[vistrails-dev] [GIT] VisTrails:

git-noreply at vistrails.org git-noreply at vistrails.org
Thu Jan 16 13:36:51 EST 2014


The project "VisTrails":

The annotated tag, v2.0.0 has been created
        at  54d307d1fb01a463718a601189fb06ceec7ab961 (tag)
   tagging  240bcab5bbcdb51758709ba8f8f4c016d9ba5df8 (commit)
 tagged by  Remi Rampin
        on  Thu Jan 16 13:35:55 2014 -0500

- Log -----------------------------------------------------------------
v2.0 release

Release Name: v2.0 build 240bcab5bbcd from v2.0 branch

Carlos Scheidegger (605):
      Moved vistrails repository to svn convention
      More moving around.
      Directory structure is now how we discussed.
      Another mass commit for which I won't bother to put decent messages. But VisTrails now runs. (type python vistrails.py from the trunk/vistrails directory)
      Removed stale packages directory.
      ModuleRegistry.sourcePortsFromDescriptor:
      resourceDirectory(): implemented
      Cosmetic changes.
      VisPipeline.buildAliasDictionary: fixed module reference.
      VisPort.makeSpec:
      QPipelineView.configureModule:
      QBuilder.addNewMethod:
      QVTKMethodScrollArea.addWidgets:
      imports core.data_structures
      VistrailController.executeWorkflow:
      Moved packages to correct directory.,
      Created a data_structures subdirectory in core, moved queue, graph, point and rect there. Created some unit tests for them.
      Moved function uniq from graph.py to common.py.
      Imports graph from core.data_structures.
      Uses fully qualified names for imports.
      moved resource files into resources directory.
      Uses fully qualified names for imports.
      moved resource files into resources directory.
      __rootDir: Computes the root directory automatically so that it's not necessary to have it in the config file anymore.
      Uses fully qualified names for imports.
      Uses fully qualified names for imports.
      Wrapped application-instancing code in "if __name__ == '__main__':" blocks
      Uses fully qualified names for imports.
      Uses fully qualified names for imports.
      Uses fully qualified names for imports.
      Removed vis_demo. run vistrails using vistrails.py instead.
      Uses new VisApplication interface.
      New file.
      Added .pyc to svn:ignore property
      __init__.py file for db/gui package.
      Script that runs the test suite for the entire VisTrails distribution.
      Expanded explanations.
      Defer initialization of Singleton to call to start_application()
      Removed stale logger import.
      Now imports all test cases, coalesces them into one big testing suite, and runs it. Also warns about modules without tests.
      Calls start_application() to initialize singleton.
      Hacked around circular dependency by inlining imports in function calls.
      Uses fully qualified names for imports.
      Updated test for current ModuleFunction layout.
      Updated test so it works from multiple directories.
      enum: Added __eq__ attribute to dynamically generated enums so that enums with the same name match, regardless of object identity. (test2 exercises this).
      getSettingsFromApp(self): Uses correct singleton from vis_application.
      Fixed test paths.
      Fixed test paths.
      dummy vistrail file for using in tests.
      Fixed test paths.
      Fixed test paths.
      Fixed test paths and vistrail paths.
      imports VistrailsInternalError
      Added bit about import *
      Fixed test paths.
      Fixed double importing bug by using correct module names.
      Fixes backslashes for windows portability.
      Respects coding conventions.
      Removed unnecessary file.
      Respects coding conventions.
      Renamed file to respect conventions.
      Added docstring, removed useless import.
      Added peps to local repository for convenience of access.
      Cosmetic changes.
      qt_version(): new function that returns the version of qt being used as a list of integers.
      start_application: now takes an optional dictionary with configuration
      Cosmetic changes.
      Tests core/system/__init__, but skips the individual files. Since core/system/__init__ will import the tests on the right architectures, this will make sure the test suite exercises the architecture-dependent tests on the right architectures but doesn't exercise the wrong ones.
      Fixed indentation problems so that it runs.
      uses fully qualified import names on link_or_copy.
      Renamed linkOrCopy to link_or_copy
      Added docstrings to module, classes and methods.
      Added docstrings to module, classes and methods.
      Added docstrings to module, classes and methods.
      Added docstrings to module, classes and methods.
      Changed defaultDotVistrails() documentation to reflect new usage.
      createBogusQtApp() uses QtCore instead of QtGui, in an effort to have test suite runnable on headless machines.
      execDotVistrails(): if a regular file named '.vistrails' exists, VisTrails tries to create a subdirectory named '.vistrails' instead and place old initialization file inside. The new initialization file is called startup.py.
      Fixed outstanding issues so that HTTP package is working and useful.
      Module.checkInputPort(): new method.
      ColorWheel: load static icons lazily on constructor.
      Some cosmetic changes to fit in 79 columns.
      execDotVistrails(): erases temporary file.
      Added Stack data structure.
      Added Stack data structure.
      Fixed bug where boolean parameter "False" would be evaluated as True.
      getDescriptorByName(): sends debug message when fails to find a module.
      ModuleError.__init__(): calls Exception constructor.
      tracemethod defines a method decorator trace_method that writes enter/exit information about methods to aid debugging.
      Adds tracemethod.
      Removed locks on setModule*() calls. (These did not solve the problem, and we're single-threaded for now anyway).
      VistrailController.sendToSpreadsheet(): executes things in the same thread.
      typeMap: uses module_registry hasModule method.
      Module.__ne__: removed unnecessary definition. (__ne__ automatically calls __eq__)
      QBuilder.changeTreeWidget: removed print.
      Added unit tests.
      Added one more test to suite.
      stop_application(): new function
      ImageViewerCell.compute() - Holds a link to the file to prevent temporary deletion.
      SVGCell.compute() - Holds a link to the file to prevent temporary deletion.
      finalize(): new function to cleanup the file pool.
      SpreadsheetWindow.__init__(): creates a file pool for temporary files.
      Calls stop_application() for cleanup./
      Removes unnecessary circular reference.
      Fixed typo core.common -> core.utils
      Imports ColorByName to unbreak vis_diff.py.
      removed unused file. (This caused the test suite to fail)
      Fixed type queryByExapmle -> queryByExample
      VistrailsApplicationSingleton.setupOptions:
      QInteractiveGraphicsView.selectModules:
      QVistrailView.__init__:
      Vistrails -> VisTrails typo.
      Fixes Ticket #14.
      Fixes Ticket #17.
      Fixes Ticket #17.
      CommandLineParserSingleton.positionalArguments: new method.
      Fixes ticket #19:
      QViewManager.currentView(): new method.
      Fixes ticket #5.
      Fixes ticket #15.
      Fixes ticket #8.
      Fixes ticket #4.
      Fixes ticket #25.
      Testing commit (ignore this).
      initialize():
      Updated to reflect GPL release, current year and current team.
      Fixed wrong year.
      Fixes ticket #29.
      Graph.inverse_immutable(): new method
      imports core.cache.hasher
      Worked around bad test cases. (not a fix: they will fail again in 2008)
      imports lock_method from lockmethod.py
      lockmethod.py: new file with lock_method decorator, a method decorator that automatically ensures a critical section is locked before entering the method, taking care of things like exception raising, etc.
      Moved Vistrail class to vistrail.py (this prevents it from being loaded when core.vistrail.* is imported)
      New file for Vistrail class.
      Connection.__init__(): Empty connection now has sensible port source and destination types.
      Removed import *.
      Package directory for caching-related things.
      Removed (everything important is now under the cache directory)
      imports necessary modules
      Refactored Interpreter.execute() into Interpreter.locked_execute and unlocked_execute.
      Removed import *.
      imports vistrail from core.vistrail.vistrail
      imports vistrail from core.vistrail.vistrail
      imports vistrail from core.vistrail.vistrail
      VistrailController.changeSelectedVersion: fixed typo in docstring.
      Mass commit that adds copyright and GPL notice header to VisTrails files.
      XMLParser.XMLParseError : new exception class to signal parsing errors in the XML handling.
      QViewManager.openVistrail(): catches XMLParser.XMLParseError and reports to user.
      Big commit: moving everything to Unix line breaks.
      Fixes ticket #34.
      Fixes ticket #34.
      xml file that's broken on purpose for use in test suite.
      no_interrupt(): new function.
      initialize(): uses core.utils.no_interrupt to try and work around race condition on OSX.
      AIRHeaderFile.get_header_annotations:
      Added missing import to fix trunk breakage.
      Hasher.connection_subpipeline_signature(): new static method.
      imports Bidict from bijectivedict.py
      new module.
      File.compute(): checks presence of input port.
      FilePool: documentation.
      ModuleError: documentation
      Added copyright notice
      aboutString(): updated to reflect open source release.
      Reflects renaming of camelcase methods to underscore-separated ones, to follow the convention.
      Pipeline.__init__: uses bijective dicts for the signature dictionaries.
      Interpreter.CachedInterpreter: new class.
      QGraphicsPortItem.mouseReleaseEvent: reflects renaming of fresh_connection_id
      createBogusQtApp: holds application instance in local variable
      DefaultTheme.__init__: Fix typo NOT_EXECUTE_MODULE_BRUSH -> NOT_EXECUTED_MODULE_BRUSH
      QViewManager.removeVistrailView: calls cleanup() on controller.
      VistrailController.__init__: stores cached interpreter (for now)
      Convert.create_output_file(): reflects renaming of create_file.
      Afront.compute(): reflects renaming of create_file.
      ImageToFile.createOutputFile(): reflects renaming of create_file.
      AlignWarp.compute(): reflects renaming of create_file.
      Added more info to module docstring.
      HTTPFile.parse_url(): reimplemented parsing of url. (previous one was wrong.)
      Runs unit tests on packages.
      New example file that uses HTTPFile and Unzip for visualizing data that lives on the web.
      File: new outputPort local_filename
      Bidict.__delitem__: resilience under nonbijectiveness
      Graph.deleteVertex(): Remove edges from other adjacency lists.
      Constant.__str__(): Changed behavior so that it's easier to debug (more consistent).
      ModuleDescriptor.__init__(): Now allows class whose "real" subclass is not the first in __bases__
      NotCacheable: new class
      NotCacheable: moved to vistrails_module.
      Module: change in documentation to reflect mixin usage
      InvalidModuleClass: new exception.
      Vistrail.deleteModule: deletes appropriate signatures from dictionary
      Uses default interpreter instead of uncached one.
      Moved interpreter to own package.
      New package directory.
      VistrailsApplicationSingleton.finishSession(): cleans up the cached interpreter.
      Cosmetic changes.
      Uses default interpreter instead of hardcoding the cached one.
      HTTPFile.compute: Some resilience against network downtime. If network is down but file is in local cache, proceeds anyway.
      Matrix.__str__(): deleted so that __str__ is more consistent.
      SpreadsheetCell: uses NotCacheable mixin to avoid caching.
      StandardWidgetTabController.openSpreadsheet: uses default interpreter instead of hard-coded non-cached one.
      vtkBaseModule.is_cacheable: new method, returns true if class subclasses from vtkAlgorithm.
      WebService.__str__(): removed method for more consistency.
      Utilities for debugging memory leaks.
      Added license header.
      Graph.dfs: reduce memory footprint by getting rid of unnecessary references.
      Added license header.
      Added license header.
      CachedInterpreter.clear(): new method.
      FilePool.__del__: removed method (interacts badly with GC)
      Module.clear(): new method
      Pipeline.clear(): new method.
      QBuilderWindow.createActions: new actions: executeCurrentWorkflowAction and flushCacheAction.
      QViewManager.removeVistrailView: calls deleteLater on view.
      Packages can now exist under ~/.vistrails/userpackages as well (ie. outside the trunk)
      Checks whether userpackages directory is present (more fixes on the way, this just prevents breakage).
      CachedInterpreter.sub_execute(): new method that executes things without erasing subpipelines. Should interact better with the abstraction mechanism.
      Module.clear(): remove useless print statement.
      AfterSearchStmt.match(): remove useless print statement.
      Vistrail.__init__(): change self.latestTime to valid number
      Vistrails.installPackages(): keeps directories in path only as long as necessary.
      iterate(): new function
      CachedInterpreter.create(): new method that performs initialization
      QBuilderWindow.flush_cache(): calls flush() instead of cleanup().
      runs tests from initialization files of subdirectories (all the __init__.py files)
      report_stack(): new decorator.
      imports report_stack decorator.
      Calls cleanup on filepool instead of just removing the reference.
      PipelineInspector.inspect(): checks for Spreadsheet package presence before getting descriptor - now works if we run VisTrails without the spreadsheet.
      Hasher.function_signature():
      Added Test to exercise wrong cache signature computation.
      cleanup(): new function
      New file with new classes PackageManager and Package.
      New file with function python_module_exists() and exception MissingRequirement().
      Added test that exercises tuple bug.
      Exposed shorthand_* functions to easily create modules for testing. (removed from test case, added to module)
      GraphContainsCycles(): new exception inside Graph
      InternalTuple: new class that represents a tuple of constant values for fast creation and access, and to avoid local registry problems with new fancy tuple.
      CachedInterpreter.unlocked_execute(): uses InternalTuple for constant values.
      Added tetra mesh contour pipeline.
      VistrailsApplicationSingleton.__init__(): Calls superclass constructor.
      Fix small typo in comment.
      package_dependencies(): new method to expose package dependencies. Signals a spreadsheet dependency if spreadsheet is present.
      Package for console_mode test suite.
      Initializes VisTrails before loading tests and finalizes it after running them.
      Testing module resiliency against bogus addresses.
      initialize():
      executable_file_exists(): new function.
      file with functions common to UNIX systems (osx and linux)
      imports executable_is_in_path from core.system.unix.
      new function executable_is_in_path (unimplemented on windows!)
      Closes ticket #51. Installs userpackages directory and correctly puts initialization file in the directory.
      Added scripts directory, populating it with a script to generate the .deb ubuntu package for VisTrails.
      imports Qt from PyQt4
      Preliminary support for automatic package installation.
      Uses smart py_import from core.bundles to automatically install necessary requirements.
      Refactoring installing functionality into separate module so it can be used by itself.
      Installs imagemagick from ubuntu packages if necessary.
      Refactoring bundles code.
      Uses bundle support to automatically install VTK when necessary.
      Moved things from scripts to dist/ubuntu, where they belogn.
      require_python_module: new function.
      installs ctypes if necessary.
      calls check_all_vistrails_requirements before trying to import things.
      Removed buggy dictionary setitem.
      ModuleRegistry.__init__:
      QGraphicsModuleItem.__init__: new field _module_shape
      Test of new python source features.
      Exercises new python source features.
      PythonSource.compute():
      ChangeParameterAction.addParameter: add assertions for types.
      fixes ticket #75.
      Fixed typo inspectAmbigiousPipeline -> inspectAmbiguousPipeline.
      QUserFunctionEditor.getValues(): Returns 'ERROR' instead of throwing exception when user-defined function fails.
      Cosmetic changes (removed unused __fields__)
      Fixes ticket #77:
      LinearInterpolator: new class
      Fixes for move from scripts to dist/ubuntu, and new revision number.
      Cosmetic changes.
      report_stack: tries to print function before reporting stack trace.
      Slightly reduced space around ports, should look a little better now.
      TestGraph.test3(): fixed bug in sourceResult.
      ModuleRegistry.addModule: support for specifying a custom leftFringe and rightFringe.
      QGraphicsModuleItem.setupModule(): uses pair of fringes instead of single one.
      New MeshQualityHistogram module
      examples with afront, matplotlib, vtk, histograms, etc.
      One more iteration over custom shape API, hopefully this one will stick.
      Bookmark.__ne__: missing method added
      Bookmark.__ne__: missing method added
      AfrontIso: new Module.
      Added the ability to run tests from individual files.
      __ne__: missing method added in enums
      imports data structures from the right place to avoid a circular dependency in the library.
      Module.__init__: defaults self.cache to 1
      Moved the logger out of vistrail_controller, console_mode, bookmarks,
      Closes ticket #84.
      Partial checkin of automatic abstraction creation. I'll resume work on
      QVerticalWidget.__init__: self._functions: new field
      XMLParser.translate0_3_0to0_3_1: new method
      core/startup.py:
      Cosmetic changes, moving code around.
      core/vistrail/action.py:
      vistrails/core/system/__init__.py:
      core/packagemanager.py:
      Updated ubuntu dist generator to newest version, now includes examples and data.
      core/interpreter/cached.py:
      Fixes ticket #89.
      packages/vtk/__init__.py:
      core/data_structures/graph.py:
      core/cache/cachemanager.py: Removed file
      core/console_mode.py:
      packages/vtk/__init__.py:
      packages/spreadsheet/spreadsheet_sheet.py:
      core.analogy: new package
      Added unit tests.
      Added correct copying and updating behavior.
      Added more unit tests.
      Point.__eq__ now tests up to a certain delta. Cosmetic changes, unit tests.
      File.compute(): tests for file presence
      ModuleDescriptor.__copy__(): new method
      Module.compute(): catch keyboard interrupt exception, and other unhandled exceptions as well.
      list2cmdline: checks types.
      list2cmdline: checks types.
      InstanceObject.__str__: new method.
      Many changes for analogy, including:
      Cosmetic changes.
      Module.__copy__: copies the registry, instead of sharing it.
      Cosmetic changes, debugging methods (show_comparison).
      Cosmetic changes, debugging methods (show_comparison).
      Added __eq__ and __ne__ operators, debugging methods.
      Added __eq__ and __ne__ operators, __copy__, debugging methods.
      Vistrail.make_actions_from_diff(): new method
      File that stores configuration objects.
      analogy icon for diff window.
      Uses core.configuration
      setModelData: fix bug where moduleId would not be set.
      QShell.__init__: gets font info from core.configuration.
      Add create analogy icon to deafult theme.
      QVersionView.dropEvent(): passes controller as well to QVisualDiff
      QVisualDiff.__init__():
      VistrailController.__init__(): stores analogy dictionary
      HTTPFile port "local_filename" is now optional.
      Passes string parameters to list2cmdline. (bugfix)
      Hooks up to core.analogy
      removed print.
      Test case for caching.
      Removed useless methods, added object_at() method.
      Uses core.configuration.
      Conversion to 0.4.0 (not ready yet)
      Removed references to mydefs. (This is still rough around the edges, but should be demoable)
      Dialogs package.
      Change the palette only on OSX.
      core/analogy/eigen.py:
      gui/pe_tab.py
      Closes ticket #94.
      new file to check information on bundles.
      Install PyQt4 if not present, install dot if not present.
      First pass at a system querying script.
      core/bundles/installbundle.py:
      gui/builder_window.py:
      gui/theme.py:
      gui/pe_table.py:
      Reorg to support abstract modules (soon)
      Added many name filters to disallow strange modules, ports and parameters.
      This checkin closes ticket #16 (abstract modules)
      This closes ticket #59.
      gui/pipeline_view.py:
      core/utils/uxml.py
      --
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      packages/spreadsheet/__init__.py:
      --
      gui/module_palette.py:
      gui/preferences.py:
      vistrails.py:
      Reorder initialization a little to get a qapplication before checking for other requirements.
      --
      core/bundles/installbundle.py
      vistrails.py:
      core/modules/module_registry.py:
      core/startup.py:
      QPackagesWidget.enable_current_package: wrap setUpdatesEnable on a try...finally so that it always sets it back, even when enable_package throws.
      gui/pipeline_tab.py:
      gui/qt.py:
      core/modules/module_registry.py:
      core/console_mode.py:
      Added new pythonsource pipeline for tests.
      --
      core/console_mode.py:
      --
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      core/packagemanager.py:
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      gui/version_view.py:
      gui/qt.py:
      core/console_mode.py
      core/system/__init__.py:
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      gui/query_tab.py:
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      createModule(): uses VTK's docstrings as documentation for package. We then get automatic documentation for all VTK modules.
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      Changed files that use volumeproperty to reflect VTK package's new overloading resolution.
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      core/modules/module_registry.py:
      This fixes a bug where any method with more than two parameters that is added
      This tries to reduce a little the amount of garbage generated by python, by replacing range() by xrange() and zip() by itertools.izip(). It's just a global search-and-replace on all these files.
      --
      core/vistrail/pipeline.py
      Removed .pyc files from rep.
      Removed .pyc files from rep.
      core/modules/module_configure.py:
      --
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      QVisualDiff.moduleSelected: fix typo
      gui/view_manager.py
      --
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      gui/pipeline_view.py:
      --
      Repository directory for outside packages, by popular request.
      My packages, currently on different levels of support, from  working to brokenness. Checking them in so I can keep track of dev on svn.
      --
      core/modules/vistrails_module.py:
      gui/method_dropbox.py
      core/query/version.py: replace .message with .args[0] to accomodate Python 2.4 and Python 2.5
      --
      packages/spreadsheet/spreadsheet_config.py: new file with configuration object
      packages/vtk/__init__.py: new module VTKRenderOffscreen to perform offscreen rendering more conveniently, like our offscreen.vt example.
      core/modules/basic_modules.py:
      gui/method_dropbox.py:
      --
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      Moving packages to the right place.
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      core/utils/__init__.py: moved imports inside of profile to workaround binary mac installs that lack the profile module.
      Removing .pycs.
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      db/services/action_chain.py:
      --
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      script to unzip a vistrail .vt to a directory, getting a pretty printed xml file
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      Enabled use of scalartree by wrapping a cusom compute method
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      Fixing typo.
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      Adding package.
      core/analogy/__init__.py:
      core/modules/basic_modules.py:
      gui/pipeline_view.py:
      gui/version_tab.py:
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      core/modules/module_registry.py:
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      Setting eolstyle to native on all pythno files.
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      scripts to help converting file paths
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      Added basic support for package management on Fedora Core through YUM. So now we can pull off the same tricks we do on Ubuntu, where we automatically install the dependencies when necessary. This is still not as good as it could be, but it does the job. One of the problems is that the user has to be in the sudoers group, which is not the default Fedora way of handling administrative tasks.
      setting svn:eol-style to native
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      Script to fix paths so that test suite can be run on macs
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      Missed file from previous commit
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      added missing file to tests/resources
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      examples for teem package
      Added UnuSlice
      Added CombineRGBA class, configuration object, and fixed GaussianBlur bug
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      Removes conditional expression constructs, so that code runs on
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      new script that uses pysvn to autogenerate release notes. not ready yet.
      <ticket>#262</ticket>
      functionality to search for ticket closes and bugfixes there
      <ticket>#274</ticket>
      --
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      moved vtksnl package, fixed issue with it running in ubuntu or fedora
      moved WebInterface to extensions subdirectory
      first shot at source tree documentation
      since vistrails/doc had documentation about more than just the main vistrails app, I am moving it to toplevel. It also makes it more visible.
      <ticket>#351</ticket>
      <feature>EXPERIMENTAL: Packages can handle workflow upgrade
      <ticket>#358</ticket>
      --
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails

