[vistrails-dev] [VisTrails/VisTrails] 299039: Introduces get_config()

GitHub noreply at github.com
Tue Oct 20 10:24:28 EDT 2015


  Branch: refs/heads/python-wrapper
  Home:   https://github.com/VisTrails/VisTrails
  Commit: 2990396864d520881ab5e063393aa66b5f820db4
      https://github.com/VisTrails/VisTrails/commit/2990396864d520881ab5e063393aa66b5f820db4
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-18 (Wed, 18 Mar 2015)

  Changed paths:
    M vistrails/core/modules/output_modules.py
    M vistrails/gui/modules/output_configuration.py
    M vistrails/packages/spreadsheet/spreadsheet_cell.py

  Log Message:
  -----------
  Introduces get_config()

OutputModule#get_mode_config() now takes an OutputMode instance, not the
subclass.


  Commit: c3a0a6820304ab675116a9102b4c6ce510f2f478
      https://github.com/VisTrails/VisTrails/commit/c3a0a6820304ab675116a9102b4c6ce510f2f478
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-18 (Wed, 18 Mar 2015)

  Changed paths:
    M vistrails/core/modules/output_modules.py

  Log Message:
  -----------
  Generates formats list in FileMode#get_config()


  Commit: 40c504ed82e044011c9341e46bcf9be5fb8e7fc1
      https://github.com/VisTrails/VisTrails/commit/40c504ed82e044011c9341e46bcf9be5fb8e7fc1
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-18 (Wed, 18 Mar 2015)

  Changed paths:
    M vistrails/core/modules/output_modules.py

  Log Message:
  -----------
  Adds RichTextToFileMode (formats = ['html'])


  Commit: 16bbb3adc98e5dbe18c95e9b91fca0d9126068df
      https://github.com/VisTrails/VisTrails/commit/16bbb3adc98e5dbe18c95e9b91fca0d9126068df
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-18 (Wed, 18 Mar 2015)

  Changed paths:
    M vistrails/core/modules/output_modules.py
    M vistrails/packages/spreadsheet/widgets/imageviewer/__init__.py
    M vistrails/packages/spreadsheet/widgets/imageviewer/imageviewer.py

  Log Message:
  -----------
  Implements ImageOutput


  Commit: 9e6fbb0bc09cdd8b66df1780e1ecb2144b0d2040
      https://github.com/VisTrails/VisTrails/commit/9e6fbb0bc09cdd8b66df1780e1ecb2144b0d2040
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-18 (Wed, 18 Mar 2015)

  Changed paths:
    M vistrails/core/modules/output_modules.py
    M vistrails/packages/spreadsheet/basic_widgets.py

  Log Message:
  -----------
  Increase spread in mode priority values


  Commit: 91d21a20f98822f0f4f56cf5043db2fba7f323bc
      https://github.com/VisTrails/VisTrails/commit/91d21a20f98822f0f4f56cf5043db2fba7f323bc
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-18 (Wed, 18 Mar 2015)

  Changed paths:
    M vistrails/core/modules/output_modules.py
    M vistrails/gui/preferences.py

  Log Message:
  -----------
  Allows overriding mode priorities in output module


  Commit: 5242e0b6d42e6064b1a6a477afad81231e711ece
      https://github.com/VisTrails/VisTrails/commit/5242e0b6d42e6064b1a6a477afad81231e711ece
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-18 (Wed, 18 Mar 2015)

  Changed paths:
    M vistrails/core/modules/output_modules.py

  Log Message:
  -----------
  Don't automatically select modes with prio<0


  Commit: 361cc204e223e2f2a15d5ab310749a149c6fae80
      https://github.com/VisTrails/VisTrails/commit/361cc204e223e2f2a15d5ab310749a149c6fae80
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-18 (Wed, 18 Mar 2015)

  Changed paths:
    M vistrails/core/modules/output_modules.py

  Log Message:
  -----------
  Makes FileToFileMode keep the extension


  Commit: 7fdbd88e9ac09c49a11a6b0ba2a385dc1af73218
      https://github.com/VisTrails/VisTrails/commit/7fdbd88e9ac09c49a11a6b0ba2a385dc1af73218
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-18 (Wed, 18 Mar 2015)

  Changed paths:
    M vistrails/core/modules/output_modules.py

  Log Message:
  -----------
  Fixes RichTextOutput's file writing mode


  Commit: 1e778b4dd90bc97fbe70f0853b097008100d2ef5
      https://github.com/VisTrails/VisTrails/commit/1e778b4dd90bc97fbe70f0853b097008100d2ef5
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-20 (Fri, 20 Mar 2015)

  Changed paths:
    M CHANGELOG
    M setup.py

  Log Message:
  -----------
  Bumps version number


  Commit: cfbc32aecbbdc8cf02250552c13d9e0a1281aaa2
      https://github.com/VisTrails/VisTrails/commit/cfbc32aecbbdc8cf02250552c13d9e0a1281aaa2
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-20 (Fri, 20 Mar 2015)

  Changed paths:
    M CHANGELOG

  Log Message:
  -----------
  Merge branch 'v2.1'


  Commit: b7bf13088e9f30dfc8efb48b64f52c0ca0fe81ef
      https://github.com/VisTrails/VisTrails/commit/b7bf13088e9f30dfc8efb48b64f52c0ca0fe81ef
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-20 (Fri, 20 Mar 2015)

  Changed paths:
    M setup.py

  Log Message:
  -----------
  Updates documentation link in long_description


  Commit: d7f3be17579ee6c82b6b3995e1e299a45843ff81
      https://github.com/VisTrails/VisTrails/commit/d7f3be17579ee6c82b6b3995e1e299a45843ff81
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-20 (Fri, 20 Mar 2015)

  Changed paths:
    A MANIFEST.in
    M setup.py

  Log Message:
  -----------
  Switch from package_data to a MANIFEST.in


  Commit: b66f0816c26c8aa5bd37de0d5d5a68ae597dd7b5
      https://github.com/VisTrails/VisTrails/commit/b66f0816c26c8aa5bd37de0d5d5a68ae597dd7b5
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-20 (Fri, 20 Mar 2015)

  Changed paths:
    M vistrails/packages/sql/init.py

  Log Message:
  -----------
  Fixes typo in DBConnection error handling


  Commit: 1d90a3a14fef5522660486939c8b89b5ec0a6381
      https://github.com/VisTrails/VisTrails/commit/1d90a3a14fef5522660486939c8b89b5ec0a6381
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-20 (Fri, 20 Mar 2015)

  Changed paths:
    M setup.py

  Log Message:
  -----------
  Adds xlrd, xlwt to setup.py


  Commit: 8757edac7de4bd0f611b538be482a5d75fc49f50
      https://github.com/VisTrails/VisTrails/commit/8757edac7de4bd0f611b538be482a5d75fc49f50
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-20 (Fri, 20 Mar 2015)

  Changed paths:
    M setup.py

  Log Message:
  -----------
  Adds xlrd, xlwt to setup.py


  Commit: aa4d46d72f5fdd731277298c51602b86946d43cb
      https://github.com/VisTrails/VisTrails/commit/aa4d46d72f5fdd731277298c51602b86946d43cb
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-20 (Fri, 20 Mar 2015)

  Changed paths:
    M dist/windows/custom/vistrails-gdal.iss
    M dist/windows/custom/vistrailsx64-gdal.iss
    M dist/windows/vistrails.iss
    M dist/windows/vistrailsx64.iss

  Log Message:
  -----------
  Fixed path to python27.dll

32bit version is in SysWOW64
64bit version is in System32


  Commit: 809307720869f61210a4ca27346fd732a0b72001
      https://github.com/VisTrails/VisTrails/commit/809307720869f61210a4ca27346fd732a0b72001
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-20 (Fri, 20 Mar 2015)

  Changed paths:
    M dist/windows/custom/vistrails-gdal.iss
    M dist/windows/custom/vistrailsx64-gdal.iss
    M dist/windows/vistrails.iss
    M dist/windows/vistrailsx64.iss

  Log Message:
  -----------
  Merge branch tag 2.1.5 into v2.1


  Commit: 4fe986148829d37db7eec71daa9071eaed489f68
      https://github.com/VisTrails/VisTrails/commit/4fe986148829d37db7eec71daa9071eaed489f68
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-20 (Fri, 20 Mar 2015)

  Changed paths:
    M dist/windows/custom/vistrailsx64-gdal.iss
    M dist/windows/vistrailsx64.iss

  Log Message:
  -----------
  Force getting dll from System32 using Sysnative


  Commit: 4a361ef11fc713ddb59c382000c2178d6a0ef7c5
      https://github.com/VisTrails/VisTrails/commit/4a361ef11fc713ddb59c382000c2178d6a0ef7c5
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-20 (Fri, 20 Mar 2015)

  Changed paths:
    M dist/windows/custom/vistrailsx64-gdal.iss
    M dist/windows/vistrailsx64.iss

  Log Message:
  -----------
  Merge tag v2.1.5 into v2.1


  Commit: 62235b98da0e32d108a250a08cda3ede1e47860a
      https://github.com/VisTrails/VisTrails/commit/62235b98da0e32d108a250a08cda3ede1e47860a
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-23 (Mon, 23 Mar 2015)

  Changed paths:
    M dist/common/prepare_release.py

  Log Message:
  -----------
  prepare_release: Update version in setup.py


  Commit: b772d7d4e5082a54aa8e6ab8e6ae6ca3f2623772
      https://github.com/VisTrails/VisTrails/commit/b772d7d4e5082a54aa8e6ab8e6ae6ca3f2623772
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-23 (Mon, 23 Mar 2015)

  Changed paths:
    A MANIFEST.in
    M scripts/dist/common/prepare_release.py
    M scripts/dist/windows/common1.iss

  Log Message:
  -----------
  Merge branch 'v2.1'

Conflicts:
	dist/windows/custom/vistrails-gdal.iss
	dist/windows/custom/vistrailsx64-gdal.iss
	dist/windows/vistrails.iss
	dist/windows/vistrailsx64.iss
	scripts/dist/common/prepare_release.py
	setup.py
	vistrails/packages/sql/init.py


  Commit: 328c4e6d3c734456744ae1709cf5d68bcb0be85b
      https://github.com/VisTrails/VisTrails/commit/328c4e6d3c734456744ae1709cf5d68bcb0be85b
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-23 (Mon, 23 Mar 2015)

  Changed paths:
    M setup.py

  Log Message:
  -----------
  Added setup.py changes missing from merge


  Commit: f2507283362e3046f787b2cc49940c8433c181a8
      https://github.com/VisTrails/VisTrails/commit/f2507283362e3046f787b2cc49940c8433c181a8
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-23 (Mon, 23 Mar 2015)

  Changed paths:
    M examples/infovis.vt
    R vistrails/packages/vtk/base_module.py
    R vistrails/packages/vtk/class_tree.py
    A vistrails/packages/vtk/common.py
    R vistrails/packages/vtk/fix_classes.py
    M vistrails/packages/vtk/identifiers.py
    M vistrails/packages/vtk/init.py
    M vistrails/packages/vtk/inspectors.py
    M vistrails/packages/vtk/offscreen.py
    A vistrails/packages/vtk/pythonclass.py
    M vistrails/packages/vtk/tf_widget.py
    R vistrails/packages/vtk/vtk_parser.py
    A vistrails/packages/vtk/vtk_wrapper/__init__.py
    A vistrails/packages/vtk/vtk_wrapper/class_tree.py
    A vistrails/packages/vtk/vtk_wrapper/fix_classes.py
    A vistrails/packages/vtk/vtk_wrapper/parse.py
    A vistrails/packages/vtk/vtk_wrapper/specs.py
    A vistrails/packages/vtk/vtk_wrapper/vtk_classes.py
    A vistrails/packages/vtk/vtk_wrapper/vtk_module.py
    A vistrails/packages/vtk/vtk_wrapper/vtk_parser.py
    A vistrails/packages/vtk/vtk_wrapper/wrapper.py
    M vistrails/packages/vtk/vtkcell.py
    M vistrails/packages/vtk/vtkhandler.py
    R vistrails/packages/vtk/vtkviewcell.py
    R vistrails/packages/vtk/wrapper.py
    M vistrails/tests/runtestsuite.py

  Log Message:
  -----------
  Merge pull request #998 from VisTrails/vtk-new-package

New vtk package with the wrapping code bundled


  Commit: 7948c2a2f2097e06841a1b61f9ad9f3b27a5bb48
      https://github.com/VisTrails/VisTrails/commit/7948c2a2f2097e06841a1b61f9ad9f3b27a5bb48
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-23 (Mon, 23 Mar 2015)

  Changed paths:
    M vistrails/gui/pipeline_view.py

  Log Message:
  -----------
  Fixes vistrail variable duplication bug


  Commit: 67acee60c5349284a11b7db78b14d3966751c49f
      https://github.com/VisTrails/VisTrails/commit/67acee60c5349284a11b7db78b14d3966751c49f
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-23 (Mon, 23 Mar 2015)

  Changed paths:
    M vistrails/packages/CLTools/wizard.py

  Log Message:
  -----------
  CLTools wizard: fixes options when swapping ports


  Commit: bec1f386be81fa3aa2d9c15bd59ba943cf0acfbc
      https://github.com/VisTrails/VisTrails/commit/bec1f386be81fa3aa2d9c15bd59ba943cf0acfbc
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-23 (Mon, 23 Mar 2015)

  Changed paths:
    M vistrails/packages/CLTools/wizard.py

  Log Message:
  -----------
  Merge branch 'v2.1' into 'master'


  Commit: 2cf6f4effd3fa183c6fd7eab47683e054e53d025
      https://github.com/VisTrails/VisTrails/commit/2cf6f4effd3fa183c6fd7eab47683e054e53d025
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-23 (Mon, 23 Mar 2015)

  Changed paths:
    R examples/scripting/README
    R examples/scripting/brain_from_script.vt
    R examples/scripting/brain_script.py
    R examples/scripting/combined_script.py
    R examples/scripting/vtk_book_3rd_p189_script.py

  Log Message:
  -----------
  Removes examples/scripting

These look like internal examples, and they don't work. They are also
superseded by the new API.


  Commit: 7d88137124371dce33a188996daa349ab0310543
      https://github.com/VisTrails/VisTrails/commit/7d88137124371dce33a188996daa349ab0310543
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-23 (Mon, 23 Mar 2015)

  Changed paths:
    M vistrails/gui/application.py
    M vistrails/tests/runtestsuite.py

  Log Message:
  -----------
  Fix VisTrails getting runtestsuite's arguments


  Commit: 4d6b056acf97fb3097245cf453a55b8464fd0473
      https://github.com/VisTrails/VisTrails/commit/4d6b056acf97fb3097245cf453a55b8464fd0473
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-24 (Tue, 24 Mar 2015)

  Changed paths:
    M vistrails/packages/vtk/vtk_wrapper/parse.py

  Log Message:
  -----------
  Added 2 disallowed classes for OpenSuSE


  Commit: cd756513937d7ca01a7c9d8535fd35f8257e0b84
      https://github.com/VisTrails/VisTrails/commit/cd756513937d7ca01a7c9d8535fd35f8257e0b84
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-24 (Tue, 24 Mar 2015)

  Changed paths:
    M vistrails/packages/vtk/vtk_wrapper/parse.py

  Log Message:
  -----------
  Merge branch 'vtk-new-package'


  Commit: 22b0e98112b09a50d3d1da591076e22a404c9c02
      https://github.com/VisTrails/VisTrails/commit/22b0e98112b09a50d3d1da591076e22a404c9c02
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-24 (Tue, 24 Mar 2015)

  Changed paths:
    M vistrails/core/debug.py
    M vistrails/core/startup.py

  Log Message:
  -----------
  Fix startup.py closing loggers: mock set_logfile()


  Commit: 1b024ce540b229a7bcd178a117c014d70141c172
      https://github.com/VisTrails/VisTrails/commit/1b024ce540b229a7bcd178a117c014d70141c172
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-24 (Tue, 24 Mar 2015)

  Changed paths:
    M vistrails/core/upgradeworkflow.py

  Log Message:
  -----------
  Fix version/package_version in upgradeworkflow.py


  Commit: dde38780a218deb13b71b1d63015d81744ac2736
      https://github.com/VisTrails/VisTrails/commit/dde38780a218deb13b71b1d63015d81744ac2736
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-24 (Tue, 24 Mar 2015)

  Changed paths:
    M vistrails/packages/gmaps/init.py

  Log Message:
  -----------
  Fix version numbers in gmaps upgrades


  Commit: 22d6287457c9437d02ea5d0e6f6e1b548968b58e
      https://github.com/VisTrails/VisTrails/commit/22d6287457c9437d02ea5d0e6f6e1b548968b58e
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-25 (Wed, 25 Mar 2015)

  Changed paths:
    M vistrails/packages/vtk/vtk_wrapper/specs.py

  Log Message:
  -----------
  Fixed spec.py tests failing when vtk package is not loaded


  Commit: 0447afec1b531c5b04f712c0962d4264d35e0b8e
      https://github.com/VisTrails/VisTrails/commit/0447afec1b531c5b04f712c0962d4264d35e0b8e
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-25 (Wed, 25 Mar 2015)

  Changed paths:
    M vistrails/packages/vtk/pythonclass.py

  Log Message:
  -----------
  Fixed VTK caching all modules

The python class wrapper ignored spec.cacheable

Fixes #1026


  Commit: 4f043417bf8ee7d8576341b48bf2db191cf20db1
      https://github.com/VisTrails/VisTrails/commit/4f043417bf8ee7d8576341b48bf2db191cf20db1
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-25 (Wed, 25 Mar 2015)

  Changed paths:
    M vistrails/gui/application.py

  Log Message:
  -----------
  Fixed querying jobs from command line

* Setting batch mode was not working
* "runJob" should be "jobInfo"
* jobInfo: Fixed getting workflow from version

Fixes #857


  Commit: 993d640cd32a3c5aa29efbc72e71f050f3d61781
      https://github.com/VisTrails/VisTrails/commit/993d640cd32a3c5aa29efbc72e71f050f3d61781
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-25 (Wed, 25 Mar 2015)

  Changed paths:
    M vistrails/db/services/io.py

  Log Message:
  -----------
  Remove two deprecated broken methods

open_abstraction_from_db() and save_abstraction_to_db() are currently
broken.

They have been deprecated since 2012.


  Commit: e23ccb1d3a06b21a6b89e63981ba22901a88b94e
      https://github.com/VisTrails/VisTrails/commit/e23ccb1d3a06b21a6b89e63981ba22901a88b94e
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-25 (Wed, 25 Mar 2015)

  Changed paths:
    M vistrails/core/modules/vistrails_module.py

  Log Message:
  -----------
  Fixes ModuleError#errorTrace attribute


  Commit: 702fa7eb2d2e7ded23469d7855beae11f31628de
      https://github.com/VisTrails/VisTrails/commit/702fa7eb2d2e7ded23469d7855beae11f31628de
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-25 (Wed, 25 Mar 2015)

  Changed paths:
    A examples-internal/broken/errors.vt
    A examples-internal/broken/invalid-package.xml
    A examples-internal/broken/too-recent.xml

  Log Message:
  -----------
  Add examples of broken workflows for testing


  Commit: 02ee32252207c930387c8bcf954a4cbf0b91477d
      https://github.com/VisTrails/VisTrails/commit/02ee32252207c930387c8bcf954a4cbf0b91477d
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-25 (Wed, 25 Mar 2015)

  Changed paths:
    M vistrails/core/modules/vistrails_module.py

  Log Message:
  -----------
  Fixes ModuleError#errorTrace attribute


  Commit: ad9e4ec0acb74382d1be2b1c613d624dd796b2cc
      https://github.com/VisTrails/VisTrails/commit/ad9e4ec0acb74382d1be2b1c613d624dd796b2cc
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-25 (Wed, 25 Mar 2015)

  Changed paths:
    M vistrails/core/api.py
    M vistrails/core/mashup/action.py
    M vistrails/core/mashup/action_annotation.py
    M vistrails/core/modules/output_modules.py
    M vistrails/gui/modules/list_configuration.py
    M vistrails/gui/modules/stringformat_configuration.py
    M vistrails/packages/CLTools/identifiers.py
    M vistrails/packages/URL/http_directory.py
    M vistrails/packages/URL/https.py
    M vistrails/packages/URL/https_if_available.py
    M vistrails/packages/controlflow/looping.py
    M vistrails/packages/dialogs/continue_prompt.py
    M vistrails/packages/gmaps/__init__.py
    M vistrails/packages/gmaps/gmap_cell.py
    M vistrails/packages/gmaps/identifiers.py
    M vistrails/packages/gmaps/init.py
    M vistrails/packages/gmaps/utils.py
    M vistrails/packages/gmaps/vis.py
    M vistrails/packages/matplotlib/__init__.py
    M vistrails/packages/matplotlib/diff.py
    M vistrails/packages/matplotlib/figure_cell.py
    M vistrails/packages/matplotlib/generate.py
    M vistrails/packages/matplotlib/init.py
    M vistrails/packages/matplotlib/mixins.py
    M vistrails/packages/matplotlib/parse.py
    M vistrails/packages/matplotlib/specs.py
    M vistrails/packages/matplotlib/widgets.py
    M vistrails/packages/parallelflow/__init__.py
    M vistrails/packages/parallelflow/api.py
    M vistrails/packages/parallelflow/engine_manager.py
    M vistrails/packages/parallelflow/init.py
    M vistrails/packages/parallelflow/map.py
    M vistrails/packages/persistent_archive/__init__.py
    M vistrails/packages/persistent_archive/cache.py
    M vistrails/packages/persistent_archive/common.py
    M vistrails/packages/persistent_archive/identifiers.py
    M vistrails/packages/persistent_archive/init.py
    M vistrails/packages/persistent_archive/persistedinput.py
    M vistrails/packages/persistent_archive/persistedoutput.py
    M vistrails/packages/persistent_archive/queriedinput.py
    M vistrails/packages/persistent_archive/queries.py
    M vistrails/packages/persistent_archive/ui.py
    M vistrails/packages/persistent_archive/widgets.py
    M vistrails/packages/sklearn/__init__.py
    M vistrails/packages/sklearn/init.py
    M vistrails/packages/sklearn/tests.py
    M vistrails/packages/sql/widgets.py
    M vistrails/packages/tabledata/convert/__init__.py
    M vistrails/packages/tabledata/convert/convert_dates.py
    M vistrails/packages/tabledata/read/__init__.py
    M vistrails/packages/tabledata/read/read_csv.py
    M vistrails/packages/tabledata/read/read_excel.py
    M vistrails/packages/tabledata/read/read_json.py
    M vistrails/packages/tabledata/read/read_numpy.py
    M vistrails/packages/tabledata/write/__init__.py
    M vistrails/packages/tabledata/write/write_csv.py
    M vistrails/packages/tabledata/write/write_excel.py
    M vistrails/packages/vtk/common.py
    M vistrails/packages/vtk/init.py
    M vistrails/packages/vtk/pythonclass.py
    M vistrails/packages/vtk/vtk_wrapper/__init__.py
    M vistrails/packages/vtk/vtk_wrapper/class_tree.py
    M vistrails/packages/vtk/vtk_wrapper/parse.py
    M vistrails/packages/vtk/vtk_wrapper/specs.py
    M vistrails/packages/vtk/vtk_wrapper/vtk_classes.py
    M vistrails/packages/vtk/vtk_wrapper/vtk_module.py
    M vistrails/packages/vtk/vtk_wrapper/vtk_parser.py
    M vistrails/tests/utils.py

  Log Message:
  -----------
  Adds missing copyright headers


  Commit: 27320ddb49bb1bda10eb3d04f81ccfffa2c1b850
      https://github.com/VisTrails/VisTrails/commit/27320ddb49bb1bda10eb3d04f81ccfffa2c1b850
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-26 (Thu, 26 Mar 2015)

  Changed paths:
    M vistrails/packages/vtk/vtk_wrapper/parse.py

  Log Message:
  -----------
  Added ignored classes for VTK 6.2


  Commit: 5c9313488d04114937c390904c00b643060e9d84
      https://github.com/VisTrails/VisTrails/commit/5c9313488d04114937c390904c00b643060e9d84
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-26 (Thu, 26 Mar 2015)

  Changed paths:
    M scripts/dist/windows/common1.iss

  Log Message:
  -----------
  Use VTK 6.2.0 in windows binaries


  Commit: c880fd468295844e3ff694303d4c4c36743ec8fb
      https://github.com/VisTrails/VisTrails/commit/c880fd468295844e3ff694303d4c4c36743ec8fb
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-26 (Thu, 26 Mar 2015)

  Changed paths:
    M vistrails/packages/vtk/vtk_wrapper/parse.py

  Log Message:
  -----------
  Fixed VTKCell being used as port even if spreadsheet is not loaded

With the new constant spec there is no way of making
this dynamic, so we replace the type with a Variant.

Now that we do not allow modules on ports,
should port types really be modules?

Fixes #1030


  Commit: 0382f99cd6316e21d96b5152e5a6511918a0fab1
      https://github.com/VisTrails/VisTrails/commit/0382f99cd6316e21d96b5152e5a6511918a0fab1
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-26 (Thu, 26 Mar 2015)

  Changed paths:
    M scripts/dist/windows/common1.iss
    M vistrails/packages/vtk/vtk_wrapper/parse.py

  Log Message:
  -----------
  Merge branch 'vtk-new-package'


  Commit: 4f9a28618e3a86350c5fa83b09247577680a9402
      https://github.com/VisTrails/VisTrails/commit/4f9a28618e3a86350c5fa83b09247577680a9402
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-26 (Thu, 26 Mar 2015)

  Changed paths:
    M vistrails/packages/vtk/init.py
    M vistrails/packages/vtk/vtk_wrapper/parse.py

  Log Message:
  -----------
  Use abstract VTKCell when spreadsheet is not loaded so that VTKCell ports work


  Commit: bce3465420ec3105278b52fc171ecfc63f6b019c
      https://github.com/VisTrails/VisTrails/commit/bce3465420ec3105278b52fc171ecfc63f6b019c
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-26 (Thu, 26 Mar 2015)

  Changed paths:
    M vistrails/packages/vtk/init.py
    M vistrails/packages/vtk/vtk_wrapper/parse.py

  Log Message:
  -----------
  Merge branch 'vtk-new-package'


  Commit: f61c34dd245c5fcf26f06799e25ab952f138ef7c
      https://github.com/VisTrails/VisTrails/commit/f61c34dd245c5fcf26f06799e25ab952f138ef7c
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-26 (Thu, 26 Mar 2015)

  Changed paths:
    M scripts/dist/windows/common1.iss

  Log Message:
  -----------
  Fixed typo in windows build script


  Commit: bd109cbae5d854b8c29ded90f1d19ab03127a521
      https://github.com/VisTrails/VisTrails/commit/bd109cbae5d854b8c29ded90f1d19ab03127a521
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-26 (Thu, 26 Mar 2015)

  Changed paths:
    M examples/matplotlib/Acorr_ex8.vt
    M examples/matplotlib/Arrow_ex9.vt
    M examples/matplotlib/Psd.vt
    M examples/matplotlib/annotate.vt
    M examples/matplotlib/axhspan_ex5.vt
    M examples/matplotlib/bar_ex1.vt
    M examples/matplotlib/cohere.vt
    M examples/matplotlib/contourf.vt
    M examples/matplotlib/hist_ex1.vt
    M examples/matplotlib/line2d_ex4.vt
    M examples/matplotlib/line2d_ex7.vt
    M examples/matplotlib/lineplot_ex3.vt
    M examples/matplotlib/pcolor.vt
    M examples/matplotlib/pie_ex1.vt
    M examples/matplotlib/polar_ex10.vt
    M examples/matplotlib/scatter.vt
    M examples/matplotlib/semilog.vt

  Log Message:
  -----------
  Examples: replace MplFigureCell -> MplFigureOutput


  Commit: b1e0f49b17dc03197bb57d993b9b72d1a9b741ed
      https://github.com/VisTrails/VisTrails/commit/b1e0f49b17dc03197bb57d993b9b72d1a9b741ed
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-26 (Thu, 26 Mar 2015)

  Changed paths:
    A examples/brain_output.xml
    A examples/coder.jpg
    A examples/imagemagick.vt
    A examples/out_html.xml
    A examples/outputs.vt
    A examples/simplemath.vt
    A examples/table.xml
    A vtapitest.ipynb

  Log Message:
  -----------
  Import from new-api_/test


  Commit: 9bea7fde8de3cfd8288eeed0a83c40b07268143e
      https://github.com/VisTrails/VisTrails/commit/9bea7fde8de3cfd8288eeed0a83c40b07268143e
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-26 (Thu, 26 Mar 2015)

  Changed paths:
    A examples/api/brain_output.xml
    A examples/api/imagemagick.vt
    A examples/api/ipython-notebook.ipynb
    A examples/api/out_html.xml
    A examples/api/outputs.vt
    A examples/api/simplemath.vt
    A examples/api/table.xml
    A examples/api/vistrails_logo.png
    R examples/brain_output.xml
    R examples/coder.jpg
    R examples/imagemagick.vt
    R examples/out_html.xml
    R examples/outputs.vt
    R examples/simplemath.vt
    R examples/table.xml
    R vtapitest.ipynb

  Log Message:
  -----------
  Turn this into examples/api/


  Commit: 4f83156abd718bfcf13a3af54269130aeffc0824
      https://github.com/VisTrails/VisTrails/commit/4f83156abd718bfcf13a3af54269130aeffc0824
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-26 (Thu, 26 Mar 2015)

  Changed paths:
    M examples/api/ipython-notebook.ipynb

  Log Message:
  -----------
  vtk example now works


  Commit: 953e84199d8ce8db9ab50150c657b5ef068ffdc2
      https://github.com/VisTrails/VisTrails/commit/953e84199d8ce8db9ab50150c657b5ef068ffdc2
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-26 (Thu, 26 Mar 2015)

  Changed paths:
    M scripts/dist/windows/common1.iss
    M scripts/dist/windows/common2.iss

  Log Message:
  -----------
  Fixed python path in windows build scripts


  Commit: b61ef9d461736e508b7390dc8496c99e2e1ecd14
      https://github.com/VisTrails/VisTrails/commit/b61ef9d461736e508b7390dc8496c99e2e1ecd14
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-26 (Thu, 26 Mar 2015)

  Changed paths:
    M scripts/dist/windows/common1.iss
    M scripts/dist/windows/common2.iss

  Log Message:
  -----------
  Merge branch 'vtk-new-package'


  Commit: 32814f2d0a20b0a1174a00f482fc8fd4ba6ef486
      https://github.com/VisTrails/VisTrails/commit/32814f2d0a20b0a1174a00f482fc8fd4ba6ef486
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-26 (Thu, 26 Mar 2015)

  Changed paths:
    M scripts/dist/mac/setup.py

  Log Message:
  -----------
  Mac build now uses VTK 6.2


  Commit: 3b14a89da4c2b09ce51f34840c665a570b930b6f
      https://github.com/VisTrails/VisTrails/commit/3b14a89da4c2b09ce51f34840c665a570b930b6f
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-26 (Thu, 26 Mar 2015)

  Changed paths:
    M scripts/dist/mac/setup.py

  Log Message:
  -----------
  	Merge branch 'vtk-new-package'


  Commit: 58019f1fffcbf43eba391af4b48d5315bc69da07
      https://github.com/VisTrails/VisTrails/commit/58019f1fffcbf43eba391af4b48d5315bc69da07
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-26 (Thu, 26 Mar 2015)

  Changed paths:
    M LICENSE

  Log Message:
  -----------
  LICENCE: Updated copyright year


  Commit: fc8bb556c8d879ab7ba83184516efaca74256db9
      https://github.com/VisTrails/VisTrails/commit/fc8bb556c8d879ab7ba83184516efaca74256db9
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-26 (Thu, 26 Mar 2015)

  Changed paths:
    R vistrails/db/versions/v0_8_1/schemas/sql/vistrails.sql.bkp

  Log Message:
  -----------
  Removes a 7-year-old .bkp file


  Commit: baab5728c2a4c204fa30e5a2eaa34cc645181896
      https://github.com/VisTrails/VisTrails/commit/baab5728c2a4c204fa30e5a2eaa34cc645181896
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-26 (Thu, 26 Mar 2015)

  Changed paths:
    M vistrails/db/bin/templates/sql_schema.sql.mako
    M vistrails/packages/matplotlib/bases.py
    M vistrails/packages/vtk/identifiers.py

  Log Message:
  -----------
  Fixes more copyright headers


  Commit: dd7a6dc16f5295d43c5c8543008fa3422b0cc7e8
      https://github.com/VisTrails/VisTrails/commit/dd7a6dc16f5295d43c5c8543008fa3422b0cc7e8
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-26 (Thu, 26 Mar 2015)

  Changed paths:
    M vistrails/gui/version_view.py

  Log Message:
  -----------
  Fixes weird typo

vistrails.gui.version_view was not imported, and it's the current file!


