[ALPS-users] Fwd: [vistrails-dev] Announcing VisTrails 1.6

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From: Emanuele Santos emanuele@sci.utah.edu Date: January 7, 2011 9:03:34 PM GMT+01:00 To: vistrails-users@sci.utah.edu Cc: vistrails-dev@sci.utah.edu Subject: [vistrails-dev] Announcing VisTrails 1.6 Reply-To: vistrails-dev@sci.utah.edu

Hello VisTrails users,

Happy new year! There is a new version of VisTrails available at http://www.vistrails.org/index.php/Downloads

The release notes listed below contain a *very long* list of enhancements and bug fixes, so we would like to highlight the coolest ones:

• A new Web Services package based on the SUDS (https://fedorahosted.org/suds/) library. Chapter 10 of the User's Guide was also updated with the new package. The old package will be removed on the next release, so please consider switching to the new package instead;
• Ability to save parameter explorations;
• Support for Workflow upgrades;
• VisTrails is now shipped with the ALPS (http://alps.comp-phys.org) package version 2.0.0rc5.

As always, if you find any problems with this release let us know!

Cheers,

-- Emanuele Santos VisTrails Developer

---

RELEASE NOTES

Release Name: v1.6 build e9f97c5908ac from v1.6 branch

Enhancements:

• Added prompt for password for database access in batch mode (06c4b63434a7)
• Please notice that the parameter separator in the command line changed again from

'&&' to '$&$' so it's consistent with the server version. (35ad76515a97)

• VisTrails now has "Check for Updates" option in Help drop-down (b80862d8a39f)
• Show port_spec.sigstring in PortMismatch error message for more detailed debugging (c28dad738abc)
• Turn off popup messages if messages window is open (62aeb9371235)
• add/delete Web Services from module palette for SUDSWebServices package (2e381a4394ed)
• Package-level context menus in the module palette (2e381a4394ed)
• Add preference for migrating tags and notes on upgrades (41177e74e687)
• Add stack trace to exception details for unexpected exceptions during change_selected_version (fd3840df3c6b)
• Added new class Chdir to prevent users from triggering side-effects by accident when using os.chdir() (4aa722db61d1)
• Added Open Recent to File menu (it works for vistrails in the file system or in the database. The maximum number of files in the list can be configured from Advanced Preferences Tab (search for maxRecentVistrails) (4aa722db61d1)
• Configuration object now supports bound methods as subscribers (4aa722db61d1)
• Debug messages now have a "details" attribute (f2911a6a6000)
• Buttons for filtering VisTrails messages (ebc728d49db3)
• Colors of message types added to theme file (ebc728d49db3)
• Improved log messages in the server log to also indicate the instance of the server that is logging the messages (762902e79b7a)
• Improved handling of log messages (037568dc5960)
• Changed all examples using relative paths to datasets to use HTTPFile (403205442fd7)
• Updated head.vt and terminator.vt example to use TransferFunction widget (403205442fd7)
• Maintain suffixes on persistent files and directories (e9b5e906e069)
• Improved debug messages (9dcd1a5a2ea8)
• Ticket #390: Add support to Latex extension to download workflows at compilation time (90ef6cee20a9)
• Improved error handling in vistrails.packages (a44800a88083)
• Improved debugging messages for vistrails.gui (25b718347ef0)
• Improved error handling in vistrails.core (2e095f36dc90)
• Debug library updated (41e3778d507e)
• Web Services package is now deprecated. Showing a warning message when the WebServices package is loaded. Message will be shown only once. (9996bba52dd1)
• Ticket #375: Add GUI support for synchronizing vistrails (4efb09fbe5bd)
• Merge 2 Vistrails from within VisTrails (4efb09fbe5bd)
• Detect changes to directories so the cache can be invalidated when they change (3058d55966f2)
• New Web Services package that uses SUDS library (0d1d3efb99da)
• Add pinch gesture support to graphics views (3d01e549f849)
• ParaView package: Converted to new VisTrails package format (65453bd92aa5)
• Updated php scripts to work with Latex extension's new features (2b53ad32a374)
• VisTrails server: added new function to return version tree as pdf (2b53ad32a374)
• Created a separate php file to store the server configuration (8d15fdbe8e1d)
• Added support for running crowdlabs and vistrails server on separate machines (still testing) (064304a99993)
• Ticket #382: Improvements to Latex extension (3123297d6a1b)
• LaTex extension: VisTrails can now embed a workflow graph or

a history tree in LaTex pdf (3123297d6a1b)