Charles Doutriaux (7):
      removed Huy's path from sources
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      tweaks to the configure to pick up locations automagically
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      ok now got it to come up under Linux, need to try under Mac...

Claudio Silva (2):
      - updated version to 0.4
      removed Utah copyright, since it really belongs to Prabhu

Claudio T. Silva (1):
      Just testing to make sure I can commit to the repository.

Claurissa (72):
      Progress on Conversion of documentation.
      mostly converted except for packages.rst and controlflow.rst
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      Initial conversion is complete.
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      Updated Version
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      Packages section done, persistence has been started
      small mistake
      Persistence and Control Flow Assistant Documentation added
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      Updated SUDS Web Service documentation and added Latex documentation
      Merge documentation added.  Latex documentation updated, but still needs some work.
      Latex documentation finally finished
      added optional port documentation
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      added documentation for the -S option
      Minor changes to documentation layout
      update
      update
      update
      added groups functionality to 2.0
      Initial 2.0 documentation changes up through Creating and Modifying Workflows
      more documentation files
      updated figures
      Merge branch 'v2.0' of vistrails.sci.utah.edu:vistrails into v2.0
      Merge branch 'v2.0' of vistrails.sci.utah.edu:vistrails into v2.0
      Merge branch 'v2.0' of vistrails.sci.utah.edu:vistrails into v2.0
      added subworkflow documentation
      Merge branch 'v2.0' of vistrails.sci.utah.edu:vistrails into v2.0
      more 2.0 updates
      Merge branch 'v2.0' of vistrails.sci.utah.edu:vistrails into v2.0
      updated image
      analogies mostly work.  They just have the same problem that we have with copying spreadsheet cells.  The example in the documentation works (using vtk_http.vt), except you need to press execute after it creates the new pipeline.
      Added images to controlflow assistant documentation and cleaned up the controlflow documentation.
      Updated groups documentation because ungrouping functionality was changed.
      Merge branch 'v2.0' of vistrails.sci.utah.edu:vistrails into v2.0
      Merge branch 'v2.0' of vgc.poly.edu:vistrails into v2.0
      Merge branch 'v2.0' of vgc.poly.edu:vistrails into v2.0
      Added Builder Window Documentation to the getting started section.
      added missing figure
      Minor edits and image updates.
      Minor updates up through the end of the Users Guide.
      Merge branch 'v2.0' of vgc.poly.edu:vistrails into v2.0
      Merge branch 'v2.0' of vgc.poly.edu:vistrails into v2.0
      Merge branch 'v2.0' of vgc.poly.edu:vistrails into v2.0
      Merge branch 'v2.0' of vgc.poly.edu:vistrails into v2.0
      Merge branch 'v2.0' of vgc.poly.edu:vistrails into v2.0
      Initial Mashups draft is created
      Updated the vtk.vt example to include cell location.
      fixed the typo in controller.py that was throwing an error when saving subworkflows. Updated the analogies documentation now that we have the visual diff functionality added.
      minor updates to querying
      Merge branch 'v2.0' of vgc.poly.edu:vistrails into v2.0
      Added provenance browser and Global Variable documentation.
      Moved groups to the vistrail view.  The pipeline now displays in a new tab.
      Tabs opened by show pipeline are now read only and the documentation is updated.
      Added documentation for vtkInstance
      Updated examples.  Cameras are still a bit off.
      Fixed broken example
      fixed some examples that didn't work properly.
      Merge branch 'v2.0' of vgc.poly.edu:vistrails into v2.0
      Added documentation for VTKmodules introduced by VisTrails (vtkInteractionHandler).
      Merge branch 'v2.0' of vgc.poly.edu:vistrails into v2.0
      Added documentation of minor features such as camera interaction, upgrade behaviors, and more details on the vtkInstance when the Interaction Handler is explained.
      query documentation is updated with new changes, but there are still some uncertainties like whether or not refine works and/or needs updated.
      Merge branch 'v2.0' of vgc.poly.edu:vistrails into v2.0
      Revert erroneous commit on Medical3.vt
      final touches on the query documentation
      Updated image for pin button
      I made some adjustments to image sizes and references.  Some image references used to be multiple sentences, but I shortened quite a few of them so there would be less interruption in the text.
      Updated image for pin button
      I made some adjustments to image sizes and references.  Some image references used to be multiple sentences, but I shortened quite a few of them so there would be less interruption in the text.

Clifton Brooks (10):
      Added a WebInterface directory which stores all file and folder necessary for the VisTrails web application.
      Added an initial version of the Vistrail Viewer.
      Finished the first version of a web application that views vistrails.
      Fixed layout issues.
      As of now, a web page that lists the available vistrails is integrated with the vistrail viewer and the workflow editor applications.
      workflows can now be executed from the workflow editor.
      Updated jQuery library from 2.6 to 3.2
      Added files needed for Vistrail and Workflow widgets.
      Finished the first version of the workflow viewer widget.  Now, as vistrails, workflows can be embedded in any web page on the internet using simple html tag syntax demonstrated in this example:
      Created simplified drawing functions for workflows and vistrails so that while the user zooms and pans, the graphs get drawn as white boxes without links.

Colin Talbert (4):
      Added two external widgets for running the Parc Module and selecting a subset of Predictors layers.  I will need to make some changes to the init module before these new widgets are implemented.  Plus my first commit with Git!
      I replaced a previous Java based version of this tool with python.
      This is the current version of the SAHM modules
      Current Version of SAHM VisTrails module.

Daniel Rees (28):
      Fixed a minor bug in XMLObject::getName().  Unbound method call was missing a 'self' reference.
      Summary:
      Summary:
      Summary:
      Added script that generates nightly source release to dist/source.
      trunk/packages/vtksnl/__init__.py
      /trunk/packages/vtksnl/__init__.py
      <bugfix>Properly track all modules in the hierarchy of a module loaded by a package for correct packing reloading</bugfix>
      This is a partial commit.  The gui changes will be committed by Emanuele.
      - Made the vtksnl package reloadable
      -Fixed the check that verified the removal of developer names (it was relying on the difference in revision number to be the same as the number of replacements, but since the CHANGELIST only includes revisions to trunk, this was incorrect)
      Added persistence for one parameter exploration per workflow.
      Changed revision var to the git equivalent of svn revision 1863
      Updated automated nightly build script to work with git instead of subversion.
      Corrected error in daily changes check in nightly build script.
      Fixed method of retrieving current revision hash in nightly build script.
      Added the ability to upgrade Subworkflow modules to the latest version in the module registry.
      Updated nightly build script to allow specification of the number of upload attempts to make (in case of an upload failure).
      Added automatic upgrades for Subworkflows (for when version changes occur in packages used by the Subworkflow).
      Fixed automatic upgrades to not crash on a missing package version, and to try to use the most recent subworkflow available as a "best effort" fix in that case.
      Added upgrade handling for 'My SubWorkflows' and outdated Package subworkflows along with namespace changes required to support these upgrades.
      Fixed 'My SubWorkflows' upgrades to be immediate even if delay is set.
      Several fixes to abstraction upgrades.
      Several fixes for upgraded package subworkflows.
      <ticket>#399</ticket>
      Added the Control Flow Assistant.
      Fixed the extra execution problem in the Control Flow Assistant.
      Added Vistrail Variables support, so that modules deriving from Constant can be used to create re-usable variables in multiple workflows within a vistrail.

