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VisTrails Changelog

What's new in VisTrails 2.2.4 Build 1519abc0ae2b

Nov 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 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
  • 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
  • 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 (Nov 12, 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 10, 2015)

  • BUG FIXES:
  • prevents introducing cycles in pipeline view (#1097)
  • Fixes OPM and PROV export (#1076) (#1075)
  • Fixes executable documents (#1088)
  • Fixed generating pipeline and version tree graphs
  • Fixes to subworkflows:
  • Fixes subworkflows failing to execute (#1065)
  • Fixes not being able to remove local subworkflows (#1101)
  • Fixes upgrading to a newer local subworkflow

New in VisTrails 2.2 Build 422e1a9bbc1c (Apr 23, 2015)

  • Enhancements:
  • zip/unzip binaries no longer needed (#862)
  • new version of tabledata package (also backported to v2.1.5)
  • new version of parallelflow package
  • adds developer debugger (enable "developerDebugger" in expert settings)
  • improves logging
  • reloading a disabled package (if you changed __init__; #714)
  • ungrouping materializes InputPort and OutputPort modules for unconnected Group ports
  • CLTools path and directory types
  • CLTools module fails if command doesn't return 0 (#957)
  • adds an icon for 'port not visible' (instead of blank)
  • sql package with SQLAlchemy
  • auto-enabling package with unmet dependencies (4a1b200b)
  • Enhancements to job submission/monitor
  • controlflow caches looped modules
  • menu to export a single spreadsheet cell
  • custom colors for version in tree
  • export version tree to graphviz dot graph
  • adds ReadFile module
  • HTTP package is now URL, validates HTTPS certificates, handles ssh://
  • fixes spreadsheet cells size resetting when resizing window
  • loads packages from pkg_resources entry points "vistrails.packages"
  • new persistent_archive package (#755)
  • new sklearn package for machine learning; http://scikit-learn.org/
  • highlight unset required ports in input ports list
  • new user API with IPython notebook integration (#24)
  • StandardOutput module can print a File's content
  • output module system: same module can output to spreadsheet, file, stdout, IPython, ...
  • output port drawn from left to right (#1006)
  • Warn when parameters have invalid values
  • New parameter widgets for editing parameters directly on modules
  • New list handling (deprecating the controlflow package): Switching views are now faster
  • New VTK package supporting up to VTK 6.2 (#998): Installers now contains VTK 6.2
  • No longer show upgrade actions in version tree (optional; #1046)
  • Associate with .vt and .vtl files on Linux
  • Added min_conns and max_conns attribute to ports
  • Bug fixes:
  • fixes strptime on system with non-English locale
  • fixes returning numpy arrays from PythonSource modules (3468998b)
  • pressing ctrl+s after loading a pipeline no longer replace it with a vistrail
  • fixed losing notes when clicking "execute" immediately from version view
  • Behavior change for package developers:
  • made Module methods python_style; updateUpstream won't work, others will work but trigger warning
  • don't use Module instances as data; pass new objects on connections
  • module upgrades can be chained (#805)
  • use output modules instead of cell/writer modules
  • output port drawn from left to right; change your sort_keys
  • constant widget use eventfilter; call installEventFilter for child widgets
  • Improved module/parameter/widget configuration APIs

New in VisTrails 2.1.5 Build 4fe986148829 (Mar 21, 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 2.0 Beta 2 (Mar 2, 2012)

