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VisTrails Changelog

What's new in VisTrails 2.2.4 Build 1519abc0ae2b

May 24, 2016
  • BUG FIXES:
  • Fix module with optional connected port having the wrong size
  • Fix InputPort with ports that have depth>0
  • ReproUnzip: actually populate 'stdout' and 'stderr' ports
  • Fix ReproUnzip not working in Mac OS binary installation
  • Fix tej failing to setup a queue in Mac OS binary installation
  • Show full stacktrace in module's "Show Error" popup
  • Fix Module Info tab showing wrong module in some cases
  • Fix Search Mode (#1149)
  • Visual query did not work without string query
  • Workflow query did not display matching modules
  • Updated Search Mode documentation
  • Upgraded pipelines will now be searched when hideUpgrades is set
  • Fix visual diff not using upgraded pipeline
  • Hide empty Mashup and Parameter exploration items in workspace
  • Fix mashup link in Workflow Info tab
  • Fix workspace not updating mashup list
  • improvements to upgrades
  • Upgrades are now correctly chained from the latest upgrade (#1164)
  • Fixed multi-step upgrades that replaces modules to other packages (#1165)
  • ENHANCEMENTS:
  • Add a TensorFlow package
  • Allow multiple versions of the same package to be installed, load the
  • latest working one
  • If loading a file with an unknown extension, assume .vt format
  • API: allow constructing vistrails.Vistrail() without argument
  • Added usage stats reporting
  • Added news widget

New in VisTrails 2.2.3 Build 02ad04a622c4 (Dec 8, 2015)

  • Bug fixes:
  • Fixed showing "invalid pipeline" instead of failure from auto-enabled package
  • Fixed responsiveness of suspended module progress bar
  • Fixed some GUI issues in the job monitor
  • Accept unicode in source configuration widgets (e.g. PythonSource's)
  • Fixed using same name for an input & output port in PythonSource
  • Fixed the spreadsheet window popping up when exiting VisTrails
  • Enhancements:
  • tej package improved & documented
  • Add "close" action in workspace context menu
  • Added a MongoDB package
  • Added a reprounzip package
  • Make FileOutput mode use the 'outputDirectory' config setting
  • Allow multiple actions in module palette's context menus by introducing 'context_menu', replacing 'contextMenuName' and 'callContextMenu'
  • Add Reshape, DictToTable and ListToTable modules to tabledata
  • Only require numpy/xlrd/xlwt when modules get executed; they now always exist Added Job Submission support to Parameter Explorations and Mashups
  • ModuleSuspended now requires a handle
  • Added Job Submission documentation, examples, and tests
  • Autosave now only stores the latest save, not a new one every 2 minutes
  • Behavior change for package developers:
  • MplFigure connections now carry the figure number (int) - ModuleSuspended now must have an associated JobHandle

New in VisTrails 2.2.2 Build 358e9a9fc33c (Jul 22, 2015)

  • Bug fixes:
  • prevents introducing cycles in pipeline view
  • Fixes to subworkflows
  • Fixes subworkflows failing to execute
  • Fixes not being able to remove local subworkflows
  • Fixes upgrading to a newer local subworkflow
  • Fixes OPM and PROV export
  • Fixes executable documents
  • Fixed generating pipeline and version tree graphs

New in VisTrails 2.1.5 Build 4fe986148829 (Mar 25, 2015)

  • Enhancements:
  • Tabledata package updated to version 0.1.5
  • New google maps cell package
  • New distribution packaging
  • Bug fixes:
  • Fixed problems with parameter explorations:
  • Using more than one unset function now works
  • Fixed update logic when switching views

New in VisTrails 2.1.4 Build 269e4808eca3 (Jan 19, 2015)

  • Bug fixes:
  • Pinch gesture was broken (2d5494ed1d10)
  • Ticket 893: "Create Version" button on the spreadsheet does not work (d3db65418fad)
  • New Parameter Exploration was created for each execution (c324acad38f9)
  • Could not load saved Parameter Explorations (c324acad38f9)
  • Ticket 762: Package.import_override.is_sys_pkg logic incorrect (bf5e20c923f7)
  • Usersguide: Fixed parameter exploration vtl links (79c3021a50b3)
  • Forces the use of PyQt4 (avoid PySide) (2460948327cc)
  • Guess whether to use su/sudo with pip (18698fa909b3)

New in VisTrails 2.1.2 build 7d8a4ed2feeb (May 16, 2014)

  • Enhancements:
  • Ticket 846: File Selection Dialog
  • Ticket 824: Workflow execution output in console
  • Adds PromptIsOkay module (WIP)
  • Adds a YesNoDialog module
  • Bug fixes:
  • Ticket 849: Autosave for existing vistrails not working
  • Saving mashups to DB corrupts them
  • CLTools wizard does not show list type field
  • Date error in workspace when using 8bit characters
  • Ticket 850: Pipeline/history view scrollbars too sensitive
  • Ticket 686: Deleting a vistrail variable breaks workflows
  • Ticket 830: Deleting a module does not delete vistrail variables connected to it
  • Ticket 825: Vistrail Variables are not copied with modules
  • Wrong view mode when switching between open vistrails
  • Ticket 828: [Windows] Pinning a panel causes it to disappear
  • Saving new vistrail caused view change
  • Could not drop module in detached vistrail variables widget
  • Vistrail Variables palette closed before it could be stickied
  • Ticket 822: Exception if PyQt is installed but PyQt.QtOpenGL isn't
  • Ticket 783: Enabling packages automatically can make a different package fail
  • Oldstyle imports did not work on vistrails server
  • Fixes adding a webservice through the context menu
  • Old mashuptrails were not deleted correctly in DB
  • Mashups: Fixes alias copy bug
  • SaveBundle did not copy mashups
  • Fixes date formatting in core.collection
  • Fixes major ImageViewerCell bug