David Koop (457):
      vistrails/core/vistrail/pipeline.py
      Removed action at time 370 which was invalid
      Updated provenance package for the second provenance challenge.  Because AIR uses (.hdr, .img) file pairs, FileSet and FileSetSink modules have been added to the original provenance package and module input/outputs updated.  The original provenance package remains available.
      * initial commit of the db code
      core/vistrail/action.py:
      core/analogy/__init__.py:
      tests/runtestsuite.py:
      * added new test file that adheres to new schema
      core/vistrail/vistrail.py:
      core/vistrail/vistrail.py:
      core/requirements.py:
      db/bin/auto_gen.py:
      core/analogy/__init__.py:
      packages/HTTP/__init__.py:
      db/services/action.py:
      db/services/vistrail.py:
      db/versions/v0_5_0/translate/v0_3_1.py:
      core/modules/module_configure.py:
      db/versions/v0_5_0/translate/v0_3_1.py:
      db/versions/v0_5_0/translate/v0_3_1.py:
      core/vistrail/module.py:
      core/vistrail/module.py:
      db/services/vistrail.py:
      core/console_mode.py:
      db/versions/v0_6_0/translate/v0_5_0.py:
      gui/vis_diff.py:
      db/versions/persistence/xml/auto_gen.py:
      core/analogy/__init__.py:
      db/versions/v0_6_0/translate/v0_5_0.py:
      core/vistrail/action.py:
      db/services/locator.py:
      gui/pe_table.py:
      gui/pe_table.py:
      Fixes for Bug 158.  Moved the registry manipulation code to the Module
      core/analogy/pipeline_utils.py:
      Fixes Ticket #164
      gui/vistrail_controller.py:
      Fixes Ticket #173
      Fixed bug in pipeline view where modules downstream of an error were
      Fixes bug where "Create Version" in the spreadsheet doesn't assign ids
      Fix for Ticket #180
      Further fixes for Ticket #180
      Fixes annoying bug where Cancel is the default button in the DB dialogs.
      db/tests/setup_db_tables.py:
      core/db/locator.py:
      Trying to fix bug on the corie.xml example
      This revision adds and revises a fair amount of stuff including:
      * Fixes the copy/paste bug with abstractions.
      * Fixes Tuple bug (Trac #183)
      Order all children of a given node in the version tree according to
      core/dotty.py:
      * Fixed write_vistrail to output pipelines with abstractions to support
      * Fixed bug where assignments with annotations wouldn't translate correctly
      * Fixes to give a better warning when a vistrail cannot be loaded
      core/db/action.py:
      gui/vistrail_controller.py:
      These fixes add namespace I/O support.  Note that they do not modify
      Switched boolean widget to use a checkbox instead of a dropdown.
      Fix to speed up database updates.
      core/vistrail/abstraction_module.py:
      Added new feature since I'm sick of bitmap captures of version trees
      Minor bug fix for the PDF feature.
      Attempted fix for bug with abstractions and namespaces.  The sigstring
      Fixed bug with abstraction module namespaces.
      Attempt to get rid of the __building_app__ flag.  We just check for
      gui/vistrail_controller.py:
      vistrails/packages/vtk/__init__.py:
      Updates the examples to access data from HTTPFile rather than a
      Code to add group/ungroup funcitonality.  This hasn't been well-tested
      Get rid of extra file.
      Added imports of Annotation and ModuleFunction to group.py.  This
      Fixes bug #203.
      Fixes Ticket #204.  This bug seems to have been introduced when we
      gui/pipeline_view.py:
      Fixes tickets #189 and #208.  Calling updatePipeline explicitly when
      Fixed group table name and also made sure that groups will save on a
      Not sure what happened to make these changes necessary, and I hope
      Updates the data layer to change the "notes" annotation to "__notes__"
      Fix for bug #226 on both the v1.2 branch and the trunk.  Error
      Fixes a bug Geoff found where the file version is not set correctly.
      Updates to support logging in vt files.  This is done by adding a
      Forgot to add the all.xml specs file.
      Updates schema and core to support plugin-specific data.
      Fixes Ticket #217.  This error was caused by optimizations in the
      Adding a script to merge two or more vistrails into a single vistrail.
      Added a new translate mechanism for the versions.  Basically, we
      Added an "Analogy" description to analogy actions.  Also added
      Removed print statements from logging code
      Added preliminary support for abstractions.  They should work locally
      Adding missing abstractions_init file.  This may be better to live in
      Add support for copy/paste/group/ungroup with relative locations.  A
      Fix logging after abstractions commit broke it.  Specifically, don't
      Fixed bug that caused "Save Workflow" to crash.
      This revision introduces a major reorg of the registry and related
      This revision adds support for "registry quickstart" which allows
      Fix PortTable combo box so that we use descriptors and not the
      Fix diff and analogy layout so that they look a bit better.
      Add support for importing workflows that have been saved as xml.  Note
      Changed a few things related to locators and fixed a bug with saving
      Made some changes that ought to further improve batch processing of
      Added new script that will update binary versions of VisTrails on the
      Added translate* methods for versions 0.9.3 and up, and updated code
      ** Note that this is work in progress.  Specifically, older database
      This revision fixes a bug where vistrails (<= v0.9.4) with groups
      Fix a bug with disabling packages.
      Fixed some db stuff related to groups and null locations.  Note that
      Added test for VistrailController.update_functions and fixed a bug in it.
      Fixes a bug with namespaces.  Also adds some new registry functionality.
      Also link vistrails.py to the svn version when updating a binary.
      More registry updates along with improved abstraction interaction.
      A few bug fixes and enhancements related to grouping and subworkflows.
      Make "Convert to SubWorkflow" work correctly and change "abstraction"
      Fixes a bug where vistrails that have incorrect port specs won't load
      Fixes to subworkflows so that nested subworkflows work correctly.
      Fixes a nasty bug with Tuples.  The ports need to be sorted, otherwise
      More permanent fix for the tuple port ordering problem.  Specifically,
      Fix a bug with packages that have namespaces with colons.
      Fixes for code that breaks on old vistrails.  Specifically, added a
      Fixed a few things with the registry.  Notably, allow registry error
      Fixed some stuff with vt files, temporary directories, and save as
      Fixes a	bug where the configuration wouldn't be	setup properly for a
      Fixed bugs with painting modules for debugging and querying.
      Added support for adding subworkflows to packages.  This includes an
      Fixed a bug with the painting of the borders of modules.  I was
      Removed module types from the theme.  Just use self.module.is_*()
      Fix the debugger so that we don't mask errors that crop up and so that
      Use a random signature for input ports so that groups inside of groups
      Fixes Ticket #241.  Problem was that we failed to match, but we don't
      Added a function to change parameters from the api along with a
      Added a *hack* so that aliases can be updated.  This will be
      Added code to allow easier programmatic change of parmaeters.
      Fixing a typo that's been there since rev 797...
      Added pc3 package for the Third Provenance Challenge.  Also includes
      Fix a bug encountered when updating PythonSource or MplPlot.  Check if
      Updated PC3 workflows to include histograms as discussed on the PC3
      Fixes Ticket #245.  gui/vistrail_controller.py was not passing old_id
      Fixes Ticket #247.  ModuleFunction real_id versus id issue.  id is
      Fixes Ticket #242.  Problem was that a group was not checking to see
      Addresses Ticket #246.  We add a display of output ports to all
      A bunch of updates added to improve control flow modules & execution
      Add scripts for converting VisTrails OPM to dot format.  Tries to
      Add the xml files used by db/services/opm.py to generate
      Fixes a bug that Fernando found.  A string is iterable, but we don't
      Should fix a few more bugs that Fernando discovered with my updates to
      Updates to the workflow logs and OPM output.  There are now two runs:
      More OPM updates.  Most focus on capturing hidden dependencies (like
      Fix a bug where loading vistrails that have groups with ports that
      Resolves Ticket #98.  We can override the "value_as_string" port on
      Fixes Ticket #219.  Need to align QSizeGrip on the right.
      Fix the annoying Mac behavior that Ctrl+W (Cmd+W on Mac) in the diff
      Change the File menu around so that all the import/export stuff is
      Fix for Ticket #228.  Pass along an iterable of versions to check when
      Fixed terminator AddPoint functions to AddPoint_1 functions.  Also
      Fix for Ticket #254.  We need to catch old package versions (esp. for
      Change OPM to use standard headers to pass validation.
      An example of loading a vistrail from a relational db and outputing it
      Fix bugs in save_to_db code in old versions.
      Fixes for Ticket #258.  We need to copy is_new and is_dirty flags
      <ticket>#260</ticket>
      <ticket>#266</ticket>
      <ticket>#268</ticket>
      <bugfix>Translate workflow_execs from previous versions correctly.
      <ticket>#270</ticket>
      <bugfix>VTKCell ModuleErrors were not constructed correctly; changed to pass the module first, then the error message.</bugfix>
      <feature>Enable more intuitive command-line interactions with
      Fixes a bug that shouldn't currently be exposed to an end-user.
      <ticket>#279</ticket>
      <ticket>#283</ticket>
      <ticket>#286</ticket>
      <ticket>#286</ticket>
      Moves the controlflow package from packages to vistrails/packages.
      <ticket>#297</ticket>
      <ticket>#300</ticket>
      <ticket>#299</ticket>
      <ticket>#305</ticket>
      <feature>Adds support for viewing web documents in a WebViewCell using
      Added a file that was missing from my last commit.
      <feature>Initial version of a persistence package that aims to cache
      <bugfix>Remove ternary operator for python 2.4 compatibility</bugfix>
      <bugfix>Fixes some of the shell interaction methods.</bugfix>
      FIxed a typo in create_port, we don't need to call the vistrails_port
      <bugfix>Fixed issue with deletes in sql persistence for versions 0.9.5
      <feature>Add support for deleting entities from the database.</feature>
      <ticket>#308</ticket>
      <ticket>#309</ticket>
      <ticket>#310</ticket>
      <ticket>#311</ticket>
      <feature>Added Path and Directory constants and updated File constant
      <ticket>#314</ticket>
      <bugfix>Analogies now replace annotations of the same key and
      <bugfix>Add version support into module signatures so that persistent
      <ticket>#319</ticket>
      <ticket>#320</ticket>
      <feature>Add a new module that allows the user to control the order of
      <ticket>#325</ticket>
      <ticket>#326</ticket>
      <ticket>#259</ticket>
      <ticket>#322</ticket>
      <ticket>#321</ticket>
      <ticket>#323</ticket>
      <bugfix>Don't disable entire vistrails when they contain **unused**
      <ticket>#276</ticket>
      <feature>Removed "Tag" entry in the method palette</feature>
      <feature>Add data provenance support for persistent files.</feature>
      <bugfix>Add copy methods to enhanced DBVistrail</bugfix>
      <feature>Better delete buttons on the parameters.</feature>
      <bugfix>DBVistrail.do_copy doesn't fail when log is None</bugfix>
      <ticket>#327</ticket>
      <feature>Allow persistence package to search for persistent entities
      <ticket>#151</ticket>
      <bugfix>Check for __init__.py in userpackages on startup.</bugfix>
      <ticket>#329</ticket>
      <ticket>#328</ticket>
      <ticket>#330</ticket>
      <ticket>#328</ticket>
      <bugfix>Add translation to new ids back after input/output remap.</bugfix>
      <feature>Initial revision of a sql scripting package</feature>
      <bugfix>Auto adding subworkflows via _subworkflows now allows
      Adding a proof-of-concept package for the SAHM project.  Supports the
      <bugfix>Ensure descriptions are updated when doing undo/redo and don't
      <ticket>#331</ticket>
      <ticket>#334</ticket>
      <ticket>#336</ticket>
      <bugfix>Move Vistrail import into load_vistrail method to avoid
      <ticket>#290</ticket>
      <ticket>#344</ticket>
      <feature>Improved package reloading support</feature>
      <bugfix>Stop creating empty actions</bugfix>
      <bugfix>Made reset query work immediately for the version search box</bugfix>
      <ticket>#346</ticket>
      <bugfix>Differentiate between init.py not existing and init.py having ImportErrors</bugfix>
      <feature>new SourceConfigurationWidget to make creating source configuration widget easier</feature>
      <feature>easier constant extensibility and customization</feature>
      <feature>easier namespace designation using _modules</feature>
      <feature>inital version of a VisTrails R package using rpy2</feature>
      <bugfix>fix incorrect port setting on Dictionary output</bugfix>
      Added an example showing how the rpy package can be utilized.
      Added a README with a couple of workarounds I needed to get rpy2 to
      Updates to SAHM from the first meeting from January.
      <bugfix>Don't require a Module to a be of type __builtin__.type to
      <bugfix>Fixed issue where module label changes were not recognized correctly and raised an exception</bugfix>
      <feature>Improved version selection handling</feature>
      <bugfix>fixed ModuleRegistry.auto_add_subworkflow so that it accepts the correct (filename, dict) format.</bugfix>
      ** EXPERIMENTAL PACKAGE **
      <ticket>#354</ticket>
      <feature>Allow QSearchBox to do non-incremental searching</feature>
      <feature>Improved string formating of nested InvalidPipeline exceptions</feature>
      <feature>Add method to allow updates of a single port rather than all ports as updateUpstream provides</feature>
      Change persistent signature to be lowercase.
      <feature>PRELIMINARY upgrade support</feature>
      <bugfix>Pass simplify argument through in create_action_from_ops</bugfix>
      <ticket>#356</ticket>
      Fixes a bug where the merge was not remapping tags correctly.
      <feature>Preferences for upgrades</feature>
      <bugfix>Fixed issue where automatic upgrades fail because a port is said to not be found even though the port does exist</bugfix>
      <bugfix>Fix issue with analogies where obselete method was being called</bugfix>
      <bugfix>Fix issue with upgrading modules that have user-added ports</bugfix>
      <bugfix>Fix issue with upgrading module functions for user-defined ports</bugfix>
      <bugfix>Pass module information through group to contained modules</bugfix>
      <bugfix>Fix bugs in displaying missing dependencies in preferences</bugfix>
      <bugfix>Fix error with handle_invalid_pipeline and subworkflows</bugfix>
      <bugfix>Band-aid for analogies to make analogies with groups or abstractions a bit more robust</bugfix>
      <bugfix>Fix issues where pipelines are not validated after certain actions like copy-paste</bugfix>
      <bugfix>Fixed issue with trying to upgrade groups introduced by upgrading port specs</bugfix>
      <ticket>#357</ticket>
      <bugfix>Don't automatically switch to pruned upgrade nodes</bugfix>
      <bugfix>Fixed issue with re-saving to the database with groups</bugfix>
      <bugfix>When pruning a node, make sure that node is removed from the version tree display</bugfix>
      <bugfix>Fixed port spec naming in new persistence package</bugfix>
      Updates to the SAHM package to match new version of java code.
      <feature>Make actions immutable by moving mutable attributes to a higher level</feature>
      <bugfix>Fix for older log files that have incorrectly moduleExec elements</bugfix>
      <ticket>#353</ticket>
      <feature>Added gui code for the interactive vistrails merge</feature>
      <feature>Move local settings for persistent paths to separate ports</feature>
      Updates to the SAHM package to allow cleanup of temporary files and
      Updates to the SAHM package for backward compatibility with the
      <bugfix>Fix issue with reading and writing the boolean parameters during persistence configuration</bugfix>
      <bugfix>Fixed issue where database was saving parent id/type pairs as NULL</bugfix>
      <bugfix>Fix issue where annotation ids weren't properly assigned</bugfix>
      Fix script that updates binaries to be python2.6-aware.  Now, the
      <bugfix>low-level merge code now allows passthrough gui references
      <feature>Add support for calling binaries in Mac bundles</feature>
      <bugfix>Added default get_executable_path to linux</bugfix>
      <ticket>#364</ticket>
      <ticket>#367</ticket>
      <ticket>#366</ticket>
      This is the first step in converting db code to use templates.  I want
      Move all of the db auto-generated code to use Mako templates (code is
      Improve the OSXSystemProfiler code to generalize the shortcut we're
      Updates to the SAHM package.  Add support for loading MAXENT
      Updates to the SAHM package.  Add support for loading MAXENT
      <ticket>#374</ticket>
      Fixed CDAT cell import.
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      <bugfix>keep selected modules after scene redraw</bugfix>
      <feature>Improved support for work with the filesystem</feature>
      <feature>Use List for controlflow now instead of ListOfSElements</feature>
      <feature>Migrating new persistence package from persistence_exp to persistence</feature>
      <bugfix>Update sql package to use List instead of ListOfElements</bugfix>
      <feature>Updated version of the rpy package</feature>
      <ticket>#377</ticket>
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      <ticket>#378</ticket>
      <bugfix>Change persistence package to use correct identifier for gui widgets</bugfix>
      <bugfix>Allow semi-translation from abstractionRef to abstraction so
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      <ticket>#369</ticket>
      <bugfix>Use git ls-files instead of cat-file to retrive hash so that we don't have issues with Windows reading from stdin</bugfix>
      <ticket>#302</ticket>
      <bugfix>Set MplFigureCell to fill spreadsheet cell</bugfix>
      <bugfix>Fixed issue with query-by-example where parameters couldn't be updated</bugfix>
      <ticket>#302</ticket>
      <ticket>#383</ticket>
      <feature>Add pinch gesture support to graphics views</feature>
      <bugfix>Expanding port specs deals with differences between descriptor and port signatures</bugfix>
      <feature>Detect changes to directories so the cache can be invalidated when they change</feature>
      <bugfix>Don't delete tag text when attempting to prune</bugfix>
      Updates to SAHM package from USGS.
      <bugfix>Fix issue with on-demand package loading leaving workflows as invalid</bugfix>
      Minor updates to SAHM package based on feedback from Colin.
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      <bugfix>With delayed upgrades, moving modules after an upgrade now generates actions in the correct order</bugfix>
      <bugfix>Fixed an issue with groups and upgrades</bugfix>
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      <bugfix>Add upgrade path for old InputPort and OutputPort modules</bugfix>
      <bugfix>Don't mask AttributeErrors when materializing pipelines</bugfix>
      <feature>Maintain suffixes on persistent files and directories</feature>
      <bugfix>Fixed issue where named intermediate persistent files/directories were not reused correctly</bugfix>
      <bugfix>Flush delayed actions (including upgrades) to fix issues with delayed upgrades and grouping upgraded workflows</bugfix>
      <bugfix>Fixed issue with spreadsheet and grouped spreadsheet cells</bugfix>
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      <bugfix>Subworkflows from packages that need upgrades are now moved to local.abstractions in the registry and picked up for workflow upgrades</bugfix>
      <bugfix>Update version tree when adding delayed actions</bugfix>
      <feature>Add preference for migrating tags and notes on upgrades</feature>
      <bugfix>Add ability to migrate tags when upgrades are not delayed</bugfix>
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      <bugfix>Fixed issue with groups and input values that evaluate to False</bugfix>
      <bugfix>Fixed problem where controlflow package would raise duplicate errors</bugfix>
      <bugfix>Fixed issue where it was not possible to ungroup a subpipeline that had an InputPort connected directly to an OutputPort</bugfix>
      <bugfix>Enable all spreadsheet cells for parameter exploration, even if they are embedded in groups or subworkflows</bugfix>
      <bugfix>Fix issue with console mode and unit tests</bugfix>
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      <feature>Added prompt for password for database access in batch mode</feature>
      Added example of enumeration module (and widget) to the SAHM package.
      <bugfix>Fixed an issue where the FilePool's local copy mechanism failed in Windows</bugfix>
      <bugfix>Better error handling for duplicate module identifiers in packages</bugfix>
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      <bugfix>Enabled with_statement for python2.5</bugfix>
      <bugfix>Preserve aliases during upgrades</bugfix>
      <bugfix>Fix issue with upgrading modules with null functions (no parameters)</bugfix>
      <bugfix>Attempt to implement VTK upgrades</bugfix>
      <bugfix>Fix parameter explorations on File parameters</bugfix>
      <feature>Improved efficiency of vtk workflow upgrades</feature>
      Initial version of a GIS package that uses QGIS.
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      New branch for 2.0 changes
      Minor updates to views.
      <feature>New manager for persistent store</feature>
      <feature>Add better provenance information for persistent entities</feature>
      Merge branch 'feature/browser' into v2.0
      Merge branch 'feature/browser' into v2.0
      <bugfix>Fix issue with caching and persistent files</bugfix>
      More updates to 2.0 branch, should have more functionality.
      <bugfix>Fix issue with enabling packages in preferences dialog</bugfix>
      <bugfix>Re-enable the double-click version capability</bugfix>
      <bugfix>Fix menubar issue on non-Mac platforms</bugfix>
      More updates to 2.0 branch.
      Fix issues with tabs and new views.
      Link more menu items to callbacks.
      <feature>Enhanced query capabilities</feature>
      <feature>Executable paper editing</feature>
      <feature>Improve query handling</feature>
      <feature>Workspace window is always visible</feature>
      <feature>Search results show up in workspace window</feature>
      <feature>Simplify visual diff and improve parameter changes display</feature>
      Cleaned up code in gui/vistrails_window.py
      Re-added undo/redo functionality.
      Re-added control flow assistant functionality.
      <feature>Added support for cross-vistrail diffs</feature>
      <bugfix>Fixed issues with spreadsheet editing for copies and analogies</bugfix>
      <bugfix>Fix issue where raw pipeline and construct from root were not working</bugfix>
      <bugfix>Fix zoom to fit for initial vistrail</bugfix>
      <bugfix>Changes to subworkflow identification</bugfix>
      <bugfix>Fixes to subworkflow upgrades and save as</bugfix>
      <bugfix>Fixed issue with cell locations in spreadsheet editing mode</bugfix>
      <bugfix>Fixed issues with upgraded subworkflows</bugfix>
      Fix issue where subworkflow wasn't being created because we weren't
      <feature>Add extensible query support</feature>
      <feature>Add extensible query support</feature>
      <bugfix>Fix issue with package subworkflows and	namespaces</bugfix>
      <feature>Improved default query support</feature>
      <bugfix>Fixed issue where numeric comparisons were being done as string compares</bugfix>
      <bugfix>Fixed issues with executing queries</bugfix>
      <bugfix>Added ability to open workflows from query results</bugfix>
      <feature>Remove gui dependencies for core.modules widgets</feature>
      <bugfix>Fixed an issue when loading a vistrail that references different versions of a subworkflow that share common ancestors</bugfix>
      <bugfix>Fixed issues with multiple versions of subworkflows appearing in the module palette</bugfix>
      <bugfix>Fixed issue where subworkflow edits could result in one-to-many port mappings.</bugfix>
      <bugfix>Fixed messages during upgrades so that upgrade info is not flagged as a warning</bugfix>
      <bugfix>Add upgrade for PythonSource to fix issue with 'self' port</bugfix>
      <bugfix>Fixed issue with ports that may have multiple functions associated with them (e.g. in the vtk package)</bugfix>
      <bugfix>Keep module position when changing visibility of ports</bugfix>
      Added more of the query results implementation.
      <feature>Expand search results to include all open vistrails</feature>
      <bugfix>Fix issue where 'layout' was an overloaded field name</bugfix>
      <bugfix>Issue correct version_selected signal after upgrades</bugfix>
      Merge branch 'master' of vistrails.org:vistrails
      <bugfix>Fix issue in ModuleDescriptor.expand_descriptor_string</bugfix>
      <bugfix>Fix issue in ModuleDescriptor.expand_descriptor_string</bugfix>
      Merge branch 'v2.0' of vgc.poly.edu:vistrails into v2.0
      <feature>Remove most PyQt4/gui dependencies in core functionality</feature>
      <feature>Add operation ids to messages about illegal operations</feature>
      <bugfix>Display more meaningful error when persistent inputs do not exist in a repository</bugfix>
      <feature>Added support to hardcode necessary packages on startup</feature>
      Fix set_needed_packages method (forgot self).
      <feature>Add separate workflow and log xml schemas</feature>
      <bugfix>Fixed typo in core.application's register_notification</bugfix>
      <bugfix>Fix issue with merging thumbnails</bugfix>
      <bugfix>Fixed issue with forced versions on modules</bugfix>
      <bugfix>Allow zero-parameter functions to be set from ports panel</bugfix>
      <bugfix>Fixed issue with vtkInteractionHandler which was not updated when the Save/Revert changes were made to source widgets</bugfix>
      <bugfix>Fixed issues with tabbing in the python editor</bugfix>
      <bugfix>Fix for remove_connection issues</bugfix>
      <feature>Add more functionality to core.api</feature>
      Fixed issue with test_abstraction_create test method.
      <bugfix>Fix issue with alternate .vistrails directory and its subdirectories</bugfix>
      <bugfix>Fix issue with deleting modules and connections</bugfix>
      <bugfix>Fix issue where reconfiguring persistent modules caused unexpected behavior.</bugfix>
      <bugfix>Add missing port labels to ports panel</bugfix>
      <bugfix>Fix logic in identifier checks in package manager</bugfix>
      <bugfix>Fix initial layout of matplotlib cells</bugfix>
      <bugfix>Fix issue with caching group modules</bugfix>
      <bugfix>Fix connection drawing issue on Mac</bugfix>
      <bugfix>Make version tree selection more intuitive</bugfix>
      <bugfix>Fix crash on undocking module info palette on Mac OS X</bugfix>
      <bugfix>Fixed issue with error message for editing package subworkflows</bugfix>
      <bugfix>Reenable refined version tree in the query view</bugfix>
      <bugfix>Fix colors in query results view</bugfix>
      <bugfix>Partial fix to make workspace more efficient</bugfix>
      <bugfix>Fix issue with executions of untagged versions</bugfix>
      <bugfix>Fix undo/redo in pipeline view</bugfix>
      <feature>Switch to pipeline view if an execution fails</feature>
      <bugfix>Fixed QPixmap scaled issue</bugfix>
      <bugfix>Change analogies to use a suitable default alpha value</bugfix>
      <bugfix>Eliminate duplicate warnings</bugfix>
      <bugfix>Fix issue with connected indicator for ports</bugfix>
      <bugfix>Fix issue with remove vistrail variable modules and connections</bugfix>
      <bugfix>Fix typo</bugfix>
      <bugfix>Fix issue with analogies that also require upgrades</bugfix>
      <bugfix>Fixed issue with creating vistrail variables in an undocked panel</bugfix>
      <bugfix>Fix issue when setting a vistrail variable on multiple modules</bugfix>
      <bugfix>Fix issue with redrawing the tree after analogies</bugfix>
      <bugfix>Add default support back in</bugfix>
      <bugfix>Ensure add_*_port can override ports in superclass port lists</bugfix>