  Commit: 7eade15486b3acae771c125e7bb9e036a7c84c44
      https://github.com/VisTrails/VisTrails/commit/7eade15486b3acae771c125e7bb9e036a7c84c44
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-27 (Fri, 27 Mar 2015)

  Changed paths:
    M vistrails/packages/vtk/init.py
    M vistrails/packages/vtk/vtkcell.py

  Log Message:
  -----------
  Re-adds Instance port on VTKCell


  Commit: 7a19c29b8322a6478d8d6bfd6b7ba2c348d51ad0
      https://github.com/VisTrails/VisTrails/commit/7a19c29b8322a6478d8d6bfd6b7ba2c348d51ad0
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-27 (Fri, 27 Mar 2015)

  Changed paths:
    M vistrails/packages/vtk/init.py
    M vistrails/packages/vtk/vtkcell.py

  Log Message:
  -----------
  Merge branch 'vtk-new-package'


  Commit: 47cf2180b9ea4cd781a7f920cd7e901b03f35385
      https://github.com/VisTrails/VisTrails/commit/47cf2180b9ea4cd781a7f920cd7e901b03f35385
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-27 (Fri, 27 Mar 2015)

  Changed paths:
    M vistrails/packages/vtk/vtk_wrapper/parse.py

  Log Message:
  -----------
  Fixes modules with the SetRenderWindow attribute

You need to remove ~/.vistrails/vtk-spec* to update schema.

>From discussion on #1032


  Commit: 5df9b9e0e1ea75a6d975d300b3e3d41a2f583f09
      https://github.com/VisTrails/VisTrails/commit/5df9b9e0e1ea75a6d975d300b3e3d41a2f583f09
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-27 (Fri, 27 Mar 2015)

  Changed paths:
    M vistrails/core/upgradeworkflow.py
    M vistrails/packages/gmaps/init.py

  Log Message:
  -----------
  Merge pull request #1027 from VisTrails/upgradeworkflow-package-version

Fixes gmaps upgrade writing invalid workflow


  Commit: df878b70f2a68bae18729332cbe28159383b0873
      https://github.com/VisTrails/VisTrails/commit/df878b70f2a68bae18729332cbe28159383b0873
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-27 (Fri, 27 Mar 2015)

  Changed paths:
    M vistrails/gui/resources/images/vistrails_splash.png

  Log Message:
  -----------
  Fixes splash image being SVG in .PNG filename


  Commit: 36c7534c6177a69fb2d8f085cb9a19eed8d9bd4f
      https://github.com/VisTrails/VisTrails/commit/36c7534c6177a69fb2d8f085cb9a19eed8d9bd4f
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-27 (Fri, 27 Mar 2015)

  Changed paths:
    M vistrails/gui/resources/images/vistrails_splash.png

  Log Message:
  -----------
  Resizes splash to correct size


  Commit: 2ab7a2e0f65d1b2332938900a29999496a1e41d6
      https://github.com/VisTrails/VisTrails/commit/2ab7a2e0f65d1b2332938900a29999496a1e41d6
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-27 (Fri, 27 Mar 2015)

  Changed paths:
    M CHANGELOG

  Log Message:
  -----------
  Updated CHANGELOG with my changes


  Commit: 518c72f167f34e3434db133030d7c837f7d2edc2
      https://github.com/VisTrails/VisTrails/commit/518c72f167f34e3434db133030d7c837f7d2edc2
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-27 (Fri, 27 Mar 2015)

  Changed paths:
    A scripts/dist/common/disclaimer.svg
    M vistrails/gui/resources/images/disclaimer.png

  Log Message:
  -----------
  Recreates disclaimer image


  Commit: 51f0c3addb089ea32d9b8861832ee42b2341e927
      https://github.com/VisTrails/VisTrails/commit/51f0c3addb089ea32d9b8861832ee42b2341e927
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-27 (Fri, 27 Mar 2015)

  Changed paths:
    A examples/api/brain_output.xml
    A examples/api/imagemagick.vt
    A examples/api/ipython-notebook.ipynb
    A examples/api/out_html.xml
    A examples/api/outputs.vt
    A examples/api/simplemath.vt
    A examples/api/table.xml
    A examples/api/vistrails_logo.png
    M examples/matplotlib/Acorr_ex8.vt
    M examples/matplotlib/Arrow_ex9.vt
    M examples/matplotlib/Psd.vt
    M examples/matplotlib/annotate.vt
    M examples/matplotlib/axhspan_ex5.vt
    M examples/matplotlib/bar_ex1.vt
    M examples/matplotlib/cohere.vt
    M examples/matplotlib/contourf.vt
    M examples/matplotlib/hist_ex1.vt
    M examples/matplotlib/line2d_ex4.vt
    M examples/matplotlib/line2d_ex7.vt
    M examples/matplotlib/lineplot_ex3.vt
    M examples/matplotlib/pcolor.vt
    M examples/matplotlib/pie_ex1.vt
    M examples/matplotlib/polar_ex10.vt
    M examples/matplotlib/scatter.vt
    M examples/matplotlib/semilog.vt

  Log Message:
  -----------
  Merge pull request #1031 from VisTrails/new-api-examples

Examples for new-api


  Commit: 5e297ea51084c8d49d8b18ecbaa57945ba3313b5
      https://github.com/VisTrails/VisTrails/commit/5e297ea51084c8d49d8b18ecbaa57945ba3313b5
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-28 (Sat, 28 Mar 2015)

  Changed paths:
    M vistrails/packages/vtk/pythonclass.py

  Log Message:
  -----------
  Fixed filePool in pythonclass wrapper


  Commit: a9bcdf874eeac64615985213915b743ad03fe09a
      https://github.com/VisTrails/VisTrails/commit/a9bcdf874eeac64615985213915b743ad03fe09a
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-30 (Mon, 30 Mar 2015)

  Changed paths:
    M vistrails/packages/vtk/offscreen.py

  Log Message:
  -----------
  Fixes VTKRendererOffscreen on VTK6


  Commit: 81e12379f703ad0f30c42694a2267c5ca4deccc9
      https://github.com/VisTrails/VisTrails/commit/81e12379f703ad0f30c42694a2267c5ca4deccc9
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-30 (Mon, 30 Mar 2015)

  Changed paths:
    M vistrails/packages/vtk/offscreen.py
    M vistrails/packages/vtk/pythonclass.py
    M vistrails/packages/vtk/vtk_wrapper/parse.py

  Log Message:
  -----------
  Merge branch 'vtk-new-package'


  Commit: a663a3aeefefa028cbcb2c5a0abb9d15b3b7f390
      https://github.com/VisTrails/VisTrails/commit/a663a3aeefefa028cbcb2c5a0abb9d15b3b7f390
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-30 (Mon, 30 Mar 2015)

  Changed paths:
    M doc/usersguide/conf.py
    M doc/usersguide/vtl/README

  Log Message:
  -----------
  Use v2.2 vtl examples


  Commit: 6951a29bb34d34a6aae91bbb13e7fa960e5363b0
      https://github.com/VisTrails/VisTrails/commit/6951a29bb34d34a6aae91bbb13e7fa960e5363b0
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-30 (Mon, 30 Mar 2015)

  Changed paths:
    M vistrails/gui/job_monitor.py

  Log Message:
  -----------
  Fixes Job refresh interval not being saved


  Commit: a6deb2c174bdc1eda1ea76e84436de5553fb4b44
      https://github.com/VisTrails/VisTrails/commit/a6deb2c174bdc1eda1ea76e84436de5553fb4b44
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-30 (Mon, 30 Mar 2015)

  Changed paths:
    M vistrails/packages/vtk/tf_widget.py

  Log Message:
  -----------
  Fixed TF points in inline widget


  Commit: 54201b1c1cf04cc343a1c4d2931c7c9f8e5d4189
      https://github.com/VisTrails/VisTrails/commit/54201b1c1cf04cc343a1c4d2931c7c9f8e5d4189
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-30 (Mon, 30 Mar 2015)

  Changed paths:
    M vistrails/core/system/osx.py

  Log Message:
  -----------
  Send OSX profiler's stderr to log


  Commit: f91fd7b1306fc0fb0c4d06e067b0844dd336a799
      https://github.com/VisTrails/VisTrails/commit/f91fd7b1306fc0fb0c4d06e067b0844dd336a799
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-03-30 (Mon, 30 Mar 2015)

  Changed paths:
    M vistrails/core/log/controller.py

  Log Message:
  -----------
  Delay Machine creation (and guess_total_memory())


  Commit: aa91cb4a2d5f420cf771afe14f177e20d29b5685
      https://github.com/VisTrails/VisTrails/commit/aa91cb4a2d5f420cf771afe14f177e20d29b5685
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-03-30 (Mon, 30 Mar 2015)

  Changed paths:
    M vistrails/core/log/controller.py
    M vistrails/core/system/osx.py

  Log Message:
  -----------
  Merge pull request #1037 from VisTrails/log-osxprofiler-errors

Log OSX system_profiler errors


  Commit: efa93b69e0ddd58ffdeea268008cabaeb89614cb
      https://github.com/VisTrails/VisTrails/commit/efa93b69e0ddd58ffdeea268008cabaeb89614cb
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-01 (Wed, 01 Apr 2015)

  Changed paths:
    M vistrails/gui/version_view.py
    M vistrails/gui/vistrail_controller.py

  Log Message:
  -----------
  Removes version layout animation


  Commit: 25f7fcdaf449de937a060edf6a3892186dabea01
      https://github.com/VisTrails/VisTrails/commit/25f7fcdaf449de937a060edf6a3892186dabea01
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-01 (Wed, 01 Apr 2015)

  Changed paths:
    M vistrails/gui/vistrail_controller.py

  Log Message:
  -----------
  Removes _previous_graph_layout


  Commit: 397af1a667e5848b5322d752f84801e1fed88dcc
      https://github.com/VisTrails/VisTrails/commit/397af1a667e5848b5322d752f84801e1fed88dcc
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-01 (Wed, 01 Apr 2015)

  Changed paths:
    M vistrails/gui/pipeline_view.py

  Log Message:
  -----------
  Handle empty current_pipeline in update_connections


  Commit: 2f38d553bb31c32b02475d3502e9bf927ec3b21b
      https://github.com/VisTrails/VisTrails/commit/2f38d553bb31c32b02475d3502e9bf927ec3b21b
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-02 (Thu, 02 Apr 2015)

  Changed paths:
    M vistrails/packages/vtk/vtk_wrapper/parse.py
    M vistrails/packages/vtk/vtk_wrapper/vtk_classes.py

  Log Message:
  -----------
  Let vtkExporters take a vtkRenderer


  Commit: fff3ad71bd4d8108bd83f42ca0ac1156ffd7b9d7
      https://github.com/VisTrails/VisTrails/commit/fff3ad71bd4d8108bd83f42ca0ac1156ffd7b9d7
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-02 (Thu, 02 Apr 2015)

  Changed paths:
    M vistrails/packages/vtk/init.py
    M vistrails/packages/vtk/vtkcell.py

  Log Message:
  -----------
  Upgrade VTKCell ports to vtkRenderer

* Removed the abstract VTKCell class
* Removed Instance port on VTKCell


  Commit: 4006bafd02d6bd2eb209828b23b66c279e84e968
      https://github.com/VisTrails/VisTrails/commit/4006bafd02d6bd2eb209828b23b66c279e84e968
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-02 (Thu, 02 Apr 2015)

  Changed paths:
    M doc/usersguide/example_guide.rst

  Log Message:
  -----------
  Updated VTK documentation


  Commit: a76fc52538455a1e2177c9d98d52d29ffb218f79
      https://github.com/VisTrails/VisTrails/commit/a76fc52538455a1e2177c9d98d52d29ffb218f79
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-02 (Thu, 02 Apr 2015)

  Changed paths:
    M vistrails/tests/utils.py

  Log Message:
  -----------
  Splits enable_package() out of tests.utils:execute


  Commit: c3481bb1b0de5f6b8449fe8d13d34bafca5cae6f
      https://github.com/VisTrails/VisTrails/commit/c3481bb1b0de5f6b8449fe8d13d34bafca5cae6f
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-02 (Thu, 02 Apr 2015)

  Changed paths:
    M vistrails/packages/vtk/vtk_wrapper/specs.py

  Log Message:
  -----------
  Enables vtk package before running vtk tests


  Commit: 9e19b1ab2ce217c91231135bd6ddf90564e18041
      https://github.com/VisTrails/VisTrails/commit/9e19b1ab2ce217c91231135bd6ddf90564e18041
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-02 (Thu, 02 Apr 2015)

  Changed paths:
    M vistrails/tests/utils.py

  Log Message:
  -----------
  Fixes enable_package()


  Commit: f2d2377119538eba2c13cac22f8d10e0f5b2aeda
      https://github.com/VisTrails/VisTrails/commit/f2d2377119538eba2c13cac22f8d10e0f5b2aeda
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-02 (Thu, 02 Apr 2015)

  Changed paths:
    M vistrails/packages/vtk/common.py
    M vistrails/packages/vtk/init.py
    M vistrails/packages/vtk/tf_widget.py
    M vistrails/packages/vtk/vtk_wrapper/specs.py

  Log Message:
  -----------
  VTK import fixes


  Commit: aceadc76650103014640decd5a539573dc7037b5
      https://github.com/VisTrails/VisTrails/commit/aceadc76650103014640decd5a539573dc7037b5
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-02 (Thu, 02 Apr 2015)

  Changed paths:
    M vistrails/packages/vtk/init.py

  Log Message:
  -----------
  Moves function definitions out of loop


  Commit: 5d22ab9ccf2b15b33877682bff01dd7ba160e200
      https://github.com/VisTrails/VisTrails/commit/5d22ab9ccf2b15b33877682bff01dd7ba160e200
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-02 (Thu, 02 Apr 2015)

  Changed paths:
    M vistrails/packages/vtk/vtk_wrapper/vtk_classes.py

  Log Message:
  -----------
  Removes globals() madness


  Commit: 3805a4b2c7ffb0ef4a3e70305be7f399df3e8fbd
      https://github.com/VisTrails/VisTrails/commit/3805a4b2c7ffb0ef4a3e70305be7f399df3e8fbd
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-02 (Thu, 02 Apr 2015)

  Changed paths:
    M vistrails/packages/tabledata/read/read_csv.py
    M vistrails/packages/tabledata/read/read_json.py

  Log Message:
  -----------
  Fixes InternalModuleError in tabledata


  Commit: 7b14450349f9620f01bb6fd6dcd1dd05281b79bf
      https://github.com/VisTrails/VisTrails/commit/7b14450349f9620f01bb6fd6dcd1dd05281b79bf
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-02 (Thu, 02 Apr 2015)

  Changed paths:
    M vistrails/packages/tabledata/common.py
    M vistrails/packages/tabledata/read/read_csv.py
    M vistrails/packages/tabledata/write/write_csv.py

  Log Message:
  -----------
  Raise a better error on invalid CSV row


  Commit: 9d643c3e8535081138f7c7631e3026b6f56bc572
      https://github.com/VisTrails/VisTrails/commit/9d643c3e8535081138f7c7631e3026b6f56bc572
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-02 (Thu, 02 Apr 2015)

  Changed paths:
    M vistrails/packages/tabledata/viewer.py

  Log Message:
  -----------
  TableCellWidget: remove columns on exception


  Commit: 97c33644c20e94442511a36de10a6c94fc7f8d72
      https://github.com/VisTrails/VisTrails/commit/97c33644c20e94442511a36de10a6c94fc7f8d72
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-02 (Thu, 02 Apr 2015)

  Changed paths:
    M vistrails/gui/version_view.py
    M vistrails/gui/vistrail_controller.py

  Log Message:
  -----------
  Merge pull request #1034 from VisTrails/remove-versiontree-timer

Removes version layout animation


  Commit: 260391967d3fa2da26d10f347a3b654440e3e1cd
      https://github.com/VisTrails/VisTrails/commit/260391967d3fa2da26d10f347a3b654440e3e1cd
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-02 (Thu, 02 Apr 2015)

  Changed paths:
    M vistrails/gui/version_view.py

  Log Message:
  -----------
  Removes refine_graph()'s argument


  Commit: 2d76b9531cfdcb4504c6c9685be288259f785375
      https://github.com/VisTrails/VisTrails/commit/2d76b9531cfdcb4504c6c9685be288259f785375
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-02 (Thu, 02 Apr 2015)

  Changed paths:
    M vistrails/gui/version_view.py

  Log Message:
  -----------
  Removes timing code from setupScene()


  Commit: b43e178d171f1e9eeea71dde670d66e90f0417b9
      https://github.com/VisTrails/VisTrails/commit/b43e178d171f1e9eeea71dde670d66e90f0417b9
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-02 (Thu, 02 Apr 2015)

  Changed paths:
    M vistrails/core/layout/tree_layout.py
    M vistrails/core/layout/version_tree_layout.py
    M vistrails/core/vistrail/controller.py

  Log Message:
  -----------
  Renames 'childs' -> 'children' in tree layout code


  Commit: d1a61a92c394375f58c1849263b77acf9d10b9a5
      https://github.com/VisTrails/VisTrails/commit/d1a61a92c394375f58c1849263b77acf9d10b9a5
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-02 (Thu, 02 Apr 2015)

  Changed paths:
    M vistrails/gui/version_prop.py

  Log Message:
  -----------
  Don't reset notes unless version really changes


  Commit: fe378b6f273bcc0bd8e26a4a6fb58f63ec618edc
      https://github.com/VisTrails/VisTrails/commit/fe378b6f273bcc0bd8e26a4a6fb58f63ec618edc
  Author: Samuel Fries <fries2 at llnl.gov>
  Date:   2015-04-02 (Thu, 02 Apr 2015)

  Changed paths:
    M vistrails/packages/vtk/vtkcell.py

  Log Message:
  -----------
  Fix case of Backspace


  Commit: d7437357bcc5a4fdb6ed1c2e86fcf2909de75d5e
      https://github.com/VisTrails/VisTrails/commit/d7437357bcc5a4fdb6ed1c2e86fcf2909de75d5e
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-02 (Thu, 02 Apr 2015)

  Changed paths:
    M vistrails/core/interpreter/cached.py
    M vistrails/core/modules/vistrails_module.py
    M vistrails/packages/vtk/init.py
    M vistrails/packages/vtk/pythonclass.py
    M vistrails/packages/vtk/vtk_wrapper/parse.py

  Log Message:
  -----------
  Add VTK package version to xml spec name


  Commit: 66e8ca7bd2d79a97281f2386f182efdf1820b1ad
      https://github.com/VisTrails/VisTrails/commit/66e8ca7bd2d79a97281f2386f182efdf1820b1ad
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-03 (Fri, 03 Apr 2015)

  Changed paths:
    M vistrails/packages/vtk/init.py

  Log Message:
  -----------
  VTK: Always use current package and identifier

The upgrade code requires using existing package version
when fetching specs and creating functions

This fix wraps those calls to always use the current version of the package.


  Commit: 5a2e0085c7483498d520b8ff6d094c18d6808e25
      https://github.com/VisTrails/VisTrails/commit/5a2e0085c7483498d520b8ff6d094c18d6808e25
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-03 (Fri, 03 Apr 2015)

  Changed paths:
    M vistrails/core/interpreter/cached.py
    M vistrails/core/modules/vistrails_module.py
    M vistrails/packages/vtk/pythonclass.py

  Log Message:
  -----------
  Removed accidental print statements


  Commit: bc2f050a0f4f3d5f94c8ef2aceb5f0ad2110e419
      https://github.com/VisTrails/VisTrails/commit/bc2f050a0f4f3d5f94c8ef2aceb5f0ad2110e419
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-03 (Fri, 03 Apr 2015)

  Changed paths:
    M vistrails/packages/vtk/init.py
    M vistrails/packages/vtk/vtkcell.py

  Log Message:
  -----------
  Added missing vtkRenderToSpreadsheet

Fixes #1042


  Commit: 20e3e9df1f1d7dafcb546e28e451bfc02e8d0c14
      https://github.com/VisTrails/VisTrails/commit/20e3e9df1f1d7dafcb546e28e451bfc02e8d0c14
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-03 (Fri, 03 Apr 2015)

  Changed paths:
    M vistrails/packages/vtk/vtk_wrapper/specs.py

  Log Message:
  -----------
  Skip VTK spec tests if VTK is not installed


  Commit: 9f67ed887390ef527cb63e185df591adcf4da598
      https://github.com/VisTrails/VisTrails/commit/9f67ed887390ef527cb63e185df591adcf4da598
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-03 (Fri, 03 Apr 2015)

  Changed paths:
    M vistrails/core/configuration.py
    M vistrails/core/modules/package.py
    M vistrails/tests/runtestsuite.py

  Log Message:
  -----------
  Introduces 'dontUnloadModules' setting

Unloading/reloading Python modules interferes with the test runner,
since TestCases have already been collected; deleting their containing
modules is not ok.


  Commit: d5f056ef53f2bd07228702c764c8aaa98f82110f
      https://github.com/VisTrails/VisTrails/commit/d5f056ef53f2bd07228702c764c8aaa98f82110f
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-03 (Fri, 03 Apr 2015)

  Changed paths:
    M vistrails/gui/mashups/mashup_app.py

  Log Message:
  -----------
  Use enable_package() in mashup test


  Commit: 43efbfc45a6cdd0927fda9d2f43d6ef87bcee676
      https://github.com/VisTrails/VisTrails/commit/43efbfc45a6cdd0927fda9d2f43d6ef87bcee676
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-03 (Fri, 03 Apr 2015)

  Changed paths:
    M scripts/dist/conda/vistrails/meta.yaml

  Log Message:
  -----------
  Adds more deps to conda package


  Commit: 032b624d9001c9c6267b13c4b809ee5419d989e0
      https://github.com/VisTrails/VisTrails/commit/032b624d9001c9c6267b13c4b809ee5419d989e0
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-03 (Fri, 03 Apr 2015)

  Changed paths:
    M vistrails/packages/vtk/vtk_wrapper/specs.py

  Log Message:
  -----------
  Removes useless classmethod() from vtk


  Commit: 07e853f1760aac5b86f65088f50ad28dadbf4dbc
      https://github.com/VisTrails/VisTrails/commit/07e853f1760aac5b86f65088f50ad28dadbf4dbc
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-03 (Fri, 03 Apr 2015)

  Changed paths:
    M vistrails/packages/vtk/vtk_wrapper/vtk_classes.py

  Log Message:
  -----------
  Removes debug filterwarnings() call


  Commit: 334bab66eed2e03c34cbc39b0e596fd64cc64f3b
      https://github.com/VisTrails/VisTrails/commit/334bab66eed2e03c34cbc39b0e596fd64cc64f3b
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-03 (Fri, 03 Apr 2015)

  Changed paths:
    M vistrails/core/console_mode.py

  Log Message:
  -----------
  Adds missing imports to console_mode.py


  Commit: b10ad8148bfe5352d4c990f0baf0b8102e7c80f7
      https://github.com/VisTrails/VisTrails/commit/b10ad8148bfe5352d4c990f0baf0b8102e7c80f7
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-06 (Mon, 06 Apr 2015)

  Changed paths:
    M scripts/add_future_import.py

  Log Message:
  -----------
  chmod +x scripts/add_future_import.py


  Commit: 6fa441a9dbae66af9de3f0b7c1d18c0ab918eca7
      https://github.com/VisTrails/VisTrails/commit/6fa441a9dbae66af9de3f0b7c1d18c0ab918eca7
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-06 (Mon, 06 Apr 2015)

  Changed paths:
    M vistrails/packages/vtk/init.py
    M vistrails/packages/vtk/vtkcell.py

  Log Message:
  -----------
  Removes vtkRendererOutput's spreadsheet ports


  Commit: dcca2109cb3d85a6556aa3a0e92e163360159e8d
      https://github.com/VisTrails/VisTrails/commit/dcca2109cb3d85a6556aa3a0e92e163360159e8d
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-06 (Mon, 06 Apr 2015)

  Changed paths:
    M vistrails/core/vistrail/controller.py
    M vistrails/core/vistrail/job.py

  Log Message:
  -----------
  Fixes weakref usage in job.py


  Commit: 6f386ccab64054eb38dd4f0ac8bbe39eb9a6ac52
      https://github.com/VisTrails/VisTrails/commit/6f386ccab64054eb38dd4f0ac8bbe39eb9a6ac52
  Author: Samuel Fries <fries2 at llnl.gov>
  Date:   2015-04-06 (Mon, 06 Apr 2015)

  Changed paths:
    M vistrails/packages/vtk/vtkcell.py

  Log Message:
  -----------
  Fixes Q/E support


  Commit: 2351b13df7911307dfbd1e7e2a159cbc20fe647b
      https://github.com/VisTrails/VisTrails/commit/2351b13df7911307dfbd1e7e2a159cbc20fe647b
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-06 (Mon, 06 Apr 2015)

  Changed paths:
    M vistrails/core/bundles/pyimport.py
    M vistrails/core/configuration.py
    M vistrails/gui/shell.py

  Log Message:
  -----------
  Store declined bundle installations in app setting

When a user declines to install an optional package (such as xlrd or
IPython), VisTrails would keep asking every time it is restarted.

We can now remember the parameter in a VisTrails setting.

If installation succeeds, the parameter is reset.


