[vistrails] 05/19: Merge tag 'upstream/2.2.4' into debian/master
Alastair McKinstry
mckinstry at moszumanska.debian.org
Sat Jul 29 14:21:53 UTC 2017
This is an automated email from the git hooks/post-receive script.
mckinstry pushed a commit to branch debian/master
in repository vistrails.
commit 4ee3f43496efeca65d969d86534d64bd1298893a
Merge: 4e47c44 b73e07c
Author: Alastair McKinstry <mckinstry at debian.org>
Date: Tue Sep 13 12:53:46 2016 +0100
Merge tag 'upstream/2.2.4' into debian/master
CHANGELOG | 81 +-
LICENSE | 2 +-
doc/coding_conventions.txt | 149 --
doc/dist/build_from_source_mac.txt | 62 -
doc/dist/build_from_source_windows.txt | 123 --
doc/dist/setup_build_system_mac.txt | 55 -
doc/dist/setup_build_system_windows.txt | 56 -
doc/module_registry.txt | 14 -
doc/package_system.txt | 99 --
doc/pep-0008.txt | 1009 -----------
doc/pep-0257.txt | 328 ----
doc/signal_mess.txt | 49 -
doc/source_tree_overview.tex | 102 --
doc/usersguide/conf.py | 4 +-
doc/usersguide/developer.rst | 1 +
doc/usersguide/example.rst | 1 +
.../figures/job_submission/job_monitor.png | Bin 0 -> 30237 bytes
doc/usersguide/figures/querying/query_vtkActor.png | Bin 55323 -> 0 bytes
.../figures/querying/query_vtkActor90.png | Bin 49397 -> 0 bytes
doc/usersguide/figures/tej/pipeline.png | Bin 0 -> 20704 bytes
doc/usersguide/job_submission.rst | 174 ++
doc/usersguide/latex.rst | 41 +-
doc/usersguide/querying.rst | 27 +-
doc/usersguide/tej.rst | 87 +
doc/usersguide/vtl/jobsubmission1.vtl | 1 +
doc/usersguide/vtl/jobsubmission2.vtl | 1 +
doc/usersguide/vtl/jobsubmission3.vtl | 1 +
doc/usersguide/vtl/mashups1.vtl | 2 +-
doc/usersguide/vtl/tej-primes.vtl | 1 +
examples/api/ipython-notebook.ipynb | 169 +-
examples/api/simplemath.vt | Bin 12437 -> 16760 bytes
examples/list-handling.vt | Bin 2995 -> 2995 bytes
examples/mongodb.vt | Bin 0 -> 143468 bytes
examples/tej-primes.vt | Bin 0 -> 2591 bytes
examples/tensorflow_mandelbrot.vt | Bin 0 -> 262822 bytes
examples/tensorflow_mnist.vt | Bin 0 -> 366488 bytes
examples/usersguide/cfassistant.vt | Bin 32336 -> 32322 bytes
examples/usersguide/job_submission.vt | Bin 0 -> 40320 bytes
examples/usersguide/mashups.vt | Bin 527175 -> 692341 bytes
examples/usersguide/parameter_exploration.vt | Bin 43687 -> 497101 bytes
extensions/http/config.php.sample | 2 +-
extensions/http/get_db_vistrail_list.php | 2 +-
extensions/http/get_vt_xml.php | 2 +-
extensions/http/get_wf_pdf.php | 2 +-
extensions/http/get_wf_xml.php | 2 +-
extensions/http/run_vistrails.php | 2 +-
extensions/latex/crowdlabs.sty | 2 +-
extensions/latex/example.tex | 2 +-
extensions/latex/example2.tex | 36 +
extensions/latex/head.pdf | Bin 133722 -> 388513 bytes
extensions/latex/head.tex | 4 +-
extensions/latex/head.vt | Bin 245975 -> 330755 bytes
extensions/latex/includecrowdlabs.py | 2 +-
extensions/latex/includevistrail.py | 22 +-
extensions/latex/test.sh | 21 +
extensions/latex/vistrails.sty | 2 +-
extensions/mediawiki/download.php | 2 +-
extensions/mediawiki/functions.php | 2 +-
extensions/mediawiki/vistrailsExtension.php | 2 +-
scripts/build_usersguide.py | 2 +-
scripts/convert_files/convert_files.sh | 2 +-
scripts/convert_files/fix_file.py | 2 +-
scripts/create_release_wiki_table.py | 43 +-
scripts/create_server_media_dir_structure.py | 3 +-
scripts/db_utils.py | 2 +-
scripts/delete_from_db.py | 2 +-
scripts/diff_package.py | 2 +-
scripts/extract.py | 2 +-
scripts/force_start_vistrails.py | 2 +-
scripts/force_start_vistrails_nonohup.py | 2 +-
scripts/gen_vtk_examples/check_diffs.py | 3 +-
scripts/gen_vtk_examples/colors.py | 2 +-
scripts/gen_vtk_examples/convert_to_vt.py | 3 +-
scripts/gen_vtk_examples/copy_vtk_examples.py | 3 +-
scripts/gen_vtk_examples/gen_vtk_examples.py | 3 +-
scripts/gen_vtk_examples/get_vtk_examples.py | 3 +-
scripts/gen_vtk_examples/vtk_imposter.py | 2 +-
scripts/gen_vtk_examples/vtk_to_vt.py | 2 +-
scripts/get_usersguide.py | 4 +-
scripts/mac_update_bin.sh | 4 +-
scripts/merge_vistrails.py | 2 +-
scripts/module_appearance/main.py | 2 +-
scripts/module_appearance/module_appearance.py | 2 +-
scripts/opm/opm2dot.py | 3 +-
scripts/release_notes.py | 2 +-
scripts/restart-vistrails-server.sh | 5 +-
scripts/retarget_mpl_libs.sh | 4 +-
scripts/run_vistrails_batch_xvfb.sh | 4 +-
scripts/sql_delete.py | 2 +-
scripts/sql_to_xml.py | 2 +-
scripts/start_vistrails.sh | 4 +-
scripts/start_vistrails_xvfb.sh | 4 +-
scripts/system_info.py | 2 +-
scripts/unzip_vistrail.sh | 4 +-
scripts/update_copyright_year.py | 5 +-
scripts/update_db.py | 4 +-
scripts/update_email_contact.py | 38 +-
scripts/update_to_mod_bsd_license.py | 3 +-
scripts/update_vistrails_command.py | 2 +-
scripts/watch_vistrail_servers.py | 2 +-