Emanuele Santos (753):
      vistrails.py
      VistrailController.pasteModulesAndConnections()
      Added Examples of docstrings
      system/__init__.py:
      Added vistrails files to examples
      basic_modules.py
      Fixed test
      Moved core/common.py to core/utils/__init__.py
      Moved core/common.py to core/utils/__init__.py
      - removed import *
      Added .pyc to svn:ignore property
      Added .pyc to svn:ignore property
      Created vistrail package inside core and moved vistrail.py to vistrail/__init__.py
      moved all vis_*.py files to core.vistrail/ and removed the Vis prefix from all files and classes.
      split vis_types in port.py, module_param.py and module_function.py and moved them to core.vistrail/
      Corrected all references to the renamed classes and modules.
      Added .pyc to svn:ignore property
      core/vistrail/__init__.py
      Removed unnecessary ImportVistrailAction class
      Removed import *
      Added Point.__eq__(self, other) and Point.__ne__(self, other) comparison methods.
      Added __eq__ and __ne__ to Module, ModuleParam and ModuleFunction.
      Removed eXist related functions and imports
      Cleaned db directory.
      Added docstrings
      Added docstrings
      Changed TestCase to not use global registry variable. This was causing a circular reference.
      core/xml_parser:
      core/console_mode.py
      renamed vis_shell
      Logger.getSettingsFromApp()
      QLegendWindow.__init__()
      VistrailsApplicationSingleton.noninteractiveMode()
      QVisualDiff.__init__()
      QBuilderWindow.createActions()
      Added back "About Vistrails"
      Added vistrails icon
      VistrailsApplicationSingleton.setupSplashScreen
      Fixed bug with SDI Mode
      Added files for windows binary distribution.
      Installed shortcuts are updated to call python.exe instead of pythonw.exe.
      Fixed ticket #27: vistrail_controller.py crash when writing a vistrail.
      Now Fixed ticket #27: vistrail_controller.py crash when writing a vistrail.
      Bug fix: alias changes were not persistent
      Updated code to work with Bookmarks Window
      added defaultBookmarksFile() to get user's bookmark file
      added generic XMLWrapper class to work with xml files in general.
      QShellDialog.closeEvent() emits a signal that it is closing, so the builder show button states correctly.
      added toolbar icon for bookmark window
      uxml.py
      fixed wrong filename
      Removed unused macro functions from parser.
      Fixed typo in docstrings
      BookmarkCollection.findBookmark()
      Added more working examples.
      Added .pyc to svn:ignore property
      Bug fix: enabling check box back in bookmarks panel
      Added more aliases to head example
      - Added Toolbar icon for removing bookmarks to the Default Theme
      image file for removing bookmarks button
      sys.stdout, sys.stderr and sys.stdin can't be capture from inside the Vistrails Shell. Now this is handled in the builder window.
      vistrails file for the web services example on the wiki.
      Added final version tag to web services vistrail.
      logger.py
      Interpreter.cached_execute: resolve aliases and record logging, like CachedInterpreter. (fix by carlos to unbreak the build)
      Updated windows distribution files to include release notes and a bookmark file example.
      changed compute method to raise a ModuleError Exception in case of failure when invoking a web service
      - Added support to QPythonValueLineEdit for selecting multiple files
      Added Parameter exploration with one dimension to Bookmarks Window
      QAliasExplorationTable
      QAliasExplorationPanel
      Fixed bug in QPythonValueLineEdit.keyPressEvent introduced in the last commit.
      Using the head data set in the Volume Rendering version for consistency.
      Fixed example to work with changed FilePool method name.
      Commented out the line adding ImageMagick Package.
      Fixed Bugs Reported on tickets #44 and #46.
      Added notes for release 389
      Changed installer script file to reflect new release.
      Example for offscreen rendering using spx data file.
      CORIE example fetching the files from the web server.
      Rearranged modules in offscreen.xml
      VistrailsApplicationSingleton.noninteractiveMode()
      Added pipelines that download an uncompressed version of the data sets.
      This commit fixes bug #38 - Duplicate aliases are allowed in the same pipeline
      Fixing ticket #62 Deleting bookmarks causes error
      Solving ticket #54
      Removed unused getClipboard functions and unused PyQT4 imports
      Moved Application icon from apllication.py to theme.py
      utils.py:
      - ported r457 (windows unzip issues and release updates) from branches/2007-02-23
      Added unzip binary files for windows
      core.system.__init__.py:
      Making Execute Current Pipeline, See Full Tree and Query By Example buttons and menus consistent with the version selection.
      Making menus (Close, Save and Save As...) consistent
      Fixed Menu issues on the spreadsheet
      Fixed small issues with button states
      Updating release notes for the next release
      Setting the release number.
      Fixing bug on disabling deleting sheets
      now the bug in the previous commit should be fixed.
      ported r452(removing windows specific pipelines) from branches/2007-02-23
      Incorporating last-minute adjustments from release 502 back to the trunk.
      Fixed typo on documentation
      theme.py:
      This should fix the problem that Carlos reported. As the pipelines were loaded on demand, if a pipeline had many actions, it could be very slow. Now pipelines are loaded only once when the bookmark is added.
      This fixes ticket #82 (Notes text panel shows "None" when there are no notes)
      Moved the logger instance from core.startup to core.logger
      This finally fixes ticket #63 (icon and menu state is not updated when operation is invalid)
      Binding the local import of MySQLdb to a global variable.
      If the query canvas was emptied before unchecking the query button the version tree status could not be restored.
      User Defined Function didn't cast types when possible (for example, returning an int when a float is expected was not allowed)
      Catching spreadsheet changes in a lower level so events generated by sheetreference are properly caught.
      Updated release information (559)
      Copying and Pasting Tuple modules was not working.
      Giving credit to the original author.
      Fixed absolute paths problem in the bookmarks.xml file.
      Added self to output ports from Tuple.\n Sorting keys when loading abstractions. (Huy)
      core/bookmark.py:
      Making sure to convert to str when reading from the xml file
      Fixed Bookmarks' parameter exploration
      BookmarkController.__init__():
      ported mac binary distribution changes and splash screen to the trunk (r 655, 656, 659, 660)
      Except for the analogies part, the branch is now consistent with the trunk.
      Work around for graphics view background problem on the Mac. We need to file a ticket to Qt.
      bookmark_panel.py, bookmark.py, noncached.py
      This fixes tickets #86 (Saving changes on quit) and
      Gui related changes for db
      - QViewManager.updateViewMenu()
      Added db section to configuration
      Icon files for db windows and buttons
      Added icons to default theme
      Added file for Open From DB Window. Not Completed yet.
      Updated menus and toolbuttons for including open from db window. The vistrails are listed but I still need to open from the database.
      Added preliminary versions of get_db_connection_list and get_db_vistrail_list.
      This fixes ticket #102 (No colors are displayed in the legend of the Visual Diff window on Macs).
      QViewManager
      - Added GUI to create a DB Connection and save it to user's startup.py
      QVTKWidget.SetRenderWindow()
      - Added "Save Vistrail to database" functionality
      Forgot to update the ignore list of some folders
      This fixes the bug that prevented the spreadsheet of adding a new version to the vistrails after performing parameter exploration.
      Fixed ticket #112 After the new vtk filters, the lung example is broken.
      Fixing bug introduced on revision 754 that prevented from saving vistrail files.
      Fixed bug that we couldn't remove methods from a module.
      This commit fixes bugs with annotations. Using a mechanism
      Now a module keeps selected after editing its configuration or annotations.
      QGraphicsConfigureItem.configure()
      Locators were getting lost when saving to DB. (Fixed by Dave)
      Fixed bug that prevented to save a vistrail after trying to quit the application.
      Fixed bug with buttons state in toolbar when opening a vistrail from the command line.
      Pipeline.__copy__()
      This fixes alias manipulation and parameter exploration of aliased parameters and fixes case inconsistencies in the Pipeline class.
      Also checking  for overloaded output ports and duplicate signatures (which occur in the latest VTK cvs version)
      Added support to new file format (.vt).
      Reverting the lung example to the previous revision. I mistakenly included it on the previous commit.
      Fixed zip / unzip issues on Windows.
      - Bug fix: Removing a module that had connections to it kept other module's dependency list inconsistent, causing copy and paste to crash. Fixed by updating the other end of connection before removing modules
      When using the timer for drag events inside QGraphicsVersionItem on Windows causes the drag event to behave improperly. So I put a conditional to use it only on other systems (Updating trunk and branch).
      .vt bug fix. Now it assumes that the name in the archive is always 'vistrail'. The tempfile is create using tempfile.mkstemp() function.
      Converted lung and brain_vistrails to new format. Removed old xml files.
      Converted more examples to .vt.
      Ported changes in rev 899-900 to the trunk.
      Added Configuration Object to the web services packages so it can be loaded on the current version.
      - Added pylab to default startup.py and startup.xml
      Removed invalid web service examples and added one that works and that is mentioned on the user's guide.
      This fixes bug #167 (Paste fails when something other than a serialized pipeline is on the clipboard) by catching exceptions thrown by the parser. Pasting something invalid will do nothing.
      Bug fix: Sometimes the vtkcell would show a blank screen when using a vtkCamera in the pipeline.
      Updated lung example and cleaned up head.vt
      Removed public domain related code from v1.0 and trunk.
      Updated scripts and release notes for Mac distribution. Also updated the icon to be consistent with the one used on Vistrails.
      Fixed wrong paths.
      Bug fix: Saving a .vt file on a path with spaces was not working on Unix systems.
      Added execute_cmdline() function to the core.system.
      Fixing analogies and saving/loading spreadsheet.
      - Updated splash screen and icons to new design.
      Updated Windows Icon File
      Putting in back code that I removed accidentally.
      Including SCI , U of U and other logos
      Added image for about box that shows all logos.
      Logos were in wrong order :/
      This adds the ability to set custom widgets to Constants in VisTrails.
      Fixed small bug that prevented from disabling packages dynamically.
      Bug fixes in Visual Query.
      Added visual hints to the transfer function widget
      Pruning the tree was not working when opening files created in v1.0 because the actions were missing the prune attribute during translation.
      - First draft of automatically generated cdat package based on xml descriptions.
      Gui part of Lauro's new tree layout.
      - Added more modules to cdat package (by adding new xml descriptions).
      - Added support for packages to create menus in the builder window and to
      - Fixed bugs in VisTrails Configuration Window (Preferences Window)
      Fixed blinking cursor in Set Methods panel.
      Lauro:
      - Added support for running Visual Diff for pipelines with
      A couple of fixes:
      Initial check in for the medleys package with part of the infra-structure and placeholders for the gui.
      Fixed focus problem in the Set Methods Panel
      This fixes ticket #193: Pasting with no version selected produces actions with prevId="-1".
      - Fixed command_line options when running in non-interactive mode.
      This fixes ticket #143: version tree is not refreshed when analogy is applied on the spreadsheet
      This fixes ticket #197: Changing name of a port on a PythonSource
      - Updated windows icons in the trunk
      - Updated mac installer scripts and release notes (mac and windows).
      Fixed annoying bug in which the methods palette would take most of the builder window size when starting vistrails.
      This should fix the viewAction problem when running Vistrails and Qt 4.4.
      Improvements in the command-line for both non-interactive and interactive mode:
      - Added support for opening vistrails files on the web (wiki integration)
      Forgot to commit this yesterday:
      Fixed bug where the Builder Window wouldn't show on top after initialization
      VistrailsApplicationSingleton.interactiveMode()
      Bug fixes:
      Bug fixes: This fixes bugs reported on tickets #205 - Refine in the search box does not work and #159 - Minor bug in query refine.
      Improvements and small bug fixes in search and refine.
      This fixes bug reported on ticket #206 - Cells not cleared in saved spreadsheets
      Increased font size in notes of some examples.
      Fixed bug in Parameter Exploration
      Analogies were broken too. I made some changes to the api so it
      Updating list of changes for next release
      Updated Windows Installer script to use Qt4.4.
      Fixed 2 of the bugs Dave reported that modules could not be dragged around when connected and the weird drawing. The dragging around problem was a setupConnection problem
      This fixes the grouping problem  and the missing port specs in both module ports and method palette (both reported by Dave)
      VistrailController.ungroup()
      Fixed analogy bug in the spreadsheet.
      Porting fixes from branch to trunk (rev 1255 and rev 1245)
      Fixed path problems on Windows.
      Ported webServices package fix (rev 1263) to trunk.
      Added files for extending latex and mediawiki with vistrails.
      - Added more documentation to the files.
      I had updated a wrong version of the pdf.
      Changed mac distribution files so they work when building the application on Leopard. My old script was Tiger only and I don't have a intel mac with tiger anymore. This means our future distributions for intel will work on Leopard only. Notice that as long as we don't have a library upgrade, I can always update the old bundle with the new vistrails file.
      Bug fixes and improvements to the VisTrails extensions for SciVis class:
      Added single instance support to VisTrails.
      Improvements to shared memory cleanup so it's not kept locked after VisTrails
      I forgot to include these files when committed in revision 1298.
      Reorganized VisTrailsApplicationSingleton code a little bit so we can reuse
      Fixed Single Instance problem on a Mac (thanks to Dave).
      Fixed bug in Parameter Exploration where the view was not updated correctly when the version was changed.
      Small bug fixes in the latex extension.
      Removed the Qt4.4 requirement.
      Bug fixes when using vistrails connected to the database.
      Added file to facilitate using vistrails as a library.  More information is in the docstring of the file.
      Added more import lines needed for the medleys
      Added more import lines needed for the medleys.
      init_for_library.py:
      This fixes a couple of bugs introduced by the abstractions changes:
      Added more import lines needed for the medleys.
      Updating in Web Services package so it works with the new registry.
      Fixed bug when removing packages that have namespaces with colons.
      Put Huy's and Tom's CDAT Gui Code in the original CDAT package.
      - Small fixes to the VTKCell so camera syncing also works on medleys
      Added more imports for medleys
      Added support to constant widgets to reset their contents
      Bug fix when loading workflow execution logs.
      This fixes Ticket #249: VTK package fails with old versions of VTK
      Just found and fixed a bug that happened when deleting a VTKCell.
      Fixes to spreadsheet package:
      - This should fix the initialization bugs we have with command line options.
      Updated copyright year
      Added script for changing the copyright year
      Updated mac distribution files to include missing libraries
      Bug fixes in the latex extension when handling tagged versions
      Removing files added by mistake.
      Bug fixes
      Removed obselete medleys package.
      Removed references to old bookmarks.
      This fixes ticket #225: Multiple optional output ports are broken
      This fixes ticket #227 Add the Color widget method version to vtkRenderer.SetBackground
      This fixes ticket #216 Request Ports not working
      This fixes ticket #199 The annotations are not updating automatically
      This fixes ticket #239 GPL license file not included with source release
      Updated windows installer script to include the license file.
      Updated splash screen for 1.3 release.
      Updated copyright year on background image of the about message.
      This solves ticket #218 Accessing environment variables from Mac Binaries
      This solves ticket #253 Running VisTrails in batch mode is broken
      This fixes tickets #230 Windows installer always creates desktop shortcut and
      This solves ticket #233 Paste menu item doesn't work in query tab
      This should fix ticket #255 Can't save vistrails files on windows because it can't find zip
      Updated copyright year in extension files (trunk)
      Bug fixes:
      Fixed typo in debug message in VistrailsStartup.create_default_directory()
      This fixes a bug that happens when you try to open a file that does not exist
      Fixed bug when trying to execute command lines where the filename had special characters on linux and mac systems, on both trunk and 1.2 branch (thanks to Juliana for spotting this bug).
      Fixed a bug I introduced in the last commit.
      This fixes the bug where VisTrails would always access the DVD Drive everytime a workflow was executed.
      This fixes ticket #257 Cannot save files on Windows when running from source
      Added new functionality to vistrails server mode to work with the VisTrails
      Fixed bug where changing the state of checkboxes for boolean
      More fixes
      Fixed flip image button in the ImageViewerCell toolbar.
      This fixes the bug where saving to the stable version was not working.
      Updated code inside MplPlot module so it works with the version of matplotlib we ship in the binaries (0.98.5.2)
      Updated Release Notes :/
      removed forgotten print.
      This fixes ticket #261 Thumbnail error on updateVersion
      <ticket>#263</ticket>
      <ticket>#267</ticket>
      Added thumbnails to the tagged versions of the example files I was able to run.
      Updated release notes and installation scripts for release.
      <bugfix>Checking for the right zip executable name on Windows</bugfix>
      Updated revision number for windows bug fix release.
      Fixed small bug that prevented load a vistrail from the database using the GUI.
      Updated VisTrails Server code in the trunk to be consistent with the server running in vistrails.sci.utah.edu (I forgot to update one of the functions when I added the functionality Clifton needed.)
      <ticket>#301</ticket>
      <ticket>#303</ticket>
      <ticket>#304</ticket>
      <ticket>#307</ticket>
      Added script to run install_name_tool on Qt plugin libs before copying them to the bundle.
      Adding set_module_persistent() to DummyView so executing a workflow from the command line does not fail with the error: 'DummyView' object has no attribute 'set_module_persistent'
      Added a local cache for DBLocators to speedup reloading (very useful for servers)
      Added missing code that checks if the db was updated before using the cached values (version r1621)
      Forgot to add necessary imports.
      <bugfix> wiki vistrails tags containing "tag" attributes were not executed on the wiki </bugfix>
      Replacing constructs that do not working in python 2.4.
      Moving the data out of the trunk and putting in the root
      Updated code to load locators using io.load_vistrail()
      Added script for (re)starting vistrails in server mode with Xvfb.
      <bugfix>Adding missing copy imports to domain/vistrail.py files </bugfix>
      bugfix>DBLog.do_copy was not returning anything</bugfix>
      <bugfix>tag "tag" was being ignored when "version" was empty in .vtl file</bugfix>
      <bugfix>Fixed exporting Log, Workflow and Registry to XML</bugfix>
      <ticket>#318</ticket>
      Added a directory input port to the vtlcreator package.
      Added new package with modules specific for portable devices (to get geographic location, images and audio snippets).
      <ticket>#332</ticket>
      Added bash script to update windows installation
      bug fixes in the mobile package.
      Improvements to the script that generates the release notes:
      Updated script for generating bundle on a Mac to be fully automatic
      Updated release notes using the script. Yay!
      Added v1.4 splash screen
      Updated Copyright message to 2010 in all source files.
      Updated release version to 1.4 and revision numbers to 1682.
      <ticket>#337</ticket>
      <bugfix>Package Web Services: expanded simple types map to
      <ticket>#338</ticket>
      <bugfix>Using VisTrails as a library: added more imports to
      Putting back an import removed by mistake.
      <ticket>#339</ticket>
      Added v1.4.1 splash screen with updated list of developers to the repository.
      Updated release version number and notes
      Found small bug in the release_notes.py script that was causing some tickets to be discarded from the release notes.
      <ticket>#341</ticket>
      <feature>SQL package also connects to a PostgreSQL database server</feature>
      <ticket>#342</ticket>
      <ticket>#345</ticket>
      <bugfix>DBLocator: Removing object name from XML serialization.
      <bugfix>Fixed a bug with opening .vtl files that embedded workflows</bugfix>
      <bugfix>Fixed bug that when enabling a package dynamically sometimes VisTrails
      <feature>Enabling access to a Web package repository.</feature>
      <ticket>#290</ticket>
      <bugfix>Fixed bugs with exception handling when enabling packages</bugfix>
      Preparing new release:
      <ticket>#347</ticket>
      <ticket>#348</ticket>
      <ticket>#349</ticket>
      <feature>Server Mode: added support for multithreading</feature>
      <bugfix>Fixed a bug in the RequestHandler.get_wf_vt_zip() function.</bugfix>
      <bugfix>Server mode: Added a global variables to store information for accessing the database</bugfix>
      <bugfix>VisTrails Server: the vistrail version was not being included in the .vt file generated by the server</bugfix>
      <feature>Views can now export the scene as a PNG image (useful for generating an image of the workflow or the version tree. Notice that this is not exposed in the builder.</feature>
      Moved the synchronization function to the vistrail level
      <bugfix>References to thumbnaisl were being shared across
      <bugfix>In VTK package: Added support for Qt4.6 to TransferFunctionWidget</bugfix>
      <bugfix>Checking whether XML element is not None before trying to evaluate it as text</bugfix>
      <feature>VTK Package: Added the ability to use the Transfer Funtion widget to
      <feature>Added support for merging vistrails on the server side</feature>
      <ticket>#317</ticket>
      <bugfix>Spreadsheet package: corrected paper size of generated pdfs</bugfix>
      <feature>Server mode: added support for executing workflows and returning
      <feature>Changed VisTrails version to 1.5</feature>
      Changed the way the spreadsheet was being imported because it was not working with the new layout of vistrails packages
      Removed NumScipy package dependency from CDAT package.
      <bugfix>Fixes for merging vistrails in server mode.</bugfix>
      <bugfix>Updated Web services code to work with HTTP package chages</bugfix>
      <bugfix>Package Web Services: Could not handle missing modules</bugfix>
      <bugfix>Sometimes matplotlib plots were not refreshed in the spreadsheet</bugfix>
      <bugfix>Removed reference to deprecated popen2 when executing command
      - Preparing release!
      - Adding extensions to releases and updpated scripts accordingly
      The directory was not completed removed in the previous commit.
      Ported changes related to python bindings in vtk package to vtksnl.
      <ticket>#365</ticket>
      <ticket>#362</ticket>
      <bugfix>ImageViewerCell: Disabling the zoom slider when playing
      <ticket>#363</ticket>
      <bugfix>log file names are now updated according to VisTrails version</bugfix>
      <bugfix>Added procedure to WIndows installer script to remove VC Redist files left behind</bugfix>
      Added Berk's changes to ParaView package.
      <bugfix>Fixed bug with thumbnails and RichTextCell</bugfix>
      <bugfix> Fixed bug where RichTextCell was not displayed when running on server mode</bugfix>
      Added VisTrails 1.5.1 splash screen
      minor bug fix in the Windows Installer script
      Updated release notes and revision number.
      <ticket>#368</ticket>
      Updated release notes and revision number to include the latest commit.
      Fixed a bug in the file dialog to export "as a single image" of
      Adding ignore patterns file to the repository
      Added workaround for reloading Web Services package.
      <bugfix>Web Services package: fixed bug in certain Complex Types</bugfix>
      - Adjusted code to use only first 12 characters from git hash key.
      <ticket>#376</ticket>
      - Added scripts specific to crowdlabs to manage vistrails server
      - More changes specific for using vistrails server together with
      - Calling the right debugging functions when error occurs
      - Addind server-side RepoSync module modifications in HTTP package (by Phillip)
      <bugfix> Persistence package: Fixed load package error on Windows</bugfix>
      <feature> Added git executable to windows repository. It will be included
      <bugfix> Spreadsheet: fixed 'RuntimeError: underlying C/C++ object has
      <bugfix>Persistence package: fixed problem where persistent files
      <ticket>#295</ticket>
      <bugfix>Fixed bug where server method get_wf_graph_png would sometimes
      Adding missing dll needed by git to Windows distribution
      Added more dependencies to git on Windows.
      <bugfix>Persistence Package: adapted use of tar command to work
      <bugfix>Persistence Package: Added code to find tar executable similar
      <bugfix> Color Constant: Initializing Color widget with default white
      <bugfix>Updated all php scripts in extensions/http to work with
      Fixed a typo in the persistence package initialize function
      <ticket>#380</ticket>
      Adding v1.6 splash screen
      Preparing Mac files for 1.6 beta binaries.
      <ticket>#381</ticket>
      - Fixed a typo in the make_app script that would generate Vistrails.app instead of VisTrails.app
      VisTrails server:
      - Adding tar to Windows installer script
      <ticket>#382</ticket>
      <feature> Updated php scripts to work with Latex extension's new features
      - Updated script that generates release notes to work with git instead of subversion.
      <feature>ParaView package: Converted to new VisTrails package format</feature>
      <feature>Web Services package is now deprecated. Showing a warning message
      <bugfix>Batch mode: On Windows, VisTrails was not executing workflows
      <bugfix>Latex extension: delaying check for a valid url so we can include
      <bugfix> VisTrails shell was not using fixed-width font </bugfix>
      - Fixed typo in debug call
      - Package initialization messages are now shown on the splash screen on the Mac
      <ticket>#390</ticket>
      <bugfix>Pasted text in VisTrails shell was being ignored</bugfix>
      <feature>Changed all examples using relative paths to datasets to use HTTPFile</feature>
      <bugfix> Added workaround for RotateFileHandler problem on Windows when some
      <ticket>#392</ticket>
      <bugfix>Forwarding force build to server so the server can also bypass
      - Changed path_exists_and_not_empty() function in php script to avoid warnings.
      - Added missing ')' to debug call in application_server.py
      <ticket>#393</ticket>
      <ticket>#394</ticket>
      <bugfix>VisTrails Server: fixed problem in caching of history tree
      <bugfix>VisTrails Server: Applied fix to caching of history tree images when
      <bugfix>Replaced svn command with git command to get current commit (if present)</bugfix>
      - Changed from QPushButtons to QCheckBoxes for filters on Messages window.
      <ticket>#397</ticket>
      <ticket>#397</ticket>
      - VisTrails server: do not scale images to a fixed size to avoid introducing artifacts in the images
      - Keeping background transparent of filter types in Messages Window on Mac,
      - Reverting unix.py to use process.poll() in a loop to see if using process.wait()
      <bugfix> Fixed bug introduced on Windowsplatforms when changed os.chdir()
      <ticket>#398</ticket>
      Merge branch 'crowdlabs'
      - Updated list of example files to be included in Windows binary
      - Updated Mac installer build script to download a specific version of ALPS libs if
      Merge branch 'master' of gitolite:vistrails
      - Fixed most of the problems in test cases.
      - Fixed all errors in unit tests
      - minor adjustments to unit tests so they work correctly on Windows and with python 2.7
      - Changed VisTrails version number to 1.6
      Fixed the ParaView Error: "Cannot compare versions whose components are not integers" by using a modified version of Berk's patch.
      ParaView package: putting GeometryRepresentation and PVLookupTable in the Rendering namespace.
      Merge branch 'master' of gitolite:vistrails
      - Fixed errors in test suite after recent changes.
      <bugfix>Wiki extension: workflows were not being embedded in .vtl file</bugfix>
      <bugfix>Latex extension: added support for running vistrails locally</bugfix>
      <ticket>#405</ticket>
      <bugfix>Added support for executing workflows even if VisTrails is already
      <ticket>#406</ticket>
      <bugfix>Replaced code that would work only on recent versions of PyQt4</bugfix>
      <bugfix>Replaced more GUI code that would work only on recent versions of Qt/PyQt4</bugfix>
      <bugfix>LaTex extension: added support to work on Windows with MikTex</bugfix>
      <ticket>#408</ticket>
      - Fixed problem where the connections were not being reset when the ports of
      Adding folder for usersguide documentation using Sphinx
      <ticket>#414</ticket>
      Merge branch 'master' of gitolite:vistrails
      <feature>ParaView package: Added server configuration window options to
      <bugfix>Changed memory size to be computed in megabytes instead of bytes
      <bugfix>LaTex extension: When generating LaTex command using the Embed panel,
      <bugfix> Fixed infovis example </bugfix>
      Added script that builds html and pdf version of User's guide.
      - Updated version of User's guide to 1.6.2
      <bugfix> VTK Package: Fixed bug when drawing TransferFunction widget</bugfix>
      <feature> ParaView package: Added ScalarBarWidgetRepresentation to Rendering
      Added icons for mashup actions.
      Created branch for mashups feature.
      Changes to VTK package: Added support to send Camera when updating the VTKCell.
      Added support for interpreter to execute a pipeline with an extra list
      Basic GUI elements for Mashups.
      Added support for instantiating a Pipeline View in read-only mode.
      Mashups: Upgraded Aliases panel to Mashups Inspector.
      Merge branch 'v2.0' into mashups
      Starting integration with v2.0 branch:
      Merge branch 'master' into mashups
      Merge branch 'v2.0' into mashups
      Merge branch 'master' into mashups
      Merge branch 'v2.0' into mashups
      Merge branch 'v2.0' into mashups
      Updated Mac installer script builder to work with new version of the libs.
      Progress in the mashups integration:
      Updated Windows installer script to work with new version of the libs.
      Forgot to remove QVistrailView* from workspace.py when emitting signal.
      Merge branch 'v2.0' into mashups
      Merge branch 'master' into mashups
      Added support for changing aliases in Module Info Palette.
      Merge remote branch 'origin/v2.0' into mashups
      Merge remote branch 'origin/master' into mashups
      Merge remote branch 'origin/v2.0' into mashups
      - Added support for Cmd+R zoom to fit in Mashups pipeline tab
      Fixed a bug in vistrail controller that was not sending aliases when a new parameter was being created without setting a value.
      - Changes in the mashup pipeline tab now create a new version in the mashuptrail and that is reflected in the panels.
      Merge remote branch 'origin/v2.0' into mashups
      Added special panel for changing aliases in Mashup View.
      Merge remote branch 'origin/v2.0' into mashups
      Adding missing files from previous commit.
      Merged mashups list and mashup properties into a same tab.
      Fixed drawing in Mashups View when switching versions in History View.
      Merge remote branch 'origin/v2.0' into mashups
      Changes to alias details now create a new version of mashup instead of changing it inplace.
      Merge remote branch 'origin/v2.0' into mashups
      Merge remote branch 'origin/v2.0' into mashups
      core.db.io.load_vistrail() now returns the mashups from .vt file
      - Added support for saving and opening mashups with vistrail files
      - Displaying available mashups on the Version properties panel (they can be executed from there).
      <bugfix>Controller was not cleaning up temporary files when discarding changes</bugfix>
      Merge remote branch 'origin/v2.0' into mashups
      Fixed typo intoroduced in last merge.
      Fixed bug when resetting aliases in pipeline in mashups view
      Updated alps version in script to build mac bundle
      - Mashups button starts disabled untill a version is selected/created
      Merge remote branch 'origin/v2.0' into mashups
      Changed splash screen to 2.0 Beta.
      Merge remote branch 'origin/v2.0' into mashups
      - Added annotations to WorkflowExec in v1.0.2 schema
      - Workflow executions are now annotated.
      - Annotating workflow execution with mashup information.
      Merge remote branch 'origin/v2.0' into mashups
      - Showing a message when generating a Preview for a mashup and the pipeline
      <bugfix>Fixed parameter exploration in v2.0</bugfix>
      Merge remote branch 'origin/v2.0' into mashups
      Disabling the execute button in the mashup view
      Fixed Publish menus, including publishing to CrowdLabs.
      Merge remote branch 'origin/v2.0' into mashups
      Fixed gpl header in some files.
      Updated file headers to the Modified BSD License.
      Updated file headers to "Modified BSD License".
      Adding script to update header files to new license.
      Updated script to generate source release with v1.6 changes.
      Updated disclaimer image with new license.
      First attempt of fixing action events
      Reverted palette's title bar to default QDockWidget.titleBarWidget
      Making sure the palette's toolbar is not floatable.
      Making sure the palette's toolbar is not movable
      Fixed inital state of Palette's actions in View Menu.
      Added support for opening a vistrail in a separate window
      The v2.0 branch now contains the mashups code.
      - Fixed bug that allowed opening the same vistrail multiple times if it was open in a detached window
      - Added support for detaching Pipeline views from tabs using the detach button on the tab
      Activating/deactivating detached pipeline views now updates state.
      Merge branch 'v2.0' of gitolite:vistrails into v2.0
      Removed detach button from tabs and using mouse double-click event to detach tabs
      Added splash screen source file to repository
      Merge branch 'v2.0' of gitolite:vistrails into v2.0
      Updated the Mac bundle builder script to include the pdf of the user's guide.
      Added support for including usersguide in windows binary
      <ticket>#448</ticket>
      Updated mac_update_bin.sh script to work with v2.0 binary
      <ticket>#440</ticket>
      <bugfix>Brought back Packages menu</bugfix>
      <bugfix>Fixed Save Camera functionality in the Spreadsheet</bugfix>
      Fixed button sizes on Palettes.
      Fixed behavior of Tools Window.
      Fixed problem when displaying visual diffs.
      Spreadsheet now starts hidden.
      Fixed bug when detaching a pipeline tab that was not the current tab.
      More bug fixes when dealing with detached tabs.
      Updated users guide to v1.7
      First version of release notes for 2.0-alpha.
      Fixed typos in Windows Installer script.
      - Fixed "Publish > To Paper..." menu option.
      <ticket>#454</ticket>
      Merge branch 'v2.0' of gitolite:vistrails into v2.0
      <bugfix>Fixed header placement in xml files that were causing tests to fail</bugfix>
      Bug fixes:
      Changed headers of files in master branch to BSD license.
      <bugfix>Fixed header placement in xml files that were causing tests to fail</bugfix>
      <ticket>#454</ticket>
      <bugfix>Allowing opening vistrail files that contain mashups. Mashups will be ignored</bugfix>
      Replaced GPL license files with BSD files.
      Updated disclaimer image and about message with current license.
      <ticket>#456</ticket>
      <ticket>#457</ticket>
      - Fixed bug where after closing a pipeline view, it was not possible to select
      Fixed mixing of tabs and spaces in file
      Merge branch 'v2.0' of gitolite:vistrails into v2.0
      Bug fixes
      Mashups bug fixes
      Added support for executing selected node in History View
      Merge branch 'v2.0' of gitolite:vistrails into v2.0
      Merge branch 'v2.0' of gitolite:vistrails into v2.0
      <bugfix> File > Export > PDF was not working </bugfix>
      <bugfix>Enabled Edit Configuration and Show Documentation from a module's
      Merge branch 'v2.0' of gitolite:vistrails into v2.0
      <ticket>#456</ticket>
      <feature>Added support for multiple PythonSource configuration windows.
      Bug fixes
      <bugfix>Enabled Embed version by default when selecting Publish > To Paper</bugfix>
      - Replaced pin radio button by a more meaningful icon.
      <feature>Displaying mashups in workspace.
      Bug fixes
      Bug fixes
      Rearranged buttons layout of PythonSource Configuration Window
      <feature>Added support for html and mediawiki extensions to
      <feature>Added support for html and mediawiki extensions to
      Pass over documentation of Embedding VisTrails Files Via Latex
      <ticket>#432</ticket>
      - Removed QLatexAssistant palette from v2.0.
      <ticket>#432</ticket>
      <ticket>#472</ticket>
      <ticket>#473</ticket>
      <ticket>#443</ticket>
      <ticket>#479</ticket>
      Merge branch 'v2.0' of gitolite:vistrails into v2.0
      Merge branch 'v2.0' of gitolite:vistrails into v2.0
      <ticket>#475</ticket>
      <ticket>#476</ticket>
      Fixed bug where VisTrails would hang upon closing
      Updated contact e-mail address to contact at vistrails.org
      Added script to update e-mail contact in file headers.
      <ticket>#478</ticket>
      Merge branch 'v2.0' of gitolite:vistrails into v2.0
      <ticket>#485</ticket>
      <ticket>#476</ticket>
      <feature>Changed "Keep" button to "Tag" in the Mashups View</feature>
      <bugfix>Updated VTK, Persistence and Matplolib packages to use
      <ticket>#491</ticket>
      <bugfix>Mashups: creating aliases in mashup view was not updating the alias table</bugfix>
      Added close_all_vistrails() to api
      Removed debug messages
      Merge branch 'v2.0' of gitolite:vistrails into v2.0
      - Updated the script to build the release notes to use www.vistrails.org
      <bugfix>Mashups: Fixed bug introduced when removing gui
      Merge branch 'v2.0' of gitolite:vistrails into v2.0
      Merge branch 'v2.0' of gitolite:vistrails into v2.0
      <bugfix>.vtl files marked to be executed when opening were not executed</bugfix>
      - Changed the Mac bundle identifier from edu.utah.sci.vistrails to org.vistrails
      Merge branch 'v2.0' of gitolite:vistrails into v2.0
      <ticket>#456</ticket>
      Added new windows installer script to build 64 binaries
      <feature>Opening exported mashups using Open menu will execute them automatically</feature>
      Merge branch 'v2.0' of gitolite:vistrails into v2.0
      <ticket>#494</ticket>
      <bugfix>VTK Package: Call to ResetCamera() in vtkRenderer was producing wrong results</bugfix>
      - Updated release notes with latest changes.
      Updated e-mail contact in all files.
      Merge branch 'v2.0'
      Updated release hashes according to the actual v2.0-alpha release.
      Merge branch 'v2.0' of gitolite:vistrails into v2.0
      <bugfix>Parameter exploration with Color Constant was not working</bugfix>
      <ticket>#472</ticket>
      <bugfix>Parameter exploration with Color Constant was not working</bugfix>
      <ticket>#472</ticket>
      Updated documentation index file to display more levels in the table of contents.
      Fixed problem in nightly build script
      <ticket>#502</ticket>
      <ticket>#502</ticket>
      <ticket>#508</ticket>
      <ticket>#508</ticket>
      Updated release notes for next bugfix release.
      <ticket>#194</ticket>
      <ticket>#194</ticket>
      <ticket>#510</ticket>
      <ticket>#510</ticket>
      <ticket>#55</ticket>
      Merge branch 'master' of gitolite:vistrails
      <ticket>#55</ticket>
      <bugfix>SpreadSheet: prompt the user to save unsaved vistrails before trying to save a spreadsheet</bugfix>
      <bugfix>SpreadSheet: prompt the user to save unsaved vistrails before trying to save a spreadsheet</bugfix>
      Small bug fix where NameError: global name 'window' is not defined would sometimes appear.
      Small bug fix where NameError: global name 'window' is not defined would sometimes appear.
      <bugfix>MultiHeads configuration was not working on 2.0 </bugfix>
      <bugfix>MultiHeads configuration was not working on 2.0 </bugfix>
      <bugfix>Fixed unable to display jpeg images in the spreadsheet
      <bugfix>Fixed unable to display jpeg images in the spreadsheet
      <bugfix>Dragging a version directly on a spreadsheet cell was not executing the workflow</bugfix>
      <bugfix>Dragging a version directly on a spreadsheet cell was not executing the workflow</bugfix>
      Added microsoft redistributable packages used by Windows installer
      <bugfix>Removed matplotlib backend selection warning</bugfix>
      Added missing file and other small fixes.
      - Added vistrails server starter script path to server.cfg file
      - Updated alpha released version.
      Merge remote-tracking branch 'origin/master' into v2.0
      Updated splash screen for beta release.
      - Commented out missing print
      Merge remote-tracking branch 'origin/master' into v2.0
      Upgraded triangle_area.vt workflow
      <bugfix>Fixed problem where unrequested vistrail temporary files were being created during test suite</bugfix>
      Upgraded triangle_area.vt workflow
      <bugfix>Fixed problem where unrequested vistrail temporary files were being created during test suite</bugfix>
      Ran dos2unix on doc/usersguide/batch.rst file.
      Added documentation about vistrails server setup.
      Merge remote-tracking branch 'origin/master' into v2.0
      Updated bacth documentation to point to new vistrails server documentation instead of crowdlabs
      Merge remote-tracking branch 'origin/master' into v2.0
      <bugfix> Accessing Module Annotate from context menu did not work</bugfix>
      Updated splash screen for beta release.
      Merge remote-tracking branch 'origin/master' into v2.0
      Updated release notes for v2.0 beta.
      Updated release version of windows files.
      Updated alps version number
      <bugfix>Mashups: editing an alias' values list had no effect</bugfix>
      Updated release notes to include mashups fixes.
      <bugfix>VTK package: fix problem when upgrading vtkCellArray.InsertNextCell input port</bugfix>
      Updated release notes for bug-fix release.
      <bugfix> Mediawiki extension: fixed undefined variable </bugfix>
      http and Mediawiki extensions: added more configuration variables to config.php
      VisTrails server: force killing vistrails if it was hanging when using startup scripts
      Fixed qt.conf problem in installer script files on Windows.
      Merge branch 'v2.0' of vgc.poly.edu:vistrails into v2.0
      <bugfix>MySQLdb was not being shipped correctly in Mac binary</bugfix>
      Updated release notes for next bug-fix release.
      <bugfix>Fixed bug in iceCream.vt example</bugfix>
      Added example fix to release notes.
      <bugfix>Parameter Exploration: Changed call to update the progress bar to be thread safe</bugfix>
      Included fix to parameter exploration progress bar into the release notes.
      <ticket>#556</ticket>
      Added rule for removing old pyalps location from Windows 32-bit install
      <ticket>#534</ticket>
      <bugfix>Decreased level of debug message when removing elements from Thumbnails cache</bugfix>
      Updated Splash screen to v2.0 release.
      Updated alps version in Mac 10.6+ binary to 2.1.0b1-r6115
      Updated alps version in Mac 10.6+ binary to 2.1.0b1-r6115
      <feature> Added alps package to VisTrails 64-bit Windows Binary </feature>
      Updated release notes to include latest changes.
      Added batchq to list of python packages to be included in the Mac 10.6 Binary
      <ticket>#562</ticket>
      <bugfix>Workspace: made loading mashups more efficient</bugfix>
      <ticket>#564</ticket>
      <ticket>#487</ticket>
      <bugfix>Workflow results that used a VTKCell were consisting of a black
      <ticket>#430</ticket>
      <feature>Added CLToolsWizard.command file to Mac Binary</feature>
      <ticket>#521</ticket>
      <ticket>#445</ticket>
      <ticket>#464</ticket>
      <bugfix>Running instance was not accepting parameters from another instance</bugfix>
      <feature>API: VisTrailsAPI.execute() now accepts the same parameters
      Updated Release Notes for 2.0 release.