  Commit: df6ea27f66ae56f867a0586b55e566d012441618
      https://github.com/VisTrails/VisTrails/commit/df6ea27f66ae56f867a0586b55e566d012441618
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-06 (Mon, 06 Apr 2015)

  Changed paths:
    M vistrails/core/bundles/pyimport.py
    M vistrails/core/configuration.py
    M vistrails/gui/shell.py

  Log Message:
  -----------
  Use a single setting for all bundles


  Commit: a7562cea09e4a8b04abeeb5b70178968718ccd3f
      https://github.com/VisTrails/VisTrails/commit/a7562cea09e4a8b04abeeb5b70178968718ccd3f
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-06 (Mon, 06 Apr 2015)

  Changed paths:
    M vistrails/packages/URL/https_if_available.py
    M vistrails/packages/tabledata/read/read_excel.py
    M vistrails/packages/tabledata/write/write_excel.py

  Log Message:
  -----------
  Use new argument for optional package deps


  Commit: 4f9703fceb1769bc8705c2b3c58b35adbe5962d6
      https://github.com/VisTrails/VisTrails/commit/4f9703fceb1769bc8705c2b3c58b35adbe5962d6
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-06 (Mon, 06 Apr 2015)

  Changed paths:
    M vistrails/core/bundles/pyimport.py
    M vistrails/core/configuration.py
    M vistrails/gui/shell.py
    M vistrails/packages/URL/https_if_available.py
    M vistrails/packages/tabledata/read/read_excel.py
    M vistrails/packages/tabledata/write/write_excel.py

  Log Message:
  -----------
  Merge branch 'bundle-install-prompts' into 'master'


  Commit: 68d0ce336fdd07754df02f0761d90aaa685ec9c7
      https://github.com/VisTrails/VisTrails/commit/68d0ce336fdd07754df02f0761d90aaa685ec9c7
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-06 (Mon, 06 Apr 2015)

  Changed paths:
    M vistrails/core/vistrail/controller.py

  Log Message:
  -----------
  Minor fixes to current terse_graph code


  Commit: db44c20a0450535a79d0a846f3353617c3cce5cd
      https://github.com/VisTrails/VisTrails/commit/db44c20a0450535a79d0a846f3353617c3cce5cd
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-06 (Mon, 06 Apr 2015)

  Changed paths:
    M vistrails/core/vistrail/controller.py

  Log Message:
  -----------
  Removes attempt to show selected pruned node

This only showed the pruned node anyway, not any of its descendants.


  Commit: 9b947117a0dbd30d3854911c5f06f58152fa78b0
      https://github.com/VisTrails/VisTrails/commit/9b947117a0dbd30d3854911c5f06f58152fa78b0
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-06 (Mon, 06 Apr 2015)

  Changed paths:
    M vistrails/core/data_structures/graph.py
    M vistrails/core/vistrail/controller.py
    M vistrails/gui/version_view.py

  Log Message:
  -----------
  Hide upgrades in tersed version tree


  Commit: 3d45aff1c1f8eab3f503582d0f15ccc528cc184c
      https://github.com/VisTrails/VisTrails/commit/3d45aff1c1f8eab3f503582d0f15ccc528cc184c
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-06 (Mon, 06 Apr 2015)

  Changed paths:
    M vistrails/core/vistrail/controller.py

  Log Message:
  -----------
  Jump over upgrades earlier


  Commit: 937a54e39171e3de3ce39de2f482e0cf58210c8f
      https://github.com/VisTrails/VisTrails/commit/937a54e39171e3de3ce39de2f482e0cf58210c8f
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-06 (Mon, 06 Apr 2015)

  Changed paths:
    M vistrails/core/vistrail/controller.py
    M vistrails/gui/version_view.py
    M vistrails/gui/vistrail_controller.py

  Log Message:
  -----------
  Adds collapsing logic to controller

This fixes the logic choosing whether to display the "collapse" button,
moving it to the controller (from the version view).

It duplicates the children-enumeration code to jump over upgrades.


  Commit: 2b03bbefb1c654fbe32d49a05b0cfaf013fd6102
      https://github.com/VisTrails/VisTrails/commit/2b03bbefb1c654fbe32d49a05b0cfaf013fd6102
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-06 (Mon, 06 Apr 2015)

  Changed paths:
    M vistrails/gui/version_view.py

  Log Message:
  -----------
  Fixes update_scene_single_node_change()


  Commit: 5f5d09f22a17c314e945028a544c30438f2f4f00
      https://github.com/VisTrails/VisTrails/commit/5f5d09f22a17c314e945028a544c30438f2f4f00
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-06 (Mon, 06 Apr 2015)

  Changed paths:
    M vistrails/core/configuration.py
    M vistrails/core/vistrail/controller.py

  Log Message:
  -----------
  Adds 'hideUpgrades' setting


  Commit: 5656d34514daba717c169e9f697a31f946ab411f
      https://github.com/VisTrails/VisTrails/commit/5656d34514daba717c169e9f697a31f946ab411f
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-06 (Mon, 06 Apr 2015)

  Changed paths:
    M vistrails/core/vistrail/controller.py
    M vistrails/gui/vistrail_controller.py

  Log Message:
  -----------
  Moves expand/collapse/prune methods to core


  Commit: bcdf0dee5a594c77175142bafe9486bfc82e7d6d
      https://github.com/VisTrails/VisTrails/commit/bcdf0dee5a594c77175142bafe9486bfc82e7d6d
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-06 (Mon, 06 Apr 2015)

  Changed paths:
    A vistrails/tests/resources/test_upgrades_layout/__init__.py
    A vistrails/tests/resources/test_upgrades_layout/init.py
    A vistrails/tests/resources/upgrades1.xml
    A vistrails/tests/resources/upgrades2.xml

  Log Message:
  -----------
  Test cases for upgrades


  Commit: 5c2eee73557f4c496b08daa50b0aefec67e90771
      https://github.com/VisTrails/VisTrails/commit/5c2eee73557f4c496b08daa50b0aefec67e90771
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-06 (Mon, 06 Apr 2015)

  Changed paths:
    M vistrails/core/vistrail/controller.py

  Log Message:
  -----------
  Change collapsible condition

Was "current node has exactly one children", now "current node would not
have been displayed if not for expand override".


  Commit: 6dcc42533088368b04dde75e3822afc4d41837bb
      https://github.com/VisTrails/VisTrails/commit/6dcc42533088368b04dde75e3822afc4d41837bb
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-06 (Mon, 06 Apr 2015)

  Changed paths:
    M vistrails/core/vistrail/controller.py

  Log Message:
  -----------
  Adds test for recompute_terse_graph()


  Commit: 9b8bc082bcd540cb687dea9b7a109d0d99ddc67d
      https://github.com/VisTrails/VisTrails/commit/9b8bc082bcd540cb687dea9b7a109d0d99ddc67d
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-07 (Tue, 07 Apr 2015)

  Changed paths:
    M vistrails/packages/vtk/vtk_wrapper/parse.py

  Log Message:
  -----------
  Blacklisted vtkOpenGLExtensionManager, vtkRenderView, vtkRenderViewBase for #1032


  Commit: a32d168839c02dbd53910b9346d6c5b9b57601db
      https://github.com/VisTrails/VisTrails/commit/a32d168839c02dbd53910b9346d6c5b9b57601db
  Author: dakoop <dakoop at users.noreply.github.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/core/modules/output_modules.py
    M vistrails/gui/modules/output_configuration.py
    M vistrails/packages/spreadsheet/spreadsheet_cell.py

  Log Message:
  -----------
  Merge pull request #1012 from VisTrails/fileoutput-format-combo

FileOutput format combo


  Commit: 4e9c3ea0d105e3ccd8cc687037b71ca1497d3217
      https://github.com/VisTrails/VisTrails/commit/4e9c3ea0d105e3ccd8cc687037b71ca1497d3217
  Author: David Koop <dkoop at umassd.edu>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M CHANGELOG
    M LICENSE
    A MANIFEST.in
    M doc/usersguide/conf.py
    M doc/usersguide/example_guide.rst
    M doc/usersguide/vtl/README
    A examples-internal/broken/errors.vt
    A examples-internal/broken/invalid-package.xml
    A examples-internal/broken/too-recent.xml
    A examples/api/brain_output.xml
    A examples/api/imagemagick.vt
    A examples/api/ipython-notebook.ipynb
    A examples/api/out_html.xml
    A examples/api/outputs.vt
    A examples/api/simplemath.vt
    A examples/api/table.xml
    A examples/api/vistrails_logo.png
    M examples/infovis.vt
    M examples/matplotlib/Acorr_ex8.vt
    M examples/matplotlib/Arrow_ex9.vt
    M examples/matplotlib/Psd.vt
    M examples/matplotlib/annotate.vt
    M examples/matplotlib/axhspan_ex5.vt
    M examples/matplotlib/bar_ex1.vt
    M examples/matplotlib/cohere.vt
    M examples/matplotlib/contourf.vt
    M examples/matplotlib/hist_ex1.vt
    M examples/matplotlib/line2d_ex4.vt
    M examples/matplotlib/line2d_ex7.vt
    M examples/matplotlib/lineplot_ex3.vt
    M examples/matplotlib/pcolor.vt
    M examples/matplotlib/pie_ex1.vt
    M examples/matplotlib/polar_ex10.vt
    M examples/matplotlib/scatter.vt
    M examples/matplotlib/semilog.vt
    R examples/scripting/README
    R examples/scripting/brain_from_script.vt
    R examples/scripting/brain_script.py
    R examples/scripting/combined_script.py
    R examples/scripting/vtk_book_3rd_p189_script.py
    M scripts/add_future_import.py
    A scripts/dist/common/disclaimer.svg
    M scripts/dist/common/prepare_release.py
    M scripts/dist/conda/vistrails/meta.yaml
    M scripts/dist/mac/setup.py
    M scripts/dist/windows/common1.iss
    M scripts/dist/windows/common2.iss
    M scripts/release_notes.py
    M setup.py
    M vistrails/core/api.py
    M vistrails/core/bundles/pyimport.py
    M vistrails/core/configuration.py
    M vistrails/core/console_mode.py
    M vistrails/core/debug.py
    M vistrails/core/layout/tree_layout.py
    M vistrails/core/layout/version_tree_layout.py
    M vistrails/core/log/controller.py
    M vistrails/core/mashup/action.py
    M vistrails/core/mashup/action_annotation.py
    M vistrails/core/modules/output_modules.py
    M vistrails/core/modules/package.py
    M vistrails/core/modules/vistrails_module.py
    M vistrails/core/startup.py
    M vistrails/core/system/osx.py
    M vistrails/core/upgradeworkflow.py
    M vistrails/core/vistrail/controller.py
    M vistrails/core/vistrail/job.py
    M vistrails/db/bin/templates/sql_schema.sql.mako
    M vistrails/db/services/io.py
    R vistrails/db/versions/v0_8_1/schemas/sql/vistrails.sql.bkp
    M vistrails/gui/application.py
    M vistrails/gui/job_monitor.py
    M vistrails/gui/mashups/mashup_app.py
    M vistrails/gui/modules/list_configuration.py
    M vistrails/gui/modules/output_configuration.py
    M vistrails/gui/modules/stringformat_configuration.py
    M vistrails/gui/paramexplore/param_view.py
    M vistrails/gui/paramexplore/pe_inspector.py
    M vistrails/gui/paramexplore/pe_table.py
    M vistrails/gui/paramexplore/pe_view.py
    M vistrails/gui/pipeline_view.py
    M vistrails/gui/resources/images/disclaimer.png
    M vistrails/gui/resources/images/vistrails_splash.png
    M vistrails/gui/shell.py
    M vistrails/gui/version_prop.py
    M vistrails/gui/version_view.py
    M vistrails/gui/vistrail_controller.py
    M vistrails/gui/vistrails_window.py
    M vistrails/packages/CLTools/identifiers.py
    M vistrails/packages/CLTools/wizard.py
    M vistrails/packages/URL/http_directory.py
    M vistrails/packages/URL/https.py
    M vistrails/packages/URL/https_if_available.py
    M vistrails/packages/controlflow/looping.py
    M vistrails/packages/dialogs/continue_prompt.py
    M vistrails/packages/gmaps/__init__.py
    M vistrails/packages/gmaps/gmap_cell.py
    M vistrails/packages/gmaps/identifiers.py
    M vistrails/packages/gmaps/init.py
    M vistrails/packages/gmaps/utils.py
    M vistrails/packages/gmaps/vis.py
    M vistrails/packages/matplotlib/__init__.py
    M vistrails/packages/matplotlib/bases.py
    M vistrails/packages/matplotlib/diff.py
    M vistrails/packages/matplotlib/figure_cell.py
    M vistrails/packages/matplotlib/generate.py
    M vistrails/packages/matplotlib/init.py
    M vistrails/packages/matplotlib/mixins.py
    M vistrails/packages/matplotlib/parse.py
    M vistrails/packages/matplotlib/specs.py
    M vistrails/packages/matplotlib/widgets.py
    M vistrails/packages/parallelflow/__init__.py
    M vistrails/packages/parallelflow/api.py
    M vistrails/packages/parallelflow/engine_manager.py
    M vistrails/packages/parallelflow/init.py
    M vistrails/packages/parallelflow/map.py
    M vistrails/packages/persistent_archive/__init__.py
    M vistrails/packages/persistent_archive/cache.py
    M vistrails/packages/persistent_archive/common.py
    M vistrails/packages/persistent_archive/identifiers.py
    M vistrails/packages/persistent_archive/init.py
    M vistrails/packages/persistent_archive/persistedinput.py
    M vistrails/packages/persistent_archive/persistedoutput.py
    M vistrails/packages/persistent_archive/queriedinput.py
    M vistrails/packages/persistent_archive/queries.py
    M vistrails/packages/persistent_archive/ui.py
    M vistrails/packages/persistent_archive/widgets.py
    M vistrails/packages/sklearn/__init__.py
    M vistrails/packages/sklearn/init.py
    M vistrails/packages/sklearn/tests.py
    M vistrails/packages/spreadsheet/spreadsheet_cell.py
    M vistrails/packages/sql/widgets.py
    M vistrails/packages/tabledata/common.py
    M vistrails/packages/tabledata/convert/__init__.py
    M vistrails/packages/tabledata/convert/convert_dates.py
    M vistrails/packages/tabledata/read/__init__.py
    M vistrails/packages/tabledata/read/read_csv.py
    M vistrails/packages/tabledata/read/read_excel.py
    M vistrails/packages/tabledata/read/read_json.py
    M vistrails/packages/tabledata/read/read_numpy.py
    M vistrails/packages/tabledata/viewer.py
    M vistrails/packages/tabledata/write/__init__.py
    M vistrails/packages/tabledata/write/write_csv.py
    M vistrails/packages/tabledata/write/write_excel.py
    R vistrails/packages/vtk/base_module.py
    R vistrails/packages/vtk/class_tree.py
    A vistrails/packages/vtk/common.py
    R vistrails/packages/vtk/fix_classes.py
    M vistrails/packages/vtk/identifiers.py
    M vistrails/packages/vtk/init.py
    M vistrails/packages/vtk/inspectors.py
    M vistrails/packages/vtk/offscreen.py
    A vistrails/packages/vtk/pythonclass.py
    M vistrails/packages/vtk/tf_widget.py
    R vistrails/packages/vtk/vtk_parser.py
    A vistrails/packages/vtk/vtk_wrapper/__init__.py
    A vistrails/packages/vtk/vtk_wrapper/class_tree.py
    A vistrails/packages/vtk/vtk_wrapper/fix_classes.py
    A vistrails/packages/vtk/vtk_wrapper/parse.py
    A vistrails/packages/vtk/vtk_wrapper/specs.py
    A vistrails/packages/vtk/vtk_wrapper/vtk_classes.py
    A vistrails/packages/vtk/vtk_wrapper/vtk_module.py
    A vistrails/packages/vtk/vtk_wrapper/vtk_parser.py
    A vistrails/packages/vtk/vtk_wrapper/wrapper.py
    M vistrails/packages/vtk/vtkcell.py
    M vistrails/packages/vtk/vtkhandler.py
    R vistrails/packages/vtk/vtkviewcell.py
    R vistrails/packages/vtk/wrapper.py
    M vistrails/tests/runtestsuite.py
    M vistrails/tests/utils.py

  Log Message:
  -----------
  Merge branch 'master' into imageoutput

Conflicts:
	vistrails/core/modules/output_modules.py


  Commit: 17bf71bb9531b69dbb3a944382e3297f8f929b62
      https://github.com/VisTrails/VisTrails/commit/17bf71bb9531b69dbb3a944382e3297f8f929b62
  Author: David Koop <dkoop at umassd.edu>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/core/modules/output_modules.py
    M vistrails/gui/preferences.py
    M vistrails/packages/spreadsheet/basic_widgets.py
    M vistrails/packages/spreadsheet/widgets/imageviewer/__init__.py
    M vistrails/packages/spreadsheet/widgets/imageviewer/imageviewer.py

  Log Message:
  -----------
  Merge branch 'imageoutput'


  Commit: 0449382268b78becf2869e8b8d392fa1f5343089
      https://github.com/VisTrails/VisTrails/commit/0449382268b78becf2869e8b8d392fa1f5343089
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/core/modules/output_modules.py

  Log Message:
  -----------
  Fixes merge

Looks like there was a conflict, my bad.

fileoutput-format-combo added a RichTextToFileMode, which uses the
formats list.
This branch, imageoutput, adds an HtmlToFileMode, which uses the
default_file_extension string.

David kept the former, this commits switchs to the latter.


  Commit: 4344501a2d48bc6b48b23c9d9f6961044b39a9b6
      https://github.com/VisTrails/VisTrails/commit/4344501a2d48bc6b48b23c9d9f6961044b39a9b6
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/core/modules/output_modules.py
    M vistrails/packages/matplotlib/bases.py

  Log Message:
  -----------
  Fixes IPythonMode priority

After 9e6fbb0b


  Commit: f61ebbda35d9bbd04ccf3eb07bb34db598f925fb
      https://github.com/VisTrails/VisTrails/commit/f61ebbda35d9bbd04ccf3eb07bb34db598f925fb
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/core/modules/output_modules.py
    M vistrails/packages/matplotlib/bases.py

  Log Message:
  -----------
  Merge pull request #1013 from VisTrails/imageoutput

Implements ImageOutput and fixes output mode priorities


  Commit: 5740c249129c882ffb4bd59defff6f66a5b75c60
      https://github.com/VisTrails/VisTrails/commit/5740c249129c882ffb4bd59defff6f66a5b75c60
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/core/configuration.py
    M vistrails/core/data_structures/graph.py
    M vistrails/core/vistrail/controller.py
    M vistrails/gui/version_view.py
    M vistrails/gui/vistrail_controller.py
    A vistrails/tests/resources/test_upgrades_layout/__init__.py
    A vistrails/tests/resources/test_upgrades_layout/init.py
    A vistrails/tests/resources/upgrades1.xml
    A vistrails/tests/resources/upgrades2.xml

  Log Message:
  -----------
  Merge pull request #1046 from VisTrails/hide-upgrades

Hide upgrades in the version tree


  Commit: 1af1ba777cc44974120a8d19339d6734e96e1f35
      https://github.com/VisTrails/VisTrails/commit/1af1ba777cc44974120a8d19339d6734e96e1f35
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/core/inspector.py
    M vistrails/core/modules/utils.py
    M vistrails/core/system/__init__.py
    M vistrails/core/utils/__init__.py
    M vistrails/core/vistrail/pipeline.py

  Log Message:
  -----------
  Unrelated imports cleanup


  Commit: 5b74b245f54604c041e94cc0b0974416045eeb5c
      https://github.com/VisTrails/VisTrails/commit/5b74b245f54604c041e94cc0b0974416045eeb5c
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/core/inspector.py
    M vistrails/core/system/__init__.py
    M vistrails/core/vistrail/pipeline.py
    M vistrails/db/services/opm.py
    M vistrails/gui/paramexplore/pe_tab.py
    M vistrails/gui/vistrail_controller.py
    M vistrails/packages/vtk/init.py

  Log Message:
  -----------
  Don't use get_vistrails_default_pkg_prefix()

The whole point of identifiers is to be a unique immutable string
identifying a module. Dynamically computing it defeats the purpose.

They should not change and code should rely on that fact. VisTrails has
already been made tolerant to changes in identifiers via the
old_identifiers and can_handle_identifier() mechanisms.


  Commit: 519f8a6ea12f6e923e0f8a1940a2efbba0889d85
      https://github.com/VisTrails/VisTrails/commit/519f8a6ea12f6e923e0f8a1940a2efbba0889d85
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/core/modules/utils.py
    M vistrails/core/system/__init__.py

  Log Message:
  -----------
  Remove legitimate use in parse_descriptor_string()


  Commit: 3e7b4d3d4cdd38fbeb7bf46e25ddff6fcd341cbf
      https://github.com/VisTrails/VisTrails/commit/3e7b4d3d4cdd38fbeb7bf46e25ddff6fcd341cbf
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/packages/spreadsheet/identifiers.py
    M vistrails/packages/spreadsheet/init.py

  Log Message:
  -----------
  Upgrades RichTextCell to RichTextOutput


  Commit: 1c27a43525e7968fb173571bf7f588b6c5cdbafb
      https://github.com/VisTrails/VisTrails/commit/1c27a43525e7968fb173571bf7f588b6c5cdbafb
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/packages/vtk/init.py

  Log Message:
  -----------
  Upgrades VTKCell to vtkRendererOutput


  Commit: a12c2e0b43011fe217279346b2b74cf781c2ad40
      https://github.com/VisTrails/VisTrails/commit/a12c2e0b43011fe217279346b2b74cf781c2ad40
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/packages/tabledata/identifiers.py
    M vistrails/packages/tabledata/init.py

  Log Message:
  -----------
  Upgrades TableCell to TableOutput


  Commit: 60bd849a5e70e2af3ff407b3ee66c57740a7a7e6
      https://github.com/VisTrails/VisTrails/commit/60bd849a5e70e2af3ff407b3ee66c57740a7a7e6
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/packages/matplotlib/identifiers.py
    M vistrails/packages/matplotlib/init.py

  Log Message:
  -----------
  Upgrades MplFigureCell to MplFigureOutput


  Commit: 9e45a9f3b509e67e6f1c18880f1fba06a08d9495
      https://github.com/VisTrails/VisTrails/commit/9e45a9f3b509e67e6f1c18880f1fba06a08d9495
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/packages/spreadsheet/init.py

  Log Message:
  -----------
  Introduces upgrade_cell_to_output()

Checks whether upgrade from Cell module to Output module can be
performed safely (i.e. no input ports besides the object to be output is
connected or set).


  Commit: 18c8f5894163bbae266e080ba8a246d08e330a7a
      https://github.com/VisTrails/VisTrails/commit/18c8f5894163bbae266e080ba8a246d08e330a7a
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/packages/vtk/init.py

  Log Message:
  -----------
  Upgrades VTKCell using upgrade_cell_to_output


  Commit: e142e504d5c504a20f7098c89671c3145af595e8
      https://github.com/VisTrails/VisTrails/commit/e142e504d5c504a20f7098c89671c3145af595e8
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/packages/tabledata/init.py

  Log Message:
  -----------
  Upgrade TableCell using upgrade_cell_to_output


  Commit: abe52347c29f471b69558e021d569e0341df1be4
      https://github.com/VisTrails/VisTrails/commit/abe52347c29f471b69558e021d569e0341df1be4
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/packages/matplotlib/init.py

  Log Message:
  -----------
  Upgrade MplFigureCell using upgrade_cell_to_output


  Commit: 82c911fbeefb30e74e1cdaf405684000f00b9cde
      https://github.com/VisTrails/VisTrails/commit/82c911fbeefb30e74e1cdaf405684000f00b9cde
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/core/upgradeworkflow.py

  Log Message:
  -----------
  Implements copying upgrade objects


  Commit: efdef0aed98682a3f15a80f40413cec242f81e24
      https://github.com/VisTrails/VisTrails/commit/efdef0aed98682a3f15a80f40413cec242f81e24
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/packages/spreadsheet/init.py

  Log Message:
  -----------
  Switches to UpgradeModuleRemap object

upgrade_cell_to_output() now returns an UpgradeModuleRemap object,
instead of a dict; it also handles an input of that type in addition to
dict.


  Commit: d615ef672d0c1ec21970577094deeacad6d8aa97
      https://github.com/VisTrails/VisTrails/commit/d615ef672d0c1ec21970577094deeacad6d8aa97
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/packages/spreadsheet/init.py
    M vistrails/packages/vtk/identifiers.py
    M vistrails/packages/vtk/init.py

  Log Message:
  -----------
  vtk: makes this the 1.0.0->1.0.1 transition


  Commit: f45ed1efeb069b691c155b98e441dfbbc0734858
      https://github.com/VisTrails/VisTrails/commit/f45ed1efeb069b691c155b98e441dfbbc0734858
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/packages/vtk/init.py

  Log Message:
  -----------
  vtk: works around limitations in upgrades system

We need to make sure we get to 1.0.1 via explicit upgrades.


  Commit: 9dd7af4f932002b3453ee548712609d8c88e2bf8
      https://github.com/VisTrails/VisTrails/commit/9dd7af4f932002b3453ee548712609d8c88e2bf8
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/packages/spreadsheet/init.py

  Log Message:
  -----------
  Upgrades ImageViewerCell to ImageOutput


  Commit: d70e440a0cde03123fb9699ee4378c954bd4ca16
      https://github.com/VisTrails/VisTrails/commit/d70e440a0cde03123fb9699ee4378c954bd4ca16
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/packages/spreadsheet/init.py

  Log Message:
  -----------
  Handle functions as well as incoming connections


  Commit: 3c44bd7de7ffa86f55ca1db50109c45521091256
      https://github.com/VisTrails/VisTrails/commit/3c44bd7de7ffa86f55ca1db50109c45521091256
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/packages/spreadsheet/init.py

  Log Message:
  -----------
  Fixes output_version

Using the end_version as output_version is very broken because the new
module can be from a different package (with different versions).


  Commit: bd71beac2b11d7ce59733ce06b85bc822e47ea3f
      https://github.com/VisTrails/VisTrails/commit/bd71beac2b11d7ce59733ce06b85bc822e47ea3f
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/core/vistrail/controller.py

  Log Message:
  -----------
  Removes debug output from 5740c24


  Commit: 543afc0714e41ac484c3dca35d87c8f4d01bd769
      https://github.com/VisTrails/VisTrails/commit/543afc0714e41ac484c3dca35d87c8f4d01bd769
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/core/upgradeworkflow.py
    M vistrails/packages/matplotlib/identifiers.py
    M vistrails/packages/matplotlib/init.py
    M vistrails/packages/spreadsheet/identifiers.py
    M vistrails/packages/spreadsheet/init.py
    M vistrails/packages/tabledata/identifiers.py
    M vistrails/packages/tabledata/init.py
    M vistrails/packages/vtk/identifiers.py
    M vistrails/packages/vtk/init.py

  Log Message:
  -----------
  Merge pull request #1017 from VisTrails/upgrade-to-output-modules

Module upgrades for output modules


  Commit: 386a94158754326aba18235e84e1d6bdb7f7ea79
      https://github.com/VisTrails/VisTrails/commit/386a94158754326aba18235e84e1d6bdb7f7ea79
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Log Message:
  -----------
  Merge branch 'v2.1' into 'master'

Conflicts:
	vistrails/core/modules/vistrails_module.py


  Commit: 5c2f00e7eb21c9930e9ed0e1f68db6e1326c03a1
      https://github.com/VisTrails/VisTrails/commit/5c2f00e7eb21c9930e9ed0e1f68db6e1326c03a1
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M CHANGELOG

  Log Message:
  -----------
  Updates CHANGELOG

[skip ci]


  Commit: b8be36e5458e5765dee15d3d44b90f14d803b219
      https://github.com/VisTrails/VisTrails/commit/b8be36e5458e5765dee15d3d44b90f14d803b219
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/packages/spreadsheet/widgets/webview/webview.py

  Log Message:
  -----------
  Adds button to open webcell in browser


  Commit: c54dc424ba7457f18023f97f5bcd1759f99d5b25
      https://github.com/VisTrails/VisTrails/commit/c54dc424ba7457f18023f97f5bcd1759f99d5b25
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-08 (Wed, 08 Apr 2015)

  Changed paths:
    M vistrails/packages/spreadsheet/celltoolbar.qrc
    M vistrails/packages/spreadsheet/celltoolbar_rc.py
    A vistrails/packages/spreadsheet/images/new-window.png
    M vistrails/packages/spreadsheet/widgets/webview/webview.py

  Log Message:
  -----------
  New window icon (well, I tried)


  Commit: d872787883f3a7639df755a7dfcd7b07ad1fc10c
      https://github.com/VisTrails/VisTrails/commit/d872787883f3a7639df755a7dfcd7b07ad1fc10c
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-09 (Thu, 09 Apr 2015)

  Changed paths:
    M CHANGELOG

  Log Message:
  -----------
  Updated CHANGELOG


  Commit: 150101ec3db02f2d2755186c8d0cece354a99af0
      https://github.com/VisTrails/VisTrails/commit/150101ec3db02f2d2755186c8d0cece354a99af0
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-09 (Thu, 09 Apr 2015)

  Changed paths:
    M examples/terminator.vt

  Log Message:
  -----------
  Updated terminator.vt:Isosurface for VTK 6

VTK code in PythonSource now upgrades SetInput -> SetInputData when needed
VTK classes now need to call Update() explicitly.


