Development

2013

April 17, 2013

Updates

[TE] Done with checking schema conversion and creating tests
[TE] Started generating new v2.0 binaries
[RR] DAT: data provenance viewer implemented

Items to Discuss

[JF] The LaTeX extension issues
- uses the weather example
- [ES] related to CLTools package?
[TE] No known v2.0 bugs that need to be fixed
[TE] What is left to do for v2.1beta release?
- are some bugs
[DK] need to look at merging the new matplotlib package
- need to add MplScript module
cannot run parallelflow on multiple machines?
- we should set features before releasing the v2.0 version
have root-level API?
- move the logic to core/gui as needed, and have the root-level import depending on mode
- need to separate concerns as necessary
try to make the switch to the org.vistrails prefix
- keep the old identifiers and have both point to the same package?
three types of subworkflow-like pieces: mashups, subworkflows, DAT
- maybe more implementation-level differences
- can we comine the infrastructure for these?
- should we try to use a similar API?
- for visual compression, more of a conceptual change rather than create new group/ungroup each time

April 10, 2013

Updates

[DK] Fixed the matplotlib cell resizing issue in current and new mpl packages.

Items to Discuss

v2.0 Release:
- [DK] matplotlib cell size issue should be fixed
- Any reported bugs that are not fixed?
- add v1.0.3 -> v1.0.2 translation in the v2.0 release
v2.1 Beta:
- What are the new features we should include?
  - auto-connection
  - visual port feedback (i.e. parameter set)
  - different port shapes
  - vistrails.-prefix
  - new matplotlib package?
  - mashup integration?
  - parameter exploration serialization
  - new schema for port spec
  - parallel flow, multiprocessing work?
  - what else?
  - add matplotlib examples inside the examples directory
  - add tests for the new features
- What needs to be checked before a beta is released?
  - want to make sure users that create vistrails in the beta can use them later
  - need to freeze the schema---are we happy with what is there?
  - need to check the schema v1.0.3 <-> v1.0.2 translations: are they robust?
    - [TE] I am checking by using the vistrail files on vis-7, but the update_db script needs to be updated.
    - v2.0 should support importing the v1.0.3 schema
  - add tests for things like schema
- matplotlib package
  - have Sunitha add some documentation about how to use the mpl package
  - still need legend updates, patch support, colorbars, script support
- DAT VTK issue with flickering

April 3, 2013

Updates

[BB] Working on UV-CDAT bugs, release mid-April
[RR] Working on the VTKCell Overlay

Items to Discuss

[DK] Better DOT_VISTRAILS management. Why not have "modes" which correspond to certain package sets?
- USGS users have some requirements here (sometimes run with SAHM, other times without)
- It's really annoying to have to update the enabled packages each time
- That way, if I am interested in running without the spreadsheet, etc., I can just run in a given mode and when I want the spreadsheet and VTK, etc. back, I just switch back
- basically, just segment out the packages part of startup.xml and make multiples of these
- also add command-line flag
- [TE} maybe ony specify only whether some packages are enabled or disabled?
- [TE} maybe just point to a different user-packages directory
- what about just making command-line flags to enable/disable packages

[DK] Latest VTK version
- Has anyone tested how the latest version of VTK runs with VisTrails?
- Huy ran into an error about "no concrete implementation..."
- [TE] May just need to ignore the class causing this issue
- [ES] Seems like the 5.10 master also had this issue before the release but perhaps they removed the features

[DK] Installing packages/python dependencies?
- [ES] can install distutils into the Mac binary?
- WIndows has a full python install so this isn't as much of a problem.
- Just have a menu-item in VisTrails that sets the right configuration variables for the installer (point to the setup.py that the user wants to install)
- Want to install to a VisTrails library directory that lives outside of the binary.
- How to deal with python dependencies for compiled pieces?

[TE] Ryan Danks on vistrails-users: I've been trying to get Vistrails to work in parallel both by using the server instructions found in the documentation as well as by using the standard Python multiprocessing.Pool objects within my module. Neither of these approaches seem to work. Has anybody successfully run their Vistrails code in parallel? If so, how?
- Tommy to check with Fernando on whether ParallelFlow satisfies these requires
- Is ParallelFlow ready for release?

March 27, 2013

Updates

[BB]Online/Incremental layout
- Added option to prevent any gaps in layers between connected modules. This in addition to preserving horizontal order seems to produce nice layouts from version to version.
[RR] working on DAT: multiple variables per port working
- Also added variable number of inputs on List module
- Also did some changes on the controlflow package
- Also made some changes to the VT GUI as suggested by Juliana last week to the PythonSource and List modules
- Also updated DAT to use matplotlib plots and add conversion typecasts if variable types don't match

Items to Discuss

[JF] Update to package API documentation
- Need to write documentation with this in mind
[DK] Colin (USGS) asked about installing packages into VisTrails's python distribution. What is the status of the easy_install work; are there other solutions?
- need to talk to Emanuele/Tommy about this
[DK] UV-CDAT Scripting. Is there anyone who can take this on? Charles is planning a meeting for early April to show what he would like to see for this.
- Part of this is just designing meaningful modules (the wrapping side of things)
- The other side is what can be done to make the scripting interface more like a normal python script
- Currently, the scripting interface just builds a workflow. This is somewhat unintuitive if you expect that things act like a normal python shell...
- Do we support partial execution as modules are added?
- What to do if a call is not wrapped?
- Perhaps a good starting point is the VTK example scripts. I converted these to workflows by tracking all the calls. Why don't we see if the scripting interface can convert these on-the-fly?
- Also, I want to keep in mind numerical ops and numpy. Typing expressions is often much easier but we don't have a great way to represent this in a workflow. What should be done?
- python has a built-in abstract syntax tree (ast) for itself that is user-facing. Could we use this to better translate scripts to workflows?
[BB] Add auto layout to api calls?
- Possble flag for this so that the user can choose whether things are laid out or not
- Also try to use this for the auto-snap feature in the GUI, BUT need to be careful to animate this as users will not be able to follow what is going on otherwise.
- the layout code now runs without any GUI dependencies but can still use QFontMetrics (like for the Cmd+L call)
VirtualBox issues on the testing machine? Emanuele is trying to fix, may need to contact Fernando

March 20, 2013

Updates

[TE] Save Camera (and similar) now works for unsaved and "saved as" vistrails using the new ensureController method
[TE] DB Mashups merged into master
- working to upgrade the older mashups
[TE] Added JobSubmission entry to FAQ
[ES] Planning to have the binary ready for testing on Friday
[DK] Work on matplotlib
[DK] Help answer Charles's UV-CDAT questions

Items to Discuss

[RR] Control flow modules:
- Lists vs multiple connections
- Using 'self' ports on ungrouped modules
- along each port to take a list or a single change a la Taverna
- try to write a new module to dynamically create a set of connections from a list
- do this in the interpreter? (need to modify the executing pipeline, not the specification
[RR] Issue with "self" port connected (emailed Fernando)
[DK] Similarly, should we try to add some method for ordering connections?
- Could display the order using a number overlay when a user moves the mouse over the port
- Then, selecting connection, could move up/down like illustrator...
- Probably would require an additional attribute to be stored in the workflow
- Rémi suggests mirroring Tuple here, (set number and type)
[DK] Dynamic ports behind the scenes?
- Problem: Would like to have both stronger container types (e.g. List<String>) as well as flexible types (e.g. Float|List)
- Idea: Don't change anything about the current registry, but allow this at the interface layer and dynamically add the port to the module/registry when needed?
- For flexible types, could create myportFloat or myportList ports depending on the connection and then map these back to the same port before compute call...
- For container types, could only add a port type to the registry when it is actually used so we don't have to materialize everything beforehand.
[JF] PythonSource/Tuple port types
- cannot type to search for port types -- have to type fast
- use a completer in the text field for this?
- drag and drop from module list?
[BB] Online layout and gui-free layout
- Am close to a working solution that just uses the old layout but optionally preserves order of specified modules
- Having an issue with saving the positions, and strange issue with newly dragged modules vs modules loaded from file

March 13, 2013

Updates

Juliana's visit to Brookhaven National Labs
- interested in climate data analysis on observational data (also light source data)
- need to have executino on parallel machines, not able to find batchq package
- batchQ seems to be pure python and should not be hard to install, need to specify which version to install, add to FAQ
- UV-CDAT Sandy demo: Sandy YouTube video
[TE] Saving mashups to DB works, but there is still a bug with tagging a mashup, the interface is redrawn while tagging and a new mashup version is created.
[TE] Working on getting spreadsheet "to version" method work with unsaved vistrails
- Added an "ensureController" method for loading a view from a controller object
- Getting the spreadsheet to work with controllers is difficult because it uses the locator everywhere and still needs the locator for things like saving the spreadsheet.
[DK] More progress on matplotlib updates
[RR] Fixed the bugs on DAT, trying to bring in more examples from VTK

Items to Discuss

It seems the ALPS package is not included in the Linux binary distribution. Is this a bug or is it omitted by design?
- [DK] Is it included in other distributions? I thought ALPS provided its own installers that update VisTrails with the necessary support for ALPS.
- Ask Emanuele and/or Matthias about this to see what the current setup is
We used to have a scripting window in VisTrails and also in an early version of UV-CDAT. What is the status of the support for shell-like commands in VisTrails?
- [DK] core.api has some support for commands like this. See the FAQ
[DK] How to best deal with importing Modules from other packages. For example, if I want to subclass a Module in matplotlib, I can use the registry (ugly, see FAQ, or I could try to directly import from vistrails.packages (e.g. import MplFigureManager from vistrails.packages.pylab). While the second method is nicer, it is also not very robust because

it does not enforce package dependencies. I can import from pylab even if that package has not been imported.
It does not work great for a package that might be in packages or $DOTVISTRAILS/userpackages depending on how it was installed (e.g. ALPS). A developer would have to check both places.