New in VisTrails 2.1.1 Build 90975fc00211 (Jan 18, 2014)

  • Bug fixes:
  • Ticket 814: Parameter Exploration Broken (13da70d0b35f)
  • Fixes early gui import in application_server (3b2f6186cea9)
  • Ticket 816: Saved vistrail doesn't appear in 'my vistrails' (784414a617d2)
  • Fix font issue for OS X 10.9. (22c0f0cca937)

New in VisTrails 2.1 Beta 2 (Oct 10, 2013)

  • Bug fixes: - Ticket #735: Windows dulwich install via pip fails (14d362a695df)
  • Ticket #718: persistence can't handle directories (2a668a6e9881)
  • Fix issue with persistent paths in Windows (2a668a6e9881)
  • Ticket #728: Upgrading vistrail with disabled package (b28c85b718ac)
  • Fix issue with subworkflows using disabled packages (b28c85b718ac)
  • Fix issue with staging persistent directories (6cddde545965)
  • Fixed module upgrades not working with dynamic packages (bf997c6bb0c6)
  • Fix issue with transfer function widget (11213143752c)
  • Rewrites error-prone code for GitRepo#add_commit() (c1d2f60cc10d)
  • Persistence sets up a Git username if none is set (f37129976ba5)
  • Fixes default values on optional Boolean ports (34365eb22800)
  • Ticket #705: zip.exe not found in Windows binary (69a16e3c5b84)
  • Ticket #700: Upgrades with package identifier changes fail (32f934bef698)
  • Ticket #716: The new IPython console does not receive console output (96d65c1d0e80)
  • Ticket #699: Base classes for parameter config widgets do not enforce defaults (6e1a5624b2ae)
  • Fix BooleanWidget default handling (6e1a5624b2ae)
  • Fixed tricky upgrade bug (1385b1d04f4b)
  • Ticket #626: Passing parameters to single instance still opens second instance of VisTrails (334c743f3c33)
  • Fix issue with package identifier changes and upgrades (32f934bef698)
  • run.py/fix_paths was broken (16aeafb32399)
  • Looping over a failing PythonSource caused logger to fail (2b5ff8105562) - Fixes line-endings for TestUnzip (05a41335f050)
  • Disables deleting from the persistence store (3c816e2734b8)
  • Adds tests for type-checking, using PythonSources (3f0c602b003a)
  • Disables type-checking for InputPort modules (4cdad5f113df)
  • module_info now shows a module's id (0c504fe06615)
  • Limits copy and paste in module_info (b99c674c8494)
  • Detects cycles when computing pipeline signature (3a0fe0b5a880)
  • Adds some more checks for persistent path type (846631436bd0)
  • Raises a ModuleError if persisting an empty dir (d3d8b2193b5f)
  • Makes type-checking optional (30659a8b6525)
  • Fixes adding a directory to persistence (0c26c5b68ee6)
  • While requires *or* ConditionPort or MaxIterations (bdcd04e3366c)
  • Fixes a package_dependencies() crashing VisTrails (3263be2d2a52)
  • Lets PythonSource use the default source (7684997bd888)
  • PythonSource configuration dialog now uses default (3dff503ce8ce)
  • Fixes StringWidget not showing default correctly (49d9dbd161f0)
  • Restores read-only mode removed by previous merge (4bdf4705a669)
  • Removes most of the persistence_exp package (90c70ee525e6)
  • Fixes matplotlib not able to reuse cells (243ae02dd499)
  • Makes UntitledLocator inherit CoreLocator (fc863650a893)
  • Fixes looping modules (34d3029f3419)
  • Minor changes to persistence code (96a605e0ca3f)
  • Adds back PersistentPath#git_command() (295f9ade09cf)
  • Fixes an issue with fix_dates() (3ad431172b47)
  • More fixes to found_another_instance_running() (916cdeb23f6f)
  • Makes fix_dates static in PersistentRefModel (56dec62ea2aa)
  • Fixes persistence view (1bbb9bfb5f45)
  • Adds tests for Unzip and UnzipDirectory (22c9d361b78b)
  • Makes HTTPFile cacheable again (5bc3619d5cba)
  • Fixes running the CLTools wizard standalone (77bf72286a8c)
  • Fixes CLTools test on Windows releases (c503e4df5cf9)
  • Fixes UnicodeDecodeErrors in DebugView (5ce4fd3515d7)
  • Adds an UnzipDirectory module (634e6415a62e)
  • Fixes Unzip code (10a2a3753185)
  • Fixes runtestsuite.py ignoring *system* (b1210c5dc5c7)
  • ImageMagick fixes (b0994f0e5684)
  • Cleans disabled packages from cache (51a4cf021a31)
  • Removes QPackagesWidget#erase_cache attribute (2919064fcce2)
  • Don't expand the module palette on package load (890b6796e4a2)
  • Re-enables type checking after all (ec6539366bbd)
  • Fixes optional tabledata->spreadsheet dependency (511ab651ad93)
  • Makes numpy arrays valid Lists (6425d8d7a286)
  • Merge branch 'optimize-module' into 'master' (906a6edf8e73)
  • Minor fixes to installers (ba9550bb44f2)
  • Moves rgb2hsv and hsv2rgb out of paramexplore (f00a710f2424)
  • PythonSource now sets unconnected output ports (75f4d085c57f)
  • Adds a Delay port on the While module (07087da25339)
  • Renames 'optimization.py' to 'looping.py' (b4b2183e3bab)
  • Renames Optimize to While, inverts condition (0a07b43c7a2f)
  • Adds state output/input ports (e6f57d0f4999)
  • Adds the Optimize module to ControlFlow (ea4ebd43293c)
  • ExecuteInOrder now uses the ControlFlow style (3d286c21a17d)
  • Adds a Delay port on the While module (2b2648c08820)
  • Makes log-related flags not fold-specific (954c984cca31)