Erik ANderson (54):
      Moved SciPy modules into new architecture.  Simply added core. to various paths as necessary
      Fixed import paths to work with new vistrails architecture
      Added the core. pathing to the modules and registry to reflect the change in organization.
      Separated out the filter types and added a watershed-based segmentation filter
      Added support for DICOM series reading.  Tested with 3 and 4 D datasets.  Cannot do anything with them yet, but we can read them.
      Added Region selection and full DICOM slice-based exploration
      Bugfixing for DICOM Slicing.
      Added CastImageFilter to allow writing of images that are natively in unsigned short (or other incompatible formats.  This provides a way to view mostly accurate MRI images from DICOM volumes.  However, I have discovered that indexing into the DICOM volume is NOT straightforward.
      Added ExtractImageFilter to collapse a dimension from the DICOM volume.
      DICOM volume loading works.  DICOMReader was deprecated by ITK so we now use GDCMImageIO/Reader.  Unfortunately, there seems to exist no way to generate valid volumes without intervention as multiple, embedded volumes cannot be separated it seems.
      scipy uses smart memory management.  This broke pipelines that counted on matrix manipulations happening down the pipeline to the initial input matrix.  To rectify this, I make sure to call .copy() on appropriate data products.  Files Touched:  Matrix.py, MatrixOperations.py
      Added CurvatureAnisotropicDiffusionImageFilter to provide edge-preserving smoothing filtering.  This will later be coupled with edge detection to provide semi-automatic segmentation
      Fixed up some Matrix subclasses and included some more accessors
      Fixed Matlab import to support multiple Matlab versions exporting .mat files.  The ordering and number of header fields changed between matlab versions 6.5 and 7.2  All formats I've encountered are now supported.
      More filters for help with segmentation.
      Added CurvatureFlowImageFilter to the smoothing filter set.  This will be used during the image smoothing step of the segmentation algorithms.
      Removed the optional part of the pixeltype and dimension outputs.  This streamlines the pipline creation quite a bit.
      Added Segmentation Filter ConfidenceConnectedImageFilter used for 3D segmentation with 1 seed point.  This does NOT require a scalar range be used as input so can be done more automatically across runs.
      SciPy version 0.5.2 moved fft functions out of the fft modules and into the global namespace.  Previously, from scipy import fft would import the fft module required fft.fft(...) to be used.  Now we check to see if the import results in fft being a function or a module to prevent this error
      Fixed Open File button problem on Windows. This is a temporary fix. I'll implement Jason's suggestion later. (Manu)
      Added basic support for morphological operation.
      Fixed tabification before changes to .emacs file made it automatic.
      Removed import of core.logger
      Changed the ElementMultiply module to function as expected when given
      Added support for 2D FFT and automatic Windowed Fourier Transform.  The 2D FFT module is FFT2 and provides output in the form of a 2D matrix of the appropriate size.  THe WindowedFourierTransform module takes as inputs the Signal and Sampling Rate of the input and outputs a SparseMatrix where the rows are the timeslices and the columns are the FFT output for that timeslice.  If the user wants more control over this, there are optional inputs Window Size and Stride.  The Window Size input controls the size of the sliding window and the Stride input controls the number of samples the window moves per time-slice.  The default to the sampling rate and the samplingrate/2 respectively.
      Added STFT with multiple window parameters
      Added the initial version of namespaced Numpy and Scipy.  This will be evolving a great deal over the next few weeks, but so far it seems to be working properly.  This package is meant as a total replacement for the current SciPy package, but these changes are far-reaching and it should not be switched out quite yet.
      Added several DSP classes to the new package.  The ShortTimeFourierTransform is still not functional, but FFT and FFTN have both been tested for the cases of single signal and signal ensemble inputs.
      Fixed FFT and FFTN to properly handle signal ensembles.  FFTN is NOT appropriate for use with ensembles as the frequency content gets distributed to all output phasors instead of representing the unique signals properly.  To fix this, I implemented the FFT in a loop over the signal array (if necessary) so the frequency content remains unique for the single input signal
      Fixed problems with STFT of both single signals as well as Ensembles.  The package is much more unified in terms of dealing with both single signal and ensemeble inputs.  All modules now handle either one transparently.  STFT has been tested with some generated signals and performs as expected.
      Allowed vtkScaledTransferFunction to take either a vtkAlgorithmOutput or vtkDataSet object as inputs.  If input is supplied on both of these ports, the vtkAlgorithmOutput port is treated preferentially and the vtkDataSet-based port is ignored.
      Added Dataset port to vtkScaledTransferFunction in order to provide use with vtkDataSet objects instead of just vtkAlgorithmOutput types.
      Fixed some typos in error message relating to adding modules to the registry
      Fixed SetFileName requirement for the vtkDICOMReader.
      Merge the NumSciPy package with my local repository.  This represents
      Added support for reading of nrrds into numpy array types.  Currently,
      Added support for vtkTIFFReader to allow volumetric (slice-based) reads.  This is necessary as the underlying vtk class
      Provide general bug-fixes and additional modules to reflect more of
      Added method to the Module base class in order to fascilitate package
      Changed the method:
      Bringing the distributed NumSciPy package up to date with my (stable) development copy.
      Re-ordered Module initialization to fix Convert bug
      Fixed vtk import problem by adding a mapping from long -> Integer.  This mapping was not there causing things that returned vtkIdTypes to map to None, which in turn caused problems at initialization-time.
      Additional modules added to the ArrayOperations namespace:
      Changed __init__.py to use import _____ instead of from _____ import *
      Added support for Picking in a VisTrails cell.  By default, the vtkRenderWindow contains a picker.
      Modified Files:
      Fixed visual diff bug introduced by the debugger:  The QGraphicsModuleItem.bp_shape variable was not properly initialized.
      Update of NumSciPy package to latest stable development version
      Updates to NumSciPy trunk package to bring it up to current development
      Added comments and docstrings to the Plotting package and fixed a bug preventing multiple datasets to properly be plotted in a scatterplot
      Added better PNG writing support through the scipy.misc toolchains.
      Added support for hiding the standard Matplotlib Toolbar.  This is an optional input
      Initial (functional) ParaView package