scripts/win_update_bin.sh | 4 +-
vistrails/__init__.py | 2 +-
vistrails/api/__init__.py | 4 +-
vistrails/core/__init__.py | 2 +-
vistrails/core/analogy/__init__.py | 2 +-
vistrails/core/analogy/eigen.py | 2 +-
vistrails/core/analogy/pipeline_utils.py | 2 +-
vistrails/core/api.py | 57 +-
vistrails/core/application.py | 15 +-
vistrails/core/bundles/__init__.py | 2 +-
vistrails/core/bundles/installbundle.py | 2 +-
vistrails/core/bundles/pyimport.py | 5 +-
vistrails/core/cache/__init__.py | 2 +-
vistrails/core/cache/hasher.py | 46 +-
vistrails/core/cache/utils.py | 2 +-
vistrails/core/collection/__init__.py | 2 +-
vistrails/core/collection/entity.py | 2 +-
vistrails/core/collection/mashup.py | 2 +-
vistrails/core/collection/parameter_exploration.py | 2 +-
vistrails/core/collection/schema.sql | 2 +-
vistrails/core/collection/search.py | 2 +-
vistrails/core/collection/thumbnail.py | 2 +-
vistrails/core/collection/vistrail.py | 2 +-
vistrails/core/collection/workflow.py | 2 +-
vistrails/core/collection/workflow_exec.py | 2 +-
vistrails/core/common.py | 2 +-
vistrails/core/configuration.py | 119 +-
vistrails/core/console_mode.py | 45 +-
vistrails/core/data_structures/__init__.py | 2 +-
vistrails/core/data_structures/bijectivedict.py | 2 +-
vistrails/core/data_structures/graph.py | 76 +-
vistrails/core/data_structures/point.py | 2 +-
vistrails/core/data_structures/queue.py | 2 +-
vistrails/core/data_structures/rect.py | 2 +-
vistrails/core/data_structures/stack.py | 2 +-
vistrails/core/db/__init__.py | 2 +-
vistrails/core/db/action.py | 2 +-
vistrails/core/db/io.py | 2 +-
vistrails/core/db/locator.py | 51 +-
vistrails/core/debug.py | 15 +-
vistrails/core/external_connection.py | 2 +-
vistrails/core/inspector.py | 44 +-
vistrails/core/interpreter/__init__.py | 2 +-
vistrails/core/interpreter/base.py | 2 +-
vistrails/core/interpreter/cached.py | 57 +-
vistrails/core/interpreter/default.py | 2 +-
vistrails/core/interpreter/noncached.py | 2 +-
vistrails/core/interpreter/utils.py | 2 +-
vistrails/core/keychain.py | 2 +-
vistrails/core/layout/__init__.py | 2 +-
vistrails/core/layout/tree_layout.py | 2 +-
vistrails/core/layout/version_tree_layout.py | 2 +-
vistrails/core/layout/workflow_layout.py | 2 +-
vistrails/core/log/__init__.py | 2 +-
vistrails/core/log/controller.py | 30 +-
vistrails/core/log/group_exec.py | 2 +-
vistrails/core/log/log.py | 2 +-
vistrails/core/log/loop_exec.py | 2 +-
vistrails/core/log/machine.py | 2 +-
vistrails/core/log/module_exec.py | 2 +-
vistrails/core/log/opm_graph.py | 2 +-
vistrails/core/log/prov_document.py | 2 +-
vistrails/core/log/workflow_exec.py | 2 +-
vistrails/core/mashup/__init__.py | 2 +-
vistrails/core/mashup/action.py | 2 +-
vistrails/core/mashup/action_annotation.py | 2 +-
vistrails/core/mashup/alias.py | 2 +-
vistrails/core/mashup/component.py | 2 +-
vistrails/core/mashup/controller.py | 2 +-
vistrails/core/mashup/mashup.py | 2 +-
vistrails/core/mashup/mashup_trail.py | 2 +-
vistrails/core/modules/__init__.py | 2 +-
vistrails/core/modules/abstraction.py | 34 +-
vistrails/core/modules/basic_modules.py | 11 +-
vistrails/core/modules/config.py | 2 +-
vistrails/core/modules/constant_configuration.py | 2 +-
vistrails/core/modules/module_configure.py | 2 +-
vistrails/core/modules/module_descriptor.py | 2 +-
vistrails/core/modules/module_registry.py | 37 +-
vistrails/core/modules/module_utils.py | 2 +-
vistrails/core/modules/output_modules.py | 53 +-
vistrails/core/modules/package.py | 91 +-
vistrails/core/modules/paramexplore.py | 2 +-
vistrails/core/modules/python_source_configure.py | 2 +-
vistrails/core/modules/query_configuration.py | 2 +-
vistrails/core/modules/source_configure.py | 2 +-
vistrails/core/modules/sub_module.py | 53 +-
vistrails/core/modules/tuple_configuration.py | 2 +-
vistrails/core/modules/utils.py | 2 +-
vistrails/core/modules/vistrails_module.py | 103 +-
vistrails/core/packagemanager.py | 234 +--
vistrails/core/packagerepository.py | 2 +-
vistrails/core/param_explore.py | 2 +-
vistrails/core/paramexplore/__init__.py | 2 +-
vistrails/core/paramexplore/function.py | 2 +-
vistrails/core/paramexplore/param.py | 2 +-
vistrails/core/paramexplore/paramexplore.py | 2 +-
vistrails/core/publishing/__init__.py | 2 +-
vistrails/core/publishing/parse_latex.py | 2 +-
vistrails/core/query/__init__.py | 2 +-
vistrails/core/query/combined.py | 52 +-
vistrails/core/query/multiple.py | 22 +-
vistrails/core/query/version.py | 86 +-
vistrails/core/query/visual.py | 15 +-
vistrails/core/recent_vistrails.py | 2 +-
vistrails/core/reportusage.py | 333 ++++
vistrails/core/repository/__init__.py | 2 +-
vistrails/core/repository/poster/__init__.py | 2 +-
vistrails/core/repository/poster/encode.py | 2 +-