- One option is to make any import of vistrails.packages use the registry method but hide it from the user. Not sure how this works for non-modules, however.
- Another option is to have vistrails.packages import all of $DOTVISTRAILS/userpackages which means a developer has to use the "from vistrails.packages import" syntax to access items.
- Other ideas?
- Just limit the way an import occurs (only the "from vistrails.packages import <package_name>" syntax)
[TE] Should we add BatchQ to VisTrails?
- Users are having problems because only the stable branch of BatchQ works with JobSubmission
- Could we use git submodule?

March 06, 2013

Updates

[RR] DAT can now execute operations on variables
[ES] Build Machine: Windows 32-bit setup is ready, but the 3D Texture Mapping doesn't work on the VM. I will test if the problem will be present in the binary.
[TE] Saving mashups to DB now works
- Will add more tests and then merge into master
- After that update crowdlabs to use it

Items to Discuss

[ES] Build machine:
- Do we have to include the patched version of SUDS in the binaries? (I noticed the example that required it was removed from the repository)
  - It was decided to keep it
- Do we have to support old packages (for example, NumSciPy)?
  - It was decided to use the prebuilt binaries for now
[TE] Adding locators to unsaved vistrails
- This will fix view switching issues with spreadsheet and vtk
- We should be able to add a MemoryLocator class to unsaved vistrails
- It was decided to store a translation from controller/view to locator

Feb 27, 2013

Updates

[TE] Working on mashup bug fixes and DB support

Items to Discuss

[TE] Animation support for Matplotlib cells?
[TE] Will look at adding locator for unsaved vistrails

Feb 20, 2013

Updates

[TE] Added PBS support to BatchQ master branch
- Troels working on a few performance items
[TE] Also working on adding mashp
[BB] Looked into some existing graph libraries for layout (NetworkX, igraph, boost graph tools, ...)
[DK] Checked in WIP on the new matplotlib package (include README about how things are generated)
- [DK] Need to clean up the specs for this package
- [DK] Figure out what the new student can help with
[RR] Determining how to type data

Items to Discuss

need some type of dataset standard for use with the DAT
what about list of (floats, strings, any type of VisTrails object)
require some additional wrapping for the DAT right now
also think about numpy/scipy operations

Feb 13, 2013

Updates

[TE] Job Monitor Improvements (New DEMO?)
- need some documentation
- Troels is working on some features for multiple jobs (100+) because each job creates a new connection
- also going to change a bunch in the implementation
- some projects need PBS submission capabilities to be using VisTrails
[DK] matplotlib work improving (a few things still missing but working, mostly automated)

Items to Discuss

[DK] vistrails prefix and numpy issue that Remi found
[DK] online pipeline layout code
[JF] shape for File module
[JF] Sunitha to work on examples for matplotlib

Feb 06, 2013

Updates

[FC] Working on the package for SciCumulus
- Widget to query run-time provenance from the cloud (almost done)
- Use ModuleSuspended in the execution (to be done)

[TE] BatchQ-PBS
- Finished a Job Monitor Widget for VisTrails (DEMO?)
- Need to add provenance gathering

[DK] Fixed minor issue with upgrades (USGS)
[DK] Working on matplotlib bindings

Items to Discuss

DAT project
- Basic functionality is there, some small example packages
- How do we handle multiple projects?
- How do we support multiple 'layered' plots per cell? (UV-CDAT needs this)
- [BB] Configuration widget
  - show ports pane for each module in plot subworkflow
- [CS] Automatic labeling of the pipelines
- [CS] Also try to auto-generate some of the code that is used to specify ports in the DAT
- Talk to Jerry and Tom about what they like about UV-CDAT, what can be improved as feedback for the DAT (talk about refactor)

Jan 30, 2013

Updates

[DK] Fix for older packages to run using new vistrails. prefix
[DK] Finished dulwich translation of persistence package
[BB] working on DAT)
[FC] working on integration between VisTrails and SciCumulous
[TE] BatchQ and PBS, module suspended state
[TE] way of mointorining jobs
[TE] mashups on crowdlabs in database, Emanuele will help on this

Items to Discuss

[DK] Need to update documentation for vistrails. prefix
- check vtl files here
[DK] Ticket #649

Jan 23, 2013

Updates

DataONE Updates
- obseleted tags
[TE] First version of BatchQ-PBS ready. Waiting for feedback.
- forked on github, no changes to the VisTrails package
[DK} Fixed Python dependency determination
[DK] Added a branch with UUIDs as identifiers
[DK] Working on using dulwich (git implmentation in python) for peristence package
[FC] Updates in PROV exporter
[FC] Start integration between SciCumulus and VisTrails
[RR] Multiple projects in DAT?
- Some way to tie cells back to the project is needed
- Global/local mismatch is an issue here (if I drag a variable from one project and combine it with a variable from another project, which project does the new vis/data below to?)

Items to Discuss

[JF] Update on package David worked on for USGS (control/suspend execution, support execution on different computational environments) -- msg data 12/18/2012
- methods to fork off processes and to condor
- need to track the settings for condor/asynchronous runs in provenance
- more general modules for this?
- abstraction mechanism for subworkflows to split up workflows (mixed execution models)
- better indication of when a module has been started but is not completed.
- BatchQ shows "suspended" state for this, stops executed this branch.

[TE] Specifying python dependencies and py_import at the same time is confusing. We could probably call py_import from the package loader if the needed information was specified in the dependencies.
- merge these two things for packages (otherwise have issues with specifying new dependencies and trying to import them)
[TE] Will new import structure and UUID:s go into 2.1?
- Synchronization issue
[DK] Nix ideas?
- we should at least record some hash of the wrappers/packages in the provenance

Jan 16, 2013

Updates

[TE] WebGL port issue: Wendel added fallback mode (use pre-rendered data), is now helping me getting it to work using port 80 through apache.
[DK] DataONE package
Rémi's progress on the DAT
- working on VisTrails code to modify the spreadsheet
- GUI is usable except that the interface doesn't execute VisTrails pipelines
- Has a document available in Google Docs documenting progress
[BB] All critical open bugs for UVCDAT are complete, one minor bug and some enhancements left

Items to Discuss

WebGL on crowdLabs
- try to send cached images through port 80 if necessary
- need to inform users why an issue comes up (e.g. port is closed, using cached image)
Remove the sci mailing lists finally?
Building VisTrails on a NASA supercomputer?
Web interface aka ClimatePipes

Jan 9, 2013

Updates

Emanuele resumed setting up the build machine for Windows.
[TE] crowdlabs now uses rendered image in vistrail tab if available
[TE] Discussing WebGL port issue with Wendel
- One possibility is to use port 80 on another server and use a proxy
[TE] Working with Troels on adding PBS support to BatchQ
[BB] 5 Bugs remaining with UVCDAT
[DK] DataONE work

Items to Discuss

Uploading Mashups to crowdLabs from VisTrails
- For this to work need to complete relational support for Mashups (see ticket #611). The code is in mashups branch and needs to be updated with the current master (it was branched from old schema-v1_0_3 branch and not updated since then).
- Need someone to work on this for Matthias
- Not just relational support here, want to improve the schema
- Could just dump xml as a blob into the database, but were trying to make things work better
Cleaning up older files (see last week)
UV-CDAT Bug #69:
- The variables are global; cdat has a global dictionary
- thus closing a project has no effect on the dictionary
- if you have two projects that reference the same variable name, you run into issues
- discuss this with Charles
UV-CDAT undo button:
- should be ok, just remember to update cell version

Jan 2, 2013

Updates

Items to Discuss

Rémi went through the code to find modules that are no longer used
- core.modules.module_configure and related have been moved to gui, can we remove the core redirects? Problem is that this could break older packages
  - need to update documentation and add to FAQ
- should we continue to maintain third-party packages (those in /packages not /vistrails/packages) or should these be moved?
  - do we distribute the /packages directory with the source tarball?
  - we don't want to be responsible for keeping these packages up-to-date, but at the same time, we shouldn't distribute packages that do not work with our releases...

crowdLabs issues?
- Trying to make ALPS server work with VisTrails
- Thumbnails: make these higher resolution
- Issue with ports and WebGL?
  - need an error message if this is a port issue
  - should be solutions/workarounds to use "standard" ports with the WebGL data

2012

Dec 19, 2012

Updates

[DK] USGS Work:
- Modules that use package settings
- Modules that do not update when input ports are not set

[DK] Reproducibility Workshop

[TE] Using a vistrail to test VisTrails (the approach adopted by UV-CDAT)

[TE] Parallel VisTrails (Remote PBS)
- Trying to add PBS support to BatchQ
- Have a working PBS server for testing

[BB] UV-CDAT Bug status
- 2 critical bugs and 5 minor bugs/enhancements remaining

Items to Discuss

iPython-style faceted output:
- iPython has a very nice feature where output can have multiple facets meaning the output in a command-line environment is different from that in a GUI environment
- Basically, an output is actually a dictionary where keys are mime-types and values is the corresponding output for that type
- A similar approach would be very useful for cases where we wish to run a VTK workflow that on the GUI appears in the spreadsheet cell but on the command-line generates a file, and in crowdLabs uses Wendel's WebGL solution
- That way, a user writes one workflow that runs everywhere
- I think the output dictionary should be mime-type -> function, however, as we don't want to produce all the outputs if we only need one at a time
- Could also have modules that lookup the output types and could be used for configuring output types.
- Should use the same cell names for output

Merge refactor-add-vistrails-prefix branch?
- Want to discuss with Rémi

Python on menubar for UV-CDAT
- [ES] Only way to change this is to change this in a plist directory of the python being run
- [ES] Sent this to Charles at some point, will forward to Ben

Global variables in UV-CDAT
- Can have multilpe projects open at once, each should have its own set of variables
- Possibility of copying variable from one project to another?