Fernando Seabra (14):
      Simple fix in the module_descriptor file, so the modules could have
      New module added to the controlflow package.
      The modules, except the VTK ones, didn't have an output port that
      A few changes inside control flow package, just to make the code
      A few more changes in the control flow package.
      A few more changes in the controlflow package. Due to these changes, the
      The triangle_area.vt example was modified to show the Cross module and
      A bug was fixed inside the controlflow package. More specifically, if
      A "print" line, used for debugging, was deleted from controlflow.py.
      Just a new organization for the controlflow package; a folder was
      Now, if the workflow has a loop, the execution log keeps track of this
      Commiting many changes that I did in the trunk...
      A bug was fixed inside fold.py, something I had forgotten.
      Commiting an example that is being used in the user's guide file. It's a

Fernando Seabra Chirigati (1):
      <bugfix>Now persistent cache works after one execution</bugfix>

Geoff Draper (2):
      Bugfix (resolves Ticket #209): The Create button on the Database Connection dialog now listens to all text fields. Done by adding the following lines to QConnectionDBSetupWindow::connectSignals(self) in the file open_db_window.py:
      Two small bugfixes for command-line switches:

Huy T. Vo (13):
      Merging with PCMDI repo
      Changes for ParaView and CDAT integration
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      Corrected the last commit and commit message.
      Removed the example GUI from cdat package.
      On the Mac, associate each vtk render window to a QWidget to avoid the conflicts of Qt's event loop distributed events to deleted windows.
      Added an Internet Explorer Cell, IECell, to the spreadsheet. This makes use of ActiveQt and ActiveX, so it's only available on Windows, but can be used to view Flash and PDF contents.
      Fixed a typo on the usage of issubclass() which prevented subclassed sheets to be used by the spreadsheet
      <bugfix>Fixed crash when running VisTrails 64-bit on Windows with more than 4GB of RAM</bugfix>
      test changing widget name
      <bugfix>Fixed the issue of being unable to activate windows under Mac OS X Lion.</bugfix>

