Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 3f15d5af213d4ba59e75f51c11b1aef4ed101428
https://github.com/galaxyproject/galaxy/commit/3f15d5af213d4ba59e75f51c11b1…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-02-24 (Wed, 24 Feb 2016)
Changed paths:
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/history_contents.py
M lib/galaxy/model/__init__.py
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/history/history-view.js.map
M static/maps/mvc/history/multi-panel.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-view.js
M static/scripts/mvc/history/multi-panel.js
Log Message:
-----------
UI, histories: rework update system to check contents based on update times of contents and only stop checking when history has no more running jobs
Commit: 7855e0009d21dad14b998bae974d0978ff43c6c9
https://github.com/galaxyproject/galaxy/commit/7855e0009d21dad14b998bae974d…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-02-24 (Wed, 24 Feb 2016)
Changed paths:
M client/galaxy/scripts/galaxy.library.js
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folder-view.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/ui/popup-menu.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view-node.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/style/less/library.less
M config/datatypes_conf.xml.sample
M doc/source/project/organization.rst
M lib/galaxy/config.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/display_applications/application.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/ngsindex.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/deferred/data_transfer.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/taggable.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/metadata.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/sanitize.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/parser/output_collection_def.py
M lib/galaxy/tools/test.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/visualization/data_providers/registry.py
M lib/galaxy/visualization/plugins/config_parser.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/helpers/__init__.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/translogger.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/visualizations.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/requests_admin.py
M lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/galaxy/controllers/tag.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/webapps/tool_shed/model/mapping.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy_utils/sequence/fasta.py
M lib/galaxy_utils/sequence/fastq.py
M lib/pulsar/client/interface.py
M lib/pulsar/client/manager.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/util/basic_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/encoding_util.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/util/workflow_util.py
M static/maps/galaxy.library.js.map
M static/maps/layout/masthead.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-folder-view.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/ui/popup-menu.js.map
M static/maps/mvc/workflow/workflow-terminals.js.map
M static/maps/mvc/workflow/workflow-view-node.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/galaxy.library.js
M static/scripts/layout/masthead.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/ui/popup-menu.js
M static/scripts/mvc/workflow/workflow-terminals.js
M static/scripts/mvc/workflow/workflow-view-node.js
M static/scripts/utils/utils.js
M static/style/blue/base.css
M static/style/blue/library.css
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/galaxy/history/display.mako
M test/api/test_tools.py
M test/base/twilltestcase.py
M test/functional/test_admin_features.py
M test/functional/test_data_security.py
M test/functional/test_dataset_features.py
M test/functional/test_get_data.py
M test/functional/test_library_features.py
M test/functional/test_library_security.py
M test/functional/test_library_templates.py
M test/functional/test_metadata_editing.py
M test/functional/test_sample_tracking.py
M test/functional/test_tags.py
M test/functional/test_ucsc_table_browser.py
M test/functional/test_user_info.py
M test/qunit/tests/masthead_tests.js
M test/qunit/tests/workflow_editor_tests.js
M test/tool_shed/base/twilltestcase.py
M test/tool_shed/functional/test_0000_basic_repository_features.py
M test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py
M test/tool_shed/functional/test_0020_basic_repository_dependencies.py
M test/tool_shed/functional/test_0030_repository_dependency_revisions.py
M test/tool_shed/functional/test_0040_repository_circular_dependencies.py
M test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py
M test/tool_shed/functional/test_0060_workflows.py
M test/tool_shed/functional/test_0070_invalid_tool.py
M test/tool_shed/functional/test_0080_advanced_circular_dependencies.py
M test/tool_shed/functional/test_0090_tool_search.py
M test/tool_shed/functional/test_0100_complex_repository_dependencies.py
M test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py
M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py
M test/tool_shed/functional/test_0130_datatype_converters.py
M test/tool_shed/functional/test_0140_tool_help_images.py
M test/tool_shed/functional/test_0150_prior_installation_required.py
M test/tool_shed/functional/test_0160_circular_prior_installation_required.py