NASA work
- use batchq and pbs, batchq uses lsf instead of pbs
- batchq uses suspended state
- execute workflow and run in the background

Thumbnails and mime type issue
- python2.7 issue?

Dec 12, 2012

Updates

[TE] Finished Vistrail Variable support for Parameter explorations

[TE] Finished Improving interface for uploading to crowdlabs

[TE] Talking with Eduardo and Troyer about adding support for PBS to BatchQ

[BB] UVCDAT Bugs

format pipeline automatically
multi-variable drag'n'drop
plot and variable drag'n'drop behavior

Items to Discuss

[BB] UVCDAT 'Python' in menu bar on mac

Dec 05, 2012

Updates

[FC] New version of PROV exporter, now generating a PROV-XML from a VisTrails workflow

[TE] Working on Vistrail Variable support for Parameter explorations

[TE] Working on improving interface for uploading to crowdlabs

Items to Discuss

VisTrails: parallel and remote execution (Tommy will lead the discussion)
- A way of running multiple workflows in parallel in vistrails
- Add support for cluster frameworks: BatchQ/Hadoop/MapReduce/Remote PBS
Idea for parallel execution: use/extend the persistent sub-system so that "make-like dependencies" can be tracked. The spreadsheet should probably be avoided in the middle layers of such parallel executions.
VisTrails and usability: http://www.wolfram.com/mathematica/new-in-9 (Claudio will lead the discussion)

Nov 28, 2012

Updates

[BB] UV-CDAT bug fixes
- Redirected python output to a session log, and added command line flag to change the default log file or redirect back to std.out
- Initial work on setting up vistrails as a git submodule of a new uvcdat-vistrails git repo
[ES] Package Installation
- easy-install branch should work on all platforms (not tested on Linux).
- currently working on making it platform aware (running easy_install on Windows x on Mac, for example)
[TE] Working on VisTrails bug fixes
- Which ones are most urgent?
[DK] DataONE package, a bit of UV-CDAT

Items to Discuss

[BB] ParaView releasing new version 3.98

[BB] Ideas for VisTrails "DAT" - generalization of UV-CDAT

Nov 21, 2012

Updates

[FC] ParallelFlow -- working on creating SSH engines through VisTrails
- I'm using vgchead for the tests, because there is no zmq (a required module) available for webdb1 (as it is an outdated version Suse)

[TE] SubWorkflows now work on crowdlabs

[ES] Package Installation
- branch easy-install works on a Mac 10.7 and above using a binary built with python 2.7.2 (it's in tests area in sourceforge)
  - the problem is that py2app does not support setuptools and we have to use easy_install available on the system. We require python 2.7 and it is included by default on Mac only starting on version 10.7. If you install python 2.7 on 10.6 it will also work on that system.
- after I commit my changes it will also work on Windows (it will use easy_install available on the binary)

[DK] spreadsheet analogy bug, group caching issue, switch to uuid

[BB] UV-CDAT bug fixes
- Fixed calculator command line related bug
- Added a simple cdms file cache to prevent files from loading/downloading twice, along with a GUI widget to selectively delete cached cdms files

Items to Discuss

[JF] Upgrades
- Developer usability---make it easier to find and define the upgrades
- Improve error messages
- Also, want to get to the point where we detect changes in packages and alert developers & users to changes that could be important for provenance

[FC] ParallelFlow -- IPython engines must be started remotely, and we also need to copy a configuration file from localhost (controller) to the machine where the ssh engines are located, before the execution starts
- paramiko is a nice Python module that connects to a remote machine, being able to execute commands and transfer files
- Is it ok to use this module, or a solution that does not use an external module is preferred?
- Talk about this next meeting, also see Joel Daniel's work on pushing data over ssh?

[ES] Package Installation
- Just have Snow Leopard users install python 2.7
- Dealing with scripts and/or executables installed by easy_install
  - Where to put them? The location needs to be added to PATH
  - Put this in the user manual, do not add to PATH by default
- [DK] what about frameworks/libraries?
  - how would you deal with links to dynamic libraries?
- still need to work on package repository on vistrails.org
  - support indirection so that we don't have to host the packages
  - also put architectures supported in this repository

[JF] Do we have configuration for environment variables in VisTrails?

[BB] Moving uvcdat branch to it's own github repo

Nov 14, 2012

Updates

[DK] Refactored to be vistrails. imports
- rope (Python refactoring tool) is awesome

[DK] Package installation
- met with Tommy and Emanuele on Thursday
- Emanuele is working on detailing the process for installing to ~/.vistrails/Python directory
- [ES] I made some progress but also found some issues that I would like to discuss
  - When running VisTrails with the same interpreter used by easy_install, when enabling a package that supports easy_install, VisTrails will install it and enable it at runtime. This is using the same infrastructure to install python packages on linux systems but should work on any platform:

  rpy_dict = {'easy_install': 'rpy2',
               'linux-ubuntu': 'python-rpy2'}
  rpy2 = py_import('rpy2', rpy_dict)

[DK] DataONE Package
- GitHub
- Now supports uploading data to DataONE

[TE] JobSubmission
- Eduardo would like to have synchronous job submission (wait until finished).

[TE] DB SubWorkflows is working. Will test on vis-7 then add to crowdlabs.

[BB] Added two new command line flags to uvcdat
- -P --noDebugPopups prevents dialog popups from happening when debug/error messages occur
- -T TIME --time=TIME runs the gui for the specified TIME in seconds and then quits, useful for basic testing
- Should these be added to the vistrails master as well?

[BB] Calculator commands related bug in uvcdat
- Likely needs to be largely refactored to prevent further bugs with these

Items to Discuss

UV-CDAT Repo?
- Charles is moving the LLNL repo to GitHub
- Wants to know if we want to move our UV-CDAT code too
- We should probably not refactor this now, but we could move the branches?
- Any reason not to move the branches as is?

Issues with calculated variables in UV-CDAT
- open file from calculator example
- Ben will ask Charles about information to CDMS variable

VisTrails Package Installation
- It seems that we can't start an interpreter different from the one we are running. Does anybody know about this?
  - Because of the issue above, I couldn't execute system's easy_install from the VisTrails bundle
  - My solution would be to ship easy_install in the VisTrails bundle and use it when installing extra packages
- Need to test from the binary and frmo Windows
- Interrupted system call error
  - R_HOME = tmp.readlines() IOError: [Errno 4] Interrupted system call
  - ok when you enable from preferences

Refactoring
- branch where everything uses vistrails. imports
- e.g. "import core.vistrail.module" becomes "import vistrails.core.vistrail.module"
- Makes installing into a system python much more straightforward
  - doesn't require PYTHONPATH tweaks
  - deoesn't overlap with other libraries as easily

[vistrails-users]
- I would like to ask if it is possible to build stand alone applications based on vistrails?
  - Emanuele will answer, we can, just not sure what example is best here
- To try and avoid reinventing the wheel, I am asking if anyone has developed, or knows of a development, of a "text" module. By this I mean, a module that is somewhat equivalent to a String module, but capable of allowing the input of multi-line text in a very simple editor. At this time, plain text is more than adequate (i.e. for handling configuration files, or multi-line test data), but the module should have the capacity to write out the data strings to file.
  - Tommy will answer, String type is not the problem, just want a subclass of String that can have the multi-line entry as its widget. Also suggest having a WriteStringToFile module that writes to temp file (FileSink persists as normal). Could submit a pull request to github.

Nov 7, 2012

Updates

[FC] ParallelFlow
- ParallelFlow can execute a module (or a subworkflow) for different parameters, in different IPython engines (embarrassingly parallelism).
- It is assumed that, in the machines where the engines are started, we have both VisTrails and IPython. Also, it is assumed that VisTrails is in PYTHONPATH.
- If IPython engines are local, this means that different threads are created for each engine - these threads are automatically created by IPython. This is particularly useful for multicore machines.
- IPython engines can also be created in a remote machine using SSH - this functionality still needs to be tested though.
- Modules can now define serialize and deserialize methods in case they need to be retrieved from the engines (e.g.: 'self' output port). In this case, each module needs to define its own methods. For instance, VTK modules need to implement these methods using VTK's serialization routines.

[FC] PROV exporter
- First version of the PROV exporter in VisTrails - this exporter will be used by the DataONE ProvWG.

[TE] JobSubmission
- Eduardo working with Troels to add features to BatchQ

[TE] Add SubWorkflow support to DB
- Almost done, need to fix some issues with upgrades.