  • Enhancements:
  • Added VisTrails Server documentation (611f2082f98d)
  • Add more functionality to core.api (26c775f0a7bb)
  • Ticket #518: Need to fix VTK ports with no parameters (9a985c40f6a2)
  • Add separate workflow and log xml schemas (04cb36cc5305)
  • Added support to hardcode necessary packages on startup (834e28f7cfa4)
  • CLTools: Added enviroment variable and default directory support (5a6e1b0daba3) (7c9a113040c2)
  • Add operation ids to messages about illegal operations (087b235e32de)
  • Remove most PyQt4/gui dependencies in core functionality (e6ada340cc15)
  • Ticket #55: Spreadsheet should have more shortcut icons (5f4db41dc8f2) (127037be178f)
  • Ticket #284: Capturing Module Errors (60c055eff8f5)
  • Display module toolTip errors in module stack trace dialog (60c055eff8f5)
  • Wizard for CLToolsgui for wrapper creation (a7a1db436fd0)
  • Added support for html and mediawiki extensions to
  • access a remote vistrails server (dd7456507ab4)
  • Bug fixes:
  • Mashups: editing an alias' values list had no effect (c485a7433dde)
  • Mashups: slider and numericstepper widgets are only displayed for
  • numeric aliases (c485a7433dde)
  • Mashups: Validating Min Max and Step edit boxes so they accept only
  • numbers (c485a7433dde)
  • Accessing Module Annotate from context menu did not work (ac100b566d84)
  • Fixed problem where unrequested vistrail temporary files were being created during test suite (445e2b68d9e6) (1a539cad8a9a)
  • Fix issue with alternate .vistrails directory and its subdirectories (7d26c36ef77a)
  • Fixed MissingRequirement path and ubuntu detection (11dd911b66a3)
  • Ticket #528: Install bundle fails with the new core_no_gui changes (87f9e83772ea)
  • Rendering version and workflow view in server failed because of new gui in 2.0 (e149aa955dd5)
  • save_many_to_db failed when list of objects were empty (ed257eb2d523)
  • Vistrail server need to initialize theme after core_no_gui changes (c4d2809d9a09)
  • Fixed server mode after merge with core_no_gui (4c2cad40c30f)
  • Ticket #522: remove_connection failure (cc038a500e3c)
  • Fix for remove_connection issues (cc038a500e3c)
  • Fixed issues with tabbing in the python editor (c046c86bf0af)
  • Fixed issue with vtkInteractionHandler which was not updated when the Save/Revert changes were made to source widgets (8abbfb8a51e9)
  • Allow zero-parameter functions to be set from ports panel (9a985c40f6a2)
  • Fixed issue with forced versions on modules (4ae602caa09e)
  • Fix issue with merging thumbnails (5bcaa7e75c6d)
  • Fixed typo in core.application's register_notification (42c7ae6b0e25)
  • Argument error caused gui/vistrail_controller test to fail (e447e02b37ca)
  • CHEBI wsdl changed (a7f1ab43159d) (6e00beb17ce6)
  • Removed matplotlib backend selection warning (23a6e3a89001)
  • Dragging a version directly on a spreadsheet cell was not executing
  • the workflow (3395a01a2139) (66d49a064e59)
  • Fixed unable to display jpeg images in the spreadsheet
  • due to a wrong Qt plugins configuration (a6a1950024a7) (333456765278)
  • Display more meaningful error when persistent inputs do not exist in a repository (1c905da96eb1)
  • Fix issue in ModuleDescriptor.expand_descriptor_string (7b973b4a4aeb) (35f1feb4d853)
  • Add icons to CLTools so that they not only work on X11 (a6a08bc1dd4e) (69110931c4e3)
  • SourceConfigurationWidget silently fails when code contains
  • non-ascii characters (0c020878edf3) (768fc8ed4df5)
  • MultiHeads configuration was not working on 2.0 (669957620bdc) (07e9672e6186)
  • Ticket #513: Add detachHistoryView back (f238870a17fe) (38a3b95d1b5d)
  • Added back detachHistoryView option (f238870a17fe) (38a3b95d1b5d)
  • Removed configuration options that are only used in non-interactive mode
  • from Expert Configuration (bb0046fe6f49)
  • Ticket #515: opening a specific version from the command line does
  • not work (20ab44a5a4ce) (468fe95d351f)
  • Fixed opening a specific version from the command line (20ab44a5a4ce) (468fe95d351f)
  • Ticket #512: Add how to create alias to users guide (83e49a3d487b)
  • (d56e02d30133) (a6249193e674) (f5b881191441)
  • Ticket #421: db version import error handling (a6eb8ae65052) (6ac6c0abec6e)
  • Detect between when a db version is missing and when it contains
  • an error (a6eb8ae65052) (6ac6c0abec6e)
  • Ticket #391: Module colors in Visual Diff are wrong after upgrades (6b16033351a9) (c28166f2110b)
  • diff view did not use correct brush for non-upgraded modules (6b16033351a9) (c28166f2110b)
  • autosave feature caused "new file" action to fail (9b19a0fc5193) (6c49e4329b8a)
  • Ticket #511: "export workflow as xml" adds extension as "..xml" (two dots) if
  • not explicitly specified (39d605e721e5) (fb2061eec506)
  • get_save_file_locator_from_gui was adding two dots (39d605e721e5) (fb2061eec506)
  • SpreadSheet: prompt the user to save unsaved vistrails before trying
  • to save a spreadsheet (d296dae6e508) (5e29113d0694)
  • Ubuntu Unity did not restore menu bar after being closed (3d702340c1fa) (719ad4dd22b5)
  • Param Exploration User-defined function did not work because of new python
  • editor interface (8354a9340944) (0f62ec4023c7)
  • Ticket #510: The Spreadsheet can't open/save spreadsheets (9259d3b8d619) (ae73b7e48971)
  • Ticket #194: Copy and paste duplicates aliases (7419092665c4) (27ee5e68a7e3)
  • Ticket #480: Executions button doesn't work (c6a9a6ac15cf)
  • Ticket #500: Double-clicking the Execute button causes VisTrails to Hang (e024a352c6ce)
  • Double clicking execute button no longer hangs vistrails (e024a352c6ce)
  • Ticket #508: Add port documentation back to ports panel (01f189a1a184)
  • Ticket #505: Version notes are not always visible after an upgrade (d16b3c834c47)
  • Issue correct version_selected signal after upgrades (d16b3c834c47)
  • Ticket #502: change_selected_version causes key error in adjacency_list (25104a599816)
  • Ticket #472: parameters in parameter exploration are reset if not executed (d07bcbd5104b)
  • Parameter exploration with Color Constant was not working (b0e0da8cc61b)
  • Ticket #462: Ungrab mouse error after editing subworkflow (2ffac0767f88)
  • Ticket #432: Problem with labeling groups (2ffac0767f88)
  • 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 1.2.1.1337 (Oct 24, 2008)

