galaxy-commits January 2016

galaxy-commits@lists.galaxyproject.org

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[galaxyproject/galaxy] f5fbe1: Client: remove older compiled backbone/backbone.js...
by GitHub 23 Jan '16

23 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: f5fbe1c5020fb432346ce6340833937d13cbf6d0 https://github.com/galaxyproject/galaxy/commit/f5fbe1c5020fb432346ce6340833… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-model.js M config/plugins/visualizations/charts/Gruntfile.js M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako R static/maps/libs/backbone/backbone.js.map M static/maps/mvc/visualization/visualization-model.js.map R static/scripts/libs/backbone/backbone.js M static/scripts/mvc/visualization/visualization-model.js Log Message: ----------- Client: remove older compiled backbone/backbone.js, update scatterplot and charts for same; Visualizations: fix visualization-model url; Scatterplot: fix title bug and Galaxy var Commit: 1b7462644d0352d44b36e2d790d6d10d906e7be4 https://github.com/galaxyproject/galaxy/commit/1b7462644d0352d44b36e2d790d6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-22 (Fri, 22 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-model.js M config/plugins/visualizations/charts/Gruntfile.js M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako R static/maps/libs/backbone/backbone.js.map M static/maps/mvc/visualization/visualization-model.js.map R static/scripts/libs/backbone/backbone.js M static/scripts/mvc/visualization/visualization-model.js Log Message: ----------- Merge pull request #1558 from carlfeberhard/release_16.01 [16.01] Fix redundant backbone and visualizations Compare: https://github.com/galaxyproject/galaxy/compare/fe96255022f4...1b7462644d03

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[galaxyproject/galaxy] 4a61a4: UI, Histories: use links for file inputs shown in ...
by GitHub 22 Jan '16

22 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4a61a4cb472f740ce98ead7fca44dcf82847c050 https://github.com/galaxyproject/galaxy/commit/4a61a4cb472f740ce98ead7fca44… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/list/list-view.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/list/list-view.js M templates/show_params.mako Log Message: ----------- UI, Histories: use links for file inputs shown in show_params (the 'i' button in the datasets of histories) that, when clicked, 1) scroll the history to the dataset shown and 2) open *that* datasets info/show_params in the center panel Commit: 017b97b7dc998151ec42c2dca919feb37d5a674d https://github.com/galaxyproject/galaxy/commit/017b97b7dc998151ec42c2dca919… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 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 M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- (repack bundles) Commit: 1275dfd09955c254b801e7be2b741d8845fa4432 https://github.com/galaxyproject/galaxy/commit/1275dfd09955c254b801e7be2b74… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-01-22 (Fri, 22 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/list/list-view.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/list/list-view.js M templates/show_params.mako Log Message: ----------- Merge pull request #1561 from carlfeberhard/input-walking show_params input walking Compare: https://github.com/galaxyproject/galaxy/compare/a162f91447dc...1275dfd09955

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[galaxyproject/galaxy] 2b97a6: History manager: prototype history contents as a s...
by GitHub 22 Jan '16