[BB] More UV-CDAT bug fixing

[DK] UV-CDAT bugs, DataONE additions, Inc report/updates

Items to Discuss

[DK] VisTrails packages
- Emanuele recently asked the py2app developers about making it easier to install other packages (and their dependencies into VisTrails)
- Reply is here: http://mail.python.org/pipermail/pythonmac-sig/2012-October/023744.html
- I like the idea of having system-wide and local user vistrails directories for added packages
- This needs to be integrated with a much easier installation process. Ideally, this looks something like:
  - Users goes to package manager and clicks "Install Package".
  - We have a vistrails.org-based list of available packages that appears as a list.
  - User selects a package and VisTrails determines any VisTrails, python, or other dependencies.
  - We use setuptools or something like it to install the package and its dependencies into the local directories
- Ideally, this also works for system-based python installs as well, this probably means separate python 2.x directories for VisTrails packages.
- Also, for "import vistrails" style use of VisTrails, it would be nice to be able to specify which packages will be used instead of relying on the ~/.vistrails/startup.xml settings
- Potential issues include packages that use external libraries. Can these also be installed into the package directories?
- Developer support: how does a developer build an installer for a more involved package (e.g. SAHM, ALPS)?
- [JF] VTK and such will be difficult.
- [DK] user-hosted packages
- how does this work for packages?
- Dave, Tommy, and Emanuele will meet on this

Oct 31, 2012

[DK] scripting support (UV-CDAT)
- dependencies?
- allow scripting to automatically load dependencies
- GUI dependencies here:
- .vistrails clashes between scripting and GUI
[JF] organizing workshop on reproducibility
- need to understand what is out there (actually how they work and fit into big picture)
- others will need to help with this
- proposals are out
[TE] Added git access as: git://vistrails.org/git/vistrails.git
- this mirrors the http://vistrails.org/git/vistrails.git
- UV-CDAT wants access via http
- http access adds a /git subdirectoy
[TE] Subworkflows on crowdlabs not working
- they are not stored in the database
- need to have a unique identifier
- could also copy to the .vistrails directory, possible name clashes
- in the long-term, nice to have vistrails access to database
[BB] Added new uvcdat-next and uvcdat-master branches
- mirror the LLNL uvcdat development structure
- allows us to test new features in next before they go into master
[BB] packages were failing on the UV-CDAT side
- shouldn't try and import package when package requirements are not met
- .uvcdat directory or a sub-directory of .vistrails (as a project-specific directory)
- [CS} don't do anything right now, need a stable release
- [CS] need a UV-CDAT workshop
[BB] most of the remaining bugs are not crashing things, just annoyances
[CS] get Fabio started on DAT
[FC] ParallelFlow package
- execution in the engines not always working
- starting engines using ssh, could also use webdb machines

Oct 24, 2012

[ES] Update: Package distribution
- Installing extra python packages to be used in the binary
- easy_install configuration that installs in a custom folder in user's home directory
- worked for R, rpy
- possible issues with compiled things
- should work for all platforms
[ES] New problem with rpy package (other than RVector)
- globalenv variable has changed--capitalization
[ES] SourceForge VisTrails Project upgrade
- new features: https://sourceforge.net/p/allura/wiki/Features/
- do we just move everything to github?
[FC] Parallel Flow
- Local controller and local engines are now started using VisTrails GUI (under Packages menu)
- Trying now SSH engines (IPython also supports MPI and PBS)
- Local controller needs to be stopped when VisTrails closes (in case user forgets)
  - if controller is not stopped, will have issues upon restarting because controllers are still there
  - cannot stop controller outside of vistrails
- Outer subworkflows are transformed into groups -- for inner subworkflows, needs to be recursive
  - problem is that the xml files that define the subworkflows cannot be found on remote machines
  - [DK} look for code that finds the subworkflows
- have an example, can test with Emanuele's new package idea
- have test workflow where module takes 10 seconds, executing 4 times with ipython also takes 10 seconds!
- execution logs from engines are being insereted into provenance
- machines are also being added for all engines
[TE] posted issue on github with temporary directories, added configuration option
[TE] crowdlabs executable workflows, external ALPS server is not accessible
- script to check external error
- string object not callable error
- one Titan workflow made non-executable
[TE} check email addresses for github for the fixes/closes shorthand
[BB] working on UV-CDAT issues
- checking on mountain lion build
- expects variables to be cdms variables
- how to handle all variables (python-based)
[BB] Visit: no callbacks on the c++ side coming through, issue with linking to the correct global variables

Oct 17, 2012

[FC] paraflow
- New commit
- No more startup code
- Add start/stop menu options
[FC] Remoting package
- Our solution cover this
[BB] uvcdat calculator commands
- Need to talk to Emanuele about making this more robust, and what capabilities it should have.
[BB] visit plugin
- Need to find how to access to methods used to implement the "isWorking" function originally created specially for the python VisTrails plugin
- Need to see if threading is still needed for the C++ version

Oct 10, 2012

Update the People page: http://vistrails.org/index.php/People
- Also publications are likely out of date
Mailing List
- Huy will check for anyone who signed up on the old vistrails-users list at SCI after we moved the list
- Then we can write Nick to shutdown the SCI list
Remoting package:
- Terrence's solution: http://code.google.com/p/rpyc4vistrails/
- NASA and weather forecasting
Parallel Execution
- Startup code in engines is possible (it executes a script before the initialization of the engines), but still not working. There was an issue before with it, that was apparently solved, but some other people still complained - waiting answer in mailing list
- Currently changing schema to add the notion of parallel execution
- Provenance capture:
  - make a new parallel execution entry, or
  - annotate that module was executed in parallel, can annotate each module execution with machine information
  - what about trying to determine which modules were tied to the same parallel execution
- Still going to look into serialization of some output values (e.g.: self)
- IPython shipped with VisTrails?
  - How big is iPython? 10-20 MBs
Package distribution
- Ideally, users could download supplemental installers to add packages into binaries
- Hard to know which pieces belong to each package
- py2app selects only modules that we are using, hard to separate out particular packages
- could we tell py2app to install a full python distribution?
[DK] bugs, UV-CDAT, NASA meeting, helping Fernando
[BB] working on UV-CDAT
[ES] working on builds
[HV] finishing parallel execution in parallel, not locking GUI when doing execution
[TE[ looking into making crowdlabs examples work, gridfields and ALPS

Oct 3, 2012

UV-CDAT development
- status of bug fixing (Ben)
  - to do: msg with summary
- release date (do we know?)
- code re-org plans (David)
  - git submodule for vistrails core code
  - refactoring some code where we have added features (e.g. in CDMSPipelineHelper)
  - list issues
  - planning for what Fabio, Jorge, and Feng
- proposal for interface improvements (Claudio)
  - can we bring in other analysis here?
  - have a start on improving matplotlib support (could better integrate this into VisTrails)
- discussion of interface improvements for supporting Jorge's workflows
VisTrails and IPython
- Singleton pattern in VisTrails: should it be really changed? Is there a way to destroy the global state?
- If output port is an object (e.g.: self), serialize it and send it back?
- How to include the execution (performed in the IPython engines) in the log?
- How engines should be started?
website (www.vistrails.org)
- The header was updated and the source files added to the master branch
- Need to decide about the sponsors (currently they have a section on the main page).
2.0.1 release
- Matthias fixed the ALPS package and the release should be out today
Including packages with dependencies
- how to best support this for developers and users
- ideally, users have automated or double-click installers
- developers need to be able to match and compile against the existing libraries inside the binaries

Sep 26, 2012

github
- add README to github
- fixes #NN for issues? [DK] didn't seem to close the issue when I used this
website (www.vistrails.org)
- do we have access to the original illustrator? header
- documentation link should go to the current release sphinx documentation now? (even if not, the documentation page should point to the web version)
[DK] MissingPackage errors: made to ignore module_id so we do not get duplicates
[FC] Parallel execution
- Using iPython and serializing workflow pieces and sending the xml to the engines
- Execution happens in workflow batch mode
- vtl is a wrapper for a vt file or a workflow, documentation
[ES] 2.0.1 release
- almost done, checking ALPS package on Windows
- need tp test Mac version
- also should test SAHM package
- documenting the build and installation instructions
Still need to have machines for other Mac OS-es (10.6, 10.8)
- signing the application: need to create certificates on developer
[TE] BuildBot bugs when execcuting multiple instances at the same time
- disable some of the timing tests (e.g. for memoization)
- could configure branches to use different .vistrails directories
[TE] Fixed the single-instance checks
[TE] testing for crowdlabs workflows
- Titan package not working right now -- check with Wendel?, is this in VTK now?
- fixes for the crowdlabs web page (description overflowing, workflow names truncated)
[BB]: working on the UV-CDAT colormap code: adding the module in code...

Sep 19, 2012

No known items?