Huy Vo (205):
      Removed import system
      gui/pipeline_view.py:
      trunk/vistrails/packages/spreadsheet/spreadsheet_sheet.py:
      trunk/vistrails/gui/qbuilder.py:
      trunk/vistrails/gui/generate_module_tree.py:
      trunk/vistrails/core/common.py:
      trunk/vistrails/core/data_structures/graph.py:
      trunk/vistrails/gui/vis_application.py:
      trunk/vistrails/gui/vis_application.py:
      trunk/vistrails/core/data_structures/graph.py,
      - Re-org code and added comments/docstrings to follow our coding convention
      packages/spreadsheet/images:
      trunk/vistrails/gui/qbuilder.py:
      Moved builder_utils.py to core.utils as color.py
      vistrails/gui/shape.py
      vistrails/core/utils/color.py:
      trunk/vistrails/core/utils/color.py:
      Separate Paramter Exploration into GUI and functionality. Changed bulk_changes.py to param_explore.py, removed pipeline_analyzer.py
      vistrails/gui/param_explore.py:
      Just a temporary check-in for a working search frame, these will be replaced later
      This is a change to a new Vistrail GUI system. Handles multiple vistrails in either SDI or tabbed view. Still need more unit tests
      Deleted more old GUI files
      Added files that are supposed to be added in the previous check-in
      gui/method_dropbox.py:
      Added back Parameter Explorations and fixed bugs
      Added back the color codes in the version tree view
      vistrails/gui/theme.py:
      Added Query By Example, it is now a tab next to Pipeline view and Version Tree view. It is only performing query for each vistrail, not all vistrails opened. Need a separate widget to perform on all opened vistrails
      vistrails/gui/pipeline_view.py:
      vistrails/gui/builder_window.py:
      vistrails/gui/builder_window.py:
      vistrails/gui/graphics_view.py:
      vistrails/core/vistrail/pipeline.py:
      vistrails/gui/vistrail_controller.py:
      vistrails/packages/spreadsheet/spreadsheet_tabcontroller.py:
      vistrails/gui/method_dropbox.py:
      vistrails/gui/method_dropbox.py:
      vistrails/gui/pipeline_view.py:
      Fixed bugs in connecting modules only in one way (source to destination port)
      Fixed using the wrong function for update version notes
      vistrails/gui/theme.py:
      vistrails/gui/vistrail_controller.py:
      Fixed Ticket #10: (From cornell) Setting ports in PythonSource
      Fixed Ticket #23: VisTrails Diff between two version whose common parent is the empty version doesn't work
      Fixed Ticket #27: (From cornell) Deleted panels don't come back
      Removed unused SetParentInfo
      trunk/vistrails/gui/builder_window.py:
      Fixed test case
      Put cursor shapes side-by-side instead of a drop-box
      Added accidentally removed View Full Tree Action
      Added QTimer and dragging distance to avoid QGraphicsView stalling on
      Fixed Ticket #35 by replacing Alt+Click with Meta (or Shift+Alt) + Click
      trunk/vistails/gui/vistrail_toolbar.py:
      trunk/vistails/core/system/__init__.py:
      Uses activateWindow instead of setActiveWindow
      Fixed memory leaks when closing vistrails
      Fixed memory leak on QVTKWidget and perform minor spreadsheet code re-org
      Removed a print command
      First version of enabling SubModule in VisTrails. Run and demo-able but still missing ways to handle some interactions from users.
      vistrails/core/vistrail/module.py:
      vistrails/packages/spreadsheet/spreadsheet_sheet.py:
      Removed type token from module connectors, create a new output result: InvalidOutput for use with Variant
      Recovered animation feature of VTK cells. Fixed multi-screen positioning bug
      Optimize the code to initialize VTK faster
      Fixed synchronization in the spreadsheet under Linux. Flip event Y position (if neccessary) in QVTKWidget::getActiveRenderer()
      Added Matplotlib package and its example to VisTrails
      Tuple is running and fixed bugs about serialization of Tuples
      trunk/vistrails/core/modules/module_registry.py
      Fixed bug of un-store stripped values
      Untabify all tabs
      Moved QVTKWidget into vtk package
      Moved VTKCell from the spreadsheet package to vtk package, add spreadsheet dependencies on the pylab module
      trunk/vistrails/packages/HTTP/__init__.py:
      Forgot to add vtkcell files from last commit
      Fixed pylab package doesn't show up on the spreadsheet. Make sure to set back-end to Qt4 before importing pylab.
      The startup process is now separated from the Qt QApplication code to core.startup. Thus, it is possible to import vistrails without running a QApplication in a python script (sample in core.inspector.py).
      Added a missing update call to showPrompt()
      Added inspectParameters() code
      Added InteractionHandler to VTKCell.
      Allow the spreadsheet to run in non-interactive mode if the user want to
      Added serialization of local registry. This should fix copy & paste of PythonSource as well as Tuple module.
      Fixed another bug with copy subnetwork containing a PythonSource or Tuple
      Use the logger from core.startup.logger
      Make the spreadsheet interacts more intuitively in the console mode
      Fixed several sub module bugs and loading vistrail doesn't need package dependencies, only loading pipeline.
      Added widgets for the new parameter exploration interface. This is in progress.
      Show tool tip while snapping ports
      More progress on the new parameter interface
      Delete resolveAliases calls from pipelines. Fixed Spreadsheet open bug.
      vistrails/gui/pipeline_view.py
      vistrails/core/system/windows.py:
      Fixed Bugs in naming ports in abstraction
      Added method 'name' for OutputPort
      Use name for OutputPort
      Added checking for Variant type for serialization
      Progress on the Parameter Exploration UI
      Parameter Exploration Run icon
      Parameter Exploration is fully functional and waiting for its first ticket.
      Workaround for now to create temp file
      Bug fixed on the spreadsheet. It should be able to load a saved sheet now.
      Show the spreadsheet on demand when there is no builder
      Fixed bug when selecting 'Skip' for a parameter in parameter exploration
      Fixed the long text showing of Float type when using user-defined function in parameter exploration
      Fixed the parameter exploration bug with time dimension
      Fixed bug when dragging virtual cell with multiple types of cells that happens to share a same annotated id
      Removed reference to the sheet widget when removed a sheet from the spreadsheet
      Several bug fixes on the parameter explorations, caching and search widgets (working with Carlos)
      In parameter exploration, formally edit the pipeline by actions to avoid mangled module ids in the interpreter. This fixed the swapped cells problem
      Enable scrollbar when there are too many widgets
      Fixed Module.updateType.summonCall setting is_cacheable in a wrong place (result vs. self)
      Only import MySQLdb when nologger is False
      Fixed uncommited item delegate bug for list table
      Allow searching for local directory in Path on Windows
      Removed widget from self._functions when the users remove a method
      Fixed bug of port ordering in local registry
      Work around for using port orders at Module Instance
      Used wrong function to remove an item from a dictionary
      Added CORIE examples and fixed some bugs on the vtk cell. Multiple interaction handlers are supported now as well as start and end interaction event.
      Fixed signature for parameter. Each module can have a description to show below the module name in the pipeline view. The description is extracted from the key '__desc__' from the module annotation.
      Several bug fixes for releasing a binary version for the CORIE group
      Fixed to use relative path for CORIE data files
      Fixed error handling bug on the Parameter Exploration and resizing bugs (for Linux) on the spreadsheet. Write a new base class for spreadsheet cell widget.
      Fixed memory leaks with VTK to run large CORIE data files. Also fixed method drop box deleting bug.
      Wrongly removed the assignment while debugging. Fixed now.
      Workaround for freeing vtk widget bug for now. There might be some VTK leaking under Linux. Fixed the tuple type for noncache interpreter.
      Improved the query by example to take module parameters into the query:
      Check reg exp query to match the whole string (instead of a substring)
      Added query to visible empty-name versions (terseGraph)
      Added handlers for all vtkCommand events to use in interaction widgets. We only had InteractionEvent, StartInteractionEvent and EndInteractionEvent before.
      New tackle at the editing mode on the spreadsheet using drag and drop. Parameter exploration can be pushed back to the version tree on the builder. Added the analogy API. For now, we can only apply to a single cell. The interface will be tweaked to apply to the whole column and selected cells.
      Fixed crashing when moving VTK cell across sheet
      Fixed spreadsheet several editing-mode bugs for new release
      Added 'InteractorStyle' input port to VTKCell to allow different vtkInteractorStyle for VTKCell (e.g. vtkInteractorStyleImage)
      Re-capture instead of use cached pixmap in editing mode
      Fixed the spreadsheet title bar problem.
      Some changes on Linux to support con-current update on interactive widget (flush before switching to Windows)
      Work around scipy bugs on Windows: always cast scipy.ones and scipy.zeros to float (Carlos)
      Fixed the open/save problem on the spreadsheet causing by Editing Mode
      Fixed bugs on Editing Mode caused by my commit yesterday. Hopefully I'm not making a recursive bug loop again...
      Added Undo, Prune versions and saved queries. The saved queries interaface is still being improved with query thumbnails and query editing...
      Remodel the saved query lists. Query By Example can also be saved. Added Preview and Edit actions for each saved query.
      Fixed Mac-related issues with editing mode
      Fixed synchronization bug on the Mac (seems to be faster than both Linux and Windows). There are still problems with cell toolbar and resizer that has not been fixed yet.
      Explicitly called vtkCarbonRenderWindow::UpdateGLRegion to fix overlapping problems when resizing the VTK cell.
      Disabled un-matched parent items
      Fixed toolbar not showing bug. Moved the handler code from sheet-level to tab-level. Hopefully fixed the Mac problem.
      Added an item delegate to the Preferences menu. Fixed some warnings in the VTK package.
      Fixed ticket #58: Viewing a non-synced cell messes up camera in synced cells
      Addressed multiple issues with Parameter Exploration in ticket #80 and #144.
      Make sure to removed temporary files attached to the cell widgets. This fixed ticket #110
      Fixed ticket #80 again. This has been tested on Windows/Suse and Mac OS X. Ignore the garbage painting state of the cell toolbar in Mac OS X since this will be gone in the next change to the spreadsheet.
      Several improves on the spreadsheet to avoid the annoying of holding the Ctrl key while selecting and interacting.
      Fixed the spreadsheet issue on Ubuntu.
      Fixed crashing Matplotlib on Ubuntu.
      Added 'Save camera' into VTK cell widget
      Added default spreadsheet size into preference dialog
      Fixed bugs on the spreadsheet on trunk and branch:
      Fixed the minor annoying bug of losing focus when dragging a module into the pipeline view
      Fixed the selection bug when click on the Select All button on the spreadsheet
      Fixed Parameter Exploration bugs where parameter widgets did not update correctly when changes are made to the pipeline. Fixed in trunk, v1.0 and cs5630 branches.
      Forgot to clear the exploration tab when no pipeline is selected. Fixed in trunk, cs5630 and v1.0 branches
      Work-around for the issue with Constant class outside basic package. Need a more general solution in the future.
      Added a 'Locate' button on the Edit Mode to show the version that has generated a particular cell
      Set up the exporters to take the VTKCell class for exporting the scene
      Added "Set Module Label" feature (through the configuration pop-up menu of the GUI)
      Changed the behavior of selecting new cell locations on the spreadsheet (cycling vs. always (0,0))
      Added getCurrentVersion() to get the current version number on VisTrails to use with Maya plug-in
      Made Vistrail::getFirstCommonVersion(v1, v2) return 0 when either v1 or v2 is -1
      Added a flag if we want to click on the background to unselect everything
      Handled double click event separately for unselecting background
      Replace the close tab button to look more Windows on Windows (similar to Qt and Firefox)
      Made the overlay version prop click through
      Made QBuilderWindow::quitVisTrails() to return True when it can quit but Qt doesn't possess the main event loop
      Added the flag QInteractiveGraphicsView::canSelectRectangle to specify whether or not we are allowing click & drag selection on the canvas
      Restored the "Clear Recent Searches" in the QSearchBox
      Moved propagatingEvents to class definition and swap condition checks to avoid events arrived before initialization.
      Made the Builder Window the parent of confirmation dialogs
      Added width and height to the offscreen rendering output. By default, it outputs 512x512. We need the newest VTK installed if we want to output the image size larger than the physical screen,
      Spreadsheet maintenance and bug fixes. Also included exporting images
      Merged changes from the plugin into trunk (wrong optimization and event filter), fix forwarding mouse event forwarding.
      Changes to store the spreadsheet cell thumbnail along with the widget.
      The timer for the version tree animation never gets terminated after its first use, causing high CPU usage after that. The terminating condition for the timerEvent() is fixed now.
      Commit many changes (since a very long time) from my local machine to
      Fixed a typo in calling tupleModule.set_input_port() causing ModuleError on setting module functions
      Added support of InfoVis to VTKCell, current the saving camera feature is not working with InfoVis (because there are no direct SetCamera port for InfoVis classes).
      Fixed incorrectly-sized matplotlib cells after dumping images to files.
      Forced update on resizing matplotlib figure using the new API.
      Fixed the _find_get_set_methods signature for newer VTK
      Added VTKViewCell for displaying vtkRenderView compatible with the current VTK trunk. Just connect vtkRenderView to VTKViewCell. First attempt, only tested on Linux.
      Added the InfoVis example using the new VTKViewCell.
      Fixed the pipeline execution mechanism in the spreadsheet that didn't work with the new interpreter interface.
      Specifically enabled the 'SetInputArrayToProcess' method of vtkAlgorithm class to use for the InfoVis package. This port was disallowed earlier for some reason, so we have to watch if this will cause any issue.
      Removed SetInputArrayToProcess from the disallowed port
      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.
      <feature>Allow the history view to be detached from the builder window through the command line options -D or --detachHistoryView</feature>
      <bugfix>Fixed Python Wrapping issue with VTK 5.7.0</bugfix>
      Kitware has put back the Python signatures to method docstrings. We no longer need the temporary fix of parsing C++ signatures into Python
      Added an example package showing how to add GUI elements to VisTrails (from a packacge). This is a GUI for pythonCalc which lets users specify parameters, preview calculations and add a PythonCalc module into the current pipeline.
      Use hwprefs to get memory size instead of the system_profiler which is a bit heavier with CD/DVD drive probing. Still fall back on system_profilerif hwprefs is not available.
      Added a package to demonstrating our API for manipulating vistrails and pipelines.
      Use 'system_profiler SPHardwareDataType' instead of 'hwprefs' as Dave suggested to get the physical amount of RAM
      <bugfix>Fixed the flickering issues of VTKCell on Windows</bugfix>
      Fixed a typo on platform types
      A script to extract resource files from xxxx_rc.py
      Apply the patch from Berk to enable VTKCell to work with the ParaView package in cilent-sever mode!

Jason Callahan (10):
      Cosmetic changes to enforce coding standars.
      More Cosmetic changes to enforce coding standard.
      Cosmetic changes to enfore coding standards applied to
      Cosmetic changes to enforce coding standards applied to
      Comsmetic changes to enforce coding standard.  Applied to /core/util and all coresponding files.
      Cosmetic changes to enforce coding standard, applied to
      Cosmetic changes to enforce coding standard.
      Cosmetic changes to enforce coding standard.
      core/modules/module_registry.py:
      This is the SCIRun package. It still needs a viewercell before it will be read

Jason Shepherd (3):
      ENH: Update to exclude vtk class
      ENH: adding vtksnl sandbox package
      Enabling "SetInputArrayToProcess" for vtksnl.

Kathryn Rodgers (2):
      Initial check in of the analytics package for VisTrails.
      Change in a module of the analytics package for Vistrails.

Lauro Lins (1):
      A    vistrails/core/vistrails_tree_layout_lw.py

Lorena Carlo (12):
      Hi,
      commit 07f3d05694dabebfd34779a024e0c5c788f42233
      I think, there was a problem with the name (white spaces).  I am sending it again.
      Bug found by Tommy in the webservices package.  If the user put white spaces between a ";" and a web service url, in the startup.xml file, then the white space was considered as part of the namespace. It is fixed now trimming the urls from wsdlList.
      Hello,
      webServices package performance improvement:  The data of the methods and complex types is serialized in a configuration file.  The wsdl remote file is parsed only when the configuration file is created.  This file is created if any of the following conditions are met:  The configuration file does not exist; the ZSI stub files are outdated in comparison with the modification date of the web service; there is no information about the modification date of the web service.
      Bug fixed:  The name of the port self had a conflict with the name of one of the ports.  Whenever this happens the program add a _number to the original name.  I loaded all of the noaa web services in the link he gave us and they could be loaded without problems.  I created a small demo and the following web service is needed:  http://opendap.co-ops.nos.noaa.gov/axis/services/WaterLevelVerifiedSixMin?wsdl
      DataTransformation_webservice.vt:  Change in demo, instead of using File module, the demo now uses HTTPFile module to be able to get the xsl file from the web (the file was uploaded to VisTrails web site).
      EMBOSS_webservices.vt:  This example used abstractions and with the new features (grouping/ungrouping) it didn't work, so now is working.
      Documentation was added to the notes of the nodes of the version tree of each of the web services demos.  This will help the users to know which web services have to be configured in VisTrails for the demo to work and also how to do this configuration.
      A bug in the demo EMBOSS_webservices.vt was fixed.  It was only showing one of the images of the array of images in the prettyplot workflow.
      __init__.py:  Fixes in the package. Validations, exceptions capturing and more descriptive error messages.  Support for attributes inside complex types, these are not common, but just in case.  Correction of a bug in repetition of names in the stub generated files.

Martin Cole (13):
      add package that wraps TetGen, Note: the makefile contains local paths since I am not sure yet how to handle configuration in vistrails, the issue likely goes away when we aren't forced to create packages in this directory
      remove mistakenly added file
      add check for file generated by dotty, print error msg if file does not exist, before continuing on to exception
      workaround for subprocess wait race condition
      order ports on the module icon in the order they were added to the registry
      fix MissingModulePackage exception, add MissingBaseClass exception, replace assert, with the new exception
      add SCIRun Viewer cell for the spreadsheet, fix ShowField interface
      use non threaded interface for the SCIRun Viewer, add a timer to trigger updates
      sync with latest scirun
      sync with SCIRun
      update for use with new python module interface, abstract categories inheritance, remove module and type scirun_ prefix for more natural scirun user interface
      new init file generated from the new algorithm xml description files in scirun, cm2view is not yet functional.
      add base for rendering widgets

Matthias Troyer (2):
      <bugfix>Fixed arguments of get_wf_graph_png rpc call</bugfix>
      vtlcreator package: fixed a bug when locator is None

Nathan Smith (2):
      ensemble_pipelines.py - contains the EnsemblePipelines class.
      Fixed import path.