vistrails/core/repository/poster/streaminghttp.py | 2 +-
vistrails/core/requirements.py | 2 +-
vistrails/core/startup.py | 2 +-
vistrails/core/system/__init__.py | 7 +-
vistrails/core/system/common.py | 2 +-
vistrails/core/system/linux.py | 2 +-
vistrails/core/system/mac_site.py | 2 +-
vistrails/core/system/osx.py | 2 +-
vistrails/core/system/unix.py | 2 +-
vistrails/core/system/windows.py | 2 +-
vistrails/core/theme.py | 2 +-
vistrails/core/thumbnails.py | 5 +-
vistrails/core/upgradeworkflow.py | 170 +-
vistrails/core/utils/__init__.py | 6 +-
vistrails/core/utils/color.py | 2 +-
vistrails/core/utils/enum.py | 2 +-
vistrails/core/utils/expression.py | 2 +-
vistrails/core/utils/gcutils.py | 2 +-
vistrails/core/utils/timemethod.py | 2 +-
vistrails/core/utils/tracemethod.py | 2 +-
vistrails/core/utils/uxml.py | 2 +-
vistrails/core/vistrail/__init__.py | 2 +-
vistrails/core/vistrail/abstraction.py | 2 +-
vistrails/core/vistrail/action.py | 2 +-
vistrails/core/vistrail/action_annotation.py | 2 +-
vistrails/core/vistrail/annotation.py | 2 +-
vistrails/core/vistrail/connection.py | 3 +-
vistrails/core/vistrail/controller.py | 684 +++++---
vistrails/core/vistrail/group.py | 2 +-
vistrails/core/vistrail/job.py | 85 +-
vistrails/core/vistrail/location.py | 2 +-
vistrails/core/vistrail/module.py | 6 +-
vistrails/core/vistrail/module_control_param.py | 2 +-
vistrails/core/vistrail/module_function.py | 2 +-
vistrails/core/vistrail/module_param.py | 2 +-
vistrails/core/vistrail/operation.py | 2 +-
vistrails/core/vistrail/pipeline.py | 44 +-
vistrails/core/vistrail/plugin_data.py | 2 +-
vistrails/core/vistrail/port.py | 2 +-
vistrails/core/vistrail/port_spec.py | 3 +-
vistrails/core/vistrail/port_spec_item.py | 2 +-
vistrails/core/vistrail/tag.py | 2 +-
vistrails/core/vistrail/vistrail.py | 34 +-
vistrails/core/vistrail/vistrailvariable.py | 2 +-
vistrails/db/__init__.py | 2 +-
vistrails/db/bin/__init__.py | 2 +-
vistrails/db/bin/auto_gen_objects.py | 2 +-
vistrails/db/bin/generate.py | 8 +-
vistrails/db/bin/parser.py | 4 +-
vistrails/db/bin/sql_gen_objects.py | 2 +-
vistrails/db/bin/templates/domain.py.mako | 2 +-
vistrails/db/bin/templates/sql.py.mako | 2 +-
vistrails/db/bin/templates/sql_delete.sql.mako | 2 +-
vistrails/db/bin/templates/sql_schema.sql.mako | 2 +-
vistrails/db/bin/templates/xml.py.mako | 2 +-
vistrails/db/bin/templates/xml_schema.xsd.mako | 2 +-
vistrails/db/bin/xml_gen_objects.py | 2 +-
vistrails/db/domain/__init__.py | 2 +-
vistrails/db/persistence/__init__.py | 2 +-
vistrails/db/services/__init__.py | 2 +-
vistrails/db/services/abstraction.py | 2 +-
vistrails/db/services/action.py | 2 +-
vistrails/db/services/action_chain.py | 2 +-
vistrails/db/services/io.py | 2 +-
vistrails/db/services/locator.py | 117 +-
vistrails/db/services/log.py | 2 +-
vistrails/db/services/opm.py | 202 ++-
vistrails/db/services/prov.py | 119 +-
vistrails/db/services/query.py | 2 +-
vistrails/db/services/registry.py | 2 +-
vistrails/db/services/vistrail.py | 6 +-
vistrails/db/services/workflow.py | 2 +-
vistrails/db/specs/all.xml | 2 +-
vistrails/db/tests/__init__.py | 2 +-
vistrails/db/tests/setup_db_tables.py | 2 +-
vistrails/db/tests/sql_to_xml.py | 2 +-
vistrails/db/tests/xml_to_sql.py | 2 +-
vistrails/db/versions/__init__.py | 2 +-
vistrails/db/versions/v0_3_0/__init__.py | 2 +-
vistrails/db/versions/v0_3_0/domain/__init__.py | 2 +-
vistrails/db/versions/v0_3_0/domain/auto_gen.py | 2 +-
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.../db/versions/v0_3_0/persistence/xml/__init__.py | 2 +-
.../db/versions/v0_3_0/persistence/xml/auto_gen.py | 2 +-
vistrails/db/versions/v0_3_0/persistence/xml/io.py | 2 +-
.../db/versions/v0_3_0/persistence/xml/xml_dao.py | 2 +-
.../db/versions/v0_3_0/schemas/xml/vistrail.xsd | 2 +-
vistrails/db/versions/v0_3_0/specs/action.xml | 2 +-
.../db/versions/v0_3_0/specs/addConnection.xml | 2 +-
vistrails/db/versions/v0_3_0/specs/addModule.xml | 2 +-
.../db/versions/v0_3_0/specs/addModulePort.xml | 2 +-
.../db/versions/v0_3_0/specs/changeAnnotation.xml | 2 +-
.../db/versions/v0_3_0/specs/changeParameter.xml | 2 +-
.../db/versions/v0_3_0/specs/deleteAnnotation.xml | 2 +-
.../db/versions/v0_3_0/specs/deleteConnection.xml | 2 +-
.../db/versions/v0_3_0/specs/deleteFunction.xml | 2 +-
.../db/versions/v0_3_0/specs/deleteModule.xml | 2 +-
.../db/versions/v0_3_0/specs/deleteModulePort.xml | 2 +-
vistrails/db/versions/v0_3_0/specs/moveModule.xml | 2 +-
vistrails/db/versions/v0_3_0/specs/tag.xml | 2 +-
vistrails/db/versions/v0_3_0/specs/vistrail.xml | 2 +-
vistrails/db/versions/v0_3_1/__init__.py | 2 +-
vistrails/db/versions/v0_3_1/domain/__init__.py | 2 +-
.../db/versions/v0_3_1/persistence/__init__.py | 2 +-