New in VisTrails 2.0.3 (Aug 30, 2013)

  • Bug fixes:
  • Ticket #639: Package details are not updated when a disabled package is selected in preferences panel (49db740c7a8c)
  • Logging fails when Group executed by Map fails (fcb6d4b1b637)
  • VisTrails Server: fixed generating a pdf from a vistrail tree (0a3d02e92b48)
  • PipelineView: Execution exceptions were not caught which caused jobView to lock up execution (91bd58c44897)
  • open_many_from_db should not be used with pre 1.0.2 schemas (e2b247f2c588)
  • Updated latex example files to use crowdlabs instead of vistrails.org (0314ecf38606)
  • Fixed generating an image of workflow graph from the command line (3f40090c5e12)
  • Fix issue with intermediate persistent files not being found in the store when a uuid is already assigned. (72c89f5aa6ca)
  • io.save_vistrail_to_db was using "Vistrail"-specific methods (db662d585a3e)

New in VisTrails 2.1 Beta (May 13, 2013)

  • Enhancements:
  • Incremental/Online Layout
  • Spreadsheet: "Find Version" and "Save Camera" now works for unsaved, closed, and "saved as" vistrails
  • DB support for Mashups
  • Support backward compatibility for packages that have not been updated to use the "vistrails." prefix when importing.
  • Updated persistence package to use dulwich, a pure python implementation of git
  • PROV document can now be exported using the command line (script)
  • Ticket #604: Add vistrail variable support to parameter exploration
  • Added PROV entities for input and output data
  • Using Dublin Core metadata for PROV document (PROV exporter)
  • New version of the PROV exporter
  • First version of PROV exporter
  • Serializable mixin class for modules
  • User does not need to create IPython controller manually anymore
  • Added support for SSH IPython engines in parallel flow
  • IPython controller is stopped when closing VisTrails or disabling the package
  • Ongoing work on the exporter for the PROV model
  • IPython controller and engines are now started from VisTrails
  • Added information about the machine from each IPython engine
  • Map (parallel flow) can execute an outer subworkflow in IPython engines
  • First version of package 'parallel flow'
  • Module / Group executions from the IPython engines are added to the provenance
  • Added some modifications in the code to allow the execution of workflow in IPython engines
  • Forward error messages when connecting to other instance
  • Add uniform method for building descriptor, port_spec strings
  • Allow selected portions of the workflow to be relaid out
  • Add option to nicely layout workflows automatically
  • runtestsuite now returns 0 for passed test runs
  • Ticket #606: Copy parameter explorations between workflows
  • Updates to parameter explorations
  • Ticket #603: Parameter Exploration from command line
  • Ticket #545: Make unset parameters accessible from the Parameter Exploration view
  • Ticket #547: Migrate parameter exploration persistence to schema and controller
  • Unset parameters can be used in parameter explorations
  • New schema for parameter explorations
  • Parameter explorations can be named
  • Parameter explorations are visible in the workspace
  • Parameter explorations can be accessed without the gui
  • Improve exception message for invalid port specification
  • Improve error messages during package loading
  • API: VisTrailsAPI.execute() now accepts the same parameters in core VistrailController.execute_current_workflow()
  • LaTex Extension: Added support for relative .vtl links in pdf and relative filenames in .vtl files
  • AutoConnect: when dragging a new module into a workflow, try to connect it
  • Allow port_and_port_spec_match to match two port specs
  • Ticket #555: Move package-specific missing package handlers
  • Support enumerations for parameters
  • Add gui support for different port shapes
  • Show when ports are set by darkening the port
  • Add visual cues for the number of connections set/needed/allowed
  • Added port docstrings to the VTK package
  • Updated port documentation
  • Add schema support for max/min connections for ports
  • Native schema for Vistrail Variables
  • Add load_package method to API
  • Add load_workflow method to api
  • Bug fixes:
  • Vistrail Variable list was changing while being iterated over
  • Saving log to previous version failed
  • Fixed update_db script to work with master
  • Allow reading different versions of subworkflows from DB
  • Fixed loading wrong abstraction DB version
  • Fixed trying to write empty workflow list to DB
  • PipelineView: Execution exceptions were not caught which caused jobView to lock up execution
  • Mashups: controller_changed caused widget to be redrawn even when the controller did not change
  • Ticket #656: Control Flow Wizard is broken
  • Fixed deleting mashup alias using Del/Backspace key
  • color picker widget gets orphaned in the alias inspector
  • Fixed bug on PROV exporter
  • Fix issue with Mac binary and the vistrails.py sys.path changes
  • Save log to xml action was not enabled in menu
  • Ticket #641: PersistentInputFile not recognizing changes in the file contents
  • Fix issue where file changes were not being recognized
  • Ticket #639: Package details are not updated when a disabled package is selected in preferences panel
  • Execution of workflows in IPython engines
  • Groups and Subworkflows can now have their execution log annotated
  • Ticket #635: Error translating from schema 1.0.2 to 1.0.3
  • Fix issue with whitespace between port spec items
  • Ticket #577: Publish window always shows grayed out snippet
  • Ticket #633: Automatic package download is not working on master
  • Ticket #626: Passing parameters to single instance still opens second instance of VisTrails
  • CLTools: Modules were not reloaded after reloading scripts
  • CLTools: "env" option was not reset in wizard when loading other tool
  • Server mashup request need to use db user with write access
  • MissingPackageVersion exceptions need to be tied to specific modules
  • Ticket #629: Issue with namespace