M test/tool_shed/functional/test_0170_complex_prior_installation_required.py
M test/tool_shed/functional/test_0300_reset_all_metadata.py
M test/tool_shed/functional/test_0310_hg_push_from_api.py
M test/tool_shed/functional/test_0400_repository_component_reviews.py
M test/tool_shed/functional/test_0410_repository_component_review_access_control.py
M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py
M test/tool_shed/functional/test_0430_browse_utilities.py
M test/tool_shed/functional/test_0440_deleting_dependency_definitions.py
M test/tool_shed/functional/test_0450_skip_tool_tests.py
M test/tool_shed/functional/test_0460_upload_to_repository.py
M test/tool_shed/functional/test_0470_tool_dependency_repository_type.py
M test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py
M test/tool_shed/functional/test_0490_export_import_repositories.py
M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py
M test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py
M test/tool_shed/functional/test_0520_import_export_circular_dependencies.py
M test/tool_shed/functional/test_0530_repository_admin_feature.py
A test/tool_shed/functional/test_0540_get_all_metadata_from_api.py
M test/tool_shed/functional/test_1000_install_basic_repository.py
M test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py
M test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py
M test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py
M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py
M test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py
M test/tool_shed/functional/test_1060_install_repository_with_workflow.py
M test/tool_shed/functional/test_1070_invalid_tool.py
M test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py
R test/tool_shed/functional/test_1085_repository_dependency_handling.py
R test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py
R test/tool_shed/functional/test_1090_install_tool_from_tool_search.py
A test/tool_shed/functional/test_1090_repository_dependency_handling.py
R test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py
A test/tool_shed/functional/test_1100_install_updated_repository_dependencies.py
R test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py
A test/tool_shed/functional/test_1110_install_tool_from_tool_search.py
A test/tool_shed/functional/test_1120_install_repository_with_complex_dependencies.py
R test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py
R test/tool_shed/functional/test_1130_datatype_converters.py
A test/tool_shed/functional/test_1130_install_repository_with_invalid_repository_dependency.py
A test/tool_shed/functional/test_1140_simple_repository_dependency_multiple_owners.py
R test/tool_shed/functional/test_1140_tool_help_images.py
A test/tool_shed/functional/test_1150_datatype_converters.py
R test/tool_shed/functional/test_1150_prior_installation_required.py
R test/tool_shed/functional/test_1160_circular_prior_installation_required.py
A test/tool_shed/functional/test_1160_tool_help_images.py
R test/tool_shed/functional/test_1170_complex_prior_installation_required.py
A test/tool_shed/functional/test_1170_prior_installation_required.py
A test/tool_shed/functional/test_1180_circular_prior_installation_required.py
A test/tool_shed/functional/test_1190_complex_prior_installation_required.py
M test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py
M test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
M test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py
M test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
M test/tool_shed/functional/test_1300_reset_all_metadata.py
M test/tool_shed/functional/test_1400_review_migration_stages.py
M test/tool_shed/functional/test_1410_update_manager.py
M test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py
M test/tool_shed/functional/test_1430_repair_installed_repository.py
M test/tool_shed/functional/test_1440_missing_env_sh_files.py
M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py
M test/tool_shed/functional/test_1460_data_managers.py
M test/tool_shed/functional/test_1470_updating_installed_repositories.py
A test/tool_shed/test_data/0540_files/column_maker/column_maker.tar
A test/tool_shed/test_data/0540_files/column_maker/repository_dependencies.xml
A test/tool_shed/test_data/0540_files/convert_chars/convert_chars.tar
A test/tool_shed/test_data/0540_files/convert_chars/tool_dependencies.xml
A test/tool_shed/test_data/0540_files/package_bwa/tool_dependencies.xml
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_parameter_parsing.py
Log Message:
-----------
(merge conflicts)
Commit: 22148c26c11a30174a6fb9cab23dd96c15fe4984
https://github.com/galaxyproject/galaxy/commit/22148c26c11a30174a6fb9cab23d…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-03-04 (Fri, 04 Mar 2016)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/py3_sources.txt
M .travis.yml
M Makefile
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/onload.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/fontawesome/core.less
M client/galaxy/style/less/ui/icon-btn.less
M client/grunt-tasks/style.js
M client/package.json
M config/galaxy.ini.sample
M create_db.sh
M doc/source/releases/16.01.rst
M doc/source/releases/16.01_announce.rst
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/exceptions/error_codes.json