  Commit: ecf1647943d56cf95230b67862651da81c0844bd
      https://github.com/VisTrails/VisTrails/commit/ecf1647943d56cf95230b67862651da81c0844bd
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-09 (Thu, 09 Apr 2015)

  Changed paths:
    M CHANGELOG

  Log Message:
  -----------
  Updates CHANGELOG


  Commit: 5a299b40fef9b793ae6c514dfd67a454e887beb6
      https://github.com/VisTrails/VisTrails/commit/5a299b40fef9b793ae6c514dfd67a454e887beb6
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-09 (Thu, 09 Apr 2015)

  Changed paths:
    M .travis.yml

  Log Message:
  -----------
  Explicitly requests sudo in Travis config


  Commit: 6c1b74949c1c577e1065748f041abaf650c5fa67
      https://github.com/VisTrails/VisTrails/commit/6c1b74949c1c577e1065748f041abaf650c5fa67
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-09 (Thu, 09 Apr 2015)

  Changed paths:
    M requirements.txt

  Log Message:
  -----------
  Use PyPI file_archive source in dev requirements


  Commit: 53df12c26b4a3d87816a4fc2ca528a41ce9be26d
      https://github.com/VisTrails/VisTrails/commit/53df12c26b4a3d87816a4fc2ca528a41ce9be26d
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-09 (Thu, 09 Apr 2015)

  Changed paths:
    M vistrails/gui/version_view.py

  Log Message:
  -----------
  Fixes version tree not highlighting current node

If the currently selected node has a materialized upgrade, it would
previously not be highlighted.


  Commit: fcc862cfbbb5f8009d84f30c98e90b15cd96137d
      https://github.com/VisTrails/VisTrails/commit/fcc862cfbbb5f8009d84f30c98e90b15cd96137d
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-09 (Thu, 09 Apr 2015)

  Changed paths:
    M vistrails/core/vistrail/controller.py
    M vistrails/gui/version_view.py

  Log Message:
  -----------
  Introduces current_base_version in controller

It points to the base version in the upgrade chain. Useful so that the
view doesn't have to recompute it (which is expensive because we walk
the upgrade annotations *backwards*, O(nb_annotations)), since the
controller knows it anyway (used it when computing the terse tree).


  Commit: edd8a9a2d3411592903d9467e479e194e88e580f
      https://github.com/VisTrails/VisTrails/commit/edd8a9a2d3411592903d9467e479e194e88e580f
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-09 (Thu, 09 Apr 2015)

  Changed paths:
    A .dockerignore
    A Dockerfile
    M Vagrantfile

  Log Message:
  -----------
  Adds Dockerfile


  Commit: 4b06d36aa61844dbd586ddcfaaa1c2e0d9381c77
      https://github.com/VisTrails/VisTrails/commit/4b06d36aa61844dbd586ddcfaaa1c2e0d9381c77
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-09 (Thu, 09 Apr 2015)

  Changed paths:
    M Dockerfile

  Log Message:
  -----------
  Removes print sys.path from Dockerfile -- it works


  Commit: c6ba1f3ec9423a97dc24a866e4067923a4703e9d
      https://github.com/VisTrails/VisTrails/commit/c6ba1f3ec9423a97dc24a866e4067923a4703e9d
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-10 (Fri, 10 Apr 2015)

  Changed paths:
    M scripts/dist/conda/conda.sh

  Log Message:
  -----------
  Make the conda build script accept -pre versions

v2.2-pre-9-g4b06d36 -> 2.2.pre.9


  Commit: 444b26f19153d6091d1e74f268a0e8a0e2f1fc9d
      https://github.com/VisTrails/VisTrails/commit/444b26f19153d6091d1e74f268a0e8a0e2f1fc9d
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-10 (Fri, 10 Apr 2015)

  Changed paths:
    M vistrails/gui/version_prop.py

  Log Message:
  -----------
  Fix separator lines


  Commit: c458cb6c98eb391973cd9e59ef760e2a965aeea5
      https://github.com/VisTrails/VisTrails/commit/c458cb6c98eb391973cd9e59ef760e2a965aeea5
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-10 (Fri, 10 Apr 2015)

  Changed paths:
    M vistrails/gui/vistrail_controller.py

  Log Message:
  -----------
  Mark controller as changed for notes


  Commit: 48b3eebb5fe15b10aa8fdf855eb5084c6713b77f
      https://github.com/VisTrails/VisTrails/commit/48b3eebb5fe15b10aa8fdf855eb5084c6713b77f
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-10 (Fri, 10 Apr 2015)

  Changed paths:
    M vistrails/core/vistrail/vistrail.py

  Log Message:
  -----------
  Adds Vistrail#search_upgrade_versions()


  Commit: d14d6b5c7a4923a350b1848a28ac525de27c5143
      https://github.com/VisTrails/VisTrails/commit/d14d6b5c7a4923a350b1848a28ac525de27c5143
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-10 (Fri, 10 Apr 2015)

  Changed paths:
    M vistrails/gui/version_prop.py

  Log Message:
  -----------
  Implements following upgrades in version_prop


  Commit: 26c78f715dfce86644aec0957e5d3a7fde0cdf9b
      https://github.com/VisTrails/VisTrails/commit/26c78f715dfce86644aec0957e5d3a7fde0cdf9b
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-10 (Fri, 10 Apr 2015)

  Changed paths:
    M vistrails/gui/vistrail_controller.py

  Log Message:
  -----------
  Implements following upgrades in gui controller


  Commit: c3e7da210809fa937cfeaec0b7240afc7b3a24f1
      https://github.com/VisTrails/VisTrails/commit/c3e7da210809fa937cfeaec0b7240afc7b3a24f1
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-10 (Fri, 10 Apr 2015)

  Changed paths:
    M vistrails/gui/vistrail_controller.py

  Log Message:
  -----------
  Tag/add notes to base_version


  Commit: 27ad929ca8cb1ec6626a93e172e26d4f3892c47d
      https://github.com/VisTrails/VisTrails/commit/27ad929ca8cb1ec6626a93e172e26d4f3892c47d
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-11 (Sat, 11 Apr 2015)

  Changed paths:
    M vistrails/core/vistrail/vistrail.py
    M vistrails/gui/version_prop.py
    M vistrails/gui/vistrail_controller.py

  Log Message:
  -----------
  Merge pull request #1053 from VisTrails/fix-version-prop

Fixes the GUI issues made apparent by #1046.


  Commit: f1029aac5a2f0e3dae09d989362a9046c5929fa1
      https://github.com/VisTrails/VisTrails/commit/f1029aac5a2f0e3dae09d989362a9046c5929fa1
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-13 (Mon, 13 Apr 2015)

  Changed paths:
    M scripts/dist/common/prepare_release.py

  Log Message:
  -----------
  Lowercase prepare_release: upper is for constants


  Commit: 58a08e6dbd31b1c0c1b45aef917d2dbac893aa10
      https://github.com/VisTrails/VisTrails/commit/58a08e6dbd31b1c0c1b45aef917d2dbac893aa10
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-13 (Mon, 13 Apr 2015)

  Changed paths:
    M scripts/dist/windows/Input/runvistrails.py

  Log Message:
  -----------
  Fixes PATH setup in runvistrails.py (Windows)


  Commit: 0219fc76b399b0ae4bc43124b70db496a3a3fd15
      https://github.com/VisTrails/VisTrails/commit/0219fc76b399b0ae4bc43124b70db496a3a3fd15
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-13 (Mon, 13 Apr 2015)

  Changed paths:
    M vistrails/core/vistrail/vistrail.py
    M vistrails/gui/version_prop.py

  Log Message:
  -----------
  Show ID/date/username of original version


  Commit: 86324e95a8335eb5b1528cd9342f0f336f097131
      https://github.com/VisTrails/VisTrails/commit/86324e95a8335eb5b1528cd9342f0f336f097131
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-14 (Tue, 14 Apr 2015)

  Changed paths:
    M vistrails/packages/CLTools/init.py

  Log Message:
  -----------
  Fixes unicode issue reloading CLTools modules


  Commit: 425224b312019f1e78023b6fdc8a954be487f6f1
      https://github.com/VisTrails/VisTrails/commit/425224b312019f1e78023b6fdc8a954be487f6f1
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-15 (Wed, 15 Apr 2015)

  Changed paths:
    M vistrails/gui/version_prop.py

  Log Message:
  -----------
  Make sure not to save HTML for empty notes


  Commit: dfe3a2518801dacbc89d7bdc76dfdfa7df10d9eb
      https://github.com/VisTrails/VisTrails/commit/dfe3a2518801dacbc89d7bdc76dfdfa7df10d9eb
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-16 (Thu, 16 Apr 2015)

  Changed paths:
    M scripts/dist/mac/setup.py

  Log Message:
  -----------
  Added sklearn to mac build script


  Commit: f1981d71b99de25961d610937e3c764c69ba34b5
      https://github.com/VisTrails/VisTrails/commit/f1981d71b99de25961d610937e3c764c69ba34b5
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-16 (Thu, 16 Apr 2015)

  Changed paths:
    M scripts/dist/windows/common2.iss

  Log Message:
  -----------
  Call runvistrails.py when starting normally on windows.

This makes sure the paths are set up correctly.


  Commit: 6848fe92177afaff4eea66feb70ad8e729084bb9
      https://github.com/VisTrails/VisTrails/commit/6848fe92177afaff4eea66feb70ad8e729084bb9
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-16 (Thu, 16 Apr 2015)

  Changed paths:
    M scripts/dist/mac/make_app

  Log Message:
  -----------
  Updated ALPS version in mac binary


  Commit: 5a028306919eb59fabc6879f355faa031504c79e
      https://github.com/VisTrails/VisTrails/commit/5a028306919eb59fabc6879f355faa031504c79e
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-16 (Thu, 16 Apr 2015)

  Changed paths:
    M vistrails/packages/persistent_archive/ui.py

  Log Message:
  -----------
  Fix hardcoded keys in persistent_archive.ui


  Commit: 6ffe8c67527a7dccbc0eebb2631371952679ba90
      https://github.com/VisTrails/VisTrails/commit/6ffe8c67527a7dccbc0eebb2631371952679ba90
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-16 (Thu, 16 Apr 2015)

  Changed paths:
    M vistrails/core/resources/default_vistrails_startup_xml

  Log Message:
  -----------
  Add more packages to default startup.xml

Since 40df629, VisTrails doesn't cry for packages it can't enable on the
first run, so there's no reason not to try them.

Newly enabled packages: gmaps, CLTools, matplotlib, persistent_archive,
sklearn, sql


  Commit: 73c2455efd2f3421c6868c94705ebd339bc7770e
      https://github.com/VisTrails/VisTrails/commit/73c2455efd2f3421c6868c94705ebd339bc7770e
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-16 (Thu, 16 Apr 2015)

  Changed paths:
    M requirements.txt
    A vistrails/packages/tej/__init__.py
    A vistrails/packages/tej/init.py
    A vistrails/packages/tej/widgets.py

  Log Message:
  -----------
  Adds vistrails-tej 0.2 to VisTrails source tree


  Commit: e0d3206565e2ad31af1e025547471135e1e3fac3
      https://github.com/VisTrails/VisTrails/commit/e0d3206565e2ad31af1e025547471135e1e3fac3
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-16 (Thu, 16 Apr 2015)

  Changed paths:
    M vistrails/packages/tej/init.py

  Log Message:
  -----------
  Get tej through py_import()


  Commit: 3f1e4b4e7ff5a98327c174e96e8521369332a05e
      https://github.com/VisTrails/VisTrails/commit/3f1e4b4e7ff5a98327c174e96e8521369332a05e
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-16 (Thu, 16 Apr 2015)

  Changed paths:
    M vistrails/core/resources/default_vistrails_startup_xml

  Log Message:
  -----------
  Enable tej in default startup.xml


  Commit: c4b75bd56620049d0affbecd0318c2067c1541ad
      https://github.com/VisTrails/VisTrails/commit/c4b75bd56620049d0affbecd0318c2067c1541ad
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-16 (Thu, 16 Apr 2015)

  Changed paths:
    M scripts/dist/windows/common2.iss

  Log Message:
  -----------
  Fixes call to runvistrails.py


  Commit: b83946776c32527bffd1f11fb4f31537ce4f1f6b
      https://github.com/VisTrails/VisTrails/commit/b83946776c32527bffd1f11fb4f31537ce4f1f6b
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-16 (Thu, 16 Apr 2015)

  Changed paths:
    M requirements.txt
    M vistrails/core/resources/default_vistrails_startup_xml
    A vistrails/packages/tej/__init__.py
    A vistrails/packages/tej/init.py
    A vistrails/packages/tej/widgets.py

  Log Message:
  -----------
  Merge branch 'tej' into 'v2.2'


  Commit: 86f919bf26c4a497da792d87aac9f8a1fa1e5571
      https://github.com/VisTrails/VisTrails/commit/86f919bf26c4a497da792d87aac9f8a1fa1e5571
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-16 (Thu, 16 Apr 2015)

  Changed paths:
    M scripts/dist/windows/Input/runvistrails.py
    M scripts/dist/windows/common2.iss

  Log Message:
  -----------
  Fixes runvistrails.py


  Commit: 95f79ecb9ef67fb1a51a30b0390b34478b8d6cb2
      https://github.com/VisTrails/VisTrails/commit/95f79ecb9ef67fb1a51a30b0390b34478b8d6cb2
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-17 (Fri, 17 Apr 2015)

  Changed paths:
    M scripts/dist/mac/setup.py

  Log Message:
  -----------
  Added tej to mac build script


  Commit: 4f4ee6fa379a9c916475fbeb4c2b495cccebd377
      https://github.com/VisTrails/VisTrails/commit/4f4ee6fa379a9c916475fbeb4c2b495cccebd377
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-17 (Fri, 17 Apr 2015)

  Changed paths:
    M scripts/dist/mac/setup.py

  Log Message:
  -----------
  Fixes tej include for py2app


  Commit: 106f7a3d1a2c8e941d1322c297bd4b6ea3c90e6c
      https://github.com/VisTrails/VisTrails/commit/106f7a3d1a2c8e941d1322c297bd4b6ea3c90e6c
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-20 (Mon, 20 Apr 2015)

  Changed paths:
    M vistrails/gui/vistrails_window.py

  Log Message:
  -----------
  Fixes open_workflow

add_vt_window was moved to open_vistrail
Now it also need to be called in open_workflow

Fixes #1062


  Commit: c837ec80a5ac03f6a7f20d1307daa0c5d63820f1
      https://github.com/VisTrails/VisTrails/commit/c837ec80a5ac03f6a7f20d1307daa0c5d63820f1
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-20 (Mon, 20 Apr 2015)

  Changed paths:
    M vistrails/gui/vistrails_window.py

  Log Message:
  -----------
  Fixes merge_vistrails


  Commit: 89b6090f499b6223c6b5ba4bfc14c77d734a3b20
      https://github.com/VisTrails/VisTrails/commit/89b6090f499b6223c6b5ba4bfc14c77d734a3b20
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-20 (Mon, 20 Apr 2015)

  Changed paths:
    M vistrails/gui/vistrails_window.py

  Log Message:
  -----------
  Fixes typo in 106f7a3d1a2c8e


  Commit: b29fb763f234f4a9eb58ef18da6a7f23f3f6daaf
      https://github.com/VisTrails/VisTrails/commit/b29fb763f234f4a9eb58ef18da6a7f23f3f6daaf
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-20 (Mon, 20 Apr 2015)

  Changed paths:
    M vistrails/gui/vistrails_window.py

  Log Message:
  -----------
  Fixed close first vistrail in open_workflow


  Commit: 422e1a9bbc1c1570fa589dab529d9c00ecda108c
      https://github.com/VisTrails/VisTrails/commit/422e1a9bbc1c1570fa589dab529d9c00ecda108c
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-22 (Wed, 22 Apr 2015)

  Changed paths:
    M scripts/create_release_wiki_table.py
    M scripts/dist/windows/common1.iss

  Log Message:
  -----------
  Added manifest from VTK source dir to windows installer


  Commit: 4c36cd1cac5300bc534ab016984bb53b4a80be56
      https://github.com/VisTrails/VisTrails/commit/4c36cd1cac5300bc534ab016984bb53b4a80be56
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-22 (Wed, 22 Apr 2015)

  Changed paths:
    M vistrails/packages/spreadsheet/spreadsheet_execute.py

  Log Message:
  -----------
  Remove connections by port rather than module name


  Commit: d916414ef86f5f52a752bff2987c1c7bbfb4e58b
      https://github.com/VisTrails/VisTrails/commit/d916414ef86f5f52a752bff2987c1c7bbfb4e58b
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-22 (Wed, 22 Apr 2015)

  Changed paths:
    M vistrails/core/vistrail/module.py

  Log Message:
  -----------
  Adds Module#delete_function_by_real_id()


  Commit: 58a4fa88ddb3c5b616c098b0d17091e6c94c042a
      https://github.com/VisTrails/VisTrails/commit/58a4fa88ddb3c5b616c098b0d17091e6c94c042a
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-22 (Wed, 22 Apr 2015)

  Changed paths:
    M vistrails/core/inspector.py

  Log Message:
  -----------
  Sanitizes inspect_spreadsheet_cells()


  Commit: 9deb2034c8a7e86c75ab40ff4d1ad6990b1f63d6
      https://github.com/VisTrails/VisTrails/commit/9deb2034c8a7e86c75ab40ff4d1ad6990b1f63d6
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-22 (Wed, 22 Apr 2015)

  Changed paths:
    M vistrails/core/inspector.py

  Log Message:
  -----------
  Accept output mods w/ spreadsheet mode as cells

PipelineInspector#inspect_spreadsheet_cells() now accepts OutputModule
as well, if they have a 'spreadsheet' mode registered.


  Commit: 798dd4916935304809b7ed2489ba46de08604f0f
      https://github.com/VisTrails/VisTrails/commit/798dd4916935304809b7ed2489ba46de08604f0f
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-22 (Wed, 22 Apr 2015)

  Changed paths:
    M vistrails/packages/spreadsheet/spreadsheet_execute.py

  Log Message:
  -----------
  Sanitizes assignPipelineCellLocations()


  Commit: e9763334fca3dcf1d00ee0d550babb5de3ad8d61
      https://github.com/VisTrails/VisTrails/commit/e9763334fca3dcf1d00ee0d550babb5de3ad8d61
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-22 (Wed, 22 Apr 2015)

  Changed paths:
    M vistrails/packages/spreadsheet/spreadsheet_execute.py

  Log Message:
  -----------
  Handles PipelineInspector returning non-lists

PipelineInspectors returns a sequence of module ids, but returns a
single id if there is one. I don't know why this difference is made;
having a constant type is usually a good idea.


  Commit: fa08548208d94f0870e350055d2cd2d4d207d92a
      https://github.com/VisTrails/VisTrails/commit/fa08548208d94f0870e350055d2cd2d4d207d92a
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-22 (Wed, 22 Apr 2015)

  Changed paths:
    M vistrails/gui/paramexplore/virtual_cell.py
    M vistrails/packages/spreadsheet/spreadsheet_execute.py

  Log Message:
  -----------
  assignPipelineCellLocations: OutputModule support


  Commit: 545e39d2fdd6f10cb7b170c2b0c12632c5a80053
      https://github.com/VisTrails/VisTrails/commit/545e39d2fdd6f10cb7b170c2b0c12632c5a80053
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-22 (Wed, 22 Apr 2015)

  Changed paths:
    M vistrails/gui/preferences.py

  Log Message:
  -----------
  Add debugger hook: enabling package from prefs


  Commit: 34ddda735d30a9968b76637956647fcc92dea478
      https://github.com/VisTrails/VisTrails/commit/34ddda735d30a9968b76637956647fcc92dea478
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-22 (Wed, 22 Apr 2015)

  Changed paths:
    M vistrails/packages/spreadsheet/spreadsheet_execute.py

  Log Message:
  -----------
  Fixes assignCellLocations with several modules


  Commit: f1f701774801111c19b54d940670d27c3f50ee83
      https://github.com/VisTrails/VisTrails/commit/f1f701774801111c19b54d940670d27c3f50ee83
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-23 (Thu, 23 Apr 2015)

  Changed paths:
    M vistrails/core/inspector.py
    M vistrails/core/vistrail/module.py
    M vistrails/gui/paramexplore/virtual_cell.py
    M vistrails/packages/spreadsheet/spreadsheet_execute.py

  Log Message:
  -----------
  Merge branch 'paramexplore-outputmodules' into 'v2.2'


  Commit: c366dbcb640c022d14d8ca5ba1b96ed6d9730141
      https://github.com/VisTrails/VisTrails/commit/c366dbcb640c022d14d8ca5ba1b96ed6d9730141
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-23 (Thu, 23 Apr 2015)

  Changed paths:
    M CHANGELOG

  Log Message:
  -----------
  Updates CHANGELOG


  Commit: ca4f1324d48cdc213a32304ed3ca1cfeed748682
      https://github.com/VisTrails/VisTrails/commit/ca4f1324d48cdc213a32304ed3ca1cfeed748682
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-24 (Fri, 24 Apr 2015)

  Changed paths:
    M CHANGELOG
    M doc/usersguide/conf.py
    M scripts/create_release_wiki_table.py
    M scripts/dist/common/splash/splash.svg
    M scripts/dist/mac/setup.py
    M scripts/dist/source/make-vistrails-src-build.py
    M scripts/dist/windows/vistrails-gdal.iss
    M scripts/dist/windows/vistrails.iss
    M scripts/dist/windows/vistrailsx64-gdal.iss
    M scripts/dist/windows/vistrailsx64.iss
    M setup.py
    M vistrails/core/system/__init__.py
    M vistrails/gui/resources/images/vistrails_splash.png

  Log Message:
  -----------
  Updated to v2.2.1


  Commit: f9d85e8ec3fc8e6847ceb16dbef908fd5c25bc15
      https://github.com/VisTrails/VisTrails/commit/f9d85e8ec3fc8e6847ceb16dbef908fd5c25bc15
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-24 (Fri, 24 Apr 2015)

  Changed paths:
    M scripts/dist/mac/make_app
    M scripts/dist/windows/common1.iss

  Log Message:
  -----------
  Removed git/zip/unzip from build scripts


  Commit: 507d4bc1c36da9628e9261ba5a6cb963261eb28b
      https://github.com/VisTrails/VisTrails/commit/507d4bc1c36da9628e9261ba5a6cb963261eb28b
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-25 (Sat, 25 Apr 2015)

  Changed paths:
    M vistrails/core/modules/package.py

  Log Message:
  -----------
  Fix a NameError getting package dependencies


  Commit: 6f50e1b1da4c25f5cfdf0332c284d2d9386f72b8
      https://github.com/VisTrails/VisTrails/commit/6f50e1b1da4c25f5cfdf0332c284d2d9386f72b8
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-25 (Sat, 25 Apr 2015)

  Changed paths:
    M vistrails/core/modules/package.py

  Log Message:
  -----------
  Package#dependencies() now logs a traceback


  Commit: 238946095f99e68d57780189378124d05289a00c
      https://github.com/VisTrails/VisTrails/commit/238946095f99e68d57780189378124d05289a00c
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-27 (Mon, 27 Apr 2015)

  Changed paths:
    M vistrails/tests/resources/test-streaming.vt

  Log Message:
  -----------
  Added subworkflow test to test_streaming.vt.


  Commit: ee3d47f23e8f491c1c864fc56521bfa237730921
      https://github.com/VisTrails/VisTrails/commit/ee3d47f23e8f491c1c864fc56521bfa237730921
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-27 (Mon, 27 Apr 2015)

  Changed paths:
    M vistrails/tests/resources/test-streaming.vt

  Log Message:
  -----------
  Revert "Added subworkflow test to test_streaming.vt."

This reverts commit 238946095f99e68d57780189378124d05289a00c.


  Commit: 51b37d775f1dcd074f5358f3ed74608468c24911
      https://github.com/VisTrails/VisTrails/commit/51b37d775f1dcd074f5358f3ed74608468c24911
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-27 (Mon, 27 Apr 2015)

  Changed paths:
    M vistrails/gui/vistrail_controller.py

  Log Message:
  -----------
  Added test_abstraction_execute


  Commit: b9d31578f0fc1d17212faef58743941f46adce65
      https://github.com/VisTrails/VisTrails/commit/b9d31578f0fc1d17212faef58743941f46adce65
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-27 (Mon, 27 Apr 2015)

  Changed paths:
    M vistrails/core/modules/sub_module.py

  Log Message:
  -----------
  Added tranfer_attrs to Abstraction

Fixes  #1065


  Commit: d66bfc75eb01acd67b90c4d523f46a68b8f041fa
      https://github.com/VisTrails/VisTrails/commit/d66bfc75eb01acd67b90c4d523f46a68b8f041fa
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-28 (Tue, 28 Apr 2015)

  Changed paths:
    M CHANGELOG

  Log Message:
  -----------
  Fix CHANGELOG branch info


  Commit: 7a71a3f5eb2edc249d888bed23076d27660a5e01
      https://github.com/VisTrails/VisTrails/commit/7a71a3f5eb2edc249d888bed23076d27660a5e01
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-28 (Tue, 28 Apr 2015)

  Changed paths:
    M vistrails/gui/vistrail_controller.py

  Log Message:
  -----------
  Fixed import bug in vistrail_controller.py


  Commit: e628f844965736ed10dc8016586d32d8bfa8cf74
      https://github.com/VisTrails/VisTrails/commit/e628f844965736ed10dc8016586d32d8bfa8cf74
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-28 (Tue, 28 Apr 2015)

  Changed paths:
    M vistrails/core/debug.py
    M vistrails/core/modules/package.py
    M vistrails/gui/module_palette.py

  Log Message:
  -----------
  Print more tracebacks

In some locations, exceptions are caught, logged and not propagated;
however, only the class and message was logged, not the traceback,
making debugging harder. A traceback is now debugged (and the debugger
triggered).


  Commit: 320fbf31c05bcb77587a882635bb05e14c764006
      https://github.com/VisTrails/VisTrails/commit/320fbf31c05bcb77587a882635bb05e14c764006
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-28 (Tue, 28 Apr 2015)

  Changed paths:
    M vistrails/core/modules/module_registry.py

  Log Message:
  -----------
  Fixes typo in error message


  Commit: 6d865f0a99de4e554ffcb99982a80b5131836368
      https://github.com/VisTrails/VisTrails/commit/6d865f0a99de4e554ffcb99982a80b5131836368
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-28 (Tue, 28 Apr 2015)

  Changed paths:
    M vistrails/api/__init__.py

  Log Message:
  -----------
  Fixed quiet flag in api.close_current_vistrail


  Commit: 49d899571d3c82f6df68e9aa898d29674a2e2667
      https://github.com/VisTrails/VisTrails/commit/49d899571d3c82f6df68e9aa898d29674a2e2667
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-28 (Tue, 28 Apr 2015)

  Changed paths:
    M vistrails/gui/vistrail_controller.py

  Log Message:
  -----------
  Clean up after test_abstraction_execute

Close open views and unload subworkflows.


  Commit: d631f25acad54c9476d12a6f6dc292fa989d601f
      https://github.com/VisTrails/VisTrails/commit/d631f25acad54c9476d12a6f6dc292fa989d601f
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-29 (Wed, 29 Apr 2015)

  Changed paths:
    M vistrails/core/modules/sub_module.py

  Log Message:
  -----------
  Add some info about what's going on in Abstraction


  Commit: aea6e385b81273d31cf98aa0ffca8330c61239f7
      https://github.com/VisTrails/VisTrails/commit/aea6e385b81273d31cf98aa0ffca8330c61239f7
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-29 (Wed, 29 Apr 2015)

  Changed paths:
    M vistrails/core/modules/sub_module.py

  Log Message:
  -----------
  Recurse into Groups when checking SubWorkflow dependencies

Fixes: 1066


  Commit: 5076da545e47a90653f6853d05e45ea2ac6ec616
      https://github.com/VisTrails/VisTrails/commit/5076da545e47a90653f6853d05e45ea2ac6ec616
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-04-30 (Thu, 30 Apr 2015)

  Changed paths:
    M vistrails/core/application.py

  Log Message:
  -----------
  Edited subworkflows were not marked as subworkflows

Subworkflows were not being saved correctly which caused errors with upgrading.

core/application.py:
 - open_vistrail:
    call to load_vistrail did not set is_abstraction


  Commit: 06d3b028704000406ed3e3ecb6e09f5277dc364e
      https://github.com/VisTrails/VisTrails/commit/06d3b028704000406ed3e3ecb6e09f5277dc364e
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-30 (Thu, 30 Apr 2015)

  Changed paths:
    M vistrails/core/modules/package.py

  Log Message:
  -----------
  'vistrails.' prefix warning: print original name


  Commit: cc65dae94c337c8e43e5b4d8160497c8dcf5343a
      https://github.com/VisTrails/VisTrails/commit/cc65dae94c337c8e43e5b4d8160497c8dcf5343a
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-04-30 (Thu, 30 Apr 2015)

  Changed paths:
    M vistrails/gui/vistrails_window.py

  Log Message:
  -----------
  Fix "subworkflow from package" warning


  Commit: 9c04ab55ac0963de89049dddc5172e32f815d562
      https://github.com/VisTrails/VisTrails/commit/9c04ab55ac0963de89049dddc5172e32f815d562
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-05-01 (Fri, 01 May 2015)

  Changed paths:
    M vistrails/core/modules/sub_module.py

  Log Message:
  -----------
  Use is_group in subworkflow dependency check

Also fixed ignored dependencies after group


  Commit: 0d98e34c4b3889d7a2655a583656006b828e8b13
      https://github.com/VisTrails/VisTrails/commit/0d98e34c4b3889d7a2655a583656006b828e8b13
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-05-01 (Fri, 01 May 2015)

  Changed paths:
    M vistrails/core/modules/sub_module.py

  Log Message:
  -----------
  Removes debug code


  Commit: d06b8379688c754c8d800f5c6944baa8048ac965
      https://github.com/VisTrails/VisTrails/commit/d06b8379688c754c8d800f5c6944baa8048ac965
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-05-05 (Tue, 05 May 2015)

  Changed paths:
    M vistrails/packages/spreadsheet/spreadsheet_sheet.py

  Log Message:
  -----------
  Fixes toolbar not going away when cell is cleared


  Commit: df96ac177b2502750567b7b2a6b4fa491befb4a2
      https://github.com/VisTrails/VisTrails/commit/df96ac177b2502750567b7b2a6b4fa491befb4a2
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-05-06 (Wed, 06 May 2015)

  Changed paths:
    M vistrails/core/modules/module_registry.py

  Log Message:
  -----------
  Fixed get_descriptor_by_name not raising MissingModule when module_version is set

This was caused by a regression in d6779b85

Loading a vistrail with an out-of-date subworkflow triggered this.