  • Fixed issue with reloading packages with namespaces
  • Allow only a single MissingPackage exception to be included in an InvalidPipeline container exception Fixed typo with ghosted pen color
  • Ticket #627: Duplicate enable package messages
  • Fix errors in parameter exploration when viewing invalid pipelines
  • Do not emit errors from the query view when the selected version changes
  • Ticket #617: Hard import from the v1_0_0 schema in opm.py makes it fail with other schemas
  • Fix OPM import
  • Windows: Saving vistrail zip xml fails when zip.exe cannot be located
  • runtestsuite.py should not care about empty string arguments
  • Fixed typo in parse/update for parameter types introduced in recent commit
  • Fixed issue with connecting tuple ports in the API
  • Ticket #621: Hidden ports that are used in connections are not set to visible
  • Fixed visibility of a connected port in ports panel
  • Fixed issue when connecting modules
  • Fixed documentation file of CLTools that was causing a failure when building the pdf version of the usersguide
  • Ticket #618: Open Workflow from DB missing in file menu
  • Ticket #614: test_abtraction_create fails in test suite
  • Preferences sometimes tried to set up a removed package
  • SplashScreen was never deleted
  • Ticket #613: triangle_area.vt fails on the map operator
  • Fix bug with obtaining port spec signature
  • Ticket #612: User-defined parameter exploration editor is problematic
  • Fix issue with modified group signatures
  • is_running_gui missing in VistrailsServerSingleton
  • Fixed issue where OPM export could not resolve ports in parent modules
  • SUDSWebServices did not handle empty configurations correctly
  • Ticket #583: CLTools: sometimes a module called CLTools is displayed
  • Empty packages could not be reloaded
  • PortSpecItem schema did not work on MySQL
  • Parameter Explorations were not being converted correctly from 1.0.2
  • Parameter Explorations were not being loaded from database correctly
  • Saving a Vistrail failed when package manager was not available
  • Ticket #601: Connection port compatibility should be checked at a lower-level
  • Check port compatibility at controller level
  • Ticket #602: core api does not work in console
  • Add missing methods to GUI application
  • Ticket #599: Missing defaults cause exception when adding a function
  • Ticket #594: Defaulted booleans added twice
  • Update color of cached modules correctly and reset colors on re-execute
  • Do not set module color back to active after it has been run
  • Ticket #591: User-decorated modules do not change color during execution
  • Module status brushes are checked first when setting the color of a module
  • Ticket #592: Dragging a Group module into a pipeline causes an invalid pipeline error
  • Guard against empty group modules
  • Spreadsheet package: Checking if the GUI is running before trying to initialize the package.
  • Catch exceptions when selecting invalid modules
  • Ticket #586: Selecting an invalid module raises exceptions
  • enabling/disabling package did not invalidate pipeline
  • Ticket #585: Failed reloading of a package does not invalidate modules
  • Fixed issue where modules were not marked as invalid before validation
  • Ticket #584: Enabling a package adds it to the enabled package list even if there are errors
  • Fix issues with package list in preferences
  • Unselect port on mouseReleaseEvent
  • SUDSWebServices: Offline Mode by storing WSDL in .vt file was not portable SUDSWebServices: Typo in handle_missing_module caused packages with wrong names
  • Ticket #575: Vistrail variables panel has an overdraw problem
  • Ticket #576: Analogies are only displayed if we change the focus out of VisTrails to another application and back
  • Ticket #539: Standard Module Configuration Widget asks to save when two ports are enabled
  • Configuration widgets will prompt to save only when the current module change, making it easier to copy text from another application
  • Ticket #569: Connected icon in Module Information does not disappear after removing connection
  • Loading an image from workflow graph or a version tree was not working in the command line
  • Workflow results that used a VTKCell were consisting of a black screen when running in batch mode
  • Ticket #487: isosurface script version of terminator.vt causes vistrails to crash
  • Ticket #540: Vistrail is not always marked as changed when containing a vistrail variable
  • Ticket #563: Temporary connection does not appear second time you create the same connection
  • Fix issue with temporary connection disappearing
  • Ticket #546: Selecting a version selects the text box instead of the version ellipse
  • Ticket #550: Workspace state_changed is slow
  • Ticket #553: Suspended module does not execute on second run even when notcacheable
  • Parameter Exploration only worked on parameters from the Basic Modules package
  • Fixed minor issue with PortSpec shape and docstring attrs Ticket #418: The database schema should use larger data types
  • Bug in translation from 1.0.3 to 1.0.2
  • Fix issue with configure item grabbing mouse.
  • Removed capitalized methods from ports in VTK
  • Parameter Exploration: Changed call to update the progress bar to be thread safe
  • Mediawiki extension: fixed undefined variable
  • WorkflowExecution.completed were set to False in the vis_log, it should be an int.
  • DBVistrail.hash*Annotation() fails when annotation values are ints
  • Fixed path_to_figures and get_wf_graph_ calls in application_server
  • Do not import VTKCell unless we have the spreadsheet
  • HTTP Package now respects alternate dotVistrails setting
  • The create analogy button is too small
  • "Show raw pipeline" and "construct from root" commands should switch to the pipeline view
  • Fix command_line argv dependency
  • Mashups: slider and numericstepper widgets are only displayed for numeric aliases
  • Mashups: Validating Min Max and Step edit boxes so they accept only numbers

New in VisTrails 2.0.2 (Apr 29, 2013)

