[vistrails-dev] [GIT] VisTrails:

git-noreply at vistrails.org git-noreply at vistrails.org
Mon Jan 6 10:27:18 EST 2014


The project "VisTrails":

The branch, dont-use-modules-as-data has been updated
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- Log -----------------------------------------------------------------
commit 8a3d2deb51a69b7fdd1acc330caf34c404951403
Merge: 6df797f 6ea1106
Author: Remi Rampin <remirampin at gmail.com>
Date:   Mon Jan 6 10:24:25 2014 -0500

Merge branch 'master' into 'dont-use-modules-as-data'

Conflicts:
vistrails/core/modules/basic_modules.py
vistrails/core/modules/module_utils.py
vistrails/packages/HTTP/init.py
vistrails/packages/persistence/init.py
vistrails/packages/rpy/init.py
vistrails/packages/spreadsheet/basic_widgets.py
vistrails/packages/tabledata/read/read_csv.py
vistrails/packages/vtk/base_module.py
vistrails/packages/vtk/inspectors.py
vistrails/packages/vtk/tf_widget.py

-----------------------------------------------------------------------

Summary of changes:
 README.md                                          |    2 +-
 contrib/NumSciPy/ArrayAccess.py                    |  104 +-
 contrib/NumSciPy/ArrayConvert.py                   |   40 +-
 contrib/NumSciPy/ArrayIO.py                        |   62 +-
 contrib/NumSciPy/ArrayInterpolate.py               |   38 +-
 contrib/NumSciPy/ArrayOperations.py                |  208 +-
 contrib/NumSciPy/ArrayPlot.py                      |  144 +-
 contrib/NumSciPy/ArrayUtilities.py                 |   48 +-
 contrib/NumSciPy/DSP.py                            |   62 +-
 contrib/NumSciPy/EnsembleOrdering.py               |   36 +-
 contrib/NumSciPy/Filters.py                        |   56 +-
 contrib/NumSciPy/Imaging.py                        |   52 +-
 contrib/NumSciPy/Matrix.py                         |   14 +-
 contrib/NumSciPy/MatrixUtilities.py                |   20 +-
 contrib/NumSciPy/Stockwell.py                      |  126 +-
 contrib/ParaView/PVBase.py                         |    6 +-
 contrib/ParaView/init.py                           |   10 +-
 contrib/ParaView/pvcell.py                         |    2 +-
 contrib/SCIRun/__init__.py                         | 6734 ++++++++++----------
 contrib/SCIRun/cm2viewcell.py                      |    2 +-
 contrib/SCIRun/viewercell.py                       |    2 +-
 contrib/SciPy/DSP.py                               |   42 +-
 contrib/SciPy/Filters.py                           |   56 +-
 contrib/SciPy/MatlabReader.py                      |    8 +-
 contrib/SciPy/MatrixConvert.py                     |   24 +-
 contrib/SciPy/MatrixInfo.py                        |    4 +-
 contrib/SciPy/MatrixOperations.py                  |   66 +-
 contrib/TetGenBridge/CreateTestSurf.py             |    2 +-
 contrib/TetGenBridge/__init__.py                   |   10 +-
 contrib/cdat/__init__.py                           | 6486 ++++++++++----------
 contrib/cdat/cdat_cell.py                          |   92 +-
 contrib/cdat/quickplot.py                          |   16 +-
 contrib/cdat/scripts/cdat_domain.py                |   24 +-
 contrib/cdat/scripts/gen_init.py                   |   38 +-
 contrib/cdat/scripts/old_cdat_init.py              |  234 +-
 contrib/edu_utah_sci_cscheid_macet/__init__.py     |   20 +-
 contrib/edu_utah_sci_cscheid_metro/__init__.py     |   20 +-
 contrib/edu_utah_sci_cscheid_teem/__init__.py      |  196 +-
 .../edu_utah_sci_eranders_proteindatabank/PDB.py   |   34 +-
 contrib/edu_utah_sci_vgc_afront/__init__.py        |   38 +-
 contrib/itk/FeatureExtractionFilters.py            |   66 +-
 contrib/itk/GradientFilters.py                     |   20 +-
 contrib/itk/ITK.py                                 |   40 +-