• LaTex extension: Caching latex instructions and images for embedding

images in case python is not available (3123297d6a1b)

• Ticket #381: Split HTTPFile.compute() method to download the file in a separate function (62d25dca3f3a)
• Add MplScatterplot and MplHistogram modules to pylab (4af6514c20d4)
• Ticket #295: Add Debug .command to Mac distribution (e835d69d8426)
• Added git executable to windows repository. It will be included

in future windows binaries for persistence package (8d9931bbbe04)

• Updated version of the rpy package (c895125216cb)
• Migrating new persistence package from persistence_exp to persistence (5b6418233dea)
• Added methods to expand shortcut string representations for module descriptors and port specs (5b6418233dea)
• Added support for shortcuts to remap modules/ports for upgrades (5b6418233dea)
• Use List for controlflow now instead of ListOfSElements (74f30460d3fe)
• Highlight invalidate port specs (74f30460d3fe)
• Improved support for work with the filesystem. Added DirectorySink module, changed FileSink module to use 'overwrite' instead of 'overrideFile', added support for getting the contents of a directory, created a new OutputPath constant with a save-style widget to select the output path, replaces OutputName on the FileSink module. Added updgrade code to translate old FileSink module to new version. Changed version of basic_modules and abstraction to static string '1.6'. (fb30dca8a15d)
• HTTPFile now supports proxies. (3799edddbb62)

Bug fixes:

• Fix issue with console mode and unit tests (a4d544eec673)
• Ticket #361: Cannot configure output cell layout for cells in groups in parameter explorations (5807414236ba)
• Enable all spreadsheet cells for parameter exploration, even if they are embedded in groups or subworkflows (5807414236ba)
• Ticket #399: Exception thrown when loading parameter exploration tab with no existing exploration (4366e52c39cf)
• Fixed exception when loading parameter exploration tab for a workflow with no saved explorations (4366e52c39cf)
• Ticket #154: vistrails should check for a new version being available and tell the user to download it (b80862d8a39f)
• Ticket #398: Failure opening vtl files (filename issue) (c52ba7adc5f8)
• Matplotlib package: if hide toolbar parameter is set after the source and there isn't an extra line at the end, the MplPlot would fail (c52ba7adc5f8)
• Ticket #398: Failure opening vtl files (filename issue) (cdfa0c97493d)
• Added escaping to filename in unzip commandline call (cdfa0c97493d)
• Fixed issue where it was not possible to ungroup a subpipeline that had an InputPort connected directly to an OutputPort (e1ea9b437507)
• Fixed problem where controlflow package would raise duplicate errors (4351b3f0102f)
• Fixed issue with groups and input values that evaluate to False (6fc007c0535d)
• Fixed ordering of PortMismatch parameters in ensure_port_specs (c28dad738abc)
• Fixed bug introduced on Windows platforms when changed os.chdir() calls by core.utils.Chdir (0a2b8a0d50d8)
• Enable the Linux theme for 'Linux' system types (57dfb4a85e7a)
• added deletion of namespaces in module palette (2e381a4394ed)
• Add ability to migrate tags when upgrades are not delayed (9c49285269ca)
• Message filter colors does not show in linux (ee8906c91039)
• Ticket #397: Save execution log when in console mode (2dae96a8f004) (1afa51d895e9)
• Update version tree when adding delayed actions (d1dbf3005499)
• Subworkflows from packages that need upgrades are now moved to local.abstractions in the registry and picked up for workflow upgrades (04476a172f61)
• Fixed issue with spreadsheet and grouped spreadsheet cells (fd3840df3c6b)
• Replaced svn command with git command to get current commit (if present) (4aa722db61d1)
• Flush delayed actions (including upgrades) to fix issues with delayed upgrades and grouping upgraded workflows (79dd982e6cef)
• VisTrails Server: Applied fix to caching of history tree images when generated as pdfs (fc0ab9f1626d)
• VisTrails Server: fixed problem in caching of history tree images (4862e1f7d18a)
• Ignoring mouse gestures when Qt version is < 4.6 (4862e1f7d18a)
• Ticket #394: VisTrails server is not detecting updates in vistrails loaded from the database (762902e79b7a)
• Restoring extensions/http/run_vistrails.php to version before merge (762902e79b7a)
• VisTrails server was ignoring the build_always variable if it found cached images (762902e79b7a)
• Using port to identify the instance of the server instead of virtual display in script that starts vistrails server using Xvfb (762902e79b7a)
• Ticket #393: Latex extension doesn't handle workflow exec. errors properly (16f522c459c5)
• Latex extension: Making sure to convert line breaks into \MessageBreak Latex commands before displaying error messages. (16f522c459c5)
• Forwarding force build to server so the server can also bypass caching (47a1105664a0)
• Ticket #392: Refactor php extensions caching logic used for wf executions (3125e0eb8e81)
• Updated mediawiki extension to work with crowdlabs server (3125e0eb8e81)
• Added workaround for RotateFileHandler problem on Windows when some packages start child processes during workflow execution (e5afc47797cb)
• Fixed issue where named intermediate persistent files/directories were not reused correctly (df3deb58a18c)
• Fixed git hash retrieval for persisted directories (df3deb58a18c)
• Pasted text in VisTrails shell was being ignored (c48e67f02ae8)
• Giving focus to VisTrails shell when showing it (c48e67f02ae8)
• Added 'VisTrails messages' button and fixed 'VisTrails debugger' button (b401b2498c74)
• Don't mask AttributeErrors when materializing pipelines (b5c3650e5ca6)
• Add upgrade path for old InputPort and OutputPort modules (8abfff56592c)
• Fixed an issue with groups and upgrades (720d93c8e3be)
• VisTrails shell was not using fixed-width font (b521e096f879)
• Latex extension: delaying check for a valid url so we can include cached images if there's no Internet connection (79296270cc86)
• Batch mode: On Windows, VisTrails was not executing workflows when an absolute path to a vt file was given (81812ac04e85)
• Minor error fixes (45b53eef1c53)
• Ticket #386: Moving modules after an upgrade generates invalid actions with delayed upgrades (ad9e029035f7)
• With delayed upgrades, moving modules after an upgrade now generates actions in the correct order (ad9e029035f7)
• Ticket #385: Workflow instantiation fails when doing on-demand package loading (aff3408c7a51)
• Fix issue with on-demand package loading leaving workflows as invalid (aff3408c7a51)
• Casting DBLocator names to string as they can store None sometimes (9996bba52dd1)
• Ticket #384: Deleting version edits version tag if delete is canceled (cc05bc9e80e5)
• Don't delete tag text when attempting to prune (cc05bc9e80e5)
• Expanding port specs deals with differences between descriptor and port signatures (c5763a437606)
• UpgradeWorkflowError tries to trim None-value (93b3be3d2a50)
• Ticket #383: Unversioned modules are not upgraded (4b3fa72869f0)
• If a module has no version, force it to be upgraded (4b3fa72869f0)
• Ticket #302: Moved modules action generated when nothing changed (3e59defe4685)
• Fixed logic so moved modules are properly detected and positions updated. (3e59defe4685)
• ParaView package: Removed hardcoded path to pvserver and mpiexec

and using configuration object for that (accessible through Menu Preferences -> Module Packages) (65453bd92aa5)

• ParaView package: Updated pv.vt example to work with current version

of the package (65453bd92aa5)

• Fixed bug in some php scripts when only the tag is passed instead of

a version number (2b53ad32a374)

• Updated all php scripts in extensions/http to work with

the current version of crowdlabs vistrails server (only local setup currently supported) (8d15fdbe8e1d)