  • Enhancements:
  • Added animation support to matplotlib/pylab
  • Job Monitor Improvements
  • Job Monitoring Tool View
  • Add support for customizing which packages are (not) reloaded
  • Testing: Validate Workflows by comparing old and new thumbnails
  • Added saving/loading SubWorkflows to/from the DB as part of a vistrail bundle
  • Ticket #628: Set the path to the vistrails tmp dir
  • Bug fixes: - Saving log to previous version failed
  • Opened vistrails were not selected
  • parallelflow: Do not deepcopy module dict
  • Fixed matplotlib spreadsheet cell resizing issue.
  • API: return result after execution
  • Job Monitor icons were set incorrectly
  • Job Monitor did not delete job when vistrail was closed
  • Workspace: Sometimes selecting an open vistrail does not select it
  • Ticket #651: Function remap upgrade operations performed in incorrect order
  • Fix ordering in function remap
  • Ticket #648: 'OutputPort' object has no attribute 'module_exec'
  • Ticket #647: ModuleSuspended does not work inside Groups
  • Ticket #645: Document py_import in dev guide
  • Ticket #646: Reloading packages fails in some cases
  • Fix issues with package reloading
  • Fixed broken mimetypes on Windows
  • Ticket #643: cannot open workflow triangle_area.vt
  • Ticket #625: Improve crowdLabs upload interface
  • Added DB version map 1.0.2->1.0.3 needed when downgrading the log
  • Saving abstractions do DB was missing version translation
  • Removed faulty import DBProvModel
  • Ticket #619: Create Analogy does not work on spreadsheet
  • Fix issue with analogy api in the spreadsheet
  • Ticket #638: Re-execution of SubWorkflow is missing parameters
  • Fix issue with subworkflow caching
  • Ticket #634: Package Documentation says port sigstring can contain spaces

New in VisTrails 2.0.1 (Apr 12, 2013)

  • Enhancements:
  • ALPS package: Updated to version 2.1.1
  • Support import of schema v1.0.3
  • CLTools: Preview command line arguments and module ports
  • CLTools: Reload modules from the wizard
  • CLTools: Add env port using wizard
  • CLTools: Extended documentation
  • CLTools: Ability to specify fixed environment variables for modules
  • CLTools: Write changes in environment variables to execution log
  • Added server function for seeing and enabling/disabling packages
  • CLTools: Ability to set working directory
  • CLTools: New arg type inputoutput that enables files be used as both input and output
  • CLTools: You can now specify file endings for output files using the suffix option
  • Ticket #582: CLTools: should support other types
  • Added single instance check as a configuration option and a command line option
  • Improved exception message for invalid port specification
  • Improved error messages during package loading
  • Bug fixes:
  • Added the missing v1_0_3 directory for schema v1_0_3 support from master branch
  • FileHooks for DBVistrail types should be skipped (94bb430fa0f0)
  • Check if package has been removed before setting package information
  • CLTools: Modules were not reloaded after reloading scripts
  • CLTools: "env" option was not reset in wizard when loading other tool
  • Server mashup request need to use db user with write access get_vt_graph_png was broken
  • Ticket #617: Hard import from the v1_0_0 schema in opm.py makes it fail with other schemas
  • Fix OPM import
  • Windows: Saving vistrail zip xml fails when zip.exe cannot be located
  • Ticket #624: unix /bin/ls check fails on fedora 17
  • Ticket #621: Hidden ports that are used in connections are not set to visible
  • Fixed visibility of a connected port in ports panel
  • Fixed documentation file of CLTools that was causing a failure when building the pdf version of the usersguide is_running_gui missing in VistrailsServerSingleton
  • Ticket #618: Open Workflow from DB missing in file menu
  • Ticket #614: test_abtraction_create fails in test suite
  • Ticket #583: CLTools: sometimes a module called CLTools is displayed
  • Empty packages could not be reloaded
  • Ticket #612: User-defined parameter exploration editor is problematic
  • Fix issue with modified group signatures
  • Ticket #464: VTK Package does not support VTK 5.10 release
  • Fixed issue where OPM export could not resolve ports in parent modules
  • Fixed issue where modifying a defaulted parameter caused a second copy of the parameter to be added
  • Ticket #602: core api does not work in console
  • Add missing methods to GUI application
  • Ticket #594: Defaulted booleans added twice
  • Fix duplicate boolean values when using defaults
  • Update color of cached modules correctly and reset colors on re-execute
  • Do not set module color back to active after it has been run
  • Ticket #591: User-decorated modules do not change color during execution
  • Module status brushes are checked first when setting the color of a module
  • Ticket #592: Dragging a Group module into a pipeline causes an invalid pipeline error
  • Guard against empty group modules
  • Spreadsheet package: Checking if the GUI is running before trying to initialize the package.
  • Ticket #586: Selecting an invalid module raises exceptions
  • Catch exceptions when selecting invalid modules
  • Enabling/disabling package did not invalidate pipeline
  • Ticket #585: Failed reloading of a package does not invalidate modules
  • Fixed issue where modules were not marked as invalid before validation
  • Ticket #584: Enabling a package adds it to the enabled package list even if there are errors
  • Fix issues with package list in preferences
  • SUDSWebServices: Offline Mode by storing WSDL in .vt file was not portable
  • SUDSWebServices: Typo in handle_missing_module caused packages with wrong names

New in VisTrails 2.0 (May 25, 2012)