 contrib/itk/Image.py                               |    8 +-
 contrib/itk/ImageReader.py                         |   44 +-
 contrib/itk/IntensityFilters.py                    |  120 +-
 contrib/itk/NeighborhoodFilters.py                 |   64 +-
 contrib/itk/PixelType.py                           |    8 +-
 contrib/itk/SegmentationFilters.py                 |  130 +-
 contrib/itk/SelectionFilters.py                    |   84 +-
 contrib/itk/SmoothingFilters.py                    |  190 +-
 contrib/itk/ThresholdFilters.py                    |   34 +-
 contrib/itk/filter_generator.py                    |   28 +-
 contrib/meshutils.py                               |   20 +-
 contrib/mobile/__init__.py                         |   74 +-
 contrib/pc3/__init__.py                            |  178 +-
 contrib/poissonrecon.py                            |   16 +-
 contrib/provenance/__init__.py                     |   40 +-
 contrib/provenance2/__init__.py                    |   66 +-
 contrib/sahm/SahmOutputViewer.py                   |   12 +-
 contrib/sahm/SahmSpatialOutputViewer.py            |   10 +-
 contrib/sahm/init.py                               |  220 +-
 contrib/sahm/utils.py                              |    8 +-
 contrib/stem/init.py                               |  134 +-
 contrib/titan/base_module.py                       |  404 +-
 contrib/titan/init.py                              |   10 +-
 contrib/titan/inspectors.py                        |  460 +-
 contrib/titan/offscreen.py                         |  120 +-
 contrib/titan/tf_widget.py                         | 1148 ++--
 contrib/titan/vtkcell.py                           | 2186 ++++----
 contrib/titan/vtkhandler.py                        |  578 +-
 contrib/titan/vtkviewcell.py                       |    2 +-
 contrib/trimesh2.py                                |   24 +-
 contrib/vtksnl/base_module.py                      |  404 +-
 contrib/vtksnl/init.py                             |   10 +-
 contrib/vtksnl/inspectors.py                       |  460 +-
 contrib/vtksnl/offscreen.py                        |  122 +-
 contrib/vtksnl/tf_widget.py                        | 1148 ++--
 contrib/vtksnl/vtkcell.py                          | 2186 ++++----
 contrib/vtksnl/vtkhandler.py                       |  580 +-
 contrib/vtksnl/vtkviewcell.py                      |    2 +-
 dist/common/splash/splash.svg                      |   26 +-
 dist/mac/Input/README                              |   50 +-
 dist/mac/make_app                                  |    2 +-
 dist/source/make-vistrails-src-release.py          |    2 +-
 dist/windows/Input/releaseNotes.txt                |   50 +-
 dist/windows/Input/runvistrails.py                 |    9 +-
 doc/usersguide/Makefile                            |    2 +-
 doc/usersguide/_static/mystyle.css                 |    6 +-
 doc/usersguide/api_documentation.rst               |  118 +
 doc/usersguide/conf.py                             |    2 +
 doc/usersguide/controlflow.rst                     |    2 +-
 doc/usersguide/creating.rst                        |    4 +-
 doc/usersguide/developer.rst                       |    1 +
 doc/usersguide/example.rst                         |    2 +-
 doc/usersguide/example_webservices.rst             |    4 +-
 .../figures/creating/module_configuration.png      |  Bin 14125 -> 0 bytes
 .../figures/packages/CustomColorShape1.png         |  Bin 24759 -> 0 bytes
 .../figures/packages/CustomColorShape2.png         |  Bin 37161 -> 0 bytes
 .../figures/packages/CustomColorShape3.png         |  Bin 21399 -> 0 bytes
 doc/usersguide/figures/packages/fancy_module1.png  |  Bin 0 -> 2787 bytes