Sept 12, 2012

Improvements to connection with CrowdLabs (see Dave's message)
- clean up interface
- currently using 2.0 on crowdLabs
- check into whether master can be translated back to 2.0
Update on CrowdLabs + WebGL
- need some better documentation here
- examples in the user's manual would also be useful
- ALPS image resolution is not good, might be using the uploaded thumbnail
- seems not to be working right now
Update on iPython and multi-threaded VisTrails
- each workflow would run on a different thread
- trying to serialize Module object
- example is executing Map concurrently
- pickling errors...
- can we push port values across only---do not need to pickle module
Feedback from Jorge on his experience with VisTrails (and the remote job submission package)
- need some documentation on using the package
- how are the UV-CDAT instances going to be running on the cluster?
- want to push a workflow and run on a cluster
- sync up with Fernando and Huy's work
- would be good to have linked views support
- add initial support from Jorge's UV-CDAT work
FIXED! mac_update_bin.sh is not working -- it does not delete the existing directories from lib/python_XY
CLTools:
- Add reload button in the wizard window
  - does the new module reload? or do I have to delete the module and add a new one?
  - try to use the upload logic here
- Add a debug mode that shows how the command will be invoked -- this should help the users understand how CLTools work and to get a wrapper working more quickly
  - want to see what the command line would look like with the settings
- We should have more examples that cover additional features of command line tools, e.g., the use additional parameters such as a flag to specify an integer value. It would also be useful to show what the module will look like in VisTrails --- this will help users understand, e.g., what the "Visible" flag means.
- It looks like the ENV var is set for the CLTools package. But what if different modules need different environments?
- In the documentation, there is mention to file "suffix". Is this related to the exchange with Remi on June 14, 2012 4:14:32 PM EDT?
Open Tickets:
- 577: grayed out when publishing until focus change
- 578: two instances of VisTrails
Testing
- BuildBot running at http://128.238.102.101:9050
- Testing section added to: https://www.vistrails.org/wiki
- People who break the build are notified by email
- To add more Virtual Machines we need more memory
[ES]: Mac builds are now working
- pytables support has been removed (not working on Lion)
- already added to the tests
Colin asked for new binaries to fix conflict with osgeo
- wants to distribute for his users

Aug 29, 2012

Mailing lists?
- should we keep the sci.utah.edu addresses?
Unicode issues [Rémi]
- sqlite filename
- configuration files
- and filenames in vistails
WebGL and crowdLabs [Wendel]
- Lis was able to add visualization
- Google bot tries to access some pages and gets sent an error
- fix the transformation
- version issues, Wendel not getting the errors when opening versions from newer versions
- make work for any workflows
Reproducibility [Fernando]
iPython [Fernando and Huy]
crowdLabs bugs [Tommy]
test machine access [Tommy]
- working on
Bugtracker on github
- how to specify branches in bugtracker
- want to add bugs for java branch
- cannot fork own repository
which version of VTK does VisTrails currently support?
- we should make it clear on the website whch versions work (or what limitations exist in which versions)?
- tracking this for provenance

Aug 22, 2012

Automated workflow layout -- done by Lauro -- Dave integrated
- https://bitbucket.org/laurolins/wflayout/wiki/Home
- piecewise layout
Serialization (pickling) Issues with IPython
- take advantage of the the multiple engines in iPython
- schedule modules to run in parallel
- Dependencies in the Module class
- Objects that stays at library level
- VTK is problematic because data is in C++ (cannot send data)
fix UV-CDAT bugs
- separate meeting for this?
- merge in latest v2.0
[RR] Java Updates
- add README file on git with link to documentation
- README is shown on main github page so this is a better link back to the documentation
- Should we maintain both the Java and PyQt interfaces?
  - problem of maintaining both
  - jpype limitations (reflection, introspection), maintenance
[DK] DataONE Package
- able to load DataONE data in a VisTrails workflow
Add Jorge's work to news page
[ES] Build machine is almost setup
- gridfields support not there
- move to Windows build
[JP] Feedback from Oak Ridge:
- Mashups do not work in UV-CDAT, vcs or DV3D
- More next week and demo
- using scikit-learn
Website maintenance:
- Update header
- Add page for contributors, contributing organizations
[WS] WebGL and crowdLabs
- update next week

Aug 15, 2012

Big Data (Huy will join the call)
- Big Data and VisTrails (let me know if you cannot access the file)
- Big Data Pipeline (let me know if you cannot access the file)
- IPython seems to be promising
- streaming and parallel execution
- simple example: parameter exploration
- ipython multithreading (python interpreter pool)
- threading helps on single machine
- for cluster, want to have "execution engine" component
- how do packages work here?
Burrito + VisTrails
- Unpacking experiment: data files inside or outside .vt? (currently, only creating xml)
- Libs and hardcoded input files: how the user can specify that? A configuration file?
Java code in our repository [Rémi]
- add java files and a Makefile to compile the jar
- need to figure out how to make sure this happens for the release (build script)
Java version of spreadsheet
- working modulo a few issues
Testing framework?
- Tommy prefers BuildBot
- Question is what mileage we get from adopting CTest? (UV-CDAT?)
Move bug tracking to github?
- for now, keep separate from our trac and see the utility

Aug 8, 2012

Java [Rémi]
- working on spreadsheet--can be used with real packages
- writing exclusively in jython, would not work via jpype
- keep GUI in java, cell widgets in Java, too
- network visualization using perfuse, could port to regular version of vistrails
Possible analogies issue in spreadsheet
Show in spreadsheet which version a cell correponds to
- show a label in upper-right corner (tag or "tag + N")
- parameter values for parameter exploration
Burrito [Fernando]
- directory names
- packaging into vistrails
Caching issue
- Dave will write an email summarizing the issue here
Big data
- Wait for Huy
crowdLabs integration
- Tommy is working with Wendel on this
Testing machine
setting up github
- Tommy is going to do this

Aug 1, 2012

testing [Tommy]
- Switched from CTest to Buildbot
- The buildbot is up and running with a few slaves:
  - http://vis-7.poly.edu:8010
  - currently linux distributions, also supports mac and windows
- can set up schedulers to run tests upon git checkins
- need windows license: both 32-bit and 64-bit?
- virtual machine with snow leopard
- virtualbox for virtual machines
- expand test coverage
- looking to test gui (mouse clicks, etc.)
- Qt has a testing framework?
VisTrails on Mac OS X 10.8 (Mountain Lion)
- possible issue with X11 dependencies
- also, how long should we continue to build for 10.5 (Leopard)
Bug #615: https://www.vistrails.org/ticket/615
- need new version of PyQt?
[Rémi] working on Java spreadsheet
- have to write JTable that supports functionality like in Qt
- have basic UI in Jython, possible to use jpype
[Fernando] burrtio and dtrace
- translate burrito script from systemtap to dtrace
- dtrace's dscript doesn't have control flow structures (only if-then-else, no for loops)
Paris report [Emanuele]
- feature request: which parameters values are used in a cell
- overlay these parameters onto
- almost like vtk to build package based on xml files from galaxy

July 25, 2012

testing [Tommy]
- CTest
  - only reports if test passes or fails
- CDash
  - http://vis-7.poly.edu/CDash/index.php?project=VisTrails&date=2012-07-20
  - set up cron jobs for the different virtual machines
  - Rémi: BuildBot -- coordinate virtual machines: http://trac.buildbot.net/wiki/ScreenShots
- coverage
  - http://vis-7.poly.edu/CDash/htmlcov_vistrails/
  - gives us coverage view of which lines are covered by the test suite
abstraction bug: possibly triggered by upgrades
[Fernando] burrito
- using DTrace on Mac, translating calls from SystemTap
- reading file, python programs read 64 files for a simple program
- need all files that are dependent on the program
- scripting virtual machines?
setting up virtual machines
- Fernando and Tommy coordinate
Rémi
- still working on spreadsheet -- need to talk to Huy
- issue with parameters updating: sometimes need to click on the version again
Big Data and VisTrails
- meeting next week?

July 18, 2012

Big data & vistrails
Publishing bug
- hangs right after the spreadsheet comes up
- Ctrl-C on command-line causes process to finish and
Java [Rémi]
- working on spreadsheet with jpype, cannot subclass java classes in python
burrito: lower barrier to adoption for VisTrails
- can build workflow that uses information from burrito
- system tap: gets all process information, dtrace for mac os
new machine for testing and releases
- virtual machines for linux distributions are setup
- create windows or mac?
vis-7 machine
- upgraded to latest suse linux
- problem updating the crowdlabs machine, poly sysadmins working on
github
- Tommy sent email on this
- goal is to have a public repository
- function to notify main developers if there is something to add
WebGL [Wendel]
- fixed issue with upgrades
- workflow does not execute, still looking into this

July 11, 2012

Big data [Fernando, Huy]
- change execution engine to allow streaming of data
- probably need to change language for execution engine in C++
Burrito [Fernando]
- if you have a program running and have process id, stores in db information about files being written, input
- mongoDB and python
- linux-based (possibly only fedora?)

Jython and Jpype [Rémi]
- Some Java functions (reflection) are not accessible and needed
- Walks jar file to see which modules can be created; writes these to a cache file
- Package needs to load this file and auto-generate VisTrails modules
- Cannot build cache file in python right now, only jython

Publishing bug [Tommy]
- Get two versions when running
- Two cases: when running VisTrails and not running VisTrails?
- Either executes or it hangs

WebGL [Wendel, Tommy]
- vis-7 issue: VTK 5.10
- after uploading, get id already used message?
- queue from xmlrpc gets full and don't receive any more commands
- Possible issue with upgrades (call change_selected_version instead of getPipeline)
- operating system on crowdlabs and vis-7 is getting old, need to upgrade these?