  • Enhancements:
  • Ticket #424: SUDSWebServices should store the WSDL spec in the .vt file to enable upgrades
  • Packages can store files in .vt zip files
  • .vt files using SUDS Web Services can now be edited offline
  • CLTools: package menu option for reloading all scripts
  • CLTools: added Open Wizard to package menu
  • Added CLToolsWizard.command file to Mac Binary
  • Ticket #430: use of absolute file names can be problematic in vtl files
  • LaTex Extension: Added support for relative .vtl links in pdf and relative filenames in .vtl files
  • Package requirement for the job submission package
  • Ticket #519: Executions in Version View that fail should change to pipeline Switch to pipeline view if an execution fails
  • Ticket #557: Password dialog
  • Ticket #559: Persistent modules do not work in groups
  • Allow modules in subpipelines to be cached
  • Added alps package to VisTrails 64-bit Windows Binary
  • Bug fixes: - Ticket #575: Vistrail variables panel has an overdraw problem Ticket #404: Overriding a port via add_*_port does not work
  • Ensure add_*_port can override ports in superclass port lists
  • Ticket #523: Default values for parameters not showing
  • Add default support back in
  • Fixed spelling in repository.py
  • SUDSWebServices: Wrong indentation caused vistrail save to fail
  • Ticket #576: Analogies are only displayed if we change the focus out of VisTrails to another application and back
  • Fix issue with redrawing the tree after analogies
  • Running instance was not accepting parameters from another instance
  • Ticket #464: VTK Package does not support VTK 5.10 release
  • Ticket #445: mashup previews is not always shown in the main window
  • Now persistent cache works after one execution
  • Ticket #573: Opened vistrail fail when reloading dependent package SUDSWebServices: Failed Web Services could not be removed
  • Execution button may hang when execution fails
  • Ticket #571: Vistrail variables cannot be used in more than one workflow
  • Fix issue when setting a vistrail variable on multiple modules
  • Ticket #574: Cannot add variable to empty detached Vistrail Variables
  • Fixed issue with creating vistrail variables in an undocked panel
  • Ticket #539: Standard Module Configuration Widget asks to save when two ports are enabled
  • Ticket #521: Annoying PythonSource behavior
  • Configuration widgets will prompt to save only when the current module change, making it easier to copy text from another application QVistrailsWindow.get_current_view() was returning the wrong view sometimes CLTools: IOErrors when executing process
  • Fix issue with analogies that also require upgrades
  • Fix typo
  • Fix issue with remove vistrail variable modules and connections
  • Ticket #569: Connected icon in Module Information does not disappear after removing connection
  • Fix issue with connected indicator for ports
  • Eliminate duplicate warnings
  • Use lil_matrix for analogies
  • Modify logic of analogy usage to use current selected version
  • Ticket #419: Analogies fail on new terminator.vt
  • Change analogies to use a suitable default alpha value
  • Ticket #567: CLTools has issues reading man pages on Mac OS X
  • Ticket #370: dataDirectory setting not used
  • Loading an image from workflow graph or a version tree was not working in the command line
  • Workflow results that used a VTKCell were consisting of a black screen when running in batch mode
  • Ticket #551: Cannot access messages window when preferences window is open
  • Ticket #487: isosurface script version of terminator.vt causes vistrails to crash
  • Ticket #564: Invalid view warning
  • Ticket #552: No visual clue when ubuntu package finishes installing
  • Ticket #540: Vistrail is not always marked as changed when containing a vistrail variable
  • Ticket #566: QPixmap scaled error message
  • Fixed QPixmap scaled issue
  • Ticket #517: Undo menu item not working
  • Fix undo/redo in pipeline view
  • Fix issue with executions of untagged versions
  • Ticket #560: Workspace has very inefficient updates
  • Workspace: made loading mashups more efficient
  • Ticket #562: "Save as" replaces items from workspace
  • Ticket #560: Workspace has very inefficient updates
  • Partial fix to make workspace more efficient
  • Ticket #565: Version labels in query results are not gray
  • Fix colors in query results view
  • Ticket #504: The Query's refine option doesn't do anything
  • Reenable refined version tree in the query view
  • Ticket #532: Edit Package Abstraction Error
  • Fixed issue with error message for editing package subworkflows
  • Ticket #541: Crash when detaching ModuleInformation dockwidget on Mac
  • Fix crash on undocking module info palette on Mac OS X
  • Ticket #546: Selecting a version selects the text box instead of the version ellipse
  • Make version tree selection more intuitive
  • Ticket #538: Pipeline Connection Drawing?
  • Fix connection drawing issue on Mac
  • Ticket #558: Group signatures cannot be based only on interface
  • Fix issue with caching group modules
  • Fix initial layout of matplotlib cells
  • Decreased level of debug message when removing elements from Thumbnails cache
  • Ticket #534: Mashups hang with auto-update on
  • Ticket #550: Workspace state_changed is slow
  • Ticket #556: Path to zip.exe not set correctly
  • Fix logic in identifier checks in package manager
  • Ticket #554: Port labels not displayed
  • Add missing port labels to ports panel
  • Ticket #553: Suspended module does not execute on second run even when notcacheable
  • Ticket #549: update_db.py script does not work
  • Parameter Exploration only worked on parameters from the Basic Modules package
  • Autoloading a SUDS Web Service no longer produce error messages
  • Ticket #513: Add detachHistoryView back
  • Ticket #543: Changes to persistence module configuration doesn't work
  • Fix issue where reconfiguring persistent modules caused unexpected behavior.
  • Show error message when trying to open a vistrail with a newer schema version
  • db_log_filename was not unset correctly for db cache
  • Ticket #531: Export To Stable Version menu does not work
  • Export to DB did not work
  • Reloading a vistrail from the database gave it the name "None"

New in VisTrails 2.0 Beta 3 (Apr 5, 2012)

  • Enhancements:
  • Mashup View: Added float slider
  • New module execution state suspended added
  • Bug fixes:
  • Parameter Exploration: Changed call to update the progress bar to be thread safe
  • Fixed bug in iceCream.vt example
  • MySQLdb was not being shipped correctly in Mac binary
  • Mashup View: integer slider did not set step size correctly
  • Cached interpreter failed when handling wrong input type
  • Mashup View: failure when handling errors in execution that does not use the spreadsheet
  • Fixed qt.conf problem in installer script files on Windows.
  • Fixed arguments of get_wf_graph_png rpc call
  • updateUpstream* failed when modules did not contain the suspended attribute Mediawiki extension: fixed undefined variable
  • WorkflowExecution.completed were set to False in the vis_log, it should be an int.