 doc/usersguide/figures/packages/fancy_module2.png  |  Bin 0 -> 3787 bytes
 doc/usersguide/figures/packages/fancy_module3.png  |  Bin 0 -> 3862 bytes
 doc/usersguide/figures/packages/fancy_ports.png    |  Bin 0 -> 3479 bytes
 doc/usersguide/intro.rst                           |   90 +-
 doc/usersguide/intro2.rst                          |   85 -
 doc/usersguide/packages.rst                        | 1155 ++--
 doc/usersguide/preface.rst                         |    4 +-
 doc/usersguide/preliminary.rst                     |    4 -
 doc/usersguide/pythoncalc.rst                      |  287 +-
 doc/usersguide/pythoncalc_file1.rst                |   22 +
 doc/usersguide/vistrails_server.rst                |   15 +-
 examples/brain_vistrail.vt                         |  Bin 192878 -> 0 bytes
 scripts/build_usersguide.py                        |   10 +-
 scripts/create_release_wiki_table.py               |    2 +-
 scripts/generate_pkg_doc.py                        |  145 +
 scripts/release_notes.py                           |    2 +-
 .../{mac_update_bin.sh => retarget_mpl_libs.sh}    |   61 +-
 scripts/update_hash.py                             |   30 +
 vistrails/core/analogy/eigen.py                    |   22 +-
 vistrails/core/api.py                              |   21 +-
 vistrails/core/application.py                      |   24 +-
 vistrails/core/cache/hasher.py                     |   19 +-
 vistrails/core/collection/search.py                |   11 +-
 vistrails/core/collection/thumbnail.py             |    4 +-
 vistrails/core/collection/workflow_exec.py         |   14 +-
 vistrails/core/common.py                           |    1 -
 vistrails/core/configuration.py                    |   14 +-
 vistrails/core/console_mode.py                     |   45 +-
 vistrails/core/data_structures/bijectivedict.py    |   14 +-
 vistrails/core/debug.py                            |   14 +-
 vistrails/core/external_connection.py              |   14 +-
 vistrails/core/interpreter/cached.py               |  494 +-
 vistrails/core/interpreter/job.py                  |  630 ++
 vistrails/core/interpreter/utils.py                |    8 -
 vistrails/core/log/controller.py                   |  505 +-
 vistrails/core/log/log.py                          |   12 -
 vistrails/core/log/loop_exec.py                    |   62 +-
 vistrails/core/log/workflow_exec.py                |   13 +
 vistrails/core/mashup/__init__.py                  |    7 +-
 vistrails/core/mashup/action.py                    |   10 +-
 vistrails/core/mashup/action_annotation.py         |   11 +-
 vistrails/core/modules/basic_modules.py            |  611 +-
 vistrails/core/modules/config.py                   |  536 ++
 vistrails/core/modules/module_descriptor.py        |   23 +
 vistrails/core/modules/module_registry.py          |  530 +-
 vistrails/core/modules/module_utils.py             |   37 +-
 vistrails/core/modules/package.py                  |    9 +-
 vistrails/core/modules/sub_module.py               |  252 +-
 vistrails/core/modules/utils.py                    |   17 +
 vistrails/core/modules/vistrails_module.py         |  530 +-
 vistrails/core/packagemanager.py                   |   22 +-
 vistrails/core/query/version.py                    |   12 +-
 vistrails/core/requirements.py                     |   15 +-
 vistrails/core/startup.py                          |   12 +-
 vistrails/core/system/__init__.py                  |  201 +-
 vistrails/core/system/common.py                    |  134 +
 vistrails/core/system/linux.py                     |  130 +-
 vistrails/core/system/osx.py                       |  164 +-
 vistrails/core/system/unix.py                      |   68 +-