.../db/versions/v0_3_1/schemas/xml/vistrail.xsd | 2 +-
vistrails/db/versions/v0_3_1/specs/action.xml | 2 +-
.../db/versions/v0_3_1/specs/addConnection.xml | 2 +-
vistrails/db/versions/v0_3_1/specs/addModule.xml | 2 +-
.../db/versions/v0_3_1/specs/addModulePort.xml | 2 +-
.../db/versions/v0_3_1/specs/changeAnnotation.xml | 2 +-
.../db/versions/v0_3_1/specs/changeParameter.xml | 2 +-
.../db/versions/v0_3_1/specs/deleteAnnotation.xml | 2 +-
.../db/versions/v0_3_1/specs/deleteConnection.xml | 2 +-
.../db/versions/v0_3_1/specs/deleteFunction.xml | 2 +-
.../db/versions/v0_3_1/specs/deleteModule.xml | 2 +-
.../db/versions/v0_3_1/specs/deleteModulePort.xml | 2 +-
vistrails/db/versions/v0_3_1/specs/moveModule.xml | 2 +-
vistrails/db/versions/v0_3_1/specs/tag.xml | 2 +-
vistrails/db/versions/v0_3_1/specs/vistrail.xml | 2 +-
vistrails/db/versions/v0_3_1/translate/__init__.py | 2 +-
vistrails/db/versions/v0_3_1/translate/v0_3_0.py | 2 +-
vistrails/db/versions/v0_5_0/__init__.py | 2 +-
vistrails/db/versions/v0_5_0/domain/__init__.py | 2 +-
vistrails/db/versions/v0_5_0/domain/auto_gen.py | 2 +-
vistrails/db/versions/v0_5_0/domain/id_scope.py | 2 +-
vistrails/db/versions/v0_5_0/domain/vistrail.py | 2 +-
vistrails/db/versions/v0_5_0/domain/workflow.py | 2 +-
.../db/versions/v0_5_0/persistence/__init__.py | 2 +-
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vistrails/db/versions/v0_5_0/persistence/xml/io.py | 2 +-
.../db/versions/v0_5_0/persistence/xml/xml_dao.py | 2 +-
.../db/versions/v0_5_0/schemas/sql/vistrails.sql | 2 +-
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vistrails/db/versions/v0_5_0/schemas/xml/log.xsd | 2 +-
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vistrails/db/versions/v0_5_0/specs/location.xml | 2 +-
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vistrails/db/versions/v0_5_0/specs/machine.xml | 2 +-
vistrails/db/versions/v0_5_0/specs/macro.xml | 2 +-
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vistrails/db/versions/v0_5_0/specs/port.xml | 2 +-
vistrails/db/versions/v0_5_0/specs/portSpec.xml | 2 +-
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vistrails/db/versions/v0_5_0/specs/workflow.xml | 2 +-
vistrails/db/versions/v0_5_0/translate/__init__.py | 2 +-
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vistrails/db/versions/v0_6_0/domain/auto_gen.py | 2 +-
vistrails/db/versions/v0_6_0/domain/id_scope.py | 2 +-
vistrails/db/versions/v0_6_0/domain/vistrail.py | 2 +-
vistrails/db/versions/v0_6_0/domain/workflow.py | 2 +-
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.../db/versions/v0_6_0/persistence/xml/__init__.py | 2 +-
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vistrails/db/versions/v0_6_0/persistence/xml/io.py | 2 +-
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.../db/versions/v0_6_0/schemas/sql/vistrails.sql | 2 +-
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.../db/versions/v0_6_0/schemas/xml/vistrail.xsd | 2 +-
vistrails/db/versions/v0_6_0/specs/abstraction.xml | 2 +-
.../db/versions/v0_6_0/specs/abstractionRef.xml | 2 +-
vistrails/db/versions/v0_6_0/specs/action.xml | 2 +-
vistrails/db/versions/v0_6_0/specs/add.xml | 2 +-
vistrails/db/versions/v0_6_0/specs/annotation.xml | 2 +-
vistrails/db/versions/v0_6_0/specs/change.xml | 2 +-
vistrails/db/versions/v0_6_0/specs/connection.xml | 2 +-
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vistrails/db/versions/v1_0_0/specs/all.xml | 2 +-
vistrails/db/versions/v1_0_0/translate/__init__.py | 2 +-
vistrails/db/versions/v1_0_0/translate/v0_9_5.py | 2 +-
vistrails/db/versions/v1_0_0/translate/v1_0_1.py | 2 +-
vistrails/db/versions/v1_0_1/__init__.py | 2 +-
vistrails/db/versions/v1_0_1/domain/__init__.py | 2 +-
vistrails/db/versions/v1_0_1/domain/auto_gen.py | 2 +-
vistrails/db/versions/v1_0_1/domain/id_scope.py | 2 +-
vistrails/db/versions/v1_0_1/domain/log.py | 2 +-
vistrails/db/versions/v1_0_1/domain/registry.py | 2 +-
vistrails/db/versions/v1_0_1/domain/vistrail.py | 2 +-
vistrails/db/versions/v1_0_1/domain/workflow.py | 2 +-
.../db/versions/v1_0_1/persistence/__init__.py | 2 +-
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vistrails/db/versions/v1_0_1/specs/all.xml | 2 +-
vistrails/db/versions/v1_0_1/translate/__init__.py | 2 +-
vistrails/db/versions/v1_0_1/translate/v1_0_0.py | 2 +-
vistrails/db/versions/v1_0_1/translate/v1_0_2.py | 2 +-
vistrails/db/versions/v1_0_2/__init__.py | 2 +-
vistrails/db/versions/v1_0_2/domain/__init__.py | 2 +-
vistrails/db/versions/v1_0_2/domain/auto_gen.py | 2 +-
vistrails/db/versions/v1_0_2/domain/id_scope.py | 2 +-
vistrails/db/versions/v1_0_2/domain/log.py | 2 +-
vistrails/db/versions/v1_0_2/domain/registry.py | 2 +-