  Commit: 7f96c12b23758c8670629b59d7d1c465493e8ecd
      https://github.com/VisTrails/VisTrails/commit/7f96c12b23758c8670629b59d7d1c465493e8ecd
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-05-15 (Fri, 15 May 2015)

  Changed paths:
    M vistrails/core/modules/sub_module.py

  Log Message:
  -----------
  Fixed Group input with depth=0->depth=1 connection failing

Groups casts inputs as Variants. Variants are never wrapped
to depth=1, so we need to get the wrapped value and pass it
on before the type information is lost.

core/modules/sub_module.py:
 - Group.compute:
   Get the final value using get_input so that it is wrapped correctly.


  Commit: 032c5684a945fdb0d5ce724f8990b86199dd6e67
      https://github.com/VisTrails/VisTrails/commit/032c5684a945fdb0d5ce724f8990b86199dd6e67
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-05-15 (Fri, 15 May 2015)

  Changed paths:
    M vistrails/gui/pipeline_view.py

  Log Message:
  -----------
  Call ungrabMouse before the view gets destroyed in the Pipeline View.

This was causing tracebacks and "not a mouse grabber" errors in the module context menu.


  Commit: f4fe536b9adb1e5790d35c5077eae148c568a6a8
      https://github.com/VisTrails/VisTrails/commit/f4fe536b9adb1e5790d35c5077eae148c568a6a8
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-05-27 (Wed, 27 May 2015)

  Changed paths:
    M vistrails/packages/spreadsheet/spreadsheet_sheet.py

  Log Message:
  -----------
  Merge pull request #1073 from VisTrails/fix-lingering-toolbar

Fixes toolbar not getting replaced if the currently selected cell widget
gets replaced (until a click on the spreadsheet selects a different (or
the same) cell).


  Commit: 7c0c7c09537e236092e578cf55ad3110f9db0dc7
      https://github.com/VisTrails/VisTrails/commit/7c0c7c09537e236092e578cf55ad3110f9db0dc7
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-05-27 (Wed, 27 May 2015)

  Changed paths:
    M vistrails/core/api.py

  Log Message:
  -----------
  Fix id_remap issue executing with inputs from API


  Commit: 9ff0d5d07ef5cf422457d69aba3da5b58b74982c
      https://github.com/VisTrails/VisTrails/commit/9ff0d5d07ef5cf422457d69aba3da5b58b74982c
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-05-27 (Wed, 27 May 2015)

  Changed paths:
    M examples/api/simplemath.vt

  Log Message:
  -----------
  Updates simplemath.vt

Makes IDs in simplemath.vt's most recent pipeline not be consecutive;
tests for #1081.


  Commit: 0f0417e3d79a3df3d6bf2d3cde58b3178a2ed095
      https://github.com/VisTrails/VisTrails/commit/0f0417e3d79a3df3d6bf2d3cde58b3178a2ed095
  Author: David Koop <dkoop at umassd.edu>
  Date:   2015-05-29 (Fri, 29 May 2015)

  Changed paths:
    M vistrails/db/services/vistrail.py

  Log Message:
  -----------
  Fixes #1080

Issue was that control parameters and annotations were not maintaining diff state in the same way as standard parameters.


  Commit: a0f96696140f2b7d8b7186da05242e8d6f393399
      https://github.com/VisTrails/VisTrails/commit/a0f96696140f2b7d8b7186da05242e8d6f393399
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-05-29 (Fri, 29 May 2015)

  Changed paths:
    M vistrails/core/bundles/pyimport.py
    M vistrails/core/thumbnails.py
    M vistrails/core/vistrail/connection.py
    M vistrails/gui/job_monitor.py

  Log Message:
  -----------
  Also update temp config when updating persistent


  Commit: cb21a4bffe208d33df7b27208fdacdf345d713d4
      https://github.com/VisTrails/VisTrails/commit/cb21a4bffe208d33df7b27208fdacdf345d713d4
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-06-01 (Mon, 01 Jun 2015)

  Changed paths:
    M vistrails/core/bundles/pyimport.py
    M vistrails/core/thumbnails.py
    M vistrails/core/vistrail/connection.py
    M vistrails/gui/job_monitor.py

  Log Message:
  -----------
  Merge pull request #1085 from VisTrails/fix-configuration-mixup

Also update temp config when updating persistent


  Commit: 5274423287685b98f08459f30a4a7fa6807cc94d
      https://github.com/VisTrails/VisTrails/commit/5274423287685b98f08459f30a4a7fa6807cc94d
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-06-01 (Mon, 01 Jun 2015)

  Changed paths:
    M vistrails/core/modules/output_modules.py
    M vistrails/packages/matplotlib/bases.py
    M vistrails/packages/matplotlib/figure_cell.py
    M vistrails/packages/spreadsheet/widgets/imageviewer/imageviewer.py
    M vistrails/packages/spreadsheet/widgets/richtext/richtext.py
    M vistrails/packages/tabledata/common.py
    M vistrails/packages/tabledata/viewer.py
    M vistrails/packages/vtk/init.py
    M vistrails/packages/vtk/vtkcell.py

  Log Message:
  -----------
  Make compute_output() 'configuration' arg required

There is no reason for this to default to None. We can rely on this
always being provided.


  Commit: 61c1bf7fd26738d0783799cd912a361370edd253
      https://github.com/VisTrails/VisTrails/commit/61c1bf7fd26738d0783799cd912a361370edd253
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-06-03 (Wed, 03 Jun 2015)

  Changed paths:
    M vistrails/core/modules/output_modules.py

  Log Message:
  -----------
  Use a more reliable way of detecting the notebook

With help from @akhmerov on Gitter.


  Commit: cd1ec811bc3c619e676ffec567c7a1f15ffb8181
      https://github.com/VisTrails/VisTrails/commit/cd1ec811bc3c619e676ffec567c7a1f15ffb8181
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-06-03 (Wed, 03 Jun 2015)

  Changed paths:
    M vistrails/core/api.py
    M vistrails/core/modules/output_modules.py

  Log Message:
  -----------
  Adds ipython_mode(True|False) to the API

This allows the user to explicitely selects if he wants to use the
notebook. It is similar to matplotlib's `%matplotlib inline` magic.

Note that the current default is to still enable IPythonMode if we think
we are running from the notebook, which right now only means that the
__main__ module exists but has no __file__ attribute, and that IPython
is installed.


  Commit: 27216c027ad81a9e55017e9eb7285a3afe42f8aa
      https://github.com/VisTrails/VisTrails/commit/27216c027ad81a9e55017e9eb7285a3afe42f8aa
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-06-03 (Wed, 03 Jun 2015)

  Changed paths:
    M vistrails/core/modules/output_modules.py

  Log Message:
  -----------
  Warn if auto-enabling IPythonMode


  Commit: 020938b47c0bbb28cad2a103338e517641372d22
      https://github.com/VisTrails/VisTrails/commit/020938b47c0bbb28cad2a103338e517641372d22
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-06-04 (Thu, 04 Jun 2015)

  Changed paths:
    M vistrails/core/api.py
    M vistrails/core/modules/output_modules.py

  Log Message:
  -----------
  Merge pull request #1090 from VisTrails/ipython-mode-detection

Fix IPythonMode auto-detection


  Commit: 48c3ccca3d0aeb2f5d01c516e0cd5353ea72c0e8
      https://github.com/VisTrails/VisTrails/commit/48c3ccca3d0aeb2f5d01c516e0cd5353ea72c0e8
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-06-04 (Thu, 04 Jun 2015)

  Changed paths:
    M vistrails/core/api.py

  Log Message:
  -----------
  Adds missing export from API


  Commit: fbfb9135beec533583235f37fcfefc28585ff4e2
      https://github.com/VisTrails/VisTrails/commit/fbfb9135beec533583235f37fcfefc28585ff4e2
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-06-04 (Thu, 04 Jun 2015)

  Changed paths:
    M examples/api/ipython-notebook.ipynb

  Log Message:
  -----------
  Adds ipython_mode(True) to example notebook


  Commit: 18c63fb8c61e2d20924809561bb2da0c85f6e784
      https://github.com/VisTrails/VisTrails/commit/18c63fb8c61e2d20924809561bb2da0c85f6e784
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-06-05 (Fri, 05 Jun 2015)

  Changed paths:
    M vistrails/packages/vtk/init.py

  Log Message:
  -----------
  Fixes render_to_image on VTK 6


  Commit: cfaff399dfa45e18f497e62f2585f62f1e14d7b6
      https://github.com/VisTrails/VisTrails/commit/cfaff399dfa45e18f497e62f2585f62f1e14d7b6
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-06-05 (Fri, 05 Jun 2015)

  Changed paths:
    M vistrails/core/api.py

  Log Message:
  -----------
  Use do_version_switch() in API

change_selected_version() eats exceptions and that is not right.


  Commit: 57c8fbb1f66094ef36709c39afddeeb0d0eb42ec
      https://github.com/VisTrails/VisTrails/commit/57c8fbb1f66094ef36709c39afddeeb0d0eb42ec
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-06-11 (Thu, 11 Jun 2015)

  Changed paths:
    M vistrails/core/modules/output_modules.py

  Log Message:
  -----------
  Don't enable IPythonMode if IPython is detected

We now require vistrails.ipython_mode(True) to be called before
IPythonMode can be used. This is similar to the %matplotlib inline
magic.

This is because there is no reliable way of detecting the notebook;
unfortunately this changes the previous behavior. Hopefully the warning
message is clear enough.


  Commit: 5b639bf6e6e316b154287ba68b9f50982ce9a8f8
      https://github.com/VisTrails/VisTrails/commit/5b639bf6e6e316b154287ba68b9f50982ce9a8f8
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-06-11 (Thu, 11 Jun 2015)

  Changed paths:
    M vistrails/core/console_mode.py

  Log Message:
  -----------
  Removed workflowInfo code

This code always executed when output_dir was set


  Commit: b1af923696fab94bc8b419742b4088c9b51ef518
      https://github.com/VisTrails/VisTrails/commit/b1af923696fab94bc8b419742b4088c9b51ef518
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-06-11 (Thu, 11 Jun 2015)

  Changed paths:
    M vistrails/gui/application.py

  Log Message:
  -----------
  Replace temp_configuration while running commands from other instance

Also updates graph generation flags.


  Commit: 8c49844fef337b4feac906e2c067de8178b6450c
      https://github.com/VisTrails/VisTrails/commit/8c49844fef337b4feac906e2c067de8178b6450c
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-06-11 (Thu, 11 Jun 2015)

  Changed paths:
    M vistrails/core/console_mode.py

  Log Message:
  -----------
  Fixes console_mode graph generation

- run_and_get_results:
Tried to used a core controller to set up a pipeline view

- get_wf_graph:
  Setting up the pipeline was not working.
  We need to set the controller manually on the pipeline?


  Commit: 974d87e9d369b0c4f222b1b82445f2709037b9cf
      https://github.com/VisTrails/VisTrails/commit/974d87e9d369b0c4f222b1b82445f2709037b9cf
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-06-11 (Thu, 11 Jun 2015)

  Changed paths:
    M vistrails/core/configuration.py
    M vistrails/gui/application.py

  Log Message:
  -----------
  Added noExecute command-line option


  Commit: 88e4c7a123267df2e5cb9cb5abfbfdc31cf6736f
      https://github.com/VisTrails/VisTrails/commit/88e4c7a123267df2e5cb9cb5abfbfdc31cf6736f
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-06-11 (Thu, 11 Jun 2015)

  Changed paths:
    M extensions/latex/includevistrail.py

  Log Message:
  -----------
  Updates latex/includevistrails.py to use OutputModule

No PDF support for results.


  Commit: 58038c17f40f3af6daca9680c36be4a2ec67bc62
      https://github.com/VisTrails/VisTrails/commit/58038c17f40f3af6daca9680c36be4a2ec67bc62
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-06-11 (Thu, 11 Jun 2015)

  Changed paths:
    M extensions/latex/head.tex

  Log Message:
  -----------
  latex/head.tex: Use relative path to run.py by default


  Commit: 50cc3bdaa29774ed731ffeed3c25875a85ed18ab
      https://github.com/VisTrails/VisTrails/commit/50cc3bdaa29774ed731ffeed3c25875a85ed18ab
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-06-11 (Thu, 11 Jun 2015)

  Changed paths:
    A extensions/latex/test.sh

  Log Message:
  -----------
  Added test script for executable documents

Requires running from source + pdflatex

Most errors will cause the script to fail.
Also checks PDF size, to catch other errors causing missing images.


  Commit: e4671b3077a9f2675b3a92a442d9564fa4150909
      https://github.com/VisTrails/VisTrails/commit/e4671b3077a9f2675b3a92a442d9564fa4150909
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-06-15 (Mon, 15 Jun 2015)

  Changed paths:
    M vistrails/core/modules/basic_modules.py

  Log Message:
  -----------
  Fix logic error in PathObject's IPython repr


  Commit: 92f1b661181b7a9ea00c8ee266d229a074902119
      https://github.com/VisTrails/VisTrails/commit/92f1b661181b7a9ea00c8ee266d229a074902119
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-06-15 (Mon, 15 Jun 2015)

  Changed paths:
    M vistrails/packages/tej/__init__.py
    M vistrails/packages/tej/widgets.py

  Log Message:
  -----------
  Add missing __future__.division imports


  Commit: ea42cda8153548360c85b222de87454c614d0dcd
      https://github.com/VisTrails/VisTrails/commit/ea42cda8153548360c85b222de87454c614d0dcd
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-06-15 (Mon, 15 Jun 2015)

  Changed paths:
    M vistrails/packages/persistent_archive/ui.py

  Log Message:
  -----------
  Fix test issue with persistent_archive.ui


  Commit: c161f3caa7c57937a1d3e7a6ba532144e18e5cb8
      https://github.com/VisTrails/VisTrails/commit/c161f3caa7c57937a1d3e7a6ba532144e18e5cb8
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-06-18 (Thu, 18 Jun 2015)

  Changed paths:
    M vistrails/db/services/prov.py

  Log Message:
  -----------
  Fixed machine error when exporting PROV

But machine info does not seem to be implemented?

fixes #1075


  Commit: 6dc172f0aad39c7c7e23d3e3a3142dffa32290e1
      https://github.com/VisTrails/VisTrails/commit/6dc172f0aad39c7c7e23d3e3a3142dffa32290e1
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-06-18 (Thu, 18 Jun 2015)

  Changed paths:
    M vistrails/db/services/prov.py

  Log Message:
  -----------
  Fixed looping in PROV export


  Commit: 5fc34c6b471f00c2895490a73eb2001dce10cd44
      https://github.com/VisTrails/VisTrails/commit/5fc34c6b471f00c2895490a73eb2001dce10cd44
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-06-20 (Sat, 20 Jun 2015)

  Changed paths:
    M vistrails/core/modules/module_registry.py

  Log Message:
  -----------
  Fix NameError in ModuleRegistry


  Commit: c50150dac53619086b2ffce72f343e12c4cc5f58
      https://github.com/VisTrails/VisTrails/commit/c50150dac53619086b2ffce72f343e12c4cc5f58
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-06-23 (Tue, 23 Jun 2015)

  Changed paths:
    M vistrails/gui/bundles/installbundle.py

  Log Message:
  -----------
  Add missing bundle message: no source for distro

Previously, you would see the "Will try to install bundle" then nothing
would happen. This makes it clear why nothing happened.


  Commit: 4b51cd4d9fb61976013cb46b83f1e9f501877b97
      https://github.com/VisTrails/VisTrails/commit/4b51cd4d9fb61976013cb46b83f1e9f501877b97
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-06-23 (Tue, 23 Jun 2015)

  Changed paths:
    M vistrails/gui/modules/python_source_configure.py

  Log Message:
  -----------
  Add Debian source for PyQt4.Qsci


  Commit: 1b236bec172a3786c81e0ce32c12659cc5791001
      https://github.com/VisTrails/VisTrails/commit/1b236bec172a3786c81e0ce32c12659cc5791001
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-06-24 (Wed, 24 Jun 2015)

  Changed paths:
    M vistrails/core/vistrail/pipeline.py
    M vistrails/gui/pipeline_view.py

  Log Message:
  -----------
  Minor formatting fixes


  Commit: 5f5dda33e75ec862efcfa0ccf72acb498d06d018
      https://github.com/VisTrails/VisTrails/commit/5f5dda33e75ec862efcfa0ccf72acb498d06d018
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-06-24 (Wed, 24 Jun 2015)

  Changed paths:
    M vistrails/core/vistrail/pipeline.py

  Log Message:
  -----------
  Fix NameError


  Commit: 8413d8cf7f2fe6b2d85b9eafcec5c8f9b0d6429f
      https://github.com/VisTrails/VisTrails/commit/8413d8cf7f2fe6b2d85b9eafcec5c8f9b0d6429f
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-06-24 (Wed, 24 Jun 2015)

  Changed paths:
    M vistrails/core/data_structures/graph.py

  Log Message:
  -----------
  Remove workaround for Python 2.0 from Graph


  Commit: f71e707ffd4cad74b6b185e5bf7f05db28f73ba6
      https://github.com/VisTrails/VisTrails/commit/f71e707ffd4cad74b6b185e5bf7f05db28f73ba6
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-06-26 (Fri, 26 Jun 2015)

  Changed paths:
    M vistrails/gui/application.py

  Log Message:
  -----------
  Fixed copy call in gui/application.py


  Commit: a8bebadf932581d5bd8554ec4be875d62e4c52a1
      https://github.com/VisTrails/VisTrails/commit/a8bebadf932581d5bd8554ec4be875d62e4c52a1
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-06-26 (Fri, 26 Jun 2015)

  Changed paths:
    M extensions/latex/head.pdf
    M extensions/latex/head.vt
    M extensions/latex/includevistrail.py
    M vistrails/core/configuration.py
    M vistrails/db/versions/v1_0_4/translate/v1_0_3.py
    M vistrails/gui/application.py

  Log Message:
  -----------
  Renamed graph-generating flags

withWorkflow -> outputPipelineGraph
withVersionTree -> outputVersionTree


  Commit: d10e231c0a505bfcbf81cbb4068b9b2eb8909342
      https://github.com/VisTrails/VisTrails/commit/d10e231c0a505bfcbf81cbb4068b9b2eb8909342
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-06-29 (Mon, 29 Jun 2015)

  Changed paths:
    M extensions/latex/head.pdf
    M extensions/latex/head.tex
    M extensions/latex/head.vt
    M extensions/latex/includevistrail.py
    A extensions/latex/test.sh
    M vistrails/core/configuration.py
    M vistrails/core/console_mode.py
    M vistrails/db/versions/v1_0_4/translate/v1_0_3.py
    M vistrails/gui/application.py

  Log Message:
  -----------
  Merge branch 'fix-executable-paper' into v2.2


  Commit: 5ffaf7a48f88a9852c59889cd82c90417dfbef3e
      https://github.com/VisTrails/VisTrails/commit/5ffaf7a48f88a9852c59889cd82c90417dfbef3e
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-06-29 (Mon, 29 Jun 2015)

  Changed paths:
    M vistrails/gui/vistrail_controller.py

  Log Message:
  -----------
  Fixed provenance export using unflushed pipeline

Fixes #1095


  Commit: 8fdbeda6b5d00f77f6434d96141c915a7b6f4564
      https://github.com/VisTrails/VisTrails/commit/8fdbeda6b5d00f77f6434d96141c915a7b6f4564
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-06-29 (Mon, 29 Jun 2015)

  Changed paths:
    M vistrails/core/data_structures/graph.py
    M vistrails/core/packagemanager.py

  Log Message:
  -----------
  Move GraphContainsCycles out of Graph


  Commit: a8f46c5c59fbc0cb7513d4a61ecefa2c73505a29
      https://github.com/VisTrails/VisTrails/commit/a8f46c5c59fbc0cb7513d4a61ecefa2c73505a29
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-06-29 (Mon, 29 Jun 2015)

  Changed paths:
    M vistrails/gui/pipeline_view.py

  Log Message:
  -----------
  Comment on what _old_{connection,module}_ids are


  Commit: 76685a11bbb14f844afb9850638eae5f6de56957
      https://github.com/VisTrails/VisTrails/commit/76685a11bbb14f844afb9850638eae5f6de56957
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-06-29 (Mon, 29 Jun 2015)

  Changed paths:
    M vistrails/core/vistrail/pipeline.py
    M vistrails/gui/pipeline_view.py

  Log Message:
  -----------
  Check that the user is not creating a cycle


  Commit: 5b6bc46ce0635d332f1a57e9bfb39afb9b261dc2
      https://github.com/VisTrails/VisTrails/commit/5b6bc46ce0635d332f1a57e9bfb39afb9b261dc2
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-06-29 (Mon, 29 Jun 2015)

  Changed paths:
    M CHANGELOG

  Log Message:
  -----------
  Updates CHANGELOG


  Commit: da7a201574f02e0d016ef353018dd17851fb4278
      https://github.com/VisTrails/VisTrails/commit/da7a201574f02e0d016ef353018dd17851fb4278
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-06-29 (Mon, 29 Jun 2015)

  Changed paths:
    M vistrails/core/vistrail/pipeline.py
    M vistrails/gui/pipeline_view.py

  Log Message:
  -----------
  Catch GraphContainsCycles from mark_list_depth()

Catch the exception in QPipelineScene.


  Commit: e09b7206a5e973b7e01f97c2b55bdc88c688017d
      https://github.com/VisTrails/VisTrails/commit/e09b7206a5e973b7e01f97c2b55bdc88c688017d
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-06-29 (Mon, 29 Jun 2015)

  Changed paths:
    M vistrails/core/vistrail/pipeline.py

  Log Message:
  -----------
  Remove mark_list_depth() optimization

This is annoying because we need to somehow update previously changed
modules when the pipeline becomes valid again.


  Commit: 7038e76638a798c7ebf1e6b3ea5a09b3e4a411e7
      https://github.com/VisTrails/VisTrails/commit/7038e76638a798c7ebf1e6b3ea5a09b3e4a411e7
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-06-29 (Mon, 29 Jun 2015)

  Changed paths:
    M vistrails/gui/pipeline_view.py

  Log Message:
  -----------
  Catch exception from execution

d836547c dropped the try/except in QPipelineView#execute(), letting
exceptions from the interpreter reach the Qt event loop without getting
logged. This puts the try/except block back.


  Commit: 4bc456332fc974306d737f52b0199191ba20ded6
      https://github.com/VisTrails/VisTrails/commit/4bc456332fc974306d737f52b0199191ba20ded6
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-06-29 (Mon, 29 Jun 2015)

  Changed paths:
    M CHANGELOG
    M vistrails/core/data_structures/graph.py
    M vistrails/core/packagemanager.py
    M vistrails/core/vistrail/pipeline.py
    M vistrails/gui/pipeline_view.py

  Log Message:
  -----------
  Merge branch 'disallow-cycles' into 'v2.2'


  Commit: 5c27c4d741896957a34f238da8eee64e1f30ad86
      https://github.com/VisTrails/VisTrails/commit/5c27c4d741896957a34f238da8eee64e1f30ad86
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-06-30 (Tue, 30 Jun 2015)

  Changed paths:
    M vistrails/core/debug.py

  Log Message:
  -----------
  Route uncaught exc. to debugger with excepthook


  Commit: 57283b134b75265435129abf7c8f091bd79fb28a
      https://github.com/VisTrails/VisTrails/commit/57283b134b75265435129abf7c8f091bd79fb28a
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-06-30 (Tue, 30 Jun 2015)

  Changed paths:
    M vistrails/db/services/opm.py

  Log Message:
  -----------
  Allow different package version when exporting OPM

A warning is printed when the exact version is not found


  Commit: 9b58ba9889a6a5cb88b02b61ea08bc9768031f06
      https://github.com/VisTrails/VisTrails/commit/9b58ba9889a6a5cb88b02b61ea08bc9768031f06
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-06-30 (Tue, 30 Jun 2015)

  Changed paths:
    M vistrails/db/services/opm.py

  Log Message:
  -----------
  Fixed OPM export for workflows using Controlflow Assistant

OPM assumes some Map inputs are functions, but CF uses connections.
In this case we cannot compute the provenance for the Map.