 vistrails/core/system/windows.py                   |  176 +-
 vistrails/core/thumbnails.py                       |   16 +-
 vistrails/core/utils/__init__.py                   |  186 +-
 vistrails/core/utils/lockmethod.py                 |   99 -
 vistrails/core/vistrail/action.py                  |   24 +-
 vistrails/core/vistrail/connection.py              |    2 +-
 vistrails/core/vistrail/controller.py              |   34 +-
 vistrails/core/vistrail/pipeline.py                |    2 +-
 vistrails/core/vistrail/vistrail.py                |    1 -
 vistrails/db/domain/__init__.py                    |    1 +
 vistrails/db/persistence/__init__.py               |    1 +
 vistrails/db/services/io.py                        |   27 +-
 vistrails/db/services/locator.py                   |   10 +-
 vistrails/db/services/opm.py                       |    2 -
 vistrails/db/services/prov.py                      |    1 -
 vistrails/db/specs/all.xml                         |  110 +-
 vistrails/db/tests/setup_db_tables.py              |    2 -
 .../db/versions/v0_3_0/persistence/xml/xml_dao.py  |    9 +-
 .../db/versions/v0_5_0/persistence/sql/sql_dao.py  |   11 +-
 .../db/versions/v0_5_0/persistence/xml/xml_dao.py  |    9 +-
 vistrails/db/versions/v0_5_0/translate/v0_3_1.py   |    4 +-
 .../db/versions/v0_6_0/persistence/sql/sql_dao.py  |   11 +-
 .../db/versions/v0_6_0/persistence/xml/xml_dao.py  |    9 +-
 vistrails/db/versions/v0_6_0/translate/v0_3_1.py   |    7 +-
 .../db/versions/v0_7_0/persistence/sql/sql_dao.py  |   11 +-
 .../db/versions/v0_7_0/persistence/xml/xml_dao.py  |    9 +-
 .../db/versions/v0_8_0/persistence/sql/sql_dao.py  |   11 +-
 .../db/versions/v0_8_0/persistence/xml/xml_dao.py  |   10 +-
 .../db/versions/v0_9_0/persistence/sql/sql_dao.py  |   11 +-
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 .../db/versions/v0_9_1/persistence/sql/sql_dao.py  |   11 +-
 .../db/versions/v0_9_1/persistence/xml/xml_dao.py  |    9 +-
 .../db/versions/v0_9_3/persistence/sql/sql_dao.py  |   10 +-
 .../db/versions/v0_9_3/persistence/xml/xml_dao.py  |    9 +-
 .../db/versions/v0_9_4/persistence/sql/sql_dao.py  |   10 +-
 .../db/versions/v0_9_4/persistence/xml/xml_dao.py  |    9 +-
 .../db/versions/v0_9_5/persistence/sql/sql_dao.py  |   10 +-
 .../db/versions/v0_9_5/persistence/xml/xml_dao.py  |    9 +-
 .../db/versions/v1_0_0/persistence/sql/sql_dao.py  |   10 +-
 .../db/versions/v1_0_0/persistence/xml/xml_dao.py  |    9 +-
 .../db/versions/v1_0_1/persistence/sql/sql_dao.py  |   10 +-
 .../db/versions/v1_0_1/persistence/xml/xml_dao.py  |    9 +-
 .../db/versions/v1_0_2/persistence/sql/sql_dao.py  |   12 +-
 .../db/versions/v1_0_2/persistence/xml/xml_dao.py  |    9 +-
 vistrails/db/versions/v1_0_3/domain/auto_gen.py    |  892 ++-
 .../db/versions/v1_0_3/persistence/sql/auto_gen.py |  382 +-
 .../db/versions/v1_0_3/persistence/sql/sql_dao.py  |   12 +-
 .../db/versions/v1_0_3/persistence/xml/auto_gen.py |  273 +-
 .../db/versions/v1_0_3/persistence/xml/xml_dao.py  |    9 +-
 .../db/versions/v1_0_3/schemas/sql/vistrails.sql   |   19 +-
 .../versions/v1_0_3/schemas/sql/vistrails_drop.sql |    2 +-
 vistrails/db/versions/v1_0_3/schemas/xml/log.xsd   |   26 +-
 vistrails/db/versions/v1_0_3/specs/all.xml         |  110 +-
 vistrails/gui/application.py                       |  206 +-
 vistrails/gui/application_server.py                |   10 +-
 vistrails/gui/bundles/installbundle.py             |    6 +-
 vistrails/gui/bundles/utils.py                     |   18 +-
 vistrails/gui/collection/vis_log.py                |   16 +-
 vistrails/gui/collection/workspace.py              |  150 +-
 vistrails/gui/controlflow_assist.py                |   12 +-