vistrails/db/versions/v1_0_2/domain/vistrail.py | 2 +-
vistrails/db/versions/v1_0_2/domain/workflow.py | 2 +-
.../db/versions/v1_0_2/persistence/__init__.py | 2 +-
.../db/versions/v1_0_2/persistence/sql/__init__.py | 2 +-
.../db/versions/v1_0_2/persistence/sql/auto_gen.py | 2 +-
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.../db/versions/v1_0_2/persistence/xml/__init__.py | 2 +-
.../db/versions/v1_0_2/persistence/xml/auto_gen.py | 2 +-
.../db/versions/v1_0_2/persistence/xml/xml_dao.py | 2 +-
.../db/versions/v1_0_2/schemas/sql/vistrails.sql | 2 +-
.../versions/v1_0_2/schemas/sql/vistrails_drop.sql | 2 +-
vistrails/db/versions/v1_0_2/schemas/xml/log.xsd | 2 +-
.../db/versions/v1_0_2/schemas/xml/vistrail.xsd | 2 +-
.../db/versions/v1_0_2/schemas/xml/vtlink.xsd | 2 +-
.../db/versions/v1_0_2/schemas/xml/workflow.xsd | 2 +-
vistrails/db/versions/v1_0_2/specs/all.xml | 2 +-
vistrails/db/versions/v1_0_2/translate/__init__.py | 2 +-
vistrails/db/versions/v1_0_2/translate/v1_0_1.py | 2 +-
vistrails/db/versions/v1_0_2/translate/v1_0_3.py | 2 +-
vistrails/db/versions/v1_0_3/__init__.py | 2 +-
vistrails/db/versions/v1_0_3/domain/__init__.py | 2 +-
vistrails/db/versions/v1_0_3/domain/auto_gen.py | 2 +-
vistrails/db/versions/v1_0_3/domain/id_scope.py | 2 +-
vistrails/db/versions/v1_0_3/domain/log.py | 2 +-
vistrails/db/versions/v1_0_3/domain/registry.py | 2 +-
vistrails/db/versions/v1_0_3/domain/vistrail.py | 2 +-
vistrails/db/versions/v1_0_3/domain/workflow.py | 2 +-
.../db/versions/v1_0_3/persistence/__init__.py | 2 +-
.../db/versions/v1_0_3/persistence/sql/__init__.py | 2 +-
.../db/versions/v1_0_3/persistence/sql/auto_gen.py | 2 +-
.../db/versions/v1_0_3/persistence/sql/sql_dao.py | 5 +-
.../db/versions/v1_0_3/persistence/xml/__init__.py | 2 +-
.../db/versions/v1_0_3/persistence/xml/auto_gen.py | 2 +-
.../db/versions/v1_0_3/persistence/xml/xml_dao.py | 2 +-
.../db/versions/v1_0_3/schemas/sql/vistrails.sql | 2 +-
.../versions/v1_0_3/schemas/sql/vistrails_drop.sql | 2 +-
vistrails/db/versions/v1_0_3/schemas/xml/log.xsd | 2 +-
.../db/versions/v1_0_3/schemas/xml/vistrail.xsd | 2 +-
.../db/versions/v1_0_3/schemas/xml/vtlink.xsd | 2 +-
.../db/versions/v1_0_3/schemas/xml/workflow.xsd | 2 +-
vistrails/db/versions/v1_0_3/specs/all.xml | 2 +-
vistrails/db/versions/v1_0_3/translate/__init__.py | 2 +-
vistrails/db/versions/v1_0_3/translate/v1_0_2.py | 2 +-
vistrails/db/versions/v1_0_3/translate/v1_0_4.py | 2 +-
vistrails/db/versions/v1_0_4/__init__.py | 2 +-
vistrails/db/versions/v1_0_4/domain/__init__.py | 2 +-
vistrails/db/versions/v1_0_4/domain/auto_gen.py | 2 +-
vistrails/db/versions/v1_0_4/domain/id_scope.py | 2 +-
vistrails/db/versions/v1_0_4/domain/log.py | 2 +-
vistrails/db/versions/v1_0_4/domain/registry.py | 2 +-
vistrails/db/versions/v1_0_4/domain/vistrail.py | 2 +-
vistrails/db/versions/v1_0_4/domain/workflow.py | 2 +-
.../db/versions/v1_0_4/persistence/__init__.py | 2 +-
.../db/versions/v1_0_4/persistence/sql/__init__.py | 2 +-
.../db/versions/v1_0_4/persistence/sql/auto_gen.py | 2 +-
.../db/versions/v1_0_4/persistence/sql/sql_dao.py | 5 +-
.../db/versions/v1_0_4/persistence/xml/__init__.py | 2 +-
.../db/versions/v1_0_4/persistence/xml/auto_gen.py | 2 +-
.../db/versions/v1_0_4/persistence/xml/xml_dao.py | 2 +-
.../db/versions/v1_0_4/schemas/sql/vistrails.sql | 2 +-
.../versions/v1_0_4/schemas/sql/vistrails_drop.sql | 2 +-
vistrails/db/versions/v1_0_4/schemas/xml/log.xsd | 2 +-
.../db/versions/v1_0_4/schemas/xml/vistrail.xsd | 2 +-
.../db/versions/v1_0_4/schemas/xml/vtlink.xsd | 2 +-
.../db/versions/v1_0_4/schemas/xml/workflow.xsd | 2 +-
vistrails/db/versions/v1_0_4/specs/all.xml | 2 +-
vistrails/db/versions/v1_0_4/translate/__init__.py | 2 +-
vistrails/db/versions/v1_0_4/translate/v1_0_3.py | 6 +-
vistrails/gui/__init__.py | 2 +-
vistrails/gui/application.py | 172 +-
vistrails/gui/application_server.py | 2 +-
vistrails/gui/base_view.py | 2 +-
vistrails/gui/bundles/__init__.py | 2 +-
vistrails/gui/bundles/installbundle.py | 3 +-
vistrails/gui/bundles/linux_debian_install.py | 2 +-
vistrails/gui/bundles/linux_fedora_install.py | 2 +-
vistrails/gui/bundles/utils.py | 2 +-
vistrails/gui/collection/__init__.py | 2 +-
vistrails/gui/collection/explorer.py | 2 +-
vistrails/gui/collection/vis_log.py | 2 +-
vistrails/gui/collection/workspace.py | 54 +-
vistrails/gui/common_widgets.py | 2 +-
vistrails/gui/configuration.py | 38 +-
vistrails/gui/controlflow_assist.py | 2 +-
vistrails/gui/debug.py | 2 +-
vistrails/gui/debugger.py | 2 +-
vistrails/gui/extras/__init__.py | 2 +-
vistrails/gui/extras/core/__init__.py | 2 +-
vistrails/gui/extras/core/db/__init__.py | 2 +-
vistrails/gui/extras/core/db/locator.py | 2 +-