• Fixed bug where server method get_wf_graph_png would sometimes

fail (064304a99993)

• Fixed bug where although DBLocators were being cached, the connections were not (b07c22d9e93d)
• Ticket #359: When using VTKRenderOffscreen module VisTrails crashes (48e477f4c1d9)
• VTK Package doesnt work with VTK version 5.7.0 (ba5e0bdbbb16)
• Fixed issue with query-by-example where parameters couldn't be updated (741b1c0d7737)
• Error using breakpoint due to new stack trace (d4f31af05a05)
• LaTex extension: removed hardcoded url for downloading vt files

upon clicking on the images in the generated pdf. It can now be set using the \vistrailsdownload in the latex file (3123297d6a1b)

• HTTP package was not handling exceptions correctly (62d25dca3f3a)
• Ticket #380: HTTPFile corrupts binary files on Windows (0a5ec2007878)
• Color Constant: Initializing Color widget with default white

color using RGB constructor instead of QtCore.Qt.White. We assume the color is always a QColor object and sometimes a GlobalColor object was being found (8565a276a353)

• Persistence Package: Added code to find tar executable similar

to the way the path to git is set up (4a2494c09ef4)

• Persistence Package: adapted use of tar command to work

on Windows (430e29bcaf2e)

• Windows binary: Including the gnu version of tar instead

of the one that comes with git (430e29bcaf2e)

• Set MplFigureCell to fill spreadsheet cell (4af6514c20d4)
• Ticket #302: Moved modules action generated when nothing changed (8f60ea9a4737)
• Dangling move actions are displayed immediately after switching versions (8f60ea9a4737)
• Ticket #331: ImportError when trying to import userpackages (bc27cdc4b171)
• "import userpackages" fixed by reordering init steps (bc27cdc4b171)
• Ticket #293: Shell copy & paste on Mac doesn't work (694c0a43fbda)
• Use git ls-files instead of cat-file to retrive hash so that we don't have issues with Windows reading from stdin (1b190225cce9)
• Persistence package: fixed problem where persistent files

couldn't be found on Windows (df8a7c2ef7d1)

• Ticket #369: picture-in-picture setting is confused when a new vistrail is opened (7ea68b3e863f)
• Check PIP preference when opening vistrails (7ea68b3e863f)
• Allow semi-translation from abstractionRef to abstraction so

old workflows (version <= 0.9.3) with subworkflows can be opened (50b9ce2b28fc)

• Spreadsheet: fixed 'RuntimeError: underlying C/C++ object has

been deleted' problem during EventFilter on Windows (93884b6a47c0)

• VTK Package: Fixed rendering context problem when embedding VTKCell in VisMashup on Linux (93884b6a47c0)
• PathChooserToolButton was not emitting proper signals necessary for

VisMashup (93884b6a47c0)

• Persistence package: Fixed load package error on Windows (4ee8f244fc79)
• Change persistence package to use correct identifier for gui widgets (9dd3ad8e0b08)
• Ticket #378: Workflow execution log contains duplicate entries (6d65daec6089)
• Fixed logging so that executions are not duplicated when saving more than once per session (6d65daec6089)
• Ticket #377: Exporting to OPM XML fails (3ee1cc842182)
• Fixed OPM output capability to work with latest object layout (3ee1cc842182)
• Update sql package to use List instead of ListOfElements (4b08dd9018db)
• Fix typo with get_package_by_name (74f30460d3fe)
• keep selected modules after scene redraw (bb5e4e6e1f45)
• Optional input ports now don't show up as output ports (bb5e4e6e1f45)
• Ticket #376: execute_cmdline broken (bbbcf19704b8)
• Fixed copyright year in background image from About box (bcd3346d8865)
• Web Services package: fixed bug in certain Complex Types (60128ff3a89a)
• Ticket #374: Web service package can't be reloaded (38976729a2a9)
• Fixed an issue with package reloading where modules imported using the "from" syntax were not added to the imported list (38976729a2a9)
• HTTPFile: Fixed error when parsing the date from the file's

header. (3799edddbb62)