 ===
'''Updates'''
 
'''Items to Discuss'''
* [TE] [https://gist.github.com/rexissimus/dfd27e466427529c385c Porting to Python 3 / PyQt5]
** Basic GUI and execution works
** Minimal work to support 2to3
** Hard to support both PyQt4 and PyQt5
 
=== January 6, 2016 ===
'''Updates'''
'''Items to Discuss'''
* Updating VisTrails dependencies
** Successfully built [https://gist.github.com/rexissimus/f1a1aada7de1c00a57c7 Win7-64/Python3/PyQt5/Qt5/WebEngine/VTK7]
*** VTK 7 is the first supporting Python 3 but is only in release candidate phase.
**** Next version of VTK 6 is rumored to support Python 3
**** There is a development branch of VTK 6 supporting Python 3
*** Can travis build this?
**** We can skip tests for WebEngine and VTK if needed
** Python 3 [https://python3wos.appspot.com/ showstoppers]
*** No MySQL-python (sqlalchemy supports mysql through other drivers)
*** No suds (there are active forks but we could also drop support?)
* Options for python2/3 support:
** Interpreter could be python2/python3 based on packages
** six layer works but not the easiest to maintain (e.g. in reprozip)
* Drop support for win-64
* Update copyright headers to 2016
 
== Older meetings ==
* [[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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