vistrails/gui/graphics_view.py | 2 +-
vistrails/gui/job_monitor.py | 643 +++++--
vistrails/gui/mashups/__init__.py | 2 +-
vistrails/gui/mashups/alias_inspector.py | 2 +-
vistrails/gui/mashups/alias_list.py | 2 +-
vistrails/gui/mashups/alias_parameter_view.py | 2 +-
vistrails/gui/mashups/controller.py | 2 +-
vistrails/gui/mashups/mashup_app.py | 90 +-
vistrails/gui/mashups/mashup_view.py | 2 +-
vistrails/gui/mashups/mashups_inspector.py | 2 +-
vistrails/gui/mashups/mashups_manager.py | 4 +-
vistrails/gui/mashups/mashups_widgets.py | 4 +-
vistrails/gui/merge_gui.py | 2 +-
vistrails/gui/module_annotation.py | 2 +-
vistrails/gui/module_configuration.py | 2 +-
vistrails/gui/module_documentation.py | 2 +-
vistrails/gui/module_info.py | 26 +-
vistrails/gui/module_options.py | 2 +-
vistrails/gui/module_palette.py | 62 +-
vistrails/gui/modules/__init__.py | 2 +-
vistrails/gui/modules/constant_configuration.py | 2 +-
vistrails/gui/modules/list_configuration.py | 2 +-
vistrails/gui/modules/module_configure.py | 8 +-
vistrails/gui/modules/output_configuration.py | 2 +-
vistrails/gui/modules/paramexplore.py | 2 +-
vistrails/gui/modules/python_source_configure.py | 6 +-
vistrails/gui/modules/query_configuration.py | 2 +-
vistrails/gui/modules/resources/__init__.py | 38 -
vistrails/gui/modules/resources/colorconfig.qrc | 5 -
vistrails/gui/modules/resources/colorconfig_rc.py | 1855 --------------------
vistrails/gui/modules/resources/colorwheel.png | Bin 28526 -> 0 bytes
vistrails/gui/modules/source_configure.py | 146 +-
vistrails/gui/modules/string_configure.py | 6 +-
.../gui/modules/stringformat_configuration.py | 2 +-
vistrails/gui/modules/tuple_configuration.py | 19 +-
vistrails/gui/modules/utils.py | 2 +-
vistrails/gui/open_db_window.py | 2 +-
vistrails/gui/paramexplore/__init__.py | 2 +-
vistrails/gui/paramexplore/param_view.py | 2 +-
vistrails/gui/paramexplore/pe_inspector.py | 2 +-
vistrails/gui/paramexplore/pe_pipeline.py | 2 +-
vistrails/gui/paramexplore/pe_tab.py | 7 +-
vistrails/gui/paramexplore/pe_table.py | 2 +-
vistrails/gui/paramexplore/pe_view.py | 2 +-
vistrails/gui/paramexplore/virtual_cell.py | 12 +-
vistrails/gui/pipeline_view.py | 219 ++-
vistrails/gui/pipeline_view_select.py | 2 +-
vistrails/gui/port_documentation.py | 2 +-
vistrails/gui/ports_pane.py | 5 +-
vistrails/gui/preferences.py | 24 +-
vistrails/gui/publishing.py | 2 +-
vistrails/gui/qt.py | 2 +-
vistrails/gui/query_view.py | 71 +-
vistrails/gui/repository.py | 2 +-
vistrails/gui/requirements.py | 2 +-
vistrails/gui/resources/__init__.py | 2 +-
vistrails/gui/resources/images/disclaimer.png | Bin 329091 -> 329346 bytes
.../gui/resources/images/vistrails_splash.png | Bin 162012 -> 161471 bytes
vistrails/gui/resources/macroicons_rc.py | 2 +-
vistrails/gui/shell.py | 2 +-
vistrails/gui/theme.py | 2 +-
vistrails/gui/utils.py | 2 +-
vistrails/gui/variable_dropbox.py | 2 +-
vistrails/gui/version_prop.py | 40 +-
vistrails/gui/version_view.py | 12 +-
vistrails/gui/vis_diff.py | 52 +-
vistrails/gui/vistrail_controller.py | 255 ++-
vistrails/gui/vistrail_variables.py | 2 +-
vistrails/gui/vistrail_view.py | 80 +-
vistrails/gui/vistrails_palette.py | 2 +-
vistrails/gui/vistrails_window.py | 6 +-
vistrails/packages/CLTools/__init__.py | 2 +-
vistrails/packages/CLTools/identifiers.py | 2 +-
vistrails/packages/CLTools/init.py | 2 +-
vistrails/packages/CLTools/wizard.py | 2 +-
vistrails/packages/ImageMagick/__init__.py | 2 +-
vistrails/packages/ImageMagick/init.py | 2 +-
vistrails/packages/RemoteQ/__init__.py | 2 +-
vistrails/packages/RemoteQ/base.py | 2 +-
vistrails/packages/RemoteQ/hdfs.py | 2 +-
vistrails/packages/RemoteQ/init.py | 2 +-
vistrails/packages/RemoteQ/streaming.py | 2 +-
vistrails/packages/SUDSWebServices/__init__.py | 2 +-
vistrails/packages/SUDSWebServices/init.py | 21 +-
vistrails/packages/URL/__init__.py | 2 +-
vistrails/packages/URL/http_directory.py | 2 +-
vistrails/packages/URL/https.py | 2 +-
vistrails/packages/URL/https_if_available.py | 2 +-
vistrails/packages/URL/identifiers.py | 2 +-
vistrails/packages/URL/init.py | 72 +-
vistrails/packages/__init__.py | 2 +-
vistrails/packages/analytics/__init__.py | 2 +-
vistrails/packages/analytics/init.py | 2 +-
vistrails/packages/controlflow/__init__.py | 9 +-
vistrails/packages/controlflow/conditional.py | 5 +-
vistrails/packages/controlflow/fold.py | 15 +-
vistrails/packages/controlflow/init.py | 14 +-
vistrails/packages/controlflow/looping.py | 5 +-
vistrails/packages/controlflow/order.py | 5 +-
vistrails/packages/controlflow/products.py | 2 +-
vistrails/packages/controlflow/utils.py | 5 +-
vistrails/packages/dialogs/__init__.py | 2 +-
vistrails/packages/dialogs/continue_prompt.py | 2 +-