 vistrails/gui/debug.py                             |   11 -
 vistrails/gui/debugger.py                          |    2 +-
 vistrails/gui/job_monitor.py                       |  458 +-
 vistrails/gui/mashups/alias_inspector.py           |   10 +-
 vistrails/gui/mashups/mashup_app.py                |    6 +-
 vistrails/gui/mashups/mashup_view.py               |    9 +-
 vistrails/gui/mashups/mashups_manager.py           |   14 +-
 vistrails/gui/mashups/mashups_widgets.py           |    2 +-
 vistrails/gui/modules/__init__.py                  |   29 +-
 vistrails/gui/modules/constant_configuration.py    |  570 +--
 vistrails/gui/modules/paramexplore.py              |   19 +-
 vistrails/gui/modules/utils.py                     |   93 +
 vistrails/gui/paramexplore/pe_tab.py               |    5 +-
 vistrails/gui/paramexplore/pe_table.py             |    6 +-
 vistrails/gui/paramexplore/virtual_cell.py         |   96 +-
 vistrails/gui/pipeline_view.py                     |  132 +-
 vistrails/gui/ports_pane.py                        |   16 +-
 vistrails/gui/qt.py                                |   36 +-
 vistrails/gui/query_view.py                        |    2 +-
 .../gui/resources/images/vistrails_splash.png      |  Bin 160080 -> 174019 bytes
 vistrails/gui/shell.py                             |   17 +-
 vistrails/gui/variable_dropbox.py                  |    2 +-
 vistrails/gui/version_view.py                      |    2 +-
 vistrails/gui/vistrail_controller.py               |  118 +-
 vistrails/gui/vistrail_view.py                     |   23 +-
 vistrails/gui/vistrails_window.py                  |   79 +-
 vistrails/index/indexworkflow.py                   |    2 +-
 vistrails/index/spec_io.py                         |    8 +-
 vistrails/packages/CLTools/init.py                 |  129 +-
 vistrails/packages/HTTP/init.py                    |   50 +-
 vistrails/packages/ImageMagick/init.py             |   93 +-
 vistrails/packages/JobSubmission/init.py           |   34 +-
 vistrails/packages/JobSubmission/machine.py        |    6 +-
 vistrails/packages/SUDSWebServices/init.py         |   46 +-
 vistrails/packages/analytics/init.py               |   20 +-
 vistrails/packages/controlflow/conditional.py      |  107 +-
 vistrails/packages/controlflow/fold.py             |  113 +-
 vistrails/packages/controlflow/looping.py          |  156 +-
 vistrails/packages/controlflow/order.py            |   49 +-
 vistrails/packages/controlflow/products.py         |  101 +-
 vistrails/packages/controlflow/utils.py            |  149 +
 vistrails/packages/dialogs/init.py                 |   16 +-
 vistrails/packages/matplotlib/artists.py           | 2052 +++---
 .../packages/matplotlib/artists_template.py.mako   |   28 +-
 vistrails/packages/matplotlib/bases.py             |  195 +-
 vistrails/packages/matplotlib/figure_cell.py       |    4 +-
 vistrails/packages/matplotlib/identifiers.py       |    2 +-
 vistrails/packages/matplotlib/mixins.py            |   10 +-
 vistrails/packages/matplotlib/mpl_plots.xml        |  473 +-
 vistrails/packages/matplotlib/mpl_plots_diff.xml   |  273 +-
 vistrails/packages/matplotlib/mpl_plots_raw.xml    |  524 +-
 vistrails/packages/matplotlib/parse.py             |   79 +-
 vistrails/packages/matplotlib/plots.py             | 2641 ++++----
 .../packages/matplotlib/plots_template.py.mako     |   29 +-
 vistrails/packages/parallelflow/map.py             |   39 +-
 vistrails/packages/persistence/init.py             |   82 +-
 vistrails/packages/pythonCalc/__init__.py          |    2 +-
 vistrails/packages/pythonCalc/init.py              |   74 +-
 vistrails/packages/qgis/init.py                    |   20 +-
 vistrails/packages/rpy/init.py                     |   62 +-