Workflow cache replacement policies? [UV-CDAT, Dave]
- measuring memory usage of python usage
- pympler: http://pypi.python.org/pypi/Pympler/

Installing binaries or into standard python

Testing
- build machine has arrived
- how to run multiple tests
- need to have some type of protocol
- create tests for new functionality
- also establish governance

July 5, 2012

Java dvelopment [Rémi]
- Weka package can be run in both jython and python via jpype
- Jython error when changing parameters (changes don't seem to happen, and trying this a second time causes db_id exception)
- Instructions to run Jython version?
- Is it possible to write a java spreadhseet that works in the python version?
Parameter Exploration Changes [Tommy]
- Added apply to other versions
- Drag and drop to apply exploration to another version
- Similar methods to apply analogies and mashups? [Add to trac]
- Also save analogies
- Apply to other versions works by module id so it won't
- Reference by tag or by unique id (resilient with unique ids)
- Visibility controlled by when there are tags
Move to github and governance
- github: can create organization
- others can fork repository, we can decide what to include or not
Survey users -- what are people using VisTrails for?
- look for old survey?
- what information are people willing to share? how to encourage?
VisTrails users' and developers' day
Status on crowd labs (Tommy will contact Wendel)
Big data: Huy, Fernando, Tommy, Juliana need to discuss

June 27, 2012

Annotations for general data identification in provenance?
IPAW and DataONE Report
Parameter Exploration Interface [Tommy]:
- save all parameter explorations for each version
- adding more metadata to the panel (user, date, exploration name)
LaTeX Issue
- Emanuele cannot reproduce the issue Juliana encountered
- Used CLTools with multiple configurations
- Tommy fixed some process blocking bug, perhaps this fixed it?
Port Documentation update from Pasteur folks
- Always in center
Rémi working on Weka package (try to use jpype here?)
Possible issue with core code in java branch --- validating pipeline and/or adding functions?
exporting VisTrails trace for DataONE working group

June 20, 2012

Move to github and governance
Survey users -- what are people using VisTrails for?
VisTrails users' and developers' day
Status on crowd labs (Tommy will contact Wendel)
Big data: Huy, Fernando, Tommy, Juliana need to discuss
Parameter exploration: apply to different versions

June 13, 2012

Tommy:
- Add support for parameter exploration on the command line---provide the user the ability to invoke a named parameter exploration
- Add support for parameter exploration from the API: this will be for users that need to customize the exploration
Remi:
- Ironing out some remaining bugs on the Weka wrapping
Emanuele:
- Working on UVCDAT improvements: ability to replace a variable
- Need to look into the issue of guiding users on what variables are needed to run a pipeline
- Will look into the latex package issue, where the workflow is not executed (maybe an issue with CLTools or Persistence Package)
David:
- global variables: can be used in the same workflow in multiple places; similar to having multiple aliases that are synched
- aliases: only set for one parameter
- Should we combine aliases and global vars?
- Currently we cannot do parameter exploration over a global variable

June 6, 2012

Tommy: Almost finished with the parameter exploration updates
- Parameter explorations show up in project list now
- Can use functions that have not been set in parameter explorations
- Also working on serialization of parameter explorations to their own schema
Wendel
- Changed combo box style for HTML5 medleys
- Using XMLRPC
- Linux python 2.7.1 issue with cElementTree?
Emanuele: API 1.7 vs. 2.0 returning execution results?
Fernando: git-annex demo
- looks to satisfy the main requirements from Matthias
- Windows haskell issues...
Rémi
- automatically wrapping Weka package
- building Weka workflows
- use Fernando's simple workflows to test this package
- jars: configure button not available before loading a package? check this?
Dave
- updates for USGS, others
- basemap example
- can we package basemap without full resolution maps?

May 23, 2012

Review remaining bugs
Issue with multiple instances
Wendel: almost done with mashups in HTML5, trying to make work on different browsers
- Emanuele will send Wendel examples for web and desktop
Juliana's issues:
- analogies are only displayed if we change the focus out of VisTrails to another application and back
- in publish window, the snippet appears grayed even if the vistrail is saved -- but if the focus is changed to the main window and back, it works
- it seems there are some issues with focus in general...
- can't run 2 instances of vistrails: Juliana managed to break Fernando's setup too
- need better viewer for persistence package: as is, it is not possible to look at values---tedious to change the length of the fields
- persistence: should allow labels in module config--can be hard to identify a file in the persistence manager
- latex extension: clicking on a figure on the PDF file (on acrobat) gives an error (is this related to the change to relative paths?)
- CLTools: should support other types, e.g., integer
- CLTools: sometimes, in the module list, under CLTools, a module called CLTools is displayed

May 16, 2012

Review remaining bugs
- Default values for parameters not showing
CLTools: allow it to be invoked from within VisTrails (Tommy will look into this)
- Emanuele created a command that makes it easier to invoke it on MacOS
Remi will demo the Java version of VisTrails and lead a discussion on design issues
Investigate connection to iRods
Mashups on iPad (ask Wendel to look into this)
- Need to translate the XML spec for the mashups into HTML5 (should be similar to what Wendel did for the automatically generated mashups he had)

May 11, 2012

Fix for issue with caching group modules
- looks to be working ok
Workspace fixes
- seem to be working ok
QPixmap:scaled error?
detaching panels issue? Cannot reproduce
Ticket #551: Make Preferences non-modal?
Ticket #539
Ticket #540: Tommy will check
Ticket #541
Ticket #517
Ticket #523: Dave with check
Ticket #532
Ticket #533: Emanuele

May 2, 2012

Performance issues with workspace reconstruction
- should be fixed, need to close ticket
Streamlining build process
- Set up virtual machines?
- Do we need to buy a dedicated server for this?
  - [ES] It could be a desktop machine, with windows and mac installed. I don't think it needs to be a dedicated machine, but we would like it to be available when a binary is built. I think it could be a mac with windows installed as a virtual machine. A 64-bit Windows has to be installed. I believe Lion allows multiple users logged in the graphical system at the same time, so if it is a powerful machine, it can be used as the development machine for another user. Also, we need to make sure the vnc port is open to the outside so a remote user can connect to it.

- Running multiple Mac versions?
  - [ES] I am not sure if a binary built on Lion will run on Snow Leopard. The contrary is true, but then if we could run snow leopard as a virtual machine would be fine. It seems that Parallels only allows running the server version of Snow Leopard as a virtual machine. If we want to create a virtual machine of Snow Leopard, we need to do some hacking (some users were able to do this).

File management
- Does git-annex work with cygwin?
- Fernando contacted author of this code, he pointed to the web page on windows requirements, thinks symbolic links are the issue
Preferences Dialog is modal and does not allow switch to error messages.
- Make preferences non-modal?
- May already be working non-modal...
- Move "Module Packages" from Preferences to "Tools" window?
Package identifier checks
- move the specific code for SUDS packages checks to the package itself
- add hooks to allow packages to identify which identifiers they can load
Enumerations
- mashups already has a widget to select from a list of existing constant values (general, not just a combo box)
Auto connect
- highlight possible ports to give the user the idea which ports are possible
- Check names of ports to try to make these connections
- Issue: when there are multiple inputs that match multiple outputs (which connection to create)

April 25, 2012

Persistent Package
- File management: discuss git-annex
  - Issue with Windows support
  - May work through cygwin, but written in Haskell which may lead to issues of integration in the Windows environment
- Make inputs of persistent modules read-only, to maintain consistency (only configure them through the configuration widget)?
- Reproducibility of workflows that have persistent inputs: get the version id from the log, put it in PersistentRef and execute the workflow?
Parameter exploration
- Do we want to add named parameter explorations and multiple explorations per version? (Tommy)

April 20, 2012

File management:
- USGS suggestion: use just files in the file system; more concerned about performance
- Git Annex may provide a good solution: http://git-annex.branchable.com/ "Fernando will look into days"
Wendel: update on Elsevier/Sciverse/Crowdlabs
- crowdlabs now uses the proper identification for workflows
- Assumption: author has already uploaded the vt to crowdlabs, and the paper refers to the workflow id, then our app would load the associated mashup and allow the user to manipulate the mashup on the browser
- Bug: random message from VisTrails--interrupt system call "Wendel will ask Emanuele for help"
- Wendel will add all vtk_examples to crowdlabs
Dave: update on additional improvements (e.g., global variables)
- Moved code from pipeline to controller
- The interaction needs to be improved so that if a var is removed, when the user clicks on a workflow, the var is automatically resolved (deleted from the workflow)
- Update Huong's example to use global variables
Discuss changes to persistence package (see email exchange)
- Also more from USGS on persistence and large files
Parallel execution
- python paralellism: for modules that serialize their output, they can be executed in different cores
- allow modules to say they are detachable--they have implement methods for reading the input and serializing output
- ask Matthias for Troels' code--USGS could test it!
Possible issue in Windows version where you need to press space bar in the console before workflows execute? (USGS)
- We need to have a Windows tester (Tommy can test this)
Defaults are not showing in the new ports panel?
Change parameter exploration to allow all parameters to be shown
- Make unset parameters accessible from a Parameter Exploration view (Tommy)
Enumerations (Pasteur group)
- Expand portspec to have subitems to better support this?
Annoying bug where selecting a version selects the text box instead of the version ellipse

April 11, 2012

Wendel gave update on Crowdlabs/WebGL
Update on persistence package and the need to support a global repository
- Juliana followed up with Matthias (see email exchange)
Schema updates going smoothly
Dave made several improvements to module attributes to handle different 'symbols' for the ports, ability to mark ports as optional, visible, etc
- discussed usability issues, including the recording of which ports are marked as visible

April 4, 2012

Fernando will look into the persistent file management
- Persistence Package notes and improvements
- We need to investigate GIT's facilities for managing metadata: http://schacon.github.com/git/git-notes.html
- To handle the metadata, one approach is to keep the local SQLite, and pull the data from GIT
Updates to schema
- Add mashups to schema (to better support crowdlabs)
- Other changes? best to make all needed changes at the same time
Bug-fix release
Crowdlabs
- Get rid of flash

Mar 21, 2012

Need to remind people at Poly about the meeting
Tommy will send an email the day before our meetings
Integer slider for Matthias (need to translate)
Schema changes

Mar 14, 2012

Mashups in the database
- Matthias's error: is there an upgrade here?
- Mashups are not currently being saved in the database, Emanuele is fixing this

Schema changes:
- Mashup changes
- Ticket on trac about schema changes
- Global variables: promote this to specified schema, not just annotations
- Port cardinality: single input or multiple input guidance
- What else should be updated in the schema?