22 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2b97a654558c95aa3ebfee4d9521c59212e67d09 https://github.com/galaxyproject/galaxy/commit/2b97a654558c95aa3ebfee4d9521… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M lib/galaxy/managers/containers.py M lib/galaxy/managers/histories.py A lib/galaxy/managers/history_contents.py A test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- History manager: prototype history contents as a separate manager - one that is a facade over the common/shared interfaces of the contained classes Commit: 7aace6dee0ddad8c0325b6ccc681f5b62035acb5 https://github.com/galaxyproject/galaxy/commit/7aace6dee0ddad8c0325b6ccc681… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/list/list-panel.js M lib/galaxy/managers/histories.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/framework/base.py M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/list/list-panel.js.map M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/list/list-panel.js Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into managers.history-contents Commit: c9a5ce7c28ef778fb68ce714806ee0e4cc5a16b3 https://github.com/galaxyproject/galaxy/commit/c9a5ce7c28ef778fb68ce714806e… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M lib/galaxy/managers/containers.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- History contents: remove HistoryAsContainer mixin Commit: 2c03d5330f0a45bb00c042b5553fa4fab9c3768b https://github.com/galaxyproject/galaxy/commit/2c03d5330f0a45bb00c042b5553f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: A .ci/check_controller.sh A .ci/check_mako.sh M .ci/flake8_blacklist.txt A .ci/flake8_py3_wrapper.sh M .ci/flake8_wrapper.sh A .ci/py3_sources.txt M .gitignore A CODE_OF_CONDUCT.md M CONTRIBUTING.md M CONTRIBUTORS.md A Makefile M README.rst A client/.docker-build.sh A client/Dockerfile M client/GruntFile.js M client/README.md M client/bower.json A client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/history-panel.js A client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/tool-panel.js R client/galaxy/scripts/base.js R client/galaxy/scripts/galaxy-app-base.js R client/galaxy/scripts/galaxy.autocom_tagging.js R client/galaxy/scripts/galaxy.base.js R client/galaxy/scripts/galaxy.frame.js A client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js R client/galaxy/scripts/galaxy.masthead.js R client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/galaxy.pages.js R client/galaxy/scripts/galaxy.panels.js R client/galaxy/scripts/galaxy.tools.js R client/galaxy/scripts/galaxy.ui.scrollPanel.js A client/galaxy/scripts/layout/masthead.js A client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/layout/modal.js A client/galaxy/scripts/layout/page.js A client/galaxy/scripts/layout/panel.js A client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/libs/IE/IE7.js R client/galaxy/scripts/libs/IE/IE8.js R client/galaxy/scripts/libs/IE/blank.gif R client/galaxy/scripts/libs/IE/excanvas.js R client/galaxy/scripts/libs/IE/ie7-recalc.js A client/galaxy/scripts/libs/backbone.js R client/galaxy/scripts/libs/backbone/backbone.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/farbtastic.js A client/galaxy/scripts/libs/jquery.sparklines.js M client/galaxy/scripts/libs/jquery/jqtouch.js M client/galaxy/scripts/libs/jquery/jquery.dynatree.js M client/galaxy/scripts/libs/jquery/select2.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/libs/tracekit.js A client/galaxy/scripts/mvc/annotation.js R client/galaxy/scripts/mvc/annotations.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js R client/galaxy/scripts/mvc/collection/collection-panel-edit.js R client/galaxy/scripts/mvc/collection/collection-panel.js A client/galaxy/scripts/mvc/collection/collection-view-edit.js A client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js R client/galaxy/scripts/mvc/data.js A client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js A client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js R client/galaxy/scripts/mvc/history/history-panel-annotated.js R client/galaxy/scripts/mvc/history/history-panel-edit-current.js R client/galaxy/scripts/mvc/history/history-panel-edit.js R client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/history-structure-view.js A client/galaxy/scripts/mvc/history/history-view-annotated.js A client/galaxy/scripts/mvc/history/history-view-edit-current.js A client/galaxy/scripts/mvc/history/history-view-edit.js A client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/job/job-model.