 vistrails/packages/spreadsheet/basic_widgets.py    |   32 +-
 vistrails/packages/spreadsheet/spreadsheet_cell.py |    3 +-
 .../spreadsheet/widgets/iebrowser/iecell.py        |    8 +-
 .../spreadsheet/widgets/imageviewer/imageviewer.py |    4 +-
 .../spreadsheet/widgets/richtext/richtext.py       |    9 +-
 vistrails/packages/spreadsheet/widgets/svg/svg.py  |    8 +-
 .../spreadsheet/widgets/webview/webview.py         |    8 +-
 vistrails/packages/sql/init.py                     |   30 +-
 vistrails/packages/tabledata/__init__.py           |    5 -
 vistrails/packages/tabledata/common.py             |   20 +-
 .../packages/tabledata/convert/convert_dates.py    |   31 +-
 vistrails/packages/tabledata/identifiers.py        |    2 +-
 vistrails/packages/tabledata/init.py               |   27 +
 vistrails/packages/tabledata/read/__init__.py      |   13 +-
 vistrails/packages/tabledata/read/read_csv.py      |   41 +-
 vistrails/packages/tabledata/read/read_excel.py    |  221 +
 vistrails/packages/tabledata/read/read_numpy.py    |   20 +-
 vistrails/packages/tabledata/test_files/xl.xls     |  Bin 0 -> 23552 bytes
 vistrails/packages/tabledata/viewer.py             |    2 +-
 vistrails/packages/vtk/base_module.py              |   12 +-
 vistrails/packages/vtk/init.py                     |   10 +-
 vistrails/packages/vtk/inspectors.py               |   30 +-
 vistrails/packages/vtk/offscreen.py                |    8 +-
 vistrails/packages/vtk/tf_widget.py                |   33 +-
 vistrails/packages/vtk/vtkcell.py                  |   12 +-
 vistrails/packages/vtk/vtkhandler.py               |    6 +-
 vistrails/packages/vtk/vtkviewcell.py              |    2 +-
 vistrails/packages/vtlcreator/init.py              |   26 +-
 vistrails/packages/webServices/init.py             |   60 +-
 vistrails/run.py                                   |    4 +
 vistrails/tests/resources/console_mode_test.py     |    8 +-
 vistrails/tests/run_on_mac.sh                      |   12 +-
 vistrails/tests/runtestsuite.py                    |   43 +-
 vistrails/tests/utils.py                           |   40 +-
 314 files changed, 25365 insertions(+), 22044 deletions(-)
 create mode 100644 doc/usersguide/api_documentation.rst
 delete mode 100644 doc/usersguide/figures/creating/module_configuration.png
 delete mode 100644 doc/usersguide/figures/packages/CustomColorShape1.png
 delete mode 100644 doc/usersguide/figures/packages/CustomColorShape2.png
 delete mode 100644 doc/usersguide/figures/packages/CustomColorShape3.png
 create mode 100644 doc/usersguide/figures/packages/fancy_module1.png
 create mode 100644 doc/usersguide/figures/packages/fancy_module2.png
 create mode 100644 doc/usersguide/figures/packages/fancy_module3.png
 create mode 100644 doc/usersguide/figures/packages/fancy_ports.png
 delete mode 100644 doc/usersguide/intro2.rst
 delete mode 100644 doc/usersguide/preliminary.rst
 create mode 100644 doc/usersguide/pythoncalc_file1.rst
 delete mode 100644 examples/brain_vistrail.vt
 create mode 100644 scripts/generate_pkg_doc.py
 copy scripts/{mac_update_bin.sh => retarget_mpl_libs.sh} (69%)
 create mode 100755 scripts/update_hash.py
 create mode 100644 vistrails/core/interpreter/job.py
 create mode 100644 vistrails/core/modules/config.py
 create mode 100644 vistrails/core/system/common.py
 delete mode 100644 vistrails/core/utils/lockmethod.py
 create mode 100644 vistrails/gui/modules/utils.py
 create mode 100644 vistrails/packages/tabledata/read/read_excel.py
 create mode 100644 vistrails/packages/tabledata/test_files/xl.xls

-- 
VisTrails
git clone git at vgc.poly.edu:vistrails


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