New in VisTrails 2.0 Beta 2 (Mar 2, 2012)

  • Bug fixes:
  • Fix issue with deleting modules and connections
  • VTK package: fix problem when upgrading vtkCellArray.InsertNextCell input port The create analogy button is too small
  • "Show raw pipeline" and "construct from root" commands should switch to the pipeline view

New in VisTrails 2.0 Build b074d3a4eb44 Beta (Feb 24, 2012)

  • Enhancements:
  • Added VisTrails Server documentation
  • Add more functionality to core.api
  • Ticket #518: Need to fix VTK ports with no parameters
  • Add separate workflow and log xml schemas
  • Added support to hardcode necessary packages on startup
  • CLTools: Added environment variable and default directory support
  • Add operation ids to messages about illegal operations
  • Remove most PyQt4/gui dependencies in core functionality
  • Ticket #55: Spreadsheet should have more shortcut icons
  • Ticket #284: Capturing Module Errors (
  • Display module toolTip errors in module stack trace dialog
  • Wizard for CLTools - gui for wrapper creation
  • Added support for html and mediawiki extensions to
  • access a remote vistrails server
  • Bug fixes:
  • Mashups: editing an alias' values list had no effect
  • Mashups: slider and numericstepper widgets are only displayed for
  • numeric aliases
  • Mashups: Validating Min Max and Step edit boxes so they accept only
  • numbers
  • Accessing Module Annotate from context menu did not work
  • Fixed problem where unrequested vistrail temporary files were being created during test suite
  • Fix issue with alternate .vistrails directory and its subdirectories
  • Fixed MissingRequirement path and ubuntu detection
  • Ticket #528: Install bundle fails with the new core_no_gui changes
  • Rendering version and workflow view in server failed because of new gui in 2.0
  • save_many_to_db failed when list of objects were empty
  • Vistrail server need to initialize theme after core_no_gui changes
  • Fixed server mode after merge with core_no_gui
  • Ticket #522: remove_connection failure
  • Fix for remove_connection issues
  • Fixed issues with tabbing in the python editor
  • Fixed issue with vtkInteractionHandler which was not updated when the Save/Revert changes were made to source widgets
  • Allow zero-parameter functions to be set from ports panel
  • Fixed issue with forced versions on modules
  • Fix issue with merging thumbnails
  • Fixed typo in core.application's register_notification
  • Argument error caused gui/vistrail_controller test to fail
  • CHEBI wsdl changed
  • Removed matplotlib backend selection warning
  • Dragging a version directly on a spreadsheet cell was not executing
  • the workflow
  • Fixed unable to display jpeg images in the spreadsheet
  • due to a wrong Qt plugins configuration
  • Display more meaningful error when persistent inputs do not exist in a repository
  • Fix issue in ModuleDescriptor.expand_descriptor_string
  • Add icons to CLTools so that they not only work on X11
  • SourceConfigurationWidget silently fails when code contains
  • non-ascii characters (0c020878edf3)
  • MultiHeads configuration was not working on 2.0
  • Ticket #513: Add detachHistoryView back
  • Added back detachHistoryView option
  • Removed configuration options that are only used in non-interactive mode
  • from Expert Configuration
  • Ticket #515: opening a specific version from the command line does
  • not work
  • Fixed opening a specific version from the command line
  • Ticket #512: Add how to create alias to users guide
  • Ticket #421: db version import error handling
  • Detect between when a db version is missing and when it contains
  • an error
  • Ticket #391: Module colors in Visual Diff are wrong after upgrades
  • diff view did not use correct brush for non-upgraded modules
  • autosave feature caused "new file" action to fail
  • Ticket #511: "export workflow as xml" adds extension as "..xml" (two dots) if not explicitly specified get_save_file_locator_from_gui was adding two dots (
  • SpreadSheet: prompt the user to save unsaved vistrails before trying
  • to save a spreadsheet
  • Ubuntu Unity did not restore menu bar after being closed
  • Param Exploration User-defined function did not work because of new python
  • editor interface
  • Ticket #510: The Spreadsheet can't open/save spreadsheets
  • Ticket #194: Copy and paste duplicates aliases
  • Ticket #480: Executions button doesn't work
  • Ticket #500: Double-clicking the Execute button causes VisTrails to Hang
  • Double clicking execute button no longer hangs vistrails
  • Ticket #508: Add port documentation back to ports panel
  • Ticket #505: Version notes are not always visible after an upgrade
  • Issue correct version_selected signal after upgrades
  • Ticket #502: change_selected_version causes key error in adjacency_list
  • Ticket #472: parameters in parameter exploration are reset if not executed
  • Parameter exploration with Color Constant was not working
  • Ticket #462: Ungrab mouse error after editing subworkflow
  • Ticket #432: Problem with labeling groups
  • Allowing opening vistrail files that contain mashups. Mashups will be ignored
  • Ticket #454: Can't interact with TransferFunction widget using Qt 4.7.*
  • Fixed header placement in xml files that were causing tests to fail

New in VisTrails 1.7 Build 51517a6cdab6 (Jul 1, 2011)

  • Enhancements:
  • VisTrails is now distributed under the "Modified BSD License"
  • VisTrails binaries are now shipped with python 2.7.1, Qt 4.7.2, sip 4.12.2, PyQt4 4.8.4, vtk 5.6.1, numpy 1.5.1, scipy 0.9.0 and matplotlib 1.0.1.
  • Current alps package version: 2.0.2-r5630
  • Bug fixes:
  • Fixed header placement in xml files that were causing tests to fail (8d74d202ad51)
  • Ticket #454: Can't interact with TransferFunction widget using Qt 4.7. (6d0ed91891d2)
  • Allowing opening vistrail files that contain mashups. Mashups will be ignored (849121dd98d4)
  • Importing basic_modules.py leads to import loop (325bfe1b517d)
  • VTK Package: Fixed bug when drawing TransferFunction widget (7722fc6727aa)