vistrails/packages/dialogs/init.py | 2 +-
vistrails/packages/gmaps/__init__.py | 2 +-
vistrails/packages/gmaps/gmap_cell.py | 6 +-
vistrails/packages/gmaps/identifiers.py | 2 +-
vistrails/packages/gmaps/init.py | 2 +-
vistrails/packages/gmaps/utils.py | 2 +-
vistrails/packages/gmaps/vis.py | 2 +-
vistrails/packages/matplotlib/__init__.py | 2 +-
vistrails/packages/matplotlib/bases.py | 28 +-
vistrails/packages/matplotlib/diff.py | 2 +-
vistrails/packages/matplotlib/figure_cell.py | 10 +-
vistrails/packages/matplotlib/generate.py | 2 +-
vistrails/packages/matplotlib/identifiers.py | 4 +-
vistrails/packages/matplotlib/init.py | 8 +-
vistrails/packages/matplotlib/mixins.py | 2 +-
vistrails/packages/matplotlib/parse.py | 2 +-
vistrails/packages/matplotlib/specs.py | 2 +-
vistrails/packages/matplotlib/update.py | 2 +-
vistrails/packages/matplotlib/widgets.py | 2 +-
vistrails/packages/mongodb/Vagrantfile | 31 +
.../{persistent_archive => mongodb}/__init__.py | 24 +-
vistrails/packages/mongodb/init.py | 291 +++
vistrails/packages/parallelflow/__init__.py | 2 +-
vistrails/packages/parallelflow/api.py | 2 +-
vistrails/packages/parallelflow/engine_manager.py | 2 +-
vistrails/packages/parallelflow/init.py | 2 +-
vistrails/packages/parallelflow/map.py | 2 +-
vistrails/packages/persistence/__init__.py | 2 +-
vistrails/packages/persistence/compute_hash.py | 2 +-
vistrails/packages/persistence/db_utils.py | 2 +-
vistrails/packages/persistence/find_files.py | 2 +-
vistrails/packages/persistence/find_workflows.py | 4 +-
vistrails/packages/persistence/identifiers.py | 2 +-
vistrails/packages/persistence/init.py | 2 +-
vistrails/packages/persistence/repo.py | 2 +-
vistrails/packages/persistence/schema.sql | 2 +-
vistrails/packages/persistence/widgets.py | 2 +-
vistrails/packages/persistent_archive/__init__.py | 2 +-
vistrails/packages/persistent_archive/cache.py | 2 +-
vistrails/packages/persistent_archive/common.py | 2 +-
.../packages/persistent_archive/identifiers.py | 2 +-
vistrails/packages/persistent_archive/init.py | 2 +-
.../packages/persistent_archive/persistedinput.py | 2 +-
.../packages/persistent_archive/persistedoutput.py | 2 +-
.../packages/persistent_archive/queriedinput.py | 2 +-
vistrails/packages/persistent_archive/queries.py | 2 +-
vistrails/packages/persistent_archive/ui.py | 11 +-
vistrails/packages/persistent_archive/widgets.py | 2 +-
vistrails/packages/pipelineEdit/__init__.py | 2 +-
vistrails/packages/pipelineEdit/init.py | 2 +-
vistrails/packages/pythonCalc/__init__.py | 2 +-
vistrails/packages/pythonCalc/init.py | 2 +-
vistrails/packages/pythonCalcQt/__init__.py | 2 +-
vistrails/packages/pythonCalcQt/init.py | 2 +-
vistrails/packages/qgis/__init__.py | 2 +-
vistrails/packages/qgis/init.py | 2 +-
vistrails/packages/reprounzip/__init__.py | 22 +
vistrails/packages/reprounzip/init.py | 165 ++
vistrails/packages/rpy/__init__.py | 2 +-
vistrails/packages/rpy/init.py | 2 +-
vistrails/packages/rpy/widgets.py | 2 +-
vistrails/packages/sklearn/__init__.py | 2 +-
vistrails/packages/sklearn/init.py | 2 +-
vistrails/packages/sklearn/tests.py | 2 +-
vistrails/packages/spreadsheet/__init__.py | 2 +-
vistrails/packages/spreadsheet/analogy_api.py | 2 +-
vistrails/packages/spreadsheet/basic_widgets.py | 2 +-
vistrails/packages/spreadsheet/cell_rc.py | 2 +-
vistrails/packages/spreadsheet/celltoolbar.qrc | 2 +
vistrails/packages/spreadsheet/celltoolbar_rc.py | 125 +-
vistrails/packages/spreadsheet/identifiers.py | 2 +-
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.../packages/spreadsheet/images/new-window.png | Bin 0 -> 619 bytes
vistrails/packages/spreadsheet/init.py | 16 +-
vistrails/packages/spreadsheet/spreadsheet_base.py | 2 +-
vistrails/packages/spreadsheet/spreadsheet_cell.py | 2 +-
.../packages/spreadsheet/spreadsheet_config.py | 2 +-
.../packages/spreadsheet/spreadsheet_controller.py | 33 +-
.../packages/spreadsheet/spreadsheet_event.py | 2 +-
.../packages/spreadsheet/spreadsheet_execute.py | 100 +-
.../packages/spreadsheet/spreadsheet_helpers.py | 2 +-
vistrails/packages/spreadsheet/spreadsheet_rc.py | 2 +-
.../packages/spreadsheet/spreadsheet_registry.py | 2 +-
.../packages/spreadsheet/spreadsheet_sheet.py | 4 +-
vistrails/packages/spreadsheet/spreadsheet_tab.py | 9 +-
.../spreadsheet/spreadsheet_tabcontroller.py | 2 +-
.../packages/spreadsheet/spreadsheet_window.py | 2 +-
vistrails/packages/spreadsheet/widgets/__init__.py | 2 +-
.../spreadsheet/widgets/iebrowser/__init__.py | 2 +-
.../spreadsheet/widgets/iebrowser/iecell.py | 2 +-
.../spreadsheet/widgets/imageviewer/__init__.py | 2 +-
.../spreadsheet/widgets/imageviewer/imageviewer.py | 4 +-
.../widgets/imageviewer/imageviewer_rc.py | 2 +-