  Commit: 8eb572d6d727a33f7172381d264cf632cd1ce5db
      https://github.com/VisTrails/VisTrails/commit/8eb572d6d727a33f7172381d264cf632cd1ce5db
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-06-30 (Tue, 30 Jun 2015)

  Changed paths:
    M vistrails/db/services/opm.py

  Log Message:
  -----------
  Fixed loop_exec in OPM export


  Commit: 1dc7ade78059e4c505c74cb8ef2b04717478396b
      https://github.com/VisTrails/VisTrails/commit/1dc7ade78059e4c505c74cb8ef2b04717478396b
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-06-30 (Tue, 30 Jun 2015)

  Changed paths:
    M vistrails/db/services/opm.py

  Log Message:
  -----------
  Fixed group typo in opm.py:create_opm:do_create_process


  Commit: e5a743edd89c02c78d75671f2ebede65ac17f3d7
      https://github.com/VisTrails/VisTrails/commit/e5a743edd89c02c78d75671f2ebede65ac17f3d7
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-07-01 (Wed, 01 Jul 2015)

  Changed paths:
    M vistrails/db/services/opm.py

  Log Message:
  -----------
  Added automatic loop handling for OPM export


  Commit: 9e0891a041a84c610961e0968be497e4a0d6f17b
      https://github.com/VisTrails/VisTrails/commit/9e0891a041a84c610961e0968be497e4a0d6f17b
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-07-06 (Mon, 06 Jul 2015)

  Changed paths:
    M vistrails/core/modules/abstraction.py

  Log Message:
  -----------
  Fixed upgrading to newer local subworkflows

We now load descriptors for all namespaces in a local subworkflow so that upgrades are detected correctly.
Also, a vistrail loaded from xml now finds upgraded local subworkflows (Fixes #1100)


  Commit: 04e41136a3ccd10c59c426a217c3e9b6cc159232
      https://github.com/VisTrails/VisTrails/commit/04e41136a3ccd10c59c426a217c3e9b6cc159232
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-07-06 (Mon, 06 Jul 2015)

  Changed paths:
    M vistrails/core/vistrail/vistrail.py
    M vistrails/gui/vistrail_controller.py

  Log Message:
  -----------
  Fixed exporting abstractions as a package

core/vistrail/vistrail.py:
  locator was not being set when converting DBVistrail

gui/vistrail_controller.py:
  Fixed abstraction export prompts having negative text checks


  Commit: f82afe43c098c5a69d234a54729722eae45d3b62
      https://github.com/VisTrails/VisTrails/commit/f82afe43c098c5a69d234a54729722eae45d3b62
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-07-07 (Tue, 07 Jul 2015)

  Changed paths:
    M vistrails/gui/module_palette.py

  Log Message:
  -----------
  Added 'remove subworkflow' context menu item

Fixes #1101


  Commit: 43dcfb0ed6ee2525951081d7cfb52f419e4bbee9
      https://github.com/VisTrails/VisTrails/commit/43dcfb0ed6ee2525951081d7cfb52f419e4bbee9
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-07-08 (Wed, 08 Jul 2015)

  Changed paths:
    M CHANGELOG

  Log Message:
  -----------
  Updated CHANGELOG


  Commit: 0cc58e054b9aeae6c36bd4198337980fa2daeb7d
      https://github.com/VisTrails/VisTrails/commit/0cc58e054b9aeae6c36bd4198337980fa2daeb7d
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-08 (Wed, 08 Jul 2015)

  Changed paths:
    M CHANGELOG

  Log Message:
  -----------
  Fix CHANGELOG


  Commit: df733413192778b78fef421a6f77d725dec4b6ee
      https://github.com/VisTrails/VisTrails/commit/df733413192778b78fef421a6f77d725dec4b6ee
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-08 (Wed, 08 Jul 2015)

  Changed paths:
    M vistrails/packages/spreadsheet/celltoolbar_rc.py
    M vistrails/packages/spreadsheet/images/new-window.png

  Log Message:
  -----------
  Lighter


  Commit: ef3ed1eb78520a1fed83ca7fe57088c39349131c
      https://github.com/VisTrails/VisTrails/commit/ef3ed1eb78520a1fed83ca7fe57088c39349131c
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-08 (Wed, 08 Jul 2015)

  Changed paths:
    M vistrails/packages/spreadsheet/celltoolbar.qrc
    M vistrails/packages/spreadsheet/celltoolbar_rc.py
    A vistrails/packages/spreadsheet/images/new-window.png
    M vistrails/packages/spreadsheet/widgets/webview/webview.py

  Log Message:
  -----------
  Merge branch 'webviewcell-open-browser' into 'v2.2'


  Commit: 1f91f2959db94a8213e5a85ea33bd1104692fd30
      https://github.com/VisTrails/VisTrails/commit/1f91f2959db94a8213e5a85ea33bd1104692fd30
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-08 (Wed, 08 Jul 2015)

  Changed paths:
    M vistrails/packages/spreadsheet/spreadsheet_tab.py

  Log Message:
  -----------
  Adds a button to stretch the spreadsheet cells


  Commit: 67c524d12b56839da8406da8db8708e6c4f46825
      https://github.com/VisTrails/VisTrails/commit/67c524d12b56839da8406da8db8708e6c4f46825
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-08 (Wed, 08 Jul 2015)

  Changed paths:
    M vistrails/packages/spreadsheet/celltoolbar.qrc
    M vistrails/packages/spreadsheet/celltoolbar_rc.py
    A vistrails/packages/spreadsheet/images/equal-sizes.png
    M vistrails/packages/spreadsheet/spreadsheet_tab.py

  Log Message:
  -----------
  Adds icon


  Commit: ba7e6a93478136bbb14633ab487712ed49fc2ace
      https://github.com/VisTrails/VisTrails/commit/ba7e6a93478136bbb14633ab487712ed49fc2ace
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-08 (Wed, 08 Jul 2015)

  Changed paths:
    M vistrails/packages/spreadsheet/celltoolbar.qrc
    M vistrails/packages/spreadsheet/celltoolbar_rc.py
    A vistrails/packages/spreadsheet/images/equal-sizes.png
    M vistrails/packages/spreadsheet/spreadsheet_tab.py

  Log Message:
  -----------
  Merge pull request #961 from VisTrails/reset-cell-sizes-button

Adds a button to stretch the spreadsheet cells


  Commit: 9bd2afa387a418da8457785ead9a4a570a9085b3
      https://github.com/VisTrails/VisTrails/commit/9bd2afa387a418da8457785ead9a4a570a9085b3
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-07-09 (Thu, 09 Jul 2015)

  Changed paths:
    M CHANGELOG

  Log Message:
  -----------
  Removes newline in CHANGELOG

The scripts needs Release Name to be on the third line


  Commit: 244ecd14ba95b0613d500b7e196d0b8dcf20b35a
      https://github.com/VisTrails/VisTrails/commit/244ecd14ba95b0613d500b7e196d0b8dcf20b35a
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-07-09 (Thu, 09 Jul 2015)

  Changed paths:
    M CHANGELOG
    M doc/usersguide/conf.py
    M scripts/create_release_wiki_table.py
    M scripts/dist/common/splash/splash.svg
    M scripts/dist/mac/make_app
    M scripts/dist/mac/setup.py
    M scripts/dist/source/make-vistrails-src-build.py
    M scripts/dist/windows/vistrails-gdal.iss
    M scripts/dist/windows/vistrails.iss
    M scripts/dist/windows/vistrailsx64-gdal.iss
    M scripts/dist/windows/vistrailsx64.iss
    M scripts/get_usersguide.py
    M setup.py
    M vistrails/core/system/__init__.py
    M vistrails/gui/resources/images/vistrails_splash.png

  Log Message:
  -----------
  Updated version for v2.2.2 release


  Commit: df4119c78468ac1de7ddf6ffdf670827bdf7b83b
      https://github.com/VisTrails/VisTrails/commit/df4119c78468ac1de7ddf6ffdf670827bdf7b83b
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-07-10 (Fri, 10 Jul 2015)

  Changed paths:
    M scripts/dist/mac/make_app

  Log Message:
  -----------
  Adds creation of missing directories in Mac installer


  Commit: 358e9a9fc33cf43dd5d66293d5b34bfa1d1bca61
      https://github.com/VisTrails/VisTrails/commit/358e9a9fc33cf43dd5d66293d5b34bfa1d1bca61
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-07-10 (Fri, 10 Jul 2015)

  Changed paths:
    M scripts/dist/mac/setup.py

  Log Message:
  -----------
  Increases recursion limit for Mac installer


  Commit: a5a41a9db22181fe75ee9d9baafa5d76f5f9b9a7
      https://github.com/VisTrails/VisTrails/commit/a5a41a9db22181fe75ee9d9baafa5d76f5f9b9a7
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-07-10 (Fri, 10 Jul 2015)

  Changed paths:
    M vistrails/core/console_mode.py

  Log Message:
  -----------
  Do not use GUI controller in run_and_get_results


  Commit: 7a8e1685d68d8c7d7cd8c19cb7dac62cc2234080
      https://github.com/VisTrails/VisTrails/commit/7a8e1685d68d8c7d7cd8c19cb7dac62cc2234080
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-11 (Sat, 11 Jul 2015)

  Changed paths:
    M .travis.yml

  Log Message:
  -----------
  Switch Travis build to container infrastructure


  Commit: 1de57e9b19bcd8620f9a3be2d779771ef0b9b5bc
      https://github.com/VisTrails/VisTrails/commit/1de57e9b19bcd8620f9a3be2d779771ef0b9b5bc
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-14 (Tue, 14 Jul 2015)

  Changed paths:
    M vistrails/core/modules/output_modules.py

  Log Message:
  -----------
  Use config 'outputDirectory' in FileMode

If file.dir is not set or is relative, the global 'outputDirectory'
setting will be used.


  Commit: 50abbf0f95e6e21c28a1f39f690b377e97f9a7c2
      https://github.com/VisTrails/VisTrails/commit/50abbf0f95e6e21c28a1f39f690b377e97f9a7c2
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-14 (Tue, 14 Jul 2015)

  Changed paths:
    M vistrails/core/console_mode.py
    M vistrails/gui/application.py

  Log Message:
  -----------
  Fix outputDirectory usage in random places


  Commit: 79381a4ba8e3be88cd22baa68bc97dbfb33931e5
      https://github.com/VisTrails/VisTrails/commit/79381a4ba8e3be88cd22baa68bc97dbfb33931e5
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-14 (Tue, 14 Jul 2015)

  Changed paths:
    M vistrails/run.py

  Log Message:
  -----------
  Remove outputDirectory condition from run.py


  Commit: 7538a499f99d844e571990d728c4b57a12100088
      https://github.com/VisTrails/VisTrails/commit/7538a499f99d844e571990d728c4b57a12100088
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-14 (Tue, 14 Jul 2015)

  Changed paths:
    M vistrails/gui/application.py

  Log Message:
  -----------
  Remove outputDirectory -> pathDumpCells assignment


  Commit: 2021a77cf66efc9cc76c032142eec80df675e100
      https://github.com/VisTrails/VisTrails/commit/2021a77cf66efc9cc76c032142eec80df675e100
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-16 (Thu, 16 Jul 2015)

  Changed paths:
    M vistrails/packages/tej/init.py

  Log Message:
  -----------
  tej.SubmitJob: check that the script file exists

To avoid future errors, check that the script exists before submitting.


  Commit: d830b45c2e25d36c277ee610575a7adac680cb26
      https://github.com/VisTrails/VisTrails/commit/d830b45c2e25d36c277ee610575a7adac680cb26
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-17 (Fri, 17 Jul 2015)

  Changed paths:
    M vistrails/gui/modules/python_source_configure.py
    M vistrails/gui/modules/source_configure.py
    M vistrails/gui/modules/string_configure.py

  Log Message:
  -----------
  Don't accept richtext in configuration widgets


  Commit: 50130fa011104806cc66331fe5a6ebc3f98c9d5c
      https://github.com/VisTrails/VisTrails/commit/50130fa011104806cc66331fe5a6ebc3f98c9d5c
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-17 (Fri, 17 Jul 2015)

  Changed paths:
    M vistrails/packages/tej/widgets.py

  Log Message:
  -----------
  Use smart text editor in tej.SubmitShellJob


  Commit: 923708231b12951c57dd416e12ee69fc16d7cfec
      https://github.com/VisTrails/VisTrails/commit/923708231b12951c57dd416e12ee69fc16d7cfec
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-20 (Mon, 20 Jul 2015)

  Changed paths:
    M vistrails/gui/modules/python_source_configure.py
    M vistrails/gui/modules/string_configure.py

  Log Message:
  -----------
  Use store_in_config for PyQt4.Qsci


  Commit: 1bda0dc1c55ddaa90bd38d2cbec90d33ce79b86f
      https://github.com/VisTrails/VisTrails/commit/1bda0dc1c55ddaa90bd38d2cbec90d33ce79b86f
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-07-21 (Tue, 21 Jul 2015)

  Changed paths:
    M vistrails/packages/vtk/init.py

  Log Message:
  -----------
  Create Ports to avoid portspec lookup on outdated vtk modules


  Commit: c27098223a8a84c1d4d758ce1aa317560f7cd0a0
      https://github.com/VisTrails/VisTrails/commit/c27098223a8a84c1d4d758ce1aa317560f7cd0a0
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-07-21 (Tue, 21 Jul 2015)

  Changed paths:
    M vistrails/core/upgradeworkflow.py

  Log Message:
  -----------
  UpgradeWorkflowHandler: Assume first upgraded module is the upgraded one

A module can be upgraded to multiple modules. The new upgrade
code allows intermediate upgrades and needs to select
the correct module to upgrade to the final version.

Previously the code selected the last added module.
This breaks some modules that upgrades to multiple modules.
We now select the first added module instead.
This seems to work, but could still be brittle.


  Commit: 89771625c9a3f6d19d903c7f3ca91b57c68d0eb1
      https://github.com/VisTrails/VisTrails/commit/89771625c9a3f6d19d903c7f3ca91b57c68d0eb1
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-07-21 (Tue, 21 Jul 2015)

  Changed paths:
    M vistrails/packages/vtk/init.py

  Log Message:
  -----------
  Do not upgrade VTKCell self->Instance


  Commit: 0365cf0975f10499dfe7683eb65af0ee8620ed6d
      https://github.com/VisTrails/VisTrails/commit/0365cf0975f10499dfe7683eb65af0ee8620ed6d
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-07-22 (Wed, 22 Jul 2015)

  Changed paths:
    M doc/usersguide/vtl/mashups1.vtl
    M examples/usersguide/mashups.vt

  Log Message:
  -----------
  updated usersguide/mashups.vt and vtl

Mashups are only supported for simple upgrades that has the
same number of deletes and adds. The example had an upgrade
with an extra add, so we need to recreate the example.


  Commit: c8493045bf746a290cf64575d52e6cf4b6b4042e
      https://github.com/VisTrails/VisTrails/commit/c8493045bf746a290cf64575d52e6cf4b6b4042e
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-07-22 (Wed, 22 Jul 2015)

  Changed paths:
    M examples/usersguide/parameter_exploration.vt
    M vistrails/core/vistrail/controller.py

  Log Message:
  -----------
  Fixed multi-step parameter exploration upgrades

vistrails/core/vistrail/controller.py:
 - PE did not support multi-step upgrades
   We need to run the upgrade until no more changes are done

examples/usersguide/parameter_exploration.vt:
 - Updated vtk port names. Since we are using port names to identify
   pe functions these are not upgraded automatically.
 - Ran the pe pipelines so that the pe:s were upgraded.


  Commit: ef19a7832281af7b2a6f713526c8de0c723e8f5e
      https://github.com/VisTrails/VisTrails/commit/ef19a7832281af7b2a6f713526c8de0c723e8f5e
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-22 (Wed, 22 Jul 2015)

  Changed paths:
    M vistrails/packages/tabledata/widgets.py

  Log Message:
  -----------
  Don't use get_vistrails_basic_pkg_id()


  Commit: dc2e98da52789e00e5d5b004f3031cc94ed73b96
      https://github.com/VisTrails/VisTrails/commit/dc2e98da52789e00e5d5b004f3031cc94ed73b96
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-22 (Wed, 22 Jul 2015)

  Changed paths:
    M vistrails/tests/utils.py

  Log Message:
  -----------
  Add tests.utils:run_file() helper


  Commit: 0f45957cc1a6c050b150e256581a796effd4c5ab
      https://github.com/VisTrails/VisTrails/commit/0f45957cc1a6c050b150e256581a796effd4c5ab
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-22 (Wed, 22 Jul 2015)

  Changed paths:
    A vistrails/packages/mongodb/__init__.py
    A vistrails/packages/mongodb/init.py

  Log Message:
  -----------
  Add a MongoDB package


  Commit: 16c9ec3df5d0bda325ae7202acfc42024a8e111f
      https://github.com/VisTrails/VisTrails/commit/16c9ec3df5d0bda325ae7202acfc42024a8e111f
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-22 (Wed, 22 Jul 2015)

  Changed paths:
    A vistrails/packages/mongodb/Vagrantfile
    M vistrails/packages/mongodb/init.py

  Log Message:
  -----------
  Add a MongoCollection module

This means you no longer pass a collection name to each module, but
rather get a MongoCollection connection in.

The MapReduce module also now returns a MongoCollection so explicit
queries can be done on it.


  Commit: d0bf7d6f39829038dd6c958a4ce48c6ee8fec5a5
      https://github.com/VisTrails/VisTrails/commit/d0bf7d6f39829038dd6c958a4ce48c6ee8fec5a5
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-22 (Wed, 22 Jul 2015)

  Changed paths:
    M vistrails/packages/tabledata/read/__init__.py
    A vistrails/packages/tabledata/read/convert.py
    M vistrails/packages/tabledata/read/read_json.py

  Log Message:
  -----------
  Add DictToTable and ListToTable to tabledata

These are the same as the JSON modules, but take live Python objects
instead of a JSON file.


  Commit: d880b4634d4facd1ad454148aad926dfe8c88967
      https://github.com/VisTrails/VisTrails/commit/d880b4634d4facd1ad454148aad926dfe8c88967
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-22 (Wed, 22 Jul 2015)

  Changed paths:
    A examples/mongodb.vt

  Log Message:
  -----------
  Add MongoDB example


  Commit: ef3ebf465fe082ad567e55a5ac4382c1defb295c
      https://github.com/VisTrails/VisTrails/commit/ef3ebf465fe082ad567e55a5ac4382c1defb295c
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-22 (Wed, 22 Jul 2015)

  Changed paths:
    M vistrails/packages/mongodb/init.py

  Log Message:
  -----------
  Add unittest to mongodb (just run the example)


  Commit: 4f7cdb3ae11e23b0be210bc6103cf13803ff571e
      https://github.com/VisTrails/VisTrails/commit/4f7cdb3ae11e23b0be210bc6103cf13803ff571e
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-07-23 (Thu, 23 Jul 2015)

  Changed paths:
    M vistrails/core/db/locator.py

  Log Message:
  -----------
  Added test for usersguide vtl files


  Commit: 04ab79de06bf873b3040ade63485dd7d223b23bf
      https://github.com/VisTrails/VisTrails/commit/04ab79de06bf873b3040ade63485dd7d223b23bf
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-23 (Thu, 23 Jul 2015)

  Changed paths:
    M vistrails/core/utils/__init__.py

  Log Message:
  -----------
  Fix deprecation warnings on Exception.message


  Commit: 8a0610dafd1632506bbf2423167c56a8e9ed6102
      https://github.com/VisTrails/VisTrails/commit/8a0610dafd1632506bbf2423167c56a8e9ed6102
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-23 (Thu, 23 Jul 2015)

  Changed paths:
    M vistrails/gui/collection/workspace.py

  Log Message:
  -----------
  Add a "close" action in the workspace context menu


  Commit: 5155573edd4c2bdc9afe298381469b7320219acc
      https://github.com/VisTrails/VisTrails/commit/5155573edd4c2bdc9afe298381469b7320219acc
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-07-23 (Thu, 23 Jul 2015)

  Changed paths:
    M vistrails/core/db/locator.py

  Log Message:
  -----------
  Revert "Added test for usersguide vtl files"

This reverts commit 4f7cdb3ae11e23b0be210bc6103cf13803ff571e.


  Commit: 8eb50ecea6603e7b06defe62645bf33e2313381a
      https://github.com/VisTrails/VisTrails/commit/8eb50ecea6603e7b06defe62645bf33e2313381a
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-07-23 (Thu, 23 Jul 2015)

  Changed paths:
    M vistrails/core/db/locator.py

  Log Message:
  -----------
  Revert "Revert "Added test for usersguide vtl files""

This reverts commit 5155573edd4c2bdc9afe298381469b7320219acc.


  Commit: a493325e082bc2898821f62b566d73e555a82cb5
      https://github.com/VisTrails/VisTrails/commit/a493325e082bc2898821f62b566d73e555a82cb5
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-24 (Fri, 24 Jul 2015)

  Changed paths:
    A vistrails/packages/reprounzip/__init__.py
    A vistrails/packages/reprounzip/init.py

  Log Message:
  -----------
  VisTrails package for reprounzip


  Commit: d64f4b9db6c69e01dab221914a2022d7ac2c157d
      https://github.com/VisTrails/VisTrails/commit/d64f4b9db6c69e01dab221914a2022d7ac2c157d
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-24 (Fri, 24 Jul 2015)

  Changed paths:
    M vistrails/packages/reprounzip/init.py

  Log Message:
  -----------
  Add version to VisTrais/reprounzip interface

Passes a version number ("1") to the reprounzip-vistrails plugin from
the VisTrails package.

This will allow reprounzip-vistrails to evolve without breaking the
VisTrails package.


  Commit: 2ae792d1bc130c299678406ce643e87f345c738e
      https://github.com/VisTrails/VisTrails/commit/2ae792d1bc130c299678406ce643e87f345c738e
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-07-27 (Mon, 27 Jul 2015)

  Changed paths:
    M examples/usersguide/cfassistant.vt

  Log Message:
  -----------
  cfassistant.vt: Fixed faulty encoding in PythonSource


  Commit: 1e2c3596ff7e10627a9f7109219a9c4b01619d3a
      https://github.com/VisTrails/VisTrails/commit/1e2c3596ff7e10627a9f7109219a9c4b01619d3a
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-07-27 (Mon, 27 Jul 2015)

  Changed paths:
    M vistrails/core/db/locator.py

  Log Message:
  -----------
  Fixed error message in vtl test


  Commit: ceb3d235135cde1a21d6e16a25d226c304dfafa5
      https://github.com/VisTrails/VisTrails/commit/ceb3d235135cde1a21d6e16a25d226c304dfafa5
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-07-27 (Mon, 27 Jul 2015)

  Changed paths:
    M examples/list-handling.vt

  Log Message:
  -----------
  list-handling.vt: Fixed PythonSource line ending encoding


  Commit: 651bebe9dd830257e68e2cdfa5d8c6a711ff863f
      https://github.com/VisTrails/VisTrails/commit/651bebe9dd830257e68e2cdfa5d8c6a711ff863f
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-27 (Mon, 27 Jul 2015)

  Changed paths:
    M vistrails/core/upgradeworkflow.py

  Log Message:
  -----------
  Makes upgrade's new_module accept ModuleDescriptor


  Commit: 3e9a49c6c512f685b206a1b7daedc42463160180
      https://github.com/VisTrails/VisTrails/commit/3e9a49c6c512f685b206a1b7daedc42463160180
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-27 (Mon, 27 Jul 2015)

  Changed paths:
    M vistrails/gui/mashups/mashup_app.py
    M vistrails/gui/version_prop.py

  Log Message:
  -----------
  Minor fixes for mashup test

Doesn't make it pass.


  Commit: e0e1c19d8633f5af728d96223f8a20f4436f909c
      https://github.com/VisTrails/VisTrails/commit/e0e1c19d8633f5af728d96223f8a20f4436f909c
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-27 (Mon, 27 Jul 2015)

  Changed paths:
    M vistrails/core/vistrail/controller.py

  Log Message:
  -----------
  Adds an unexpected_exception() call


  Commit: 32c7129583245eab066e94731f9b5d611227ab63
      https://github.com/VisTrails/VisTrails/commit/32c7129583245eab066e94731f9b5d611227ab63
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-27 (Mon, 27 Jul 2015)

  Changed paths:
    M vistrails/core/vistrail/controller.py

  Log Message:
  -----------
  Fixes controller hiding InitializationFailed

When handle_invalid_pipeline() enables a package, it did not print out
the package initialization errors.


  Commit: a65bc935c7984c0a044a0b86002d479ef93ccd0c
      https://github.com/VisTrails/VisTrails/commit/a65bc935c7984c0a044a0b86002d479ef93ccd0c
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-27 (Mon, 27 Jul 2015)

  Changed paths:
    M vistrails/core/vistrail/controller.py

  Log Message:
  -----------
  Fixes use of handle_invalid_pipeline()

do_version_switch() had lots of nested try: blocks with
handle_invalid_pipeline() calls. This probably makes it right.


  Commit: 156f96a2b7dd6aa35a7b22288a2ad35632d9172d
      https://github.com/VisTrails/VisTrails/commit/156f96a2b7dd6aa35a7b22288a2ad35632d9172d
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-07-27 (Mon, 27 Jul 2015)

  Changed paths:
    M vistrails/packages/SUDSWebServices/init.py

  Log Message:
  -----------
  Do not save WSDL for DBVistrail


  Commit: dd20e92fc48129eb2b66c22401363a4f9d8ba1c2
      https://github.com/VisTrails/VisTrails/commit/dd20e92fc48129eb2b66c22401363a4f9d8ba1c2
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-27 (Mon, 27 Jul 2015)

  Changed paths:
    M vistrails/core/vistrail/controller.py

  Log Message:
  -----------
  Formatting


  Commit: 9d10713261af6595e7cbfbd5aa256ca7dfa835c9
      https://github.com/VisTrails/VisTrails/commit/9d10713261af6595e7cbfbd5aa256ca7dfa835c9
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-27 (Mon, 27 Jul 2015)

  Changed paths:
    M vistrails/core/vistrail/controller.py

  Log Message:
  -----------
  Merge branch 'invalid-pipeline-hides-package-errors' into 'v2.2'


  Commit: 1a1179c1cf37c1d9afd35612b52b1ab7bd2a9854
      https://github.com/VisTrails/VisTrails/commit/1a1179c1cf37c1d9afd35612b52b1ab7bd2a9854
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-07-27 (Mon, 27 Jul 2015)

  Changed paths:
    M vistrails/gui/preferences.py

  Log Message:
  -----------
  preferences.py: Switched test from dialogs to URL


  Commit: 60d43bc3fdfd90221fb613fe4306610d8558dfe5
      https://github.com/VisTrails/VisTrails/commit/60d43bc3fdfd90221fb613fe4306610d8558dfe5
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-28 (Tue, 28 Jul 2015)

  Changed paths:
    M vistrails/packages/matplotlib/bases.py
    M vistrails/packages/matplotlib/figure_cell.py

  Log Message:
  -----------
  Don't pass down MplFigure objects


  Commit: adbd186c2d1a12fa6072c3ca162d31e3170ae709
      https://github.com/VisTrails/VisTrails/commit/adbd186c2d1a12fa6072c3ca162d31e3170ae709
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-28 (Tue, 28 Jul 2015)

  Changed paths:
    M vistrails/packages/matplotlib/identifiers.py
    M vistrails/packages/matplotlib/init.py

  Log Message:
  -----------
  Upgrade for MplFigure change


  Commit: 5fe2e62572ea000f8d7b5f192d5a0fe67cea41ef
      https://github.com/VisTrails/VisTrails/commit/5fe2e62572ea000f8d7b5f192d5a0fe67cea41ef
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-29 (Wed, 29 Jul 2015)

  Changed paths:
    M vistrails/packages/matplotlib/bases.py
    M vistrails/packages/matplotlib/figure_cell.py
    M vistrails/packages/matplotlib/identifiers.py
    M vistrails/packages/matplotlib/init.py

  Log Message:
  -----------
  Merge pull request #1112 from VisTrails/dont-pass-mplfigure

Don't pass MplFigure module on MplFigure connection, just pass the
figure object.


  Commit: 2e9b694be618573eaedfada6ddf49c53444e6a9b
      https://github.com/VisTrails/VisTrails/commit/2e9b694be618573eaedfada6ddf49c53444e6a9b
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-29 (Wed, 29 Jul 2015)

  Changed paths:
    A examples/mongodb.vt
    A vistrails/packages/mongodb/Vagrantfile
    A vistrails/packages/mongodb/__init__.py
    A vistrails/packages/mongodb/init.py
    M vistrails/packages/tabledata/read/__init__.py
    A vistrails/packages/tabledata/read/convert.py
    M vistrails/packages/tabledata/read/read_json.py

  Log Message:
  -----------
  Merge pull request #1106 from VisTrails/mongodb

Adds a MongoDB package using pymongo.


  Commit: e04135bdc5771a39188a2db064c0ca788adf112f
      https://github.com/VisTrails/VisTrails/commit/e04135bdc5771a39188a2db064c0ca788adf112f
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-07-29 (Wed, 29 Jul 2015)

  Changed paths:
    A vistrails/packages/reprounzip/__init__.py
    A vistrails/packages/reprounzip/init.py

  Log Message:
  -----------
  Merge pull request #1110 from VisTrails/reprounzip-pkg

Add ReproUnzip package.


  Commit: 2cb064565282fcdfbe6feab97ef3934bdf108b01
      https://github.com/VisTrails/VisTrails/commit/2cb064565282fcdfbe6feab97ef3934bdf108b01
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-07-29 (Wed, 29 Jul 2015)

  Changed paths:
    M vistrails/core/console_mode.py
    M vistrails/core/modules/output_modules.py
    M vistrails/gui/application.py
    M vistrails/run.py

  Log Message:
  -----------
  Merge branch 'output-modules-use-global-dir' into v2.2


  Commit: 09a82e311db7e907335a75be15f78f43db2ed54a
      https://github.com/VisTrails/VisTrails/commit/09a82e311db7e907335a75be15f78f43db2ed54a
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-07-30 (Thu, 30 Jul 2015)

  Changed paths:
    M vistrails/gui/preferences.py

  Log Message:
  -----------
  Specified exception type in TestPreferencesDialog


  Commit: 204e6dc6e47ca15bd6997e7b4ed9c4997739c3cc
      https://github.com/VisTrails/VisTrails/commit/204e6dc6e47ca15bd6997e7b4ed9c4997739c3cc
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-07-30 (Thu, 30 Jul 2015)

  Changed paths:
    M examples/list-handling.vt
    M examples/usersguide/cfassistant.vt
    M vistrails/core/db/locator.py
    M vistrails/gui/preferences.py
    M vistrails/packages/SUDSWebServices/init.py

  Log Message:
  -----------
  Merge branch 'vtl_test' into v2.2


  Commit: 48417312996026a98f7cbe4f4a4468923925c28e
      https://github.com/VisTrails/VisTrails/commit/48417312996026a98f7cbe4f4a4468923925c28e
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-07-31 (Fri, 31 Jul 2015)

  Changed paths:
    M vistrails/core/vistrail/controller.py

  Log Message:
  -----------
  Validate the final call to handle_invalid_pipeline


  Commit: 93b1b55df74d75333cb31ff6f6974a8a018537f6
      https://github.com/VisTrails/VisTrails/commit/93b1b55df74d75333cb31ff6f6974a8a018537f6
  Author: David Koop <dkoop at umassd.edu>
  Date:   2015-07-31 (Fri, 31 Jul 2015)

  Changed paths:
    M vistrails/db/versions/v1_0_2/persistence/sql/sql_dao.py
    M vistrails/db/versions/v1_0_3/persistence/sql/sql_dao.py
    M vistrails/db/versions/v1_0_4/persistence/sql/sql_dao.py

  Log Message:
  -----------
  Fix issue with grouped sql statements escaping

Make sure to keep each argument separately escaped


  Commit: 1745a1b1e6bf70e9ee64b9832393c23771616d2c
      https://github.com/VisTrails/VisTrails/commit/1745a1b1e6bf70e9ee64b9832393c23771616d2c
  Author: David Koop <dkoop at umassd.edu>
  Date:   2015-07-31 (Fri, 31 Jul 2015)

  Changed paths:
    M vistrails/tests/runtestsuite.py

  Log Message:
  -----------
  Fix file/dir test in runtestsuite's tempfile cleanup


  Commit: 3b3496947a9fcf34775c99aa036cf8536c100935
      https://github.com/VisTrails/VisTrails/commit/3b3496947a9fcf34775c99aa036cf8536c100935
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-08-03 (Mon, 03 Aug 2015)

  Changed paths:
    M vistrails/gui/job_monitor.py

  Log Message:
  -----------
  Fixed responsiveness of suspended module progress bar


  Commit: fbd1e2b72f18b0ecdd51bda65ff394f8c47a1d7b
      https://github.com/VisTrails/VisTrails/commit/fbd1e2b72f18b0ecdd51bda65ff394f8c47a1d7b
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-08-03 (Mon, 03 Aug 2015)

  Changed paths:
    M vistrails/core/vistrail/job.py
    M vistrails/gui/job_monitor.py

  Log Message:
  -----------
  Fixed old-style job monitoring

Restarted jobs are now correctly marked as running.
JobFinished is replaced with job.ready so that its temporary usage
can be reset when re-running the workflow.