ClimatePipes
- Demo

Mar 7, 2012

Proposal to change the interpreter to support suspended execution (Tommy will look into this and then coordinate with Troels)
- any module should be allowed to have its execution suspended --- we will have a new execution state
- modules that are declared by the developer as suspendable will have a different shape (oval?)
- during execution, suspended modules are shown in a different color (orange?)
- VisTrails should execute all other modules that do not depend on the suspended modules
- the suspension of a module should generate a log entry that states the module is suspended
- Question: how often should VisTrails polls the suspended process? Should we have a 'resume' button in the interface to allow the user to also control this manually?

Bug with updates (Dave will look into this)
export to stable menu does not work, and we need a export to XML (Emanuele will add these to trac)
Crowdlabs and upgrades: Tommy and Wendel will work on this
Emanuele is implementing support to export a single workflow. Caveat: the workflow will be detached from its original, and it will not be possible to 'update' it on Crowdlabs (this will be documented in the manual)
Oracle interface: add dialog error msg when 'reproduce' is not possible; differentiate between execution and 'reproduce' (use italics for reproduce, and keep the existing colors)

Matthias says: Troels has now found the time to finish his Python background job submission package, which can run calculations in the background locally, on remote Unix machines, and on remote clusters and supercomputers. We are integrating it into ALPS now and next want to do a VisTrails package for it. That should not be too hard, but we'll need some changes in VisTrails to be able to implement it well. If a background job starts we want to stop the execution of the downstream part of the workflow and can do that by raising an exception - but this exception should be treated differently to others. In particular we don't want to have the execution log record it as a failed execution, but maybe as "suspended" or "incomplete" or similar. One might also use another color than red to mark the status of the module and the downstream modules. Finally there might still be other branches of the workflow that could be executed and one does not have to stop all execution.

Feb 21, 2012

Wendel: 3D crowdlabs -- found some issues that have been fixed
- TODO: create a function to add a package and reload a package
- TODO: add a function to automatically modify a workflow to produce WebGL results

Tommy: Crowdlabs
- allow users to upload packages -- similar to safe workflows

Fernando: VisTrails/Oracle
- TODO: save db state ID in the log, associated with a workflow execution
- Oracle package supports all functionality of the MySQL package
- already supports 'reproduce'

Emanuele:
- Updated VisTrails doc to include info about server setup
- working on the release
- hard to use VisTrails as a server because of the dependence on X server; when one does not need the GUI, it would be nice to transform the workflow so that it could run in batch, for example, use VTK offscreen support
- caveat: requires VTK to be compiled with offscreen support
- it is not clear if this would work for matplotlib, which also requires X server
- http://stackoverflow.com/questions/4931376/generating-matplotlib-graphs-without-a-running-x-server

Feb 14, 2012

To Do:

new branch in crowdlabs for Wendel
update doc
Oracle package
release 2.0 beta
Future tasks: packaging, testing

Update on crowdlabs (Wendel and Tommy)
- Wendel had problems with black images being returned by the VisTrails server, we suspect the issue is related to the virtual frame buffer---he will investigate
- We need a script to migrate old crowdlabs information into the new format
- There is a new GIT repo for crowdlabs, currently Emanuele, Tommy, Juliana and Wendel are on the notification list
- Tommy is almost done with the update, need to clean up documentation

VisTrails + Oracle Total Recall (Fernando)
- Overview of total recall
- Having the ability to execute and reproduce
- To reproduce go through the log; only works for read-only queries

UVCDAT
- Done, except for icons

Tighter integration with scripting
- require the modules to support serialization into Python
- not clear if can use compute method as it; python serialization is simpler than compute
- need to better investigate this -- ask Dave about his implementation for the VTK scripts
- in UVCDAT there is translation only from pipeline to script, not the other way around

Tasks for new guys (Tommy):
- https://www.vistrails.org/ticket/525
- https://www.vistrails.org/ticket/526

Jan 31, 2012

Climate Tools and Provenance
Server:
- Save workflows to the server database
- Keep the parameter changes
- Add annotation that says when a version is WebGL enabled
- Just send actions that are the changes that are being made in WebGL version

Jan 24, 2012

TE: crowdLabs is running, able to upload a file from VisTrails
- still debugging, found transaction error when writing to database maybe order
defaults:
- problem is that we currently are not showing default values for modules in the port panel
- don't know if we should clutter the interface with all defaults, should we save them as provenance?
- set all defaults when a user drags in a module, this way we have provenance
- hide defaults in the interface--if user clicks on a port, show it, but don't automatically expand it
error handling:returns values and exceptions
- need to track down bug from Colin's workflow

Jan 20, 2012

Updating crowdlabs install
calling VisTrails from command-line using "python vistrails.py"
want to change this to use the VisTrails sever
create a new page, option to view visualization in 3D
send GET request to Wendel's 3D stuff
running on git version of VisTrails (so the code is up-to-date)
server currently has an issue with the change to core_no_gui code
crowdlabs, one change to have "View Vistrail in 3D" link
one new parameter to settings (ip address)
Tommy has crowdlabs code running with new versions of Django
Wendel's code is on the vgc git repo
Branch a new version for crowdlabs

January 10, 2012

need to support mandatory vs. optional attributes
find the status of remote execution
Dave will reply to question from QGIS developer
Emanuele has sent information to LLNL
To do for VisTrails
- test server version for CrowdLabs
- revisit CrowdLabs--issue: Django has evolved, many libraries no longer exist

2011

Dec 13, 2011

Change time to 11am

Derek's suggestion for "Writing VisTrails Packages"
- Split old/new way of writing modules?
- Do we still support having a package as a .py file?
- Should we document adding custom configuration screens?

Dec 6, 2011

Test suite
- our current test suite is not comprehensive
- add tests for the core that was separated from the GUI, e.g., calling update functions, ...
- focus on accuracy and reliability of the provenance that is saved
- will not create scripts for the actual GUI right now
- Action items: iterate through the directories and add the missing tests--start from controller (should document functions as the tests are created) --- start on this after UVCDAT is done

UVCDAT

Nov 29, 2011

UVCDAT

Nov 8, 2011

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

Merge core_no_gui branch with master
- Check unit tests here
- Can we merge this into master, or keep as a separate branch?

UV-CDAT
- 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

We will focus on UV-CDAT and on completing the alpha version of the system. Please read the documents Emanuele emailed.

Using different servers with CrowdLabs

Closing tickets (Tommy)

Oct 11, 2011

Bug reports:

- execute_cmdline issue: CLTools supports both

2.0 bug fixes: push new release soon (for change_selected_version bug fix)

Fix migrateTags issue and any other minor bugs, then release new version of 2.0

CLTools:
- latest is in repository
- README in package directory
- adding to online user's/developer's guide

Oct 4, 2011

We will discuss issues related to remote execution of VisTrails modules as well as multi-threaded and parallel execution of workflows
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:

start jobs and obtain id (which will be saved in VisTrails and in UFRJ's database)
poll the status of a job (if it is still running of it is completed)
copy files to and from the remote server

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.

Next steps:

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'
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

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.

September 27, 2011

Stéphane Descorps-Declere and Loic Couderc from 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
- 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
- the graph is probably being corrupted by some version not being added to the version tree, could be a single action type
- Asked Tom if he knows steps to reproduce

September 20, 2011

Tommy will give a demo of CLTools package for wrapping command line tools
- 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

Making it easier to wrap command line tools, motivated by the need to simplify the creation of executable papers
- Goal: build a wizard that guides a user on the creation of a wrapper.
- 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)
- Initially, require the user to manually provide the information---parameter names and optionally, types.
- The output of the wizard should be a machine-readable specification which could be loaded as a module in VisTrails
- Some desirable functionality:
  - 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
- provide 'smart' parsing to help in the wrapper construction, for example, extract the information from a python script

We will create a separate branch for external developers, so that they can contribute patches to VisTrails

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

Web services (EMBOSS example)
- All now works except Prophet example (<choice> bug in SUDS). Should we remove it?

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

September 7, 2011

Query mode
- need to finish this implementation

Analogy parent() issue?
- check what this was (form August 16)

Web services (EMBOSS example)
- changes with SUDS (should be easier)

VTK Examples:
- 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
- Document this
- MIgrate notes as well so that the notes and tags are migrated

August 31, 2011

Diff tab has other view modes disabled.
- Opening a version or mashup from workspace, open in new tab instead of overwriting diff

Binaries
- 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
- instead of using version numbers for untagged versions, use the same convention used in pipeline view (eg., parent_tag + 1)

Documentation
- VTK?
- At least a section in the user's guide that points the users to the right examples

Examples
- problem with examples that depend on 3rd-party packages
  - move them to the package folder?