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/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/list/list-item.js R client/galaxy/scripts/mvc/list/list-panel.js A client/galaxy/scripts/mvc/list/list-view.js A client/galaxy/scripts/mvc/tag.js R client/galaxy/scripts/mvc/tags.js A client/galaxy/scripts/mvc/tool/tool-form-base.js A client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/tool/tool-form-workflow.js A client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/tool/tool-template.js A client/galaxy/scripts/mvc/tool/tools.js R client/galaxy/scripts/mvc/tools.js R client/galaxy/scripts/mvc/tools/tools-form-base.js R client/galaxy/scripts/mvc/tools/tools-form-workflow.js R client/galaxy/scripts/mvc/tools/tools-form.js R client/galaxy/scripts/mvc/tools/tools-jobs.js R client/galaxy/scripts/mvc/tools/tools-template.js M client/galaxy/scripts/mvc/ui/popup-menu.js R client/galaxy/scripts/mvc/ui/ui-button-check.js R client/galaxy/scripts/mvc/ui/ui-button-menu.js A client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-ftp.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/ui/ui-slider.js A client/galaxy/scripts/mvc/upload/composite/composite-row.js A client/galaxy/scripts/mvc/upload/composite/composite-view.js A client/galaxy/scripts/mvc/upload/default/default-row.js A client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-model.js R client/galaxy/scripts/mvc/upload/upload-row.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/nls/zh/locale.js A client/galaxy/scripts/onload.js A client/galaxy/scripts/polyfills.js A client/galaxy/scripts/reports_webapp/run_stats.js R client/galaxy/scripts/rgenetics/checkbox_and_radiobutton.js R client/galaxy/scripts/rgenetics/helper_functions.js R client/galaxy/scripts/rgenetics/timer.js M client/galaxy/scripts/templates/compiled/panel_section.js M client/galaxy/scripts/templates/compiled/tool_form.js M client/galaxy/scripts/templates/compiled/tool_link.js M client/galaxy/scripts/templates/compiled/tool_search.js M client/galaxy/scripts/templates/tool_link.handlebars R client/galaxy/scripts/tools/rgenetics/checkbox_and_radiobutton.js R client/galaxy/scripts/tools/rgenetics/helper_functions.js R client/galaxy/scripts/tools/rgenetics/timer.js A client/galaxy/scripts/ui/autocom_tagging.js A client/galaxy/scripts/ui/editable-text.js A client/galaxy/scripts/ui/popupmenu.js A client/galaxy/scripts/ui/scroll-panel.js M client/galaxy/scripts/utils/add-logging.js M client/galaxy/scripts/utils/ajax-queue.js A client/galaxy/scripts/utils/async-save-text.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/localization.js M client/galaxy/scripts/utils/metrics-logger.js A client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/trackster/util.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/style/less/base.less M client/galaxy/style/less/bootstrap.less M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/galaxy/style/less/history.less M client/galaxy/style/less/library.less M client/galaxy/style/less/list-item.less A client/galaxy/style/less/reports.less M client/galaxy/style/less/trackster.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M client/grunt-tasks/install-libs.js M client/grunt-tasks/scripts.js M client/grunt-tasks/style.js M client/grunt-tasks/templates.js M client/package.json M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-listrow-view.js A client/webpack.config.js M config/auth_conf.xml.sample M config/datatypes_conf.xml.sample A config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.xml A config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js A config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/static/js/ipython.js M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js M config/plugins/visualizations/charts/static/charts/tools.js M config/plugins/visualizations/charts/static/library/ui-table-form.js M config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/static/views/group.js M config/plugins/visualizations/charts/static/views/viewport.js M config/plugins/visualizations/charts/templates/charts.mako A config/plugins/visualizations/csg/config/csg.xml A config/plugins/visualizations/csg/static/Detector.js A config/plugins/visualizations/csg/static/OrbitControls.js A config/plugins/visualizations/csg/static/PLYLoader.js A config/plugins/visualizations/csg/static/VTKLoader.js A config/plugins/visualizations/csg/static/dat.gui.min.js A config/plugins/visualizations/csg/static/three.min.js A config/plugins/visualizations/csg/templates/csg.mako A config/plugins/visualizations/graphviz/README.md A config/plugins/visualizations/graphviz/config/graphviz.xml A config/plugins/visualizations/graphviz/static/css/style.css A config/plugins/visualizations/graphviz/static/img/15xvbd5.png