  Commit: 69d8da4114f3a0f3920e6fa75d95146337129527
      https://github.com/VisTrails/VisTrails/commit/69d8da4114f3a0f3920e6fa75d95146337129527
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-08-03 (Mon, 03 Aug 2015)

  Changed paths:
    M vistrails/gui/job_monitor.py

  Log Message:
  -----------
  Fixed deleting second workflow job bug


  Commit: 617dd4a11abfc70d580db8dc9126d84190ffea5b
      https://github.com/VisTrails/VisTrails/commit/617dd4a11abfc70d580db8dc9126d84190ffea5b
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-08-03 (Mon, 03 Aug 2015)

  Changed paths:
    M vistrails/gui/job_monitor.py

  Log Message:
  -----------
  Add 'delete job' context menu items


  Commit: f67f7dfc41acaf8a3e4455572cbe73ccdea450ac
      https://github.com/VisTrails/VisTrails/commit/f67f7dfc41acaf8a3e4455572cbe73ccdea450ac
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-08-03 (Mon, 03 Aug 2015)

  Changed paths:
    M vistrails/core/interpreter/cached.py
    M vistrails/core/modules/sub_module.py
    M vistrails/core/modules/vistrails_module.py

  Log Message:
  -----------
  Fixed running job inside Group


  Commit: 7f08d6bf3fed606034b379c24d54b37dbf7b244a
      https://github.com/VisTrails/VisTrails/commit/7f08d6bf3fed606034b379c24d54b37dbf7b244a
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-08-03 (Mon, 03 Aug 2015)

  Changed paths:
    M vistrails/gui/job_monitor.py

  Log Message:
  -----------
  Fixed job monitor progress bar hanging on long intervals


  Commit: 2e6cd3fdb4a8af560349b532d01cb6b7d51cdd4f
      https://github.com/VisTrails/VisTrails/commit/2e6cd3fdb4a8af560349b532d01cb6b7d51cdd4f
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-05 (Wed, 05 Aug 2015)

  Changed paths:
    M vistrails/core/modules/vistrails_module.py

  Log Message:
  -----------
  ModuleSupended requires 'handle' (or 'queue') arg


  Commit: 9c0da065695583a34f530d44469b27a9a988b8ad
      https://github.com/VisTrails/VisTrails/commit/9c0da065695583a34f530d44469b27a9a988b8ad
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-06 (Thu, 06 Aug 2015)

  Changed paths:
    M vistrails/packages/tej/init.py

  Log Message:
  -----------
  tej: Fix checking for job path existence

Amends 2021a77c.


  Commit: 5dc3f2a46392667e458ea3bff3d9c9c06eb65889
      https://github.com/VisTrails/VisTrails/commit/5dc3f2a46392667e458ea3bff3d9c9c06eb65889
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-06 (Thu, 06 Aug 2015)

  Changed paths:
    M vistrails/core/modules/package.py
    M vistrails/gui/module_palette.py

  Log Message:
  -----------
  Fix package contextmenu logic

- Replaces has_contextMenuName() and has_contextMenu() with a single
has_context_menu()
- Warns if a package defines only one of contextMenuName and
callContextMenu
- Fix use of unset return value from callContextMenu in the module
palette


  Commit: 457de75a275b345c035b3a4f69ed55132c1bdd4f
      https://github.com/VisTrails/VisTrails/commit/457de75a275b345c035b3a4f69ed55132c1bdd4f
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-06 (Thu, 06 Aug 2015)

  Changed paths:
    M vistrails/core/modules/package.py
    M vistrails/gui/module_palette.py

  Log Message:
  -----------
  Allow multiple items in context menus

Packages can now define context_menu, which takes the name of the
clicked module or None (if the package name was clicked); it returns a
list of tuples (text, callback); the callback is called on click with no
argument.


  Commit: a2a95bd68f511147d5892e60d32e05877915b772
      https://github.com/VisTrails/VisTrails/commit/a2a95bd68f511147d5892e60d32e05877915b772
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-06 (Thu, 06 Aug 2015)

  Changed paths:
    M vistrails/gui/modules/source_configure.py

  Log Message:
  -----------
  Fix madness


  Commit: cf44c9d14afb27b3e31450c72171df71046abd7b
      https://github.com/VisTrails/VisTrails/commit/cf44c9d14afb27b3e31450c72171df71046abd7b
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-06 (Thu, 06 Aug 2015)

  Changed paths:
    M vistrails/gui/modules/source_configure.py

  Log Message:
  -----------
  Unicode support in SourceConfigurationWidget

I thought that was the point of urlencoding.


  Commit: e6e2120fe296d7a9ecf6313e383fec45d63ad576
      https://github.com/VisTrails/VisTrails/commit/e6e2120fe296d7a9ecf6313e383fec45d63ad576
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-07 (Fri, 07 Aug 2015)

  Changed paths:
    M vistrails/core/vistrail/job.py

  Log Message:
  -----------
  Remove NotCacheable from JobMixin


  Commit: bfaa492c900061371a4b764ae7e86d5ec8b18b55
      https://github.com/VisTrails/VisTrails/commit/bfaa492c900061371a4b764ae7e86d5ec8b18b55
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-08-07 (Fri, 07 Aug 2015)

  Changed paths:
    M vistrails/core/vistrail/job.py

  Log Message:
  -----------
  Merge pull request #1120 from VisTrails/jobmixin-cacheable

Remove NotCacheable from JobMixin


  Commit: 88900f21e69f4037b98609cc2159bff404d5d6e4
      https://github.com/VisTrails/VisTrails/commit/88900f21e69f4037b98609cc2159bff404d5d6e4
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-07 (Fri, 07 Aug 2015)

  Changed paths:
    M vistrails/core/modules/package.py
    M vistrails/gui/module_palette.py

  Log Message:
  -----------
  Merge pull request #1118 from VisTrails/palette-context-menu

Palette context menu


  Commit: 287cfad09ba979e24e18aa278956fc88a07bd2f3
      https://github.com/VisTrails/VisTrails/commit/287cfad09ba979e24e18aa278956fc88a07bd2f3
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-07 (Fri, 07 Aug 2015)

  Changed paths:
    M vistrails/packages/tej/init.py

  Log Message:
  -----------
  Remove one level of wrapping in SubmitShellJob


  Commit: fa67cc5c9c244dbedfef584e0e49d81d4e579e0f
      https://github.com/VisTrails/VisTrails/commit/fa67cc5c9c244dbedfef584e0e49d81d4e579e0f
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-07 (Fri, 07 Aug 2015)

  Changed paths:
    M doc/usersguide/example.rst
    A doc/usersguide/tej.rst

  Log Message:
  -----------
  Initial work on documentation for the tej package


  Commit: 55764a7ab8bfd0b4c98c800a2be2d120cb38ecdf
      https://github.com/VisTrails/VisTrails/commit/55764a7ab8bfd0b4c98c800a2be2d120cb38ecdf
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-07 (Fri, 07 Aug 2015)

  Changed paths:
    M vistrails/packages/tej/init.py
    M vistrails/packages/tej/widgets.py

  Log Message:
  -----------
  Add MakeDirectory module to tej


  Commit: ae4075876699295954313a4709ade59e7b8eaaad
      https://github.com/VisTrails/VisTrails/commit/ae4075876699295954313a4709ade59e7b8eaaad
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-07 (Fri, 07 Aug 2015)

  Changed paths:
    M vistrails/packages/tej/init.py

  Log Message:
  -----------
  Formatting and doc


  Commit: 13a8e41b3bd61407b3131cc4a0f8f19482199e49
      https://github.com/VisTrails/VisTrails/commit/13a8e41b3bd61407b3131cc4a0f8f19482199e49
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-07 (Fri, 07 Aug 2015)

  Changed paths:
    M vistrails/packages/tej/init.py

  Log Message:
  -----------
  Make SubmitJob accept portspecs

Additional files to be sent with the job can now be added using the
DirectoryConfigurationWidget.


  Commit: 6f39e2d290fd81b6c8a4d3deb1816398e068a046
      https://github.com/VisTrails/VisTrails/commit/6f39e2d290fd81b6c8a4d3deb1816398e068a046
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-07 (Fri, 07 Aug 2015)

  Changed paths:
    M vistrails/packages/tej/init.py

  Log Message:
  -----------
  Hide some more log messages from tej


  Commit: 1275f2261d8282d8563ca88b1f2ac9761e1b0b1c
      https://github.com/VisTrails/VisTrails/commit/1275f2261d8282d8563ca88b1f2ac9761e1b0b1c
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-07 (Fri, 07 Aug 2015)

  Changed paths:
    M vistrails/packages/tej/init.py

  Log Message:
  -----------
  'print_error' port: check status and print stderr


  Commit: 91a023a8e0de616862aae00342874530c1d2649e
      https://github.com/VisTrails/VisTrails/commit/91a023a8e0de616862aae00342874530c1d2649e
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-10 (Mon, 10 Aug 2015)

  Changed paths:
    M vistrails/packages/tabledata/convert/__init__.py
    A vistrails/packages/tabledata/convert/convert_numpy.py

  Log Message:
  -----------
  Add Reshape module


  Commit: dbee7a65908952abb6ff4fe097e3d2efd137eaa0
      https://github.com/VisTrails/VisTrails/commit/dbee7a65908952abb6ff4fe097e3d2efd137eaa0
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-08-10 (Mon, 10 Aug 2015)

  Changed paths:
    M vistrails/gui/job_monitor.py

  Log Message:
  -----------
  Removes code to check jobs without handle

This code is unused after 2e6cd3fdb4a8af560349b532d01cb6b7d51cdd4f.


  Commit: 9ab9efa1ecbcf4ea6d71cf4d25a2fe54e4d602fc
      https://github.com/VisTrails/VisTrails/commit/9ab9efa1ecbcf4ea6d71cf4d25a2fe54e4d602fc
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-10 (Mon, 10 Aug 2015)

  Changed paths:
    M vistrails/core/modules/basic_modules.py

  Log Message:
  -----------
  Allow PythonSource var name to be input *and* out

Previously, if using the same name for an input and an output port, the
input would be None instead.


  Commit: 2957b5580db7fd6d519bc4ef2ac5e52906c0b07b
      https://github.com/VisTrails/VisTrails/commit/2957b5580db7fd6d519bc4ef2ac5e52906c0b07b
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-10 (Mon, 10 Aug 2015)

  Changed paths:
    M vistrails/packages/tabledata/read/convert.py

  Log Message:
  -----------
  Fix ListToTable with numpy arrays


  Commit: 4c428872a37594c5cb69c9ae13643b74316f5617
      https://github.com/VisTrails/VisTrails/commit/4c428872a37594c5cb69c9ae13643b74316f5617
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-10 (Mon, 10 Aug 2015)

  Changed paths:
    M vistrails/packages/tabledata/__init__.py
    M vistrails/packages/tabledata/common.py
    M vistrails/packages/tabledata/identifiers.py
    M vistrails/packages/tabledata/init.py
    M vistrails/packages/tabledata/operations.py
    M vistrails/packages/tabledata/viewer.py
    M vistrails/packages/tabledata/widgets.py

  Log Message:
  -----------
  Adds missing copyright headers to tabledata


  Commit: b5ddc85e523a60c80c7d7f88b91318ebaccc1418
      https://github.com/VisTrails/VisTrails/commit/b5ddc85e523a60c80c7d7f88b91318ebaccc1418
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-10 (Mon, 10 Aug 2015)

  Changed paths:
    M vistrails/packages/tabledata/common.py
    M vistrails/packages/tabledata/convert/__init__.py
    M vistrails/packages/tabledata/convert/convert_numpy.py
    M vistrails/packages/tabledata/init.py
    M vistrails/packages/tabledata/operations.py
    M vistrails/packages/tabledata/read/__init__.py
    M vistrails/packages/tabledata/read/read_csv.py
    M vistrails/packages/tabledata/read/read_excel.py
    M vistrails/packages/tabledata/read/read_numpy.py
    M vistrails/packages/tabledata/write/__init__.py
    M vistrails/packages/tabledata/write/write_numpy.py

  Log Message:
  -----------
  tabledata: require numpy later

Always define all modules in tabledata, try to import numpy/xlrd/xlwt
when modules are executed.


  Commit: ca432693502f548fdd470d51fb4c456b96d46fff
      https://github.com/VisTrails/VisTrails/commit/ca432693502f548fdd470d51fb4c456b96d46fff
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-08-12 (Wed, 12 Aug 2015)

  Changed paths:
    M vistrails/gui/job_monitor.py

  Log Message:
  -----------
  Fixes jobs in ready state not being marked as finished


  Commit: f743973e4fcffafd4d1b921a09f660c11c63280c
      https://github.com/VisTrails/VisTrails/commit/f743973e4fcffafd4d1b921a09f660c11c63280c
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-12 (Wed, 12 Aug 2015)

  Changed paths:
    M vistrails/packages/tabledata/__init__.py
    M vistrails/packages/tabledata/common.py
    M vistrails/packages/tabledata/convert/__init__.py
    M vistrails/packages/tabledata/convert/convert_numpy.py
    M vistrails/packages/tabledata/identifiers.py
    M vistrails/packages/tabledata/init.py
    M vistrails/packages/tabledata/operations.py
    M vistrails/packages/tabledata/read/__init__.py
    M vistrails/packages/tabledata/read/read_csv.py
    M vistrails/packages/tabledata/read/read_excel.py
    M vistrails/packages/tabledata/read/read_numpy.py
    M vistrails/packages/tabledata/viewer.py
    M vistrails/packages/tabledata/widgets.py
    M vistrails/packages/tabledata/write/__init__.py
    M vistrails/packages/tabledata/write/write_numpy.py

  Log Message:
  -----------
  Merge branch 'tabledata-all-modules' into 'v2.2'


  Commit: 7190bc201baa3c0ff5f94a3cfc290a9ee6ed8582
      https://github.com/VisTrails/VisTrails/commit/7190bc201baa3c0ff5f94a3cfc290a9ee6ed8582
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-12 (Wed, 12 Aug 2015)

  Changed paths:
    M .travis.yml

  Log Message:
  -----------
  Travis: update Python environment first


  Commit: 00e6e65187317b6303f81b4b31df02fe95071256
      https://github.com/VisTrails/VisTrails/commit/00e6e65187317b6303f81b4b31df02fe95071256
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-12 (Wed, 12 Aug 2015)

  Changed paths:
    M vistrails/packages/spreadsheet/spreadsheet_controller.py

  Log Message:
  -----------
  Fixed findSpreadsheetWindow()

SpreadsheetController#findSpreadsheetWindow() looked at the top-level
widgets to find a SpreadsheetWindow even if the spreadsheetWindow global
variable was set. This causes issues if the SpreadsheetWindow gets
embedded somewhere.


  Commit: 514eec02c2900e0bcb6ec6576f8c695026221a0d
      https://github.com/VisTrails/VisTrails/commit/514eec02c2900e0bcb6ec6576f8c695026221a0d
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-12 (Wed, 12 Aug 2015)

  Changed paths:
    M vistrails/packages/spreadsheet/init.py
    M vistrails/packages/spreadsheet/spreadsheet_controller.py

  Log Message:
  -----------
  Don't show spreadsheet at exit

findSpreadsheetWindow() would previously create the spreadsheet window
and show it, meaning that finalize() was creating it just so it could
tear it down.

This adds create[=True] to findSpreadsheetWindow().

Also fixes caching in findSpreadsheetWindow(), and don't test the return
value everywhere it cannot be None anymore.


  Commit: 686f1a36a1a51fb1fd96fdd0321bdd49792a6c36
      https://github.com/VisTrails/VisTrails/commit/686f1a36a1a51fb1fd96fdd0321bdd49792a6c36
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-12 (Wed, 12 Aug 2015)

  Changed paths:
    M CHANGELOG

  Log Message:
  -----------
  Update CHANGELOG


  Commit: d61fdead91e7285e91267f629c26d837f44ff23b
      https://github.com/VisTrails/VisTrails/commit/d61fdead91e7285e91267f629c26d837f44ff23b
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-12 (Wed, 12 Aug 2015)

  Changed paths:
    A doc/usersguide/figures/tej/pipeline.png
    M doc/usersguide/tej.rst
    A doc/usersguide/vtl/tej-primes.vtl
    A examples/tej-primes.vt

  Log Message:
  -----------
  Example


  Commit: ea0b998d5c88504ef66a7c1efbfbb4bcfa9da83e
      https://github.com/VisTrails/VisTrails/commit/ea0b998d5c88504ef66a7c1efbfbb4bcfa9da83e
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-12 (Wed, 12 Aug 2015)

  Changed paths:
    M doc/usersguide/example.rst
    A doc/usersguide/figures/tej/pipeline.png
    A doc/usersguide/tej.rst
    A doc/usersguide/vtl/tej-primes.vtl
    A examples/tej-primes.vt
    M vistrails/packages/tej/init.py
    M vistrails/packages/tej/widgets.py

  Log Message:
  -----------
  Merge branch 'tej-docs' into 'v2.2'


  Commit: 75d4b7a4f35d238dec5af19899ccf06d99e396d2
      https://github.com/VisTrails/VisTrails/commit/75d4b7a4f35d238dec5af19899ccf06d99e396d2
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-08-13 (Thu, 13 Aug 2015)

  Changed paths:
    M vistrails/gui/job_monitor.py

  Log Message:
  -----------
  Improved job monitor raising logic

Job monitor will no longer be raised when nothing has changed


  Commit: 0b08fec8067d7954b46b8d4362b250de7c47c783
      https://github.com/VisTrails/VisTrails/commit/0b08fec8067d7954b46b8d4362b250de7c47c783
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-08-17 (Mon, 17 Aug 2015)

  Changed paths:
    M vistrails/gui/job_monitor.py

  Log Message:
  -----------
  Added pausing of workflow job checking

Workflow jobs can now be paused when loaded or manually in the context menu.
Paused workflows will not be checked by the timer or "Check all" button.

This partially reverts commit dbee7a65908952abb6ff4fe097e3d2efd137eaa0.


  Commit: 7703d63593e2f7bac632d18aa64206a8d1cb393f
      https://github.com/VisTrails/VisTrails/commit/7703d63593e2f7bac632d18aa64206a8d1cb393f
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-08-25 (Tue, 25 Aug 2015)

  Changed paths:
    M vistrails/core/vistrail/job.py
    M vistrails/gui/job_monitor.py
    M vistrails/gui/vistrail_controller.py

  Log Message:
  -----------
  Added Job support to Parameter Explorations

core/vistrail/job.py:
 - Fixed "Job is already running" error

gui/job_monitor.py:
  Support workflow jobs that does not reference pipeline versions

gui/vistrail_controller.py:
 - PEProgressDialog: *new
   Custom progress dialog for parameter explorations that supports jobs
 - executeParameterExplorations:
   Added job handling logic


  Commit: 03d9b5ce4cc529383c15a441569448f0fa0a5b25
      https://github.com/VisTrails/VisTrails/commit/03d9b5ce4cc529383c15a441569448f0fa0a5b25
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-08-26 (Wed, 26 Aug 2015)

  Changed paths:
    M vistrails/gui/job_monitor.py

  Log Message:
  -----------
  Removed redundant finishWorkflow calls


  Commit: 3cb5b7cc11ebbef5a1a881768b4e2f6cb70b8017
      https://github.com/VisTrails/VisTrails/commit/3cb5b7cc11ebbef5a1a881768b4e2f6cb70b8017
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-08-26 (Wed, 26 Aug 2015)

  Changed paths:
    M vistrails/gui/mashups/mashup_app.py
    M vistrails/gui/mashups/mashups_manager.py

  Log Message:
  -----------
  Added Job support to Mashups

gui/mashups/mashup_app.py:
  Added progress bar and job handling logic to mashup execution

gui/mashups/mashups_manager.py:
  Copy jobMonitor when copying vt controller


  Commit: c7782d38196dfb1d0746b33b176b3e4f44a3b355
      https://github.com/VisTrails/VisTrails/commit/c7782d38196dfb1d0746b33b176b3e4f44a3b355
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-08-27 (Thu, 27 Aug 2015)

  Changed paths:
    M vistrails/core/interpreter/cached.py
    M vistrails/gui/pipeline_view.py
    M vistrails/gui/vistrail_controller.py

  Log Message:
  -----------
  Fixed progress error in parameter exploration

Running a modified pipeline in parameter exploration
failed with the new Progress Bar. It tried to fetch
the name of the non-existing module.

vistrails/core/interpreter/cached.py:
  Added full support for job_monitor attribute

vistrails/gui/pipeline_view.py:
  QPipelineScene:
    Handle non-existing module when fetching module name for progress bar

vistrails/gui/vistrail_controller.py
  executeParameterExploration:
    Rearranged and cleaned up code
    Removed controller as argument to execution
    Added job_monitor as argument to execution


  Commit: ab73a63edc3f17b72d7ebcb37c5d573197a46c59
      https://github.com/VisTrails/VisTrails/commit/ab73a63edc3f17b72d7ebcb37c5d573197a46c59
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-08-27 (Thu, 27 Aug 2015)

  Changed paths:
    M vistrails/gui/job_monitor.py

  Log Message:
  -----------
  Removed annoying notification each time a PE cell job finishes


  Commit: cb969b1361c1cbbf5a7a9b98d882a802ec7f153c
      https://github.com/VisTrails/VisTrails/commit/cb969b1361c1cbbf5a7a9b98d882a802ec7f153c
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-27 (Thu, 27 Aug 2015)

  Changed paths:
    M scripts/create_release_wiki_table.py
    M scripts/create_server_media_dir_structure.py
    M scripts/dist/common/set_version.py
    M scripts/dist/mac/Input/CLToolsWizard.command
    M scripts/dist/mac/Input/VisTrails.command
    M scripts/dist/mac/make_app
    M scripts/dist/mac/setup_itk.py
    M scripts/gen_vtk_examples/check_diffs.py
    M scripts/gen_vtk_examples/convert_to_vt.py
    M scripts/gen_vtk_examples/copy_vtk_examples.py
    M scripts/gen_vtk_examples/gen_vtk_examples.py
    M scripts/gen_vtk_examples/get_vtk_examples.py
    M scripts/mac_update_bin.sh
    M scripts/opm/opm2dot.py
    M scripts/restart-vistrails-server.sh
    M scripts/retarget_mpl_libs.sh
    M scripts/run_vistrails_batch_xvfb.sh
    M scripts/start_vistrails.sh
    M scripts/start_vistrails_xvfb.sh
    M scripts/unzip_vistrail.sh
    M scripts/update_copyright_year.py
    M scripts/update_email_contact.py
    M scripts/update_to_mod_bsd_license.py
    M scripts/win_update_bin.sh

  Log Message:
  -----------
  Fix permissions and shebangs in scripts


  Commit: e8dbaff1519cc5f11aed553df59ab65775c09df1
      https://github.com/VisTrails/VisTrails/commit/e8dbaff1519cc5f11aed553df59ab65775c09df1
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-27 (Thu, 27 Aug 2015)

  Changed paths:
    R vistrails/gui/modules/resources/__init__.py
    R vistrails/gui/modules/resources/colorconfig.qrc
    R vistrails/gui/modules/resources/colorconfig_rc.py
    R vistrails/gui/modules/resources/colorwheel.png

  Log Message:
  -----------
  Remove unused resource file colorconfig_rc


  Commit: 02c8b7e628104901af633545c88aa8e7911353c2
      https://github.com/VisTrails/VisTrails/commit/02c8b7e628104901af633545c88aa8e7911353c2
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-27 (Thu, 27 Aug 2015)

  Changed paths:
    A scripts/dist/man/vistrails.1

  Log Message:
  -----------
  Add a manpage (from the --help screen)


  Commit: 272dacf9efdfb392d969abd96512c0892d76ed43
      https://github.com/VisTrails/VisTrails/commit/272dacf9efdfb392d969abd96512c0892d76ed43
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-27 (Thu, 27 Aug 2015)

  Changed paths:
    R doc/coding_conventions.txt
    R doc/module_registry.txt
    R doc/package_system.txt
    R doc/pep-0008.txt
    R doc/pep-0257.txt
    R doc/signal_mess.txt
    R doc/source_tree_overview.tex

  Log Message:
  -----------
  Remove old developer documents from doc/


  Commit: 1cebb74b0a6f415ef0eee5f1cb46d6a8d54ff761
      https://github.com/VisTrails/VisTrails/commit/1cebb74b0a6f415ef0eee5f1cb46d6a8d54ff761
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-27 (Thu, 27 Aug 2015)

  Changed paths:
    M scripts/dist/source/make-vistrails-src-build.py

  Log Message:
  -----------
  Don't include doc/dist/ in source tarballs


  Commit: da8ba48411f8098da15f70eded31b5eb3dbcfc44
      https://github.com/VisTrails/VisTrails/commit/da8ba48411f8098da15f70eded31b5eb3dbcfc44
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-08-27 (Thu, 27 Aug 2015)

  Changed paths:
    M vistrails/run.py

  Log Message:
  -----------
  Don't fix paths if run.py has been moved


  Commit: af05ca780b237a934088f02771f00a753fa322fb
      https://github.com/VisTrails/VisTrails/commit/af05ca780b237a934088f02771f00a753fa322fb
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-09-01 (Tue, 01 Sep 2015)

  Changed paths:
    M vistrails/db/services/locator.py

  Log Message:
  -----------
  Limit autosaves to 30

When number of autosaves reaches 60 (2h) the oldest 30 (1h) will be removed


  Commit: a0dcfc5e41555f8e8fff6d0e688b3611d8f66695
      https://github.com/VisTrails/VisTrails/commit/a0dcfc5e41555f8e8fff6d0e688b3611d8f66695
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-09-01 (Tue, 01 Sep 2015)

  Changed paths:
    M vistrails/core/console_mode.py
    M vistrails/core/vistrail/job.py
    M vistrails/gui/vistrail_controller.py

  Log Message:
  -----------
  Fixed job execution error when there are non-wf jobs

Also fixed an updating_now deadlock

vistrails/gui/vistrail_controller.py:
 Fixed updating_now deadlocks by calling it directly after "finally:"
 - execute_current_workflow:
     Handle non-workflow jobs

vistrails/core/console_mode.py:
     Handle non-workflow jobs

vistrails/core/vistrail/job.py:
  Make sure finishWorkflow always clears current workflow


  Commit: 35a29fffb1814973ebbde6e4671d75bbd5958b2f
      https://github.com/VisTrails/VisTrails/commit/35a29fffb1814973ebbde6e4671d75bbd5958b2f
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-09-03 (Thu, 03 Sep 2015)

  Changed paths:
    M scripts/dist/source/make-vistrails-src-build.py

  Log Message:
  -----------
  Fix make-vistrails-src-build.py

Fixes a typo in 1cebb74b.


  Commit: b3a5f3521cb373a3ef2bda1c19fde7cf4eccfaa9
      https://github.com/VisTrails/VisTrails/commit/b3a5f3521cb373a3ef2bda1c19fde7cf4eccfaa9
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-09-03 (Thu, 03 Sep 2015)

  Changed paths:
    M vistrails/db/services/locator.py

  Log Message:
  -----------
  Only keep a single autosave

The new one is written before deleting the old one


  Commit: 7d058e5279a4fec3b9fef8fc4eb281cbc8d4f8e7
      https://github.com/VisTrails/VisTrails/commit/7d058e5279a4fec3b9fef8fc4eb281cbc8d4f8e7
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-09-03 (Thu, 03 Sep 2015)

  Changed paths:
    M vistrails/db/services/locator.py

  Log Message:
  -----------
  Minor fixes to locator.py


  Commit: ae22e76ba404b4a200f379791a1fa02128be5716
      https://github.com/VisTrails/VisTrails/commit/ae22e76ba404b4a200f379791a1fa02128be5716
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-09-03 (Thu, 03 Sep 2015)

  Changed paths:
    M vistrails/db/services/locator.py

  Log Message:
  -----------
  Minor fixes


  Commit: dac2631e445a6aa760f3fd93a5dedb416d5786e9
      https://github.com/VisTrails/VisTrails/commit/dac2631e445a6aa760f3fd93a5dedb416d5786e9
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-09-03 (Thu, 03 Sep 2015)

  Changed paths:
    M vistrails/db/services/locator.py

  Log Message:
  -----------
  Merge pull request #1126 from VisTrails/limit_autosave

Limit number of autosaves.