Philip Mates (2):
      Added project listings to web repo options.
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails

Phillip Mates (44):
      itk package completely reorganized in order to facilitate namespaces.
      Reorganized package so that it passes around Image Wrapper Objects instead of itk Image objects, Dimension values, and PixelType objects. This eliminates a lot of redundancy when using vistrails.
      More filters and filter files have been added and a little bit of error handling has been added sporadically. A Kernel object has been added to the ITK.py file
      These two files aid in the development of the itk package.
      fixed import typo
      added help text to __init__.py, cleaned up comments on filter_generator.py.
      <feature>Added helper methods, get_inputPort_modules and get_outputPort_modules, to get modules that connect to a given input port or output port</feature>
      <feature>Added basic online web repository (crowdLabs) user authentication dialog</feature>
      <feature>New module, RepoSync, has been added to the HTTP package, which enables data files to be synced with an online repository (crowdLabs)</feature>
      <skip>
      <bugfix>Fixed Vistrail merge casting bugs</bugfix>
      <feature>User may now designate permissions when uploading vistrail to web repository</feature>
      <bugfix>Minor UI fixes to web repository dialog</bugfix>
      <bugfix>repository_vt_id now represents the crowdlabs vistrail object id instead of the vistrails db id</bugfix>
      <bugfix>Fixed web repository commit bug where updated vistrail files where not successfully loaded into VisTrails after being downloaded</bugfix>
      Typo fix and error handling for web repositroy gui
      Ability to read Config File added to vt server
      Improved error handling by returning exec status
      can now upload to projects (and vistrail servers)
      fixed typo run_vistrails.php
      changed is_local bool to be a function parameter
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      vt config webRepositoryLogin is correctly saved.
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      Added creation of dir for non-local run_from_db calls
      Refactored http modified header error handling
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      Exposed wiki ext. params showworkflow and showtree
      Support for VisTrail Server status pining
      watch_vistra...py now logs server coming back up
      Merge branch 'master' into crowdlabs
      Merge branch 'crowdlabs' of vistrails.sci.utah.edu:vistrails into crowdlabs
      Re-adding mediawiki params showworkflow and showtree in crowdlabs branch
      Comment out pingserver in application_server.py until it is fixed
      Updated Chris AtLee's poster code for py2.7
      Show port_spec sigstring in PortMismatch exception
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      <ticket>#398</ticket>
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      Switched from using pipes.quote to commands.mkarg
      <ticket>#154</ticket>
      Merged crowdlabs & master ver. of RepoSync module
      Added traceback logging to excep. in applc_server
      Removed wf indexing import/methods from appl_serve

Steven Callahan (50):
      Add example that uses an interactive clipping planes and volume slicing.
      Added a configuration button to the modules.  This now opens a menu
      Minor changes to the builder.  The largest changes are to the
      Fix uncommented line.
      pipeline_view.py: Fixed a bad case in the selection strategy by reworking the logic.
      Add Ctrl+E sequence to edit module configuration for currently
      Removed the annotations tab container and put it in a modal dialog that is
      Add undo and redo buttons
      Removed the vistrail view tab bar and associated classes.  The
      vistrail_toolbar.py:
      Moved the view toolbar to the top.  The top toolbar is now uniform in
      Add a minimum size bounding rectangle to the graphics views for nicer
      Add a software renderer to the terminator example.
      Miscellaneous GUI bug fixes and cleanup.
      Miscellaneous GUI changes to improve the consistency and look of the builder.
      Miscellaneous GUI changes to improve the consistency and look of the builder.
      Minor fixes to the query interface.  The reset query button now comes up when
      Fixed scheme for execute button and menu updates.  The states now
      Fixed version selection bugs. Drag selection now sends out the correct signals, versions and connections now behave better when drag selecting, and two version selection for the menu visual diff now uses the correct ids when executed.
      Switch to the history tab when executing a query from the qbe or pe tabs.
      Added a general preferences tab that allows the user to change a
      Minor gui changes:
      Fixed where the methods panel was not getting updated on delete in the query canvas.  Also changed the color of the skip icon in the parameter exploration tab.  Finally, removed a rogue print statement.
      Save file open and save directory to configuration.  This is replacing code that was accidentally removed with a previous reorganization.
      Fixed the saving of preferences by changing command line defaults
      Add autosave to the preferences.
      Fixed bugs with pipeline view.
      Removed separator from toolbar that used to separate bookmarks.  Branch and Trunk.
      Added an interface feature that allows tags on the version tree to be edited directly by double-clicking
      Change shortcut for reset in graphics view from r to ctrl-r so that it does not interfere with version text items.
      Add a transparent overlay to the version viewer that shows the selected version's
      Minor bug fix to disallow editing tag of root node.
      Refactored the toolbars in the builder window to make it easier to customize them.
      Remove reference to viewToolBar from api.
      Add single document support back into the builder.  This is off by
      Improvements to the version properties overlay.  An expand button is now placed
      Revisited the notes dialog to make it more user friendly.  Buttons are now included
      Minor fixes and changes to make the builder more general.
      Interactive expansion and collapsing in the version tree.  The three
      Basic support for animating version tree changes.  This is
      Compute a description for each action that is now displayed in the
      Added descriptions to the version tree.  They show up in place of
      Added hide/show functionality to the controller as a simpler and
      Add functionality to change the number of most current
      Minor bug fixes with editing version tags directly
      Fixed some bugs and annoying behavior with autosave.  A dialog
      Fixed bugs with direct tag entry.
      Search descriptions along with tags.
      Minor fix for refine. Always show current version, even when refining.
      Catch exceptions when writing file to raise dialog box if there is an error.  This fixes bug that nothing was being shown to the user in case of a bad write (ie, file permissions insufficient).

Tommy (26):
      Enable copy in VisTrails console
      Add access to stack traces from module errors
      Write module stack traces to log file as annotations
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      Show stack traces in new window
      <ticket>#293</ticket>
      Revert "<ticket>#293</ticket>"
      <ticket>#293</ticket>
      <ticket>#331</ticket>
      <bugfix>Error using breakpoint due to new stack trace</bugfix>
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      <bugfix>UpgradeWorkflowError tries to trim None-value</bugfix>
      <feature>New Web Services package that uses SUDS library</feature>
      Updated examples for new Web Services package
      <ticket>#375</ticket>
      <feature>Debug library updated</feature>
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      <bugfix>Minor error fixes</bugfix>
      <feature>Improved error handling in vistrails.core</feature>
      <feature>Improved debugging messages for vistrails.gui</feature>
      <feature>Improved error handling in vistrails.packages</feature>
      <bugfix>Added 'VisTrails messages' button and fixed 'VisTrails debugger' button</bugfix>
      <feature>Improved debug messages</feature>
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      <feature>Improved handling of log messages</feature>
      <feature>Buttons for filtering VisTrails messages</feature>

Tommy Ellqvist (193):
      <feature>Merging of vistrails files for crowdlabs.</feature>
      <bugfix>Merging of vistrails files for crowdlabs.</bugfix>
      <feature>Methods for hashing tags and annotations</feature>
      <feature>Merging action annotations</feature>
      <bugfix>Merging of vistrails did not work</bugfix>
      <feature>Interactive interface for merging two vistrails</feature>
      <feature>Handle upgrade and prune annotations during merge</feature>
      <bugfix>Vistrail merge did not copy thumbnails</bugfix>
      <bugfix>Merging thumbnails</bugfix>
      <feature>Debug messages now have a "details" attribute</feature>
      Converted MessageBox messages and print statements to core.debug calls
      <bugfix>Message filter colors does not show in linux</bugfix>
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      <feature>add/delete Web Services from module palette for SUDSWebServices package</feature>
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      made "transparent" the default for DEBUG_FILTER_BACKGROUND_COLOR
      <bugfix>Enable the Linux theme for 'Linux' system types</bugfix>
      <feature>Turn off popup messages if messages window is open</feature>
      Details to be added later
      Message will be added later
      <bugfix>Added title to console and debugger toolbars</bugfix>
      <ticket>#411</ticket>
      Latest version of Browser/Workspace
      <feature>Group SQL statements to enable faster DB communication</feature>
      merge with master
      fixed merge bug
      Merge branch 'master' into feature/browser
      <ticket>#416</ticket>
      merge with master
      Merge branch 'master' into feature/browser
      <ticket>#420</ticket>
      <bugfix>Do not import MySQLdb directly in sql_dao</bugfix>
      Merge branch 'master' into feature/browser
      Added "Workflow Execution Explorer"
      updates to explorer and vis_log
      more fixes to the explorer and vis_log
      First commit for workflow explorer
      updates to workspace, log browser, and log viewer
      <bugfix>persistence package updated to work with the new configuration widget</bugfix>
      <feature>Improved PythonEditor class using QScintilla2</feature>
      <feature>Added versioning for SUDS Web Services using content hash</feature>
      <bugfix>SUDSWebServices wsdl caching in Windows need to use pickle protocol=0</bugfix>
      <feature>Autosort module palette</feature>
      <bugfix>Made new PythonEditor use correct font</bugfix>
      <bugfix>persistence package did not show dates correctly</bugfix>
      Changed git commands in PersistencePath to static methods
      <feature>persistence package now hides file references instead of deleting them</feature>
      <bugfix>open merged vistrail in new tab and other fixes</bugfix>
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails
      <bugfix>2 bugfixes to the vistrail merge code</bugfix>
      Updates to provenance view
      <bugfix>removed self reference in static method in persistence package</bugfix>
      <feature>PythonSource editor will now indent newline to previous line</feature>
      <feature>Improved PythonEditor class using QScintilla2</feature>
      <bugfix>Made new PythonEditor use correct font</bugfix>
      <feature>PythonSource editor will now indent newline to previous line</feature>
      Merged new PythonSource editor from master.
      <bugfix>open merged vistrail in new tab and other fixes</bugfix>
      <bugfix>2 bugfixes to the vistrail merge code</bugfix>
      <feature>Added merge by dragging vistrail to vistrail</feature>
      Merge branch 'v2.0' of vistrails.sci.utah.edu:vistrails into v2.0
      <bugfix>Vistrails did not shut down properly</bugfix>
      Fixes to provenance browser and workspace
      <bugfix>initial untitled workflow was not closed correctly</bugfix>
      <bugfix>Enable vistrail save button</bugfix>
      collection/workspace.py:
      Added Vistrail Variables support, so that modules deriving from Constant can be used to create re-usable variables in multiple workflows within a vistrail.
      <feature>Autosort module palette</feature>
      <feature>Provenance browser now shows statusicon in list</feature>
      Completed merge menu option
      Fixes to interface, Log and diff
      <ticket>#441</ticket>
      <bugfix>Removed close button from Vistrails Messages view</bugfix>
      <ticket>#436</ticket>
      <feature>Enabled the provenance browser tool</feature>
      <bugfix>Fixed export/import menu options</bugfix>
      <bugfix>Importing basic_modules.py leads to import loop</bugfixed>
      Merge branch 'v2.0' of vistrails.sci.utah.edu:vistrails into v2.0
      <bugfix>Importing basic_modules.py leads to import loop</bugfixed>
      Simplified workspace panel for maintaining a list of open files
      <bugfix>Dropping vistrails variable created error</bugfix>
      <bugfix>QPipelineScene.addModule were calling addItem twice</bugfix>
      Merge branch 'v2.0' of vistrails.sci.utah.edu:vistrails into v2.0
      Merge branch 'v2.0' of vistrails.sci.utah.edu:vistrails into v2.0
      <feature>Improved workspace</feature>
      Removed none-existing import BasePEWidget
      Improved workspace
      <bugfix>Error when removing assigned Vistrail Variables</bugfix>
      <ticket>#450</ticket>
      <feature>Perform visual diff from workspace by dragging pipelines together</feature>
      <bugfix>Vistrails Messages did not show when 'Show Messages' button was clicked</bugfix>
      <feature>Workspace can show workflows in a tree view</feature>
      <ticket>#453</ticket>
      <bugfix>Workspace fixes for saving empty vistrail and closing detached vistrail</bugfix>
      <bugfix>Removed missing web service</bugfix>
      Error handling and border-case fixes
      Enable multiple New Files and ignore indexing unsaved files
      <feature>Remove workspace entry when selected file has been deleted</feature>
      <ticket>#455</ticket><bugfix>module information stretches unnaturally</bugfix>
      Merge branch 'v2.0' of vgc.poly.edu:vistrails into v2.0
      Workspace will now contain 'Workflows' and a 'Mashups' items
      <ticket>#463</ticket>
      <ticket>#465</ticket>
      SUDSWebServices: Create package even when wsdl fails to load
      <ticket>#459</ticket>
      <ticket>#466</ticket>
      <ticket>#467</ticket>
      <bugfix>Module documentation in module palette not working</bugfix>
      <bugfix>Opening xml vistrail from workspace showed open file dialog</bugfix>
      <ticket>#469</ticket>
      <ticket>#471</ticket>
      <ticket>#474</ticket> Close vistrail when Ctrl-Q is pressed in spreadsheet mode
      <ticket>#474</ticket>
      <bugfix>vtkhandler did not handle new PythonEditor correctly</bugfix>
      <ticket>#468</ticket>
      <bugfix>Double clicking a vistrail in file browser fails because of _first_view bug</bugfix>
      <ticket>#477</ticket>
      <ticket>#483</ticket>
      Merge branch 'v2.0' of vgc.poly.edu:vistrails into v2.0
      <ticket>#484</ticket>
      <feature>Make pipeline current when selected in provenance explorer</feature>
      <ticket>#468</ticket>
      <bugfix>Fixed 2 detach view bugs</bugfix>
      <bugfix>workspace.item_selected had invalid setSelected call</bugfix>
      <feature>Update executions in workspace when they are created</feature>
      <feature>Executions in provenance view are now given names based on the "tagname + n" naming scheme</feature>
      <bugfix>Do not store subworkflows in "recent files" or "My Vistrails"</bugfix>
      <feature>Open subworkflow from module palette</feature>
      <ticket>#489</ticket>
      <bugfix>get_current_view bug caused double-clicking a vistrail to fail</bugfix>
      <bugfix>sql package was not using new gui.modules.source_configure</bugfix>
      <bugfix>Remove vistrail from workspace if removed from disk</bugfix>
      <bugfix>Can now delete from workspace using backspace key</bugfix>
      SUDSWebServices - removed uninformative warning messages
      Commented out print statements related to new gui
      <feature>Show parameters for invalid modules</feature>
      <ticket>#488</ticket>
      Merge branch 'v2.0' of vgc.poly.edu:vistrails into v2.0
      <bugfix>Make provenance view read-only</bugfix>
      <ticket>#488</ticket>
      Merge branch 'v2.0' of vgc.poly.edu:vistrails into v2.0
      <ticket>#498</ticket>
      <feature>CLTools - package for wrapping command line tools</feature>
      Updated EMBOSS_webservisces.vt to include link on how to patch SUDS
      Merge branch 'v2.0' of vgc.poly.edu:vistrails into v2.0
      Updates to CLTools package
      <feature>Wizard for CLTools - gui for wrapper creation</feature>
      Updates to the CLTools package
      Added README file for package CLTools
      CLTools - removed dependency on sip
      <feature>Wizard for CLTools - gui for wrapper creation</feature>
      Updates to the CLTools package
      Added README file for package CLTools
      CLTools - removed dependency on sip
      Added Chapter for CLTools in Users Guide
      Added Chapter for CLTools in Users Guide
      Merge branch 'v2.0' of vgc.poly.edu:vistrails into v2.0
      Merge branch 'master' of vgc.poly.edu:vistrails
      <ticket>#500</ticket>
      <ticket>#480</ticket>
      <ticket>#284</ticket>
      <bugfix>Param Exploration User-defined function did not work because of new python editor interface</bugfix>
      <bugfix>Param Exploration User-defined function did not work because of new python editor interface</bugfix>
      <bugfix>Ubuntu Unity did not restore menu bar after being closed</bugfix>
      <bugfix>Ubuntu Unity did not restore menu bar after being closed</bugfix>
      <ticket>#511</ticket>
      <ticket>#511</ticket>
      <bugfix>autosave feature caused "new file" action to fail</bugfix>
      <bugfix>autosave feature caused "new file" action to fail</bugfix>
      <ticket>#391</ticket>
      <ticket>#391</ticket>
      <ticket>#421</ticket>
      <ticket>#421</ticket>
      <ticket>#512</ticket>
      <ticket>#512</ticket>
      <ticket>#512</ticket>
      <ticket>#512</ticket>
      <ticket>#515</ticket>
      <ticket>#515</ticket>
      <bugfix>Removed configuration options that are only used in non-interactive mode from Expert Configuration</bugfix>
      <ticket>#513</ticket>
      Merge branch 'master' of vgc.poly.edu:vistrails
      <ticket>#513</ticket>
      <bugfix>Fixed server mode after merge with core_no_gui</bugfix>
      <bugfix>Vistrail server need to initialize theme after core_no_gui changes</bugfix>
      <bugfix>save_many_to_db failed when list of objects were empty</bugfix>
      <bugfix>Rendering version and workflow view in server failed because of new gui in 2.0</bugfix>
      Merge branch 'master' of vgc.poly.edu:vistrails
      <ticket>#528</ticket>
      <bugfix>Fixed MissingRequirement path and ubuntu detection</bugfix>
      <ticket>#513</ticket>
      <ticket>#550</ticket>
      <ticket>#552</ticket>

Troels Roennow (4):
      Adding job submission package.
      Update of submission package
      <ticket>#557</ticket> Cacheable password dialog added.
      <feature>Package requirement for the job submission package</feature>

Wendel B Silva (2):
      <bugfix>VTK Package doesnt work with VTK version 5.7.0</bugfix>
      Merge branch 'master' of vistrails.sci.utah.edu:vistrails

Wendel Silva (5):
      Titan Toolkit package for VisTrails
      Small fix in the Titan Package. Fixed the modules that wasn't using vtkAlgorithm/vtkAlgorithmOutput
      VTK Package updated to work with the version 5.7.0.
      Titan Package updated to support the Titan based on the VTK 5.7.0
      <feature>HTTPFile now supports proxies.</feature>

root (4):
      Merge remote branch 'origin' into crowdlabs
      Revert "fixed typo run_vistrails.php"
      Merge remote branch 'origin' into crowdlabs
      Added additional ProtocolError error handling

tommy (42):
      <bugfix>SourceConfigurationWidget silently fails when code contains non-ascii characters</bugfix>
      <bugfix>SourceConfigurationWidget silently fails when code contains non-ascii characters</bugfix>
      <bugfix>Add icons to CLTools so that they not only work on X11</bugfix>
      <bugfix>Add icons to CLTools so that they not only work on X11</bugfix>
      <feature>CLTools: Added enviroment variable and default directory support</feature>
      <feature>CLTools: Added enviroment variable and default directory support</feature>
      Removed "workflowexec" print statements shown when saving a vistrail
      Removed "workflowexec" print statements shown when saving a vistrail
      <bugfix>CHEBI wsdl changed</bugfix>
      <bugfix>CHEBI wsdl changed</bugfix>
      <bugfix>Argument error caused gui/vistrail_controller test to fail</bugfix>
      <ticket>#526</ticket>
      <ticket>#525</ticket>
      <feature>New module execution state suspended added</feature>
      <bugfix>updateUpstream* failed when modules did not contain the suspended attribute</bugfix>
      <feature>Mashup View: Added float slider</feature>
      <ticket>#531</ticket>
      <bugfix>db_log_filename was not unset correctly for db cache</bugfix>
      <bugfix>Show error message when trying to open a vistrail with a newer schema version</bugfix>
      Merge branch 'v2.0' of vgc.poly.edu:vistrails into v2.0
      <bugfix>Autoloading a SUDS Web Service no longer produce error messages</bugfix>
      <bugfix>Parameter Exploration only worked on parameters from the Basic Modules package</bugfix>
      <ticket>#549</ticket>
      <ticket>#550</ticket>
      <ticket>#553</ticket>
      <ticket>#540</ticket>
      <ticket>#551</ticket>
      <ticket>#370</ticket>
      <ticket>#567</ticket>
      <feature>CLTools: added Open Wizard to package menu</feature>
      <bugfix>CLTools: IOErrors when executing process</bugfix>
      <feature>CLTools: package menu option for reloading all scripts</feature>
      Merge branch 'v2.0' of vgc.poly.edu:vistrails into v2.0
      <ticket>#573</ticket>
      <ticket>#424</ticket>
      <bugfix>SUDSWebServices: Wrong indentation caused vistrail save to fail</bugfix>
      <ticket>#575</ticket>
      <bugfix>Fixed spelling in repository.py</bugfix>
      <ticket>#575</ticket>
      <ticket>#575</ticket>
      <ticket>#575</ticket>
      <ticket>#575</ticket>

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