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/pbs.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/util/job_script/__init__.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/cwl/__init__.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/output_collection_def.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/util/__init__.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/requests_admin.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/api/categories.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/users.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/webapps/tool_shed/model/mapping.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/render.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh
M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py
M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/repository_content_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/util/workflow_util.py
M manage_db.sh
M scripts/api/common.py
M scripts/api/copy_hda_to_library_folder.py
M scripts/api/create.py
M scripts/api/data_manager_example_execute.py
M scripts/api/delete.py
M scripts/api/display.py
M scripts/api/example_watch_folder.py
M scripts/api/form_create_from_xml.py
M scripts/api/history_create_history.py
M scripts/api/history_delete_history.py
M scripts/api/import_library_dataset_to_history.py
M scripts/api/import_workflows_from_installed_tool_shed_repository.py
M scripts/api/install_tool_shed_repositories.py
M scripts/api/library_create_folder.py
M scripts/api/library_create_library.py
M scripts/api/library_upload_dir.py
M scripts/api/library_upload_from_import_dir.py
M scripts/api/load_data_with_metadata.py
M scripts/api/repair_tool_shed_repository.py
M scripts/api/request_type_create_from_xml.py
M scripts/api/requests_update_state.py
M scripts/api/reset_metadata_on_installed_repositories.py
M scripts/api/sample_dataset_update_status.py
M scripts/api/sample_update_state.py
M scripts/api/search.py
M scripts/api/sequencer_configuration_create.py
M scripts/api/update.py
M scripts/api/upload_to_history.py
M scripts/api/workflow_delete.py
M scripts/api/workflow_execute.py
M scripts/api/workflow_execute_parameters.py
M scripts/api/workflow_import.py
M scripts/api/workflow_import_from_file_rpark.py
M scripts/check_galaxy.py
M scripts/cleanup_datasets/cleanup_datasets.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/create_db.py
M scripts/data_libraries/build_lucene_index.py
M scripts/data_libraries/build_whoosh_index.py
M scripts/db_shell.py
M scripts/edam_mapping.py
M scripts/extract_dataset_part.py
M scripts/functional_tests.py
M scripts/galaxy-main
M scripts/get_platforms.py
M scripts/helper.py
M scripts/loc_files/create_all_fasta_loc.py
M scripts/manage_db.py
M scripts/manage_tools.py
M scripts/microbes/BeautifulSoup.py
M scripts/microbes/create_bacteria_loc_file.py
M scripts/microbes/create_bacteria_table.py
M scripts/microbes/create_nib_seq_loc_file.py
M scripts/microbes/get_builds_lengths.py
M scripts/microbes/harvest_bacteria.py
M scripts/microbes/ncbi_to_ucsc.py
M scripts/microbes/util.py
M scripts/migrate_tools/migrate_tools.py
M scripts/others/incorrect_gops_jobs.py
M scripts/others/incorrect_gops_join_jobs.py
M scripts/paster.py
A scripts/patch.sh
M scripts/set_dataset_sizes.py
M scripts/set_user_disk_usage.py
M scripts/tool_shed/build_ts_whoosh_index.py
M scripts/tool_shed/check_download_urls.py
M scripts/tool_shed/migrate_tools_to_repositories.py
M scripts/tools/maf/check_loc_file.py
M scripts/tools/re_escape_output.py
M scripts/transfer.py
M scripts/update_shed_config_path.py
M static/maps/mvc/workflow/workflow-view.js.map
M static/maps/onload.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/onload.js
M static/style/blue/base.css
R templates/admin/requests/select_datasets_to_transfer.mako
M templates/admin/tool_shed_repository/common.mako
M templates/webapps/galaxy/requests/common/common.mako
M templates/webapps/galaxy/requests/common/view_request_history.mako
M templates/webapps/galaxy/requests/common/view_sample_datasets.mako
M templates/webapps/galaxy/workflow/run.mako
M templates/webapps/tool_shed/repository/common.mako
M test/api/test_tools.py
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
M test/docker/base/Dockerfile
M test/docker/base/run_test_wrapper.sh
A test/functional/tools/empty_output.xml
M test/functional/tools/output_format.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/strict_shell.xml
A test/functional/tools/strict_shell_default_off.xml
A test/functional/tools/validation_empty_dataset.xml
M test/tool_shed/base/twilltestcase.py
M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py
M test/unit/jobs/test_command_factory.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/test_objectstore.py
M test/unit/tools/test_evaluation.py
A test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parsing.py
M test/unit/tools_support.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/workflows/test_render.py
M tox.ini
Log Message:
-----------
(merge conflicts)
Commit: 8078306d9af4ce4ebff5b85f20290ee11c98177a
https://github.com/galaxyproject/galaxy/commit/8078306d9af4ce4ebff5b85f2029…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-03-04 (Fri, 04 Mar 2016)
Changed paths:
M lib/galaxy/managers/histories.py
Log Message:
-----------
History manager: remove unused import
Commit: c15e5db2eca3e177febe2da43bfa41b9bcbd4455
https://github.com/galaxyproject/galaxy/commit/c15e5db2eca3e177febe2da43bfa…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-03-07 (Mon, 07 Mar 2016)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/tours.js