  • Changes:
  • Schema upgrade. Current version: 0.9.3. If you keep vt files in a database, you have to upgrade the database as well
  • VisTrails now requires Qt 4.4 or later to run
  • Adopted application single instance behavior (only one version of the VisTrails application can be executing).
  • Added Interactive expansion and collapsing in the version tree: the three lines on edges in the version tree that used to represent multiple versions has been replaced by a plus symbol. Clicking this symbol expands the link to show all the versions in between (though this may change to only a limited number later). A minus sign appears on the top of a list of untagged, non-branching, non-selected versions that will collapse that list.
  • Added descriptions to the version tree. They show up in place of a tag if one hasn't been set, but with a thinner italicized font. Double-clicking on the node allows it to be changed and turned into a tag. Showing a description for each action that is now displayed in the properties overlay. This description is still very simple (eg., Added module), though in the future it might make sense to save off more detailed descriptions for each action in the db (eg., Added vtkRenderer module)
  • Added new items to the View Menu to show and hide branches and nodes
  • Restored the "Clear Recent Searches" in the search box in the version properties
  • Added command line options to execute workflows and show only the spreadsheet when opening
  • Logging information is now stored in .vt file
  • Bug fixes:
  • Copying and Pasting dynamic modules, such as PythonSource threw an error
  • File version was not set correctly
  • Fixed a bug in analogies that sometimes corrupted vistrails files.
  • Fixed some bugs and annoying behavior with autosave. A dialog now prompts the user if they want to load autosaved data. This dialog appears when opening a file or starting up vistrails. Autosave data no longer is loaded when the user creates a new vistrail by pressing the new button.
  • Dragging versions to the spreadsheet is working again
  • Dragging a spreadsheet tab created a window that couldn't be closed or put back. A floating sheet can be docked back by simply closing it or dragging it back the spreadsheet tab bar (if exists) or just the window itself.
  • There was no obvious way to exit full screen mode in spreadsheet. The fullscreen mode can be closed either by: Pressing 'ESC', 'Ctrl-F', 'F11' or 'Alt-Enter'; Right click on the fullscreen mode and unselect 'Fullscreen'
  • Border color of selected cells in the spreadsheet is now consistent