A config/plugins/visualizations/graphviz/static/img/lite-blue-check.png A config/plugins/visualizations/graphviz/static/js/collapse.js A config/plugins/visualizations/graphviz/static/js/cytoscape.min.js A config/plugins/visualizations/graphviz/static/js/graphVis.js A config/plugins/visualizations/graphviz/static/js/jquery.qtip.js A config/plugins/visualizations/graphviz/static/js/tip_centerwindow.js A config/plugins/visualizations/graphviz/static/js/tip_followscroll.js A config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js A config/plugins/visualizations/graphviz/static/js/wz_tooltip.js A config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/trackster/config/trackster.xml A config/reports.ini.sample R config/reports_wsgi.ini.sample M config/tool_data_table_conf.xml.sample M config/tool_shed.ini.sample M contrib/galaxy_config_merger.py M 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test/qunit/tests/modal_tests.html A test/qunit/tests/modal_tests.js A test/qunit/tests/popover_tests.html A test/qunit/tests/popover_tests.js M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/base/twilltestcase.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/test_routes.py A test/unit/tools/test_conda_resolution.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into managers.history-contents Commit: cec03b8d767f8841ce26b8be2e8c5d6a984701df https://github.com/galaxyproject/galaxy/commit/cec03b8d767f8841ce26b8be2e8c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-12 (Tue, 12 Jan 2016) Changed paths: M lib/galaxy/managers/history_contents.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- History contents manager: fix tests Commit: 8e4d3845fdc6c535912d5cbca85646b367890362 https://github.com/galaxyproject/galaxy/commit/8e4d3845fdc6c535912d5cbca856… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/history_contents.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- History contents manager: (an attempt to) clarify/simplify/clean up, re-implement default_order_by and respect it Commit: 28b8816f46d4619b396a13deb21f15135b020b7b https://github.com/galaxyproject/galaxy/commit/28b8816f46d4619b396a13deb21f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py Log Message: ----------- History contents manager: fully 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lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/pulsar/client/amqp_exchange.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M setup.cfg M static/maps/utils/utils.js.map 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/utils/utils.js M test/casperjs/casperjs_runner.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into managers.history-contents Commit: bd237cd5863352faba908bbcf39529cd176601a0 https://github.com/galaxyproject/galaxy/commit/bd237cd5863352faba908bbcf395… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/managers/containers.py M lib/galaxy/managers/history_contents.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- History contents manager: add tests, fix order_by defaulting, clarify 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test/functional/tools/output_action_change_format.xml M test/qunit/tests/masthead_tests.js A test/qunit/tests/ui_tests.html A test/qunit/tests/ui_tests.js M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_execution.py M test/unit/unittest_utils/galaxy_mock.py A test/unit/web/framework/__init__.py A test/unit/web/framework/test_webapp.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into managers.history-contents Commit: 8ab1607b556b872ccedc6411790786f0a1b5db42 https://github.com/galaxyproject/galaxy/commit/8ab1607b556b872ccedc64117907… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M test/unit/managers/test_HistoryManager.py Log Message: ----------- Testing: remove unused imports in test_HistoryManager Commit: 48f45cb1853877f78eb917121c0da4fc7dc51c15 https://github.com/galaxyproject/galaxy/commit/48f45cb1853877f78eb917121c0d… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- Testing: remove egg import from test_HistoryContentsManager Commit: a162f91447dc47f89df42246ce313de1e27acd35 https://github.com/galaxyproject/galaxy/commit/a162f91447dc47f89df42246ce31… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-22 (Fri, 22 Jan 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/histories.py A lib/galaxy/managers/history_contents.py A test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge pull request #1490 from carlfeberhard/managers.history-contents An attempt to add limit/offset to history contents Compare: https://github.com/galaxyproject/galaxy/compare/0f52600583e4...a162f91447dc