  Commit: 04d26368e515c8807e7bf888226ed2efb4df1b8f
      https://github.com/VisTrails/VisTrails/commit/04d26368e515c8807e7bf888226ed2efb4df1b8f
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-09-09 (Wed, 09 Sep 2015)

  Changed paths:
    M vistrails/core/modules/vistrails_module.py

  Log Message:
  -----------
  Allow parent jobs to have no handle


  Commit: 072ac63ad74ff4285d349d8c8989588864caac98
      https://github.com/VisTrails/VisTrails/commit/072ac63ad74ff4285d349d8c8989588864caac98
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-09-09 (Wed, 09 Sep 2015)

  Changed paths:
    M vistrails/core/vistrail/job.py
    M vistrails/gui/job_monitor.py

  Log Message:
  -----------
  Add custom name to parent jobs


  Commit: 552cbbfb9f7de8c6cb1353c8f1856c6fbf92494e
      https://github.com/VisTrails/VisTrails/commit/552cbbfb9f7de8c6cb1353c8f1856c6fbf92494e
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-09-09 (Wed, 09 Sep 2015)

  Changed paths:
    M CHANGELOG

  Log Message:
  -----------
  Touch up CHANGELOG


  Commit: b9c2d8e66acf913f2bedcb7abc8515a1f4c9b56e
      https://github.com/VisTrails/VisTrails/commit/b9c2d8e66acf913f2bedcb7abc8515a1f4c9b56e
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-09-10 (Thu, 10 Sep 2015)

  Changed paths:
    M vistrails/gui/mashups/mashups_widgets.py

  Log Message:
  -----------
  Fixed QNumericStepper.contentsChanged parameters


  Commit: 244c869b0689df4a7465bb082cc8101d77cb5e1b
      https://github.com/VisTrails/VisTrails/commit/244c869b0689df4a7465bb082cc8101d77cb5e1b
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-09-10 (Thu, 10 Sep 2015)

  Changed paths:
    M vistrails/gui/mashups/mashup_app.py

  Log Message:
  -----------
  Made mashup app notifications non-blocking


  Commit: 636d3df8b2def2aaae66e73a9338f2405ee80f37
      https://github.com/VisTrails/VisTrails/commit/636d3df8b2def2aaae66e73a9338f2405ee80f37
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-09-10 (Thu, 10 Sep 2015)

  Changed paths:
    M vistrails/gui/job_monitor.py
    A vistrails/packages/myjob.py
    A vistrails/tests/resources/jobs.vt

  Log Message:
  -----------
  Job Monitor tests

This tests the following Job Submission features:
* Run a job (suspend+finish)
* Run job in Group
* Run jobs in list loop
* Run jobs in Map
* Run Parameter Exploration with Job (suspend+finish)
* Run Mashup with Job (suspend+finish)

packages/myjob.py: *new
  Example package with timed and check-based jobs

tests/resources/jobs.vt: *new
  File containing the Workflows, PEs, and Mashups to test


  Commit: 0881d7d4b1af82c5f9f3fcb528fb4548efaa47cd
      https://github.com/VisTrails/VisTrails/commit/0881d7d4b1af82c5f9f3fcb528fb4548efaa47cd
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-09-10 (Thu, 10 Sep 2015)

  Changed paths:
    M vistrails/gui/mashups/mashup_app.py

  Log Message:
  -----------
  Make mashup app warnings critical so that they get displayed


  Commit: 6419a2b5df8712b4167f47c8e58254e35db49a63
      https://github.com/VisTrails/VisTrails/commit/6419a2b5df8712b4167f47c8e58254e35db49a63
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-09-14 (Mon, 14 Sep 2015)

  Changed paths:
    M doc/usersguide/developer.rst
    A doc/usersguide/job_submission.rst
    A doc/usersguide/vtl/jobsubmission1.vtl
    A doc/usersguide/vtl/jobsubmission2.vtl
    A examples/usersguide/job_submission.vt

  Log Message:
  -----------
  Job Submission developer documentation

  doc/usersguide/developer.rst
  doc/usersguide/job_submission.rst

Examples of ModuleSuspended and JobMixin:
  examples/usersguide/job_submission.vt

Links to examples:
  doc/usersguide/vtl/jobsubmission1.vtl
  doc/usersguide/vtl/jobsubmission2.vtl


  Commit: 00837ee3e17632310d48cfab73726772832842f8
      https://github.com/VisTrails/VisTrails/commit/00837ee3e17632310d48cfab73726772832842f8
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-09-17 (Thu, 17 Sep 2015)

  Changed paths:
    A doc/usersguide/figures/job_submission/job_monitor.png

  Log Message:
  -----------
  Added missing figure job_monitor.png


  Commit: a7f70828cc9abe98ac3db8e0c0e7eec11e6c5963
      https://github.com/VisTrails/VisTrails/commit/a7f70828cc9abe98ac3db8e0c0e7eec11e6c5963
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-09-17 (Thu, 17 Sep 2015)

  Changed paths:
    M doc/usersguide/job_submission.rst
    A doc/usersguide/vtl/jobsubmission3.vtl
    M examples/usersguide/job_submission.vt
    M vistrails/gui/job_monitor.py
    R vistrails/packages/myjob.py
    A vistrails/tests/resources/myjob.py

  Log Message:
  -----------
  Moved myjob package to tests/resources

myjob.py now needs to be installed to userpackages
manually or using a workflow that does this.

tests/resources/myjob.py: *moved
vtl/jobsubmission3.vtl: *new - link to package installer
examples/usersguide/job_submission.vt: Added package installer workflow
gui/job_monitor.py: Changed test package path
job_submission.rst: Added note how to install package (with link)


  Commit: 81d43de8c2c8692977ea2574d8e93e77dc0f4067
      https://github.com/VisTrails/VisTrails/commit/81d43de8c2c8692977ea2574d8e93e77dc0f4067
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-09-18 (Fri, 18 Sep 2015)

  Changed paths:
    M doc/usersguide/developer.rst
    A doc/usersguide/figures/job_submission/job_monitor.png
    A doc/usersguide/job_submission.rst
    A doc/usersguide/vtl/jobsubmission1.vtl
    A doc/usersguide/vtl/jobsubmission2.vtl
    A doc/usersguide/vtl/jobsubmission3.vtl
    A examples/usersguide/job_submission.vt
    M vistrails/core/modules/vistrails_module.py
    M vistrails/core/vistrail/job.py
    M vistrails/gui/job_monitor.py
    M vistrails/gui/mashups/mashup_app.py
    M vistrails/gui/mashups/mashups_widgets.py
    A vistrails/tests/resources/jobs.vt
    A vistrails/tests/resources/myjob.py

  Log Message:
  -----------
  Merge pull request #1128 from VisTrails/job-dev-docs

Developer documentation for Job Submission


  Commit: 872d8277e63e57dc9ed498d6b96ecc2f463b2102
      https://github.com/VisTrails/VisTrails/commit/872d8277e63e57dc9ed498d6b96ecc2f463b2102
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-09-18 (Fri, 18 Sep 2015)

  Changed paths:
    M doc/usersguide/job_submission.rst

  Log Message:
  -----------
  Minor fixes to job documentation


  Commit: 87ced4938dbc872a6dd598ccf06270d7c293b899
      https://github.com/VisTrails/VisTrails/commit/87ced4938dbc872a6dd598ccf06270d7c293b899
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-09-18 (Fri, 18 Sep 2015)

  Changed paths:
    M vistrails/packages/mongodb/__init__.py

  Log Message:
  -----------
  Fix typo in MongoDB package requirements


  Commit: c72b8067062c80babd2f24d2fb0957506862e37f
      https://github.com/VisTrails/VisTrails/commit/c72b8067062c80babd2f24d2fb0957506862e37f
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-09-18 (Fri, 18 Sep 2015)

  Changed paths:
    M doc/usersguide/job_submission.rst
    M doc/usersguide/vtl/jobsubmission1.vtl
    M doc/usersguide/vtl/jobsubmission2.vtl
    M doc/usersguide/vtl/jobsubmission3.vtl
    M vistrails/core/db/locator.py
    M vistrails/gui/job_monitor.py

  Log Message:
  -----------
  Fixed job submission vtl test

core/db/locator.py:
- TestUsersGuideVTL:
    Sort tests by filename
    Update available packages in case one has been added

gui/job_monitor.py:
  Set up filename even if package is already loaded

Reordered example links so that package installer is first:
  doc/usersguide/job_submission.rst
  doc/usersguide/vtl/jobsubmission1.vtl
  doc/usersguide/vtl/jobsubmission2.vtl
  doc/usersguide/vtl/jobsubmission3.vtl


  Commit: df9bf200d91e8d87a0d02a9eef2845b301137740
      https://github.com/VisTrails/VisTrails/commit/df9bf200d91e8d87a0d02a9eef2845b301137740
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-09-18 (Fri, 18 Sep 2015)

  Changed paths:
    M CHANGELOG

  Log Message:
  -----------
  Updated CHANGELOG


  Commit: 5667d285c8a02fb7d3268f9d86c6fdf46d436d1d
      https://github.com/VisTrails/VisTrails/commit/5667d285c8a02fb7d3268f9d86c6fdf46d436d1d
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-09-21 (Mon, 21 Sep 2015)

  Changed paths:
    M CHANGELOG
    M doc/usersguide/conf.py
    M scripts/create_release_wiki_table.py
    M scripts/dist/common/splash/splash.svg
    M scripts/dist/mac/setup.py
    M scripts/dist/source/make-vistrails-src-build.py
    M scripts/dist/windows/vistrails-gdal.iss
    M scripts/dist/windows/vistrails.iss
    M scripts/dist/windows/vistrailsx64-gdal.iss
    M scripts/dist/windows/vistrailsx64.iss
    M setup.py
    M vistrails/core/system/__init__.py
    M vistrails/gui/resources/images/vistrails_splash.png

  Log Message:
  -----------
  Updated version number to 2.2.3


  Commit: 9bd6e055e3e29c4a4af78867468a3c57bed29a0e
      https://github.com/VisTrails/VisTrails/commit/9bd6e055e3e29c4a4af78867468a3c57bed29a0e
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-09-21 (Mon, 21 Sep 2015)

  Changed paths:
    M scripts/dist/mac/setup.py

  Log Message:
  -----------
  Added pymongo dependency to Mac installer


  Commit: 02ad04a622c4b9fd438c0f5b87f101bdc31f8aa6
      https://github.com/VisTrails/VisTrails/commit/02ad04a622c4b9fd438c0f5b87f101bdc31f8aa6
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-09-21 (Mon, 21 Sep 2015)

  Changed paths:
    M scripts/dist/mac/make_app

  Log Message:
  -----------
  Updated ALPS version in Mac installer to 2.2.b5


  Commit: 1e47bcccd2ffb3fd630a41de83933956494a65c7
      https://github.com/VisTrails/VisTrails/commit/1e47bcccd2ffb3fd630a41de83933956494a65c7
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-09-22 (Tue, 22 Sep 2015)

  Changed paths:
    M CHANGELOG

  Log Message:
  -----------
  Set release name in CHANGELOG


  Commit: 610eb6b47251f1873cb69d86ab9e33331356257e
      https://github.com/VisTrails/VisTrails/commit/610eb6b47251f1873cb69d86ab9e33331356257e
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-09-22 (Tue, 22 Sep 2015)

  Changed paths:
    M scripts/dist/conda/vistrails/meta.yaml

  Log Message:
  -----------
  Add file_archive to Conda package requirements


  Commit: 8ee6a633d7512842790377e4aac891e8804c593f
      https://github.com/VisTrails/VisTrails/commit/8ee6a633d7512842790377e4aac891e8804c593f
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-09-23 (Wed, 23 Sep 2015)

  Changed paths:
    M vistrails/packages/gmaps/gmap_cell.py

  Log Message:
  -----------
  Fix sizing of map in GMapCellWidget


  Commit: 5f7c2abf113b0370e41277ac2f28eec1f3b70430
      https://github.com/VisTrails/VisTrails/commit/5f7c2abf113b0370e41277ac2f28eec1f3b70430
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-09-23 (Wed, 23 Sep 2015)

  Changed paths:
    M vistrails/packages/gmaps/gmap_cell.py

  Log Message:
  -----------
  Use 'vh' for map height, for good measure


  Commit: 19e5bb21e1d810614487cd8a0c2d7d980422ccd7
      https://github.com/VisTrails/VisTrails/commit/19e5bb21e1d810614487cd8a0c2d7d980422ccd7
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-09-23 (Wed, 23 Sep 2015)

  Changed paths:
    M vistrails/gui/paramexplore/pe_tab.py
    M vistrails/packages/vtk/init.py

  Log Message:
  -----------
  Remove unused imports of get_vistrails_default_pkg_prefix


  Commit: ebd598ab121a6554e0bb8362372038bca94ec7ce
      https://github.com/VisTrails/VisTrails/commit/ebd598ab121a6554e0bb8362372038bca94ec7ce
  Author: Remi Rampin <remirampin at gmail.com>
  Date:   2015-09-23 (Wed, 23 Sep 2015)

  Changed paths:
    M scripts/dist/README.md

  Log Message:
  -----------
  Update the dist README


  Commit: 11db25b3f6be66c877c6c7705cf9e2ebc1bf5d32
      https://github.com/VisTrails/VisTrails/commit/11db25b3f6be66c877c6c7705cf9e2ebc1bf5d32
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-10-07 (Wed, 07 Oct 2015)

  Changed paths:
    M vistrails/core/modules/vistrails_module.py

  Log Message:
  -----------
  get_input: Do not convert lists if it can be avoided

core/modules/vistrails_module.py:
 - get_input:
   Only merge lists if there are more than one.

Fixes #1132


  Commit: fa323b45604c34225c8276eb9034b15cd04c4a54
      https://github.com/VisTrails/VisTrails/commit/fa323b45604c34225c8276eb9034b15cd04c4a54
  Author: Tommy Ellqvist <tommy.ellqvist at nyu.edu>
  Date:   2015-10-20 (Tue, 20 Oct 2015)

  Changed paths:
    A .dockerignore
    M .travis.yml
    M CHANGELOG
    A Dockerfile
    M LICENSE
    A MANIFEST.in
    M Vagrantfile
    R doc/coding_conventions.txt
    R doc/module_registry.txt
    R doc/package_system.txt
    R doc/pep-0008.txt
    R doc/pep-0257.txt
    R doc/signal_mess.txt
    R doc/source_tree_overview.tex
    M doc/usersguide/conf.py
    M doc/usersguide/developer.rst
    M doc/usersguide/example.rst
    M doc/usersguide/example_guide.rst
    A doc/usersguide/figures/job_submission/job_monitor.png
    A doc/usersguide/figures/tej/pipeline.png
    A doc/usersguide/job_submission.rst
    A doc/usersguide/tej.rst
    M doc/usersguide/vtl/README
    A doc/usersguide/vtl/jobsubmission1.vtl
    A doc/usersguide/vtl/jobsubmission2.vtl
    A doc/usersguide/vtl/jobsubmission3.vtl
    M doc/usersguide/vtl/mashups1.vtl
    A doc/usersguide/vtl/tej-primes.vtl
    A examples-internal/broken/errors.vt
    A examples-internal/broken/invalid-package.xml
    A examples-internal/broken/too-recent.xml
    A examples/api/brain_output.xml
    A examples/api/imagemagick.vt
    A examples/api/ipython-notebook.ipynb
    A examples/api/out_html.xml
    A examples/api/outputs.vt
    A examples/api/simplemath.vt
    A examples/api/table.xml
    A examples/api/vistrails_logo.png
    M examples/list-handling.vt
    M examples/matplotlib/Acorr_ex8.vt
    M examples/matplotlib/Arrow_ex9.vt
    M examples/matplotlib/Psd.vt
    M examples/matplotlib/annotate.vt
    M examples/matplotlib/axhspan_ex5.vt
    M examples/matplotlib/bar_ex1.vt
    M examples/matplotlib/cohere.vt
    M examples/matplotlib/contourf.vt
    M examples/matplotlib/hist_ex1.vt
    M examples/matplotlib/line2d_ex4.vt
    M examples/matplotlib/line2d_ex7.vt
    M examples/matplotlib/lineplot_ex3.vt
    M examples/matplotlib/pcolor.vt
    M examples/matplotlib/pie_ex1.vt
    M examples/matplotlib/polar_ex10.vt
    M examples/matplotlib/scatter.vt
    M examples/matplotlib/semilog.vt
    A examples/mongodb.vt
    R examples/scripting/README
    R examples/scripting/brain_from_script.vt
    R examples/scripting/brain_script.py
    R examples/scripting/combined_script.py
    R examples/scripting/vtk_book_3rd_p189_script.py
    A examples/tej-primes.vt
    M examples/terminator.vt
    M examples/usersguide/cfassistant.vt
    A examples/usersguide/job_submission.vt
    M examples/usersguide/mashups.vt
    M examples/usersguide/parameter_exploration.vt
    M extensions/latex/head.pdf
    M extensions/latex/head.tex
    M extensions/latex/head.vt
    M extensions/latex/includevistrail.py
    A extensions/latex/test.sh
    M requirements.txt
    M scripts/add_future_import.py
    M scripts/create_release_wiki_table.py
    M scripts/create_server_media_dir_structure.py
    M scripts/dist/README.md
    A scripts/dist/common/disclaimer.svg
    M scripts/dist/common/prepare_release.py
    M scripts/dist/common/set_version.py
    M scripts/dist/common/splash/splash.svg
    M scripts/dist/conda/conda.sh
    M scripts/dist/conda/vistrails/meta.yaml
    M scripts/dist/mac/Input/CLToolsWizard.command
    M scripts/dist/mac/Input/VisTrails.command
    M scripts/dist/mac/make_app
    M scripts/dist/mac/setup.py
    M scripts/dist/mac/setup_itk.py
    A scripts/dist/man/vistrails.1
    M scripts/dist/source/make-vistrails-src-build.py
    M scripts/dist/windows/Input/runvistrails.py
    M scripts/dist/windows/common1.iss
    M scripts/dist/windows/common2.iss
    M scripts/dist/windows/vistrails-gdal.iss
    M scripts/dist/windows/vistrails.iss
    M scripts/dist/windows/vistrailsx64-gdal.iss
    M scripts/dist/windows/vistrailsx64.iss
    M scripts/gen_vtk_examples/check_diffs.py
    M scripts/gen_vtk_examples/convert_to_vt.py
    M scripts/gen_vtk_examples/copy_vtk_examples.py
    M scripts/gen_vtk_examples/gen_vtk_examples.py
    M scripts/gen_vtk_examples/get_vtk_examples.py
    M scripts/get_usersguide.py
    M scripts/mac_update_bin.sh
    M scripts/opm/opm2dot.py
    M scripts/restart-vistrails-server.sh
    M scripts/retarget_mpl_libs.sh
    M scripts/run_vistrails_batch_xvfb.sh
    M scripts/start_vistrails.sh
    M scripts/start_vistrails_xvfb.sh
    M scripts/unzip_vistrail.sh
    M scripts/update_copyright_year.py
    M scripts/update_email_contact.py
    M scripts/update_to_mod_bsd_license.py
    M scripts/win_update_bin.sh
    M setup.py
    M vistrails/api/__init__.py
    M vistrails/core/api.py
    M vistrails/core/application.py
    M vistrails/core/bundles/pyimport.py
    M vistrails/core/configuration.py
    M vistrails/core/console_mode.py
    M vistrails/core/data_structures/graph.py
    M vistrails/core/db/locator.py
    M vistrails/core/debug.py
    M vistrails/core/inspector.py
    M vistrails/core/interpreter/cached.py
    M vistrails/core/layout/tree_layout.py
    M vistrails/core/layout/version_tree_layout.py
    M vistrails/core/log/controller.py
    M vistrails/core/mashup/action.py
    M vistrails/core/mashup/action_annotation.py
    M vistrails/core/modules/abstraction.py
    M vistrails/core/modules/basic_modules.py
    M vistrails/core/modules/module_registry.py
    M vistrails/core/modules/output_modules.py
    M vistrails/core/modules/package.py
    M vistrails/core/modules/sub_module.py
    M vistrails/core/modules/utils.py
    M vistrails/core/modules/vistrails_module.py
    M vistrails/core/packagemanager.py
    M vistrails/core/resources/default_vistrails_startup_xml
    M vistrails/core/startup.py
    M vistrails/core/system/__init__.py
    M vistrails/core/system/osx.py
    M vistrails/core/thumbnails.py
    M vistrails/core/upgradeworkflow.py
    M vistrails/core/utils/__init__.py
    M vistrails/core/vistrail/connection.py
    M vistrails/core/vistrail/controller.py
    M vistrails/core/vistrail/job.py
    M vistrails/core/vistrail/module.py
    M vistrails/core/vistrail/pipeline.py
    M vistrails/core/vistrail/vistrail.py
    M vistrails/core/wrapper/common.py
    M vistrails/core/wrapper/pythonclass.py
    M vistrails/db/bin/templates/sql_schema.sql.mako
    M vistrails/db/services/io.py
    M vistrails/db/services/locator.py
    M vistrails/db/services/opm.py
    M vistrails/db/services/prov.py
    M vistrails/db/services/vistrail.py
    R vistrails/db/versions/v0_8_1/schemas/sql/vistrails.sql.bkp
    M vistrails/db/versions/v1_0_2/persistence/sql/sql_dao.py
    M vistrails/db/versions/v1_0_3/persistence/sql/sql_dao.py
    M vistrails/db/versions/v1_0_4/persistence/sql/sql_dao.py
    M vistrails/db/versions/v1_0_4/translate/v1_0_3.py
    M vistrails/gui/application.py
    M vistrails/gui/bundles/installbundle.py
    M vistrails/gui/collection/workspace.py
    M vistrails/gui/job_monitor.py
    M vistrails/gui/mashups/mashup_app.py
    M vistrails/gui/mashups/mashups_manager.py
    M vistrails/gui/mashups/mashups_widgets.py
    M vistrails/gui/module_palette.py
    M vistrails/gui/modules/list_configuration.py
    M vistrails/gui/modules/output_configuration.py
    M vistrails/gui/modules/python_source_configure.py
    R vistrails/gui/modules/resources/__init__.py
    R vistrails/gui/modules/resources/colorconfig.qrc
    R vistrails/gui/modules/resources/colorconfig_rc.py
    R vistrails/gui/modules/resources/colorwheel.png
    M vistrails/gui/modules/source_configure.py
    M vistrails/gui/modules/string_configure.py
    M vistrails/gui/modules/stringformat_configuration.py
    M vistrails/gui/paramexplore/pe_tab.py
    M vistrails/gui/paramexplore/virtual_cell.py
    M vistrails/gui/pipeline_view.py
    M vistrails/gui/preferences.py
    M vistrails/gui/resources/images/disclaimer.png
    M vistrails/gui/resources/images/vistrails_splash.png
    M vistrails/gui/shell.py
    M vistrails/gui/version_prop.py
    M vistrails/gui/version_view.py
    M vistrails/gui/vistrail_controller.py
    M vistrails/gui/vistrails_window.py
    M vistrails/packages/CLTools/identifiers.py
    M vistrails/packages/CLTools/init.py
    M vistrails/packages/CLTools/wizard.py
    M vistrails/packages/SUDSWebServices/init.py
    M vistrails/packages/URL/http_directory.py
    M vistrails/packages/URL/https.py
    M vistrails/packages/URL/https_if_available.py
    M vistrails/packages/controlflow/looping.py
    M vistrails/packages/dialogs/continue_prompt.py
    M vistrails/packages/gmaps/__init__.py
    M vistrails/packages/gmaps/gmap_cell.py
    M vistrails/packages/gmaps/identifiers.py
    M vistrails/packages/gmaps/init.py
    M vistrails/packages/gmaps/utils.py
    M vistrails/packages/gmaps/vis.py
    M vistrails/packages/matplotlib/__init__.py
    M vistrails/packages/matplotlib/bases.py
    M vistrails/packages/matplotlib/diff.py
    M vistrails/packages/matplotlib/figure_cell.py
    M vistrails/packages/matplotlib/generate.py
    M vistrails/packages/matplotlib/identifiers.py
    M vistrails/packages/matplotlib/init.py
    M vistrails/packages/matplotlib/mixins.py
    M vistrails/packages/matplotlib/parse.py
    M vistrails/packages/matplotlib/specs.py
    M vistrails/packages/matplotlib/widgets.py
    A vistrails/packages/mongodb/Vagrantfile
    A vistrails/packages/mongodb/__init__.py
    A vistrails/packages/mongodb/init.py
    M vistrails/packages/parallelflow/__init__.py
    M vistrails/packages/parallelflow/api.py
    M vistrails/packages/parallelflow/engine_manager.py
    M vistrails/packages/parallelflow/init.py
    M vistrails/packages/parallelflow/map.py
    M vistrails/packages/persistent_archive/__init__.py
    M vistrails/packages/persistent_archive/cache.py
    M vistrails/packages/persistent_archive/common.py
    M vistrails/packages/persistent_archive/identifiers.py
    M vistrails/packages/persistent_archive/init.py
    M vistrails/packages/persistent_archive/persistedinput.py
    M vistrails/packages/persistent_archive/persistedoutput.py
    M vistrails/packages/persistent_archive/queriedinput.py
    M vistrails/packages/persistent_archive/queries.py
    M vistrails/packages/persistent_archive/ui.py
    M vistrails/packages/persistent_archive/widgets.py
    A vistrails/packages/reprounzip/__init__.py
    A vistrails/packages/reprounzip/init.py
    M vistrails/packages/sklearn/__init__.py
    M vistrails/packages/sklearn/init.py
    M vistrails/packages/sklearn/tests.py
    M vistrails/packages/spreadsheet/basic_widgets.py
    M vistrails/packages/spreadsheet/celltoolbar.qrc
    M vistrails/packages/spreadsheet/celltoolbar_rc.py
    M vistrails/packages/spreadsheet/identifiers.py
    A vistrails/packages/spreadsheet/images/equal-sizes.png
    A vistrails/packages/spreadsheet/images/new-window.png
    M vistrails/packages/spreadsheet/init.py
    M vistrails/packages/spreadsheet/spreadsheet_cell.py
    M vistrails/packages/spreadsheet/spreadsheet_controller.py
    M vistrails/packages/spreadsheet/spreadsheet_execute.py
    M vistrails/packages/spreadsheet/spreadsheet_sheet.py
    M vistrails/packages/spreadsheet/spreadsheet_tab.py
    M vistrails/packages/spreadsheet/widgets/imageviewer/__init__.py
    M vistrails/packages/spreadsheet/widgets/imageviewer/imageviewer.py
    M vistrails/packages/spreadsheet/widgets/richtext/richtext.py
    M vistrails/packages/spreadsheet/widgets/webview/webview.py
    M vistrails/packages/sql/widgets.py
    M vistrails/packages/tabledata/__init__.py
    M vistrails/packages/tabledata/common.py
    M vistrails/packages/tabledata/convert/__init__.py
    M vistrails/packages/tabledata/convert/convert_dates.py
    A vistrails/packages/tabledata/convert/convert_numpy.py
    M vistrails/packages/tabledata/identifiers.py
    M vistrails/packages/tabledata/init.py
    M vistrails/packages/tabledata/operations.py
    M vistrails/packages/tabledata/read/__init__.py
    A vistrails/packages/tabledata/read/convert.py
    M vistrails/packages/tabledata/read/read_csv.py
    M vistrails/packages/tabledata/read/read_excel.py
    M vistrails/packages/tabledata/read/read_json.py
    M vistrails/packages/tabledata/read/read_numpy.py
    M vistrails/packages/tabledata/viewer.py
    M vistrails/packages/tabledata/widgets.py
    M vistrails/packages/tabledata/write/__init__.py
    M vistrails/packages/tabledata/write/write_csv.py
    M vistrails/packages/tabledata/write/write_excel.py
    M vistrails/packages/tabledata/write/write_numpy.py
    A vistrails/packages/tej/__init__.py
    A vistrails/packages/tej/init.py
    A vistrails/packages/tej/widgets.py
    M vistrails/packages/vtk/identifiers.py
    M vistrails/packages/vtk/init.py
    M vistrails/packages/vtk/offscreen.py
    M vistrails/packages/vtk/tf_widget.py
    M vistrails/packages/vtk/vtk_wrapper/__init__.py
    M vistrails/packages/vtk/vtk_wrapper/class_tree.py
    M vistrails/packages/vtk/vtk_wrapper/parse.py
    M vistrails/packages/vtk/vtk_wrapper/vtk_classes.py
    M vistrails/packages/vtk/vtk_wrapper/vtk_module.py
    M vistrails/packages/vtk/vtk_wrapper/vtk_parser.py
    M vistrails/packages/vtk/vtkcell.py
    M vistrails/run.py
    A vistrails/tests/resources/jobs.vt
    A vistrails/tests/resources/myjob.py
    A vistrails/tests/resources/test_upgrades_layout/__init__.py
    A vistrails/tests/resources/test_upgrades_layout/init.py
    A vistrails/tests/resources/upgrades1.xml
    A vistrails/tests/resources/upgrades2.xml
    M vistrails/tests/runtestsuite.py
    M vistrails/tests/utils.py

  Log Message:
  -----------
  Merge branch 'v2.2' into python-wrapper

Conflicts:
	vistrails/packages/vtk/init.py
	vistrails/packages/vtk/vtk_wrapper/specs.py


Compare: https://github.com/VisTrails/VisTrails/compare/e2a4281c26a0...fa323b45604c


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