.../spreadsheet/widgets/richtext/__init__.py | 2 +-
.../spreadsheet/widgets/richtext/richtext.py | 4 +-
.../packages/spreadsheet/widgets/svg/__init__.py | 2 +-
vistrails/packages/spreadsheet/widgets/svg/svg.py | 2 +-
.../spreadsheet/widgets/webview/__init__.py | 2 +-
.../spreadsheet/widgets/webview/webview.py | 30 +-
vistrails/packages/sql/__init__.py | 2 +-
vistrails/packages/sql/init.py | 2 +-
vistrails/packages/sql/widgets.py | 2 +-
vistrails/packages/tabledata/__init__.py | 35 +
vistrails/packages/tabledata/common.py | 74 +-
vistrails/packages/tabledata/convert/__init__.py | 6 +-
.../packages/tabledata/convert/convert_dates.py | 2 +-
.../packages/tabledata/convert/convert_numpy.py | 108 ++
vistrails/packages/tabledata/identifiers.py | 35 +
vistrails/packages/tabledata/init.py | 45 +-
vistrails/packages/tabledata/operations.py | 47 +-
vistrails/packages/tabledata/read/__init__.py | 22 +-
vistrails/packages/tabledata/read/convert.py | 193 ++
vistrails/packages/tabledata/read/read_csv.py | 10 +-
vistrails/packages/tabledata/read/read_excel.py | 11 +-
vistrails/packages/tabledata/read/read_json.py | 129 +-
vistrails/packages/tabledata/read/read_numpy.py | 68 +-
vistrails/packages/tabledata/viewer.py | 37 +-
vistrails/packages/tabledata/widgets.py | 40 +-
vistrails/packages/tabledata/write/__init__.py | 26 +-
vistrails/packages/tabledata/write/write_csv.py | 2 +-
vistrails/packages/tabledata/write/write_excel.py | 2 +-
vistrails/packages/tabledata/write/write_numpy.py | 10 +-
vistrails/packages/tej/__init__.py | 2 +
vistrails/packages/tej/init.py | 255 ++-
vistrails/packages/tej/widgets.py | 149 +-
.../{persistent_archive => tensorflow}/__init__.py | 18 +-
vistrails/packages/tensorflow/base.py | 268 +++
vistrails/packages/tensorflow/init.py | 293 ++++
vistrails/packages/vtk/__init__.py | 2 +-
vistrails/packages/vtk/common.py | 2 +-
vistrails/packages/vtk/hasher.py | 2 +-
vistrails/packages/vtk/identifiers.py | 2 +-
vistrails/packages/vtk/init.py | 36 +-
vistrails/packages/vtk/inspectors.py | 2 +-
vistrails/packages/vtk/offscreen.py | 2 +-
vistrails/packages/vtk/pythonclass.py | 2 +-
vistrails/packages/vtk/tf_widget.py | 2 +-
vistrails/packages/vtk/vtk_wrapper/class_tree.py | 2 +-
vistrails/packages/vtk/vtk_wrapper/fix_classes.py | 2 +-
vistrails/packages/vtk/vtk_wrapper/parse.py | 2 +-
vistrails/packages/vtk/vtk_wrapper/specs.py | 2 +-
vistrails/packages/vtk/vtk_wrapper/vtk_classes.py | 2 +-
vistrails/packages/vtk/vtk_wrapper/vtk_parser.py | 2 +-
vistrails/packages/vtk/vtk_wrapper/wrapper.py | 2 +-
vistrails/packages/vtk/vtkcell.py | 4 +-
vistrails/packages/vtk/vtkhandler.py | 2 +-
vistrails/packages/vtlcreator/__init__.py | 2 +-
vistrails/packages/vtlcreator/init.py | 2 +-
vistrails/packages/webServices/__init__.py | 2 +-
.../packages/webServices/enumeration_widget.py | 2 +-
vistrails/packages/webServices/init.py | 2 +-
vistrails/run.py | 24 +-
vistrails/stop_vistrails_server.py | 2 +-
vistrails/tests/__init__.py | 2 +-
vistrails/tests/resources/__init__.py | 2 +-
vistrails/tests/resources/broken_upgrade.xml | 23 +
vistrails/tests/resources/chained_upgrade.xml | 23 +
vistrails/tests/resources/console_mode_test.py | 2 +-
vistrails/tests/resources/dummy.xml | 2 +-
vistrails/tests/resources/dummy_broken.xml | 2 +-
vistrails/tests/resources/dummy_new.xml | 2 +-
vistrails/tests/resources/dynamic_module_error.xml | 2 +-
vistrails/tests/resources/empty_bookmarks.xml | 2 +-
vistrails/tests/resources/jobs.vt | Bin 0 -> 42374 bytes
.../tests/resources/looping_upgrades/__init__.py | 0
.../resources/looping_upgrades/pkg_a/__init__.py | 3 +
.../tests/resources/looping_upgrades/pkg_a/init.py | 23 +
.../resources/looping_upgrades/pkg_b/__init__.py | 3 +
.../tests/resources/looping_upgrades/pkg_b/init.py | 23 +
.../resources/looping_upgrades/pkg_c/__init__.py | 3 +
.../tests/resources/looping_upgrades/pkg_c/init.py | 11 +
.../resources/looping_upgrades/pkg_x/__init__.py | 3 +
.../tests/resources/looping_upgrades/pkg_x/init.py | 23 +
.../resources/looping_upgrades/pkg_y/__init__.py | 3 +
.../tests/resources/looping_upgrades/pkg_y/init.py | 23 +
.../tests/resources/looping_upgrades/workflow.xml | 26 +
.../tests/resources/looping_upgrades/workflow2.xml | 26 +
vistrails/tests/resources/myjob.py | 195 ++
vistrails/tests/resources/pythonsource.xml | 2 +-
vistrails/tests/resources/test_alias.xml | 2 +-
vistrails/tests/resources/test_ticket_73.xml | 2 +-
vistrails/tests/resources/vtk.xml | 2 +-
vistrails/tests/runtestsuite.py | 30 +-
vistrails/tests/utils.py | 73 +-
vistrails/vistrails_server.py | 2 +-
1114 files changed, 8278 insertions(+), 7088 deletions(-)
--
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