M config/tool_conf.xml.main
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/external_services/result_handlers/basic.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
M lib/galaxy/jobs/transfer_manager.py
M lib/galaxy/managers/context.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/search.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/dbkeys.py
M lib/galaxy/util/json.py
M lib/galaxy/visualization/data_providers/basic.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/visualization/plugins/resource_parser.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/workflow/modules.py
M lib/tool_shed/galaxy_install/repair_repository_manager.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/workflow_util.py
M manage_tools.sh
M run_reports.sh
M run_tool_shed.sh
M scripts/check_python.py
M scripts/functional_tests.py
M scripts/transfer.py
M static/maps/layout/menu.js.map
M static/maps/mvc/tours.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/mvc/tours.js
M templates/webapps/tool_shed/repository/view_repository.mako
M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py
M test/tool_shed/base/twilltestcase.py
M tools/data_source/upload.py
Log Message:
-----------
(manually merge conflicts)
Commit: d9fc71510a4ce1c7829457f518f672859d372ed9
https://github.com/galaxyproject/galaxy/commit/d9fc71510a4ce1c7829457f518f6…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-03-08 (Tue, 08 Mar 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/workflow/workflow-canvas.js
M lib/galaxy/managers/workflows.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run_request.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/util/workflow_util.py
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/mvc/workflow/workflow-canvas.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/workflow/workflow-canvas.js
M templates/webapps/galaxy/workflow/editor.mako
M templates/webapps/galaxy/workflow/run.mako
M test/unit/workflows/test_modules.py
Log Message:
-----------
(merge conflicts)
Commit: 4fd5df6d58ac4ddab59006c5251bdf3ef723de68
https://github.com/galaxyproject/galaxy/commit/4fd5df6d58ac4ddab59006c5251b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-03-10 (Thu, 10 Mar 2016)
Changed paths:
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Rebuild client, bundles had unresolved conflicts committed previously.
Commit: effdc314da3f05908eee4770354b457505bfffb4
https://github.com/galaxyproject/galaxy/commit/effdc314da3f05908eee4770354b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-03-10 (Thu, 10 Mar 2016)
Changed paths:
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/history_contents.py
M lib/galaxy/model/__init__.py
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/history/history-view.js.map
M static/maps/mvc/history/multi-panel.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-view.js
M static/scripts/mvc/history/multi-panel.js
Log Message:
-----------
Merge branch 'history.updating' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/6b96f7d5abce...effdc314da3f
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: 4c874c3cdf1cbf6e1a3d687cafc5ee324dc7402d
https://github.com/galaxyproject/usegalaxy-playbook/commit/4c874c3cdf1cbf6e…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-03-09 (Wed, 09 Mar 2016)
Changed paths:
M roles/galaxyprojectdotorg.galaxy/README.md
M roles/galaxyprojectdotorg.galaxy/defaults/main.yml
M roles/galaxyprojectdotorg.galaxy/meta/.galaxy_install_info
M roles/galaxyprojectdotorg.galaxy/tasks/dependencies.yml
M roles/galaxyprojectdotorg.galaxy/tasks/main.yml
Log Message:
-----------
Update galaxyprojectdotorg.galaxy role
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 9b251e567b0a1d5c7600d6aae7df7f22c7831700
https://github.com/galaxyproject/galaxy/commit/9b251e567b0a1d5c7600d6aae7df…
Author: Brad Langhorst <brad(a)langhorst.com>
Date: 2016-03-08 (Tue, 08 Mar 2016)
Changed paths:
M templates/webapps/galaxy/workflow/run.mako
Log Message:
-----------
Tones down the warning message about tool changes
This looked like an error to people here. I think this proposed language is a bit softer, but still conveys the message that users can proceed but should review the changes first to make sure their results will not be affected.
Commit: 079d645bebad8b531d926f08703c5a2ae180b9d5
https://github.com/galaxyproject/galaxy/commit/079d645bebad8b531d926f08703c…
Author: Brad Langhorst <brad(a)langhorst.com>
Date: 2016-03-08 (Tue, 08 Mar 2016)
Changed paths:
M templates/webapps/galaxy/workflow/run.mako
Log Message:
-----------
typo fix
Commit: 7955a2b769d02e57ed609b636621cd76d27bc3a8
https://github.com/galaxyproject/galaxy/commit/7955a2b769d02e57ed609b636621…
Author: Brad Langhorst <brad(a)langhorst.com>
Date: 2016-03-09 (Wed, 09 Mar 2016)
Changed paths:
M templates/webapps/galaxy/workflow/run.mako
Log Message:
-----------
Update run.mako
Commit: 8311b7233f15c04596322db57ca232e8f368d318
https://github.com/galaxyproject/galaxy/commit/8311b7233f15c04596322db57ca2…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-03-09 (Wed, 09 Mar 2016)
Changed paths:
M templates/webapps/galaxy/workflow/run.mako
Log Message:
-----------
Merge pull request #1893 from bwlang/patch-1
Tones down the warning message about tool changes
Compare: https://github.com/galaxyproject/galaxy/compare/cd26a567e84b...8311b7233f15