New in VisTrails 1.7 Build c243c4044893 (Jun 28, 2011)

  • Enhancements:
  • VisTrails is now distributed under the "Modified BSD License"
  • VisTrails binaries are now shipped with python 2.7.1, Qt 4.7.2, sip 4.12.2, PyQt4 4.8.4, vtk 5.6.1, numpy 1.5.1, scipy 0.9.0 and matplotlib 1.0.1.
  • Bug fixes:
  • Importing basic_modules.py leads to import loop (325bfe1b517d)
  • VTK Package: Fixed bug when drawing TransferFunction widget (7722fc6727aa)

New in VisTrails 1.4.2.1736 (May 7, 2010)

  • Enhancements:
  • Package WebServices: Updated version to 0.9.3 (r1724)
  • Ticket #290: Reload packages without restating VisTrails (r1714)
  • Package reloading support should now be fully functional (r1714)
  • Enabling access to a Web package repository. (r1712)
  • Started adding support for Qt4.6.x (r1711)
  • Package vtlcreator: Exposing the function to create the contents
  • of a .vtl file as a static method, so it can be called from other
  • packages (r1709)
  • Added support for embedding workflows when using the Web extensions (r1709)
  • VisTrails Server: Added support for creating a .vt file for a given
  • vistrail/workflow on the DB so it can be embedded on a .vtl file (r1709)
  • New module, RepoSync, has been added to the HTTP package, which enables data files to be synced with an online repository (crowdLabs) (r1708)
  • Added basic online web repository (crowdLabs) user authentication dialog (r1707)
  • Added ability to upload VisTrail files to online web repository (crowdLabs) (r1707)
  • Improved package reloading support (r1703)
  • Added helper methods, get_inputPort_modules and get_outputPort_modules, to get modules that connect to a given input port or output port (r1701)
  • Added helper method, connections_to_module, that returns a list of all modules that connect into a given module (r1701)
  • Ticket #290: Reload packages without restating VisTrails (r1697)
  • Enable package reloading without the need to restart VisTrails. (r1697)
  • SQL package also connects to a PostgreSQL database server (r1696)
  • SQL package: added cacheResults parameter to SQLSource (r1696)
  • SQL package also handles connection timeouts (r1696)
  • Bug fixes:
  • Ticket #349: VisTrails does not ask to install missing requirements
  • via apt-get on Ubuntu (r1733)
  • Delaying the package check requirements to the beginning
  • of initialization. This is a workaround to go back to the
  • old behavior. (r1733)
  • Explicitly made the wrapped DisplayId object a null-terminated string to work with VTK Python Wrapping mechanism. This fixed the crashing of the VTKCell on VTK's trunk. (r1729)
  • Ticket #348: Sometimes VisTrails can't execute a workflow because
  • of some network configuration (r1726)
  • Handling exceptions when the machine ip address can't be obtained. (r1726)
  • Ticket #347: Web Services package fails with new package structure (r1724)
  • Package WebServices: Added support for packaging reloading.
  • If you see the error ('Error loading configuration file: ',
  • '~/.vistrails/webServices/modules.conf')
  • Just remove your ~/.vistrails/webServices and enable the package
  • again. (r1724)
  • Package WebServices: Added HTTP package to list of package
  • dependencies (r1724)
  • Differentiate between init.py not existing and init.py having ImportErrors (r1719)
  • Fixed bugs with exception handling when enabling packages (r1715)
  • Showing the VisTrails shell with no pipeline selected would throw an error (r1715)
  • Package menu items (on the toolbar) are now properly removed when the package is disabled (r1714)
  • Package lists can now be traversed with the keyboard (r1714)
  • Fixed bug that when enabling a package dynamically sometimes VisTrails
  • would say that it failed but if you just selected the version node again the
  • pipeline would be loaded without problems (r1711)
  • MAC and Qt4.6: VisTrails would fail to start when using MacBrushMetalStyle (r1711)
  • Mac and Qt4.6: There was not text anti-aliasing in modules and version
  • nodes (r1711)
  • Qt4.6: Moving a module in the pipeline view would not move the
  • connections attached to it (r1711)
  • Qt4.6: Legend Window in Visual Diff would not properly display the
  • colors (r1711)
  • Fixed a bug with opening .vtl files that embedded workflows (r1709)
  • Package vtlcreator: Fixed a bug that the version of the embedded
  • vistrail was not being set (r1709)
  • Fixed the Capitalization error in the VisTrails App Bundle name (r1709)
  • Properly track all modules in the hierarchy of a module loaded by a package for correct packing reloading (r1706)
  • Made reset query work immediately for the version search box (r1705)
  • Stop creating empty actions (r1704)
  • DBLocator: Removing object name from XML serialization.
  • This was causing inconsistencies with caching locators because we don't
  • know the name of the object before we load it (r1702)
  • Ticket #345: db connection edit bug (r1700)
  • DBLocator: Serializing also db connection user so current
  • permissions are not overriden by the cached version (r1700)
  • Ticket #344: Ungroup failing (r1699)
  • Ensure correct modules after ungrouping (r1699)
  • Ticket #342: Method responses return None in Web Services Package (r1698)
  • Complex types were ignoring the new 'self' input port when
  • unwrapping contents (r1698)
  • Ticket #341: On Ubuntu, VisTrails doesn't try to install MySQLdb (if not present) when accessing the database (r1695)
  • Move Vistrail import into load_vistrail method to avoid
  • circular imports. (r1694)