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[galaxyproject/galaxy] 5f175e: Update run_test_wrapper.sh
by GitHub 22 Jan '16

22 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5f175e35034d2a211264a2b37e9748998dc216e7 https://github.com/galaxyproject/galaxy/commit/5f175e35034d2a211264a2b37e97… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-22 (Fri, 22 Jan 2016) Changed paths: M test/docker/base/run_test_wrapper.sh Log Message: ----------- Update run_test_wrapper.sh Commit: 0f52600583e4a4776a46ad86db75fc5f56912bf2 https://github.com/galaxyproject/galaxy/commit/0f52600583e4a4776a46ad86db75… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-22 (Fri, 22 Jan 2016) Changed paths: M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge pull request #1566 from galaxyproject/upgrade_ts_db Update run_test_wrapper.sh to upgrade the toolshed database before running tests. Compare: https://github.com/galaxyproject/galaxy/compare/ce3f2b9cd18c...0f52600583e4

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[galaxyproject/galaxy] 5f175e: Update run_test_wrapper.sh
by GitHub 22 Jan '16

22 Jan '16

Branch: refs/heads/upgrade_ts_db Home: https://github.com/galaxyproject/galaxy Commit: 5f175e35034d2a211264a2b37e9748998dc216e7 https://github.com/galaxyproject/galaxy/commit/5f175e35034d2a211264a2b37e97… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-22 (Fri, 22 Jan 2016) Changed paths: M test/docker/base/run_test_wrapper.sh Log Message: ----------- Update run_test_wrapper.sh

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[galaxyproject/usegalaxy-playbook] 89cf99: update test to ce3f2b9cd18c0160ae198fe2482cd056c54...
by GitHub 22 Jan '16

22 Jan '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 89cf999d529d4c7ce698952186eccc62a0d889f5 https://github.com/galaxyproject/usegalaxy-playbook/commit/89cf999d529d4c7c… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-01-22 (Fri, 22 Jan 2016) Changed paths: M stage/group_vars/all.yml Log Message: ----------- update test to ce3f2b9cd18c0160ae198fe2482cd056c5449e86

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[galaxyproject/galaxy] 8ceb4d: Force --skip-venv if we can detect that Python is ...
by GitHub 21 Jan '16

21 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 8ceb4d8ee495d21a664e3faece1e072a88048494 https://github.com/galaxyproject/galaxy/commit/8ceb4d8ee495d21a664e3faece1e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Force --skip-venv if we can detect that Python is Conda Python. Commit: fe96255022f4fdf72f39be959a15993d014a0d38 https://github.com/galaxyproject/galaxy/commit/fe96255022f4fdf72f39be959a15… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #1554 from natefoo/conda-interop [16.01] Force --skip-venv if we can detect that Python is Conda Python. Compare: https://github.com/galaxyproject/galaxy/compare/e48388ef6cca...fe96255022f4

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[galaxyproject/galaxy]
by GitHub 21 Jan '16

21 Jan '16

Branch: refs/tags/v15.10.1 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] aad5d9: Bump 15.10 version to 15.10.1 (and apparently it h...
by GitHub 21 Jan '16

21 Jan '16

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: aad5d9a2e557e935bd88f725deb10d0ed82468d8 https://github.com/galaxyproject/galaxy/commit/aad5d9a2e557e935bd88f725deb1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Bump 15.10 version to 15.10.1 (and apparently it has been incorrectly set to 15.10.dev all this time). Commit: 868acc362f6ce8a8b3559fcb88ebb4c060321905 https://github.com/galaxyproject/galaxy/commit/868acc362f6ce8a8b3559fcb88eb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #1555 from natefoo/release_15.10 [15.10] Bump 15.10 version to 15.10.1 Compare: https://github.com/galaxyproject/galaxy/compare/c13b1c088cfb...868acc362f6c

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[galaxyproject/galaxy] cd9563: Fix #1538.
by GitHub 21 Jan '16

21 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: cd95635197eddaeee55be88f96543dc3a97e9343 https://github.com/galaxyproject/galaxy/commit/cd95635197eddaeee55be88f9654… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-20 (Wed, 20 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix #1538. Displaying subcollection mapping in tool forms was broken with #1308 - this fixes that I believe. Commit: e48388ef6cca6505d47b3daf3c2e0c4a5041b3f4 https://github.com/galaxyproject/galaxy/commit/e48388ef6cca6505d47b3daf3c2e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1545 from jmchilton/subcollection_mapping_problem [16.01] Fix #1538. Compare: https://github.com/galaxyproject/galaxy/compare/2fc982027cb3...e48388ef6cca

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