August 16, 2011

Diff tab should have other view modes disabled.
- Tab doesn't make sense to switch back to history
- Could either try to make mode buttons work or just disable the modes
- Easier to disable the other modes
- If open a version or mashup from workspace, open in new tab instead of overwriting diff
- this way, a diff view is only closed by a user explicitly closing it

Binaries for Mac
- Can build 64-bit binary and not 32-bit
- 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?
- Expand them automatically
- Mashups are meant to be shortcuts

Mashup saving
- keep does not save (workspace is not updated)
- can we emit signal to workspace so it is updated
- can we put things in memory for the workspace?
- set_changed is called so we should update the workspace when a vistrail to be changed

Subworkflows
- 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
- issue with parent() bug, Dave needs to file this

Databases
- no direct database access currently allowed at NYU
- either create localhost database or use via crowdlabs

August 9, 2011

Ticket #459
- for an empty pipeline, the exploration is not resetting correctly

Dave looking into query issues

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

Ticket #472. Setting values in the user-defined list or any other type of window
- Going to any other window causes everything to reset, after executing, focus out event causes things to reset

Subworkflows: edit bugs, Claurissa

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

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

Enhancement: spreadsheet camera reset button?

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

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

Missing example for vtk.vt for cell locations and sheet references.

Diff when upgraded doesn't work

Upgrade entire version tree? How do we preserve tree structure?

Mashups: display with pipelines? having both expanded to solve the extra click
- 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.

August 2, 2011

Ticket #459 (Tommy)
- Pipeline inspector may not get updated correctly when pipeline is empty

July 26, 2011

Zoom level in the first vistrail bug
- file on trac
- start vistrails and go to version view, history tree is not there, Cmd+R shows root node
- all vistrails after work fine

Subworkflows
- issue with adding input ports and naming
- separate issue with editing a subworkflow more than once

Analogies
- how to update the algorithm so the terminator with HTTPFile works correctly

LaTeX Assistant
- Dave's new changes (read tex file and find \vistrails tags) moved to 2.1, remove from 2.0 for now
- Add back as a new feature for 2.1

ungrabMouse in setModuleLabel
- 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

keep triangle menu initially in 2.0, may remove in later versions if we can maintain access to all features

July 19, 2011

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 12 13, 2011

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
- 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
- Tommy should check that the exceptions are propograted

July 5, 2011

Server migration is almost completed
- GIT/Wiki/Trac working fine. Machine will be relocated to get better bandwidth
- ~~Still need to update vistrails.org to point to new location~~

Some bugs from last week were fixed, still a few more to go (see trac tickets)
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

svn offline this weekend to migrate servers (Huy)
- send an email to vistrails-dev
fix bugs from demo
- fix zoom on open, change view
- detach configuration window, rename, in a read-only, non-changing state (allow copy)
- read-only controller for diff view, or use Emanuele's read-only view flag
- check for pruned versions in "(latest)" version
- failed to index error on open (possibly old version of vistrail--with filenames)

releases?
- waiting for ALPS build for Mac OS X 10.5
- allow 2.0 vt files to open in 1.7 (e.g. those with mashups)

June 21, 2011

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

Updated workspace window
- Separate open and recent files
- Delete closes an open vistrail or removes a closed one from recent file list
- Also has an "open in new open window" option for right-click, suggested "open in new window", "open in new tab" for workflows
- Want to be able to show this palette at all times? This allows better navigation, but problem is the screen space
- Try showing the workspace window in the upper left and "normal" left palettes in the lower-left.

Module Palette
- 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
- one bug on disconnecting variables

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

Diff
- Diff properties not showing up automatically, Emanuele will check
- Implement a diff in workspace window so you can do cross-vistrail diff
- Diff uses version tree for efficiency, but we can use analogy match or heuristic even when no actions are shared

Inspector window: would be nice to keep this window smaller (certain tabs keep it large)

June 14, 2011

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

Global Variables
- 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
- Can we use normal version/pipeline views as result views?
  - Which view to start with? history/pipeline
  - Show the workspace panel instead of history view
  - Show results in the query panel (as pipeline or workspace as appropriate)
- Should we always combine "keyword" and "visual" queries?
  - 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
  - get back to the search window after seeing results (need a button here)
- What interactivity do we want? Open pipeline when matching version is double-clicked?
  - yes, single-click shows in results view, double-click opens as normal vistrail
- Dave will look at query view

Add read-only PythonSource

Workspace: keep closed vistrails here too
- 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

Status of 2.0

May 31, 2011

Go over bugs and new features for 2.0

May 17, 2011

Add comments, bugs, critiques, etc. about the 2.0 changes here

Global variables
- Check issue on MacOS
- Add documentation

Mashups [Emanuele]
- 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]
- read all provenance right now
- create an index file in the vt to load pieces of provenance on demand
- enhancement idea: highlight errors in the list view of Log Details
- tooltips in the browser view show large icons
- search for provenance browser
- fix issues with the left box
- number of search boxes...

Update splash screen [Juliana will talk to Nathan]

Go over Jan's feedback on the PythonSource editor

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.

May 2, 2011

Demos of new 2.0 functionality:
- Mashup
  - log issue: break the link between vistrail.log and controller.log...
  - 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
- Web services
  - upgrades are working
  - Upgrades are in a separate package
  - hooks in vistrails to allow detection when a package is not loaded

Apr 26, 2011

Updates:
- Mashup
  - easier ways to generate package wrappers
  - working on merging code
- Provenance browser
  - fixed thumbnails to show larger thumbnails
  - via tooltip?
  - keeping separate branch right now, detailed commit message on merge
- Persistence Package
  - 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
  - keep mashups off master
  - merging is pretty good using git
  - changing to a single-window interface, adding menus back

Decide:
- PythonSource editor
  - try Eric or some QScintilla-based approach

Apr 18, 2011

2.0 Release: new features to be included and bug fixes
- Mashup
  - if already have alias, carry these over
  - 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
- Workflow search [Tommy]
  - can now save multiple objects to the database in two round trips (modulo number of groups)
  - 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

Workflow search [Tommy]
- Thumbnails in search
- 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
- need more documentation
- better ways to view and navigate still needed

Documentation [Claurissa]
- Persistence
- 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]

Interface changes [Dave]

PythonSource updates [Emanuele]
- DeVide, Eric4

HTTPDirectory
- create a manifest file that can be used for HTTP directory
- check with Matthias for how this works, not supported by HTTP

Apr 1, 2011

Meeting time change suggestion to 10AM (Tommy) -- sorry Tommy, only now I saw this item...
- Next week: meet if need be
- Move future meetings to 10am if room is possible (Juliana checking with Deb)
Workflow Execution Explorer demo (Tommy)
- search interface for workflow executions
- 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

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
- [DK] Note that mashups are higher-level objects than workflows. It would seem that mashups should include vistrails.
- [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
- [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)
- abstractions==subworkflows? Some error messages still refer to abstractions
- Logic for merging subworkflows from different sources? (Upgrading issues?)
Control Flow Assistant feedback (Tommy)
From Matthias:
- 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?
- 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

database to file: works for log now
database: save subworkflows to the database
add uuids for vistrails, subworkflows, merges
merging: same uuid and data changed
look into distributed algorithm
merge should possibly include logs
allow additional metadata to be controlled, possible to have a 1-1 correspondence

speedup on database queries to speed up joins over entities, combine different attributes
loops on module executions
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
how to handle users that want to contribute code or examples

[Dan] committing control flow assistant soon, issue with database version (see trac commit from today)

Mar 8, 2011

DB speedup finished? [Tommy]
- Speedup done.
- Looking into issues with saving log
- Execution Provenance API

Control flow [Dan]
- 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]
- check in guide to git

Mar 1, 2011

Documentation Log

Updating the relational DB (Tommy)
- Import vistrail from DB is now very fast.
- Mostly done with export vistrail to DB. Still a few issues.

Feb 22, 2011

Python Source widget (Emanuele)

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.
- Please add any undocumented features as well any (informal/incomplete) descriptions you might have to the following page: Undocumented Features

- focus issue (will ask Huy if he knows a good solution for this)

Browser updates (Tommy)
- project browser, workspace

Updating the relational DB (Tommy)
- insert size: Tommy tested with 60,000 inserts
- 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)
- add tutorial for this loop

mailing list emails
- Dan: keep track of which emails and update the FAQ with answers
- Could think about putting this into a system eventually, but for now it's low-traffic enough

Feb 8, 2011

LaTex extension demo (Emanuele)

- New embed dialog

Non-modal PythonSource windows (link to discussion)

- make it non-modal, single window
- update selection on click

Where to keep User's guide and other documentation

- Sphinx, commit to doc directory

Log Explorer demo (Tommy)

Log_API RFC (Tommy)

Control Flow Assistant (Daniel)

Feb 1, 2011

Execution Provenance View (Tommy)

Control flow assistant (Daniel)

Script Interaction (Emanuele)
- CDAT feature that might be useful in other settings

Port/parameter management (Dave)
- 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

2010

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 The Dataverse Network or maybe 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 The Dataverse Network or maybe 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 --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

Welcome Tommy!

Update on subworkflow (Daniel)

Issues raised by Matthias:

- 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.

- explorations do not detect an MplFigureCell embedded in a subworkflow.