January 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 932e68: Revert "Remove handlebars and rely solely on under...
by GitHub 19 Jan '16

19 Jan '16

Branch: refs/heads/revert-1537-handlebars.removal Home: https://github.com/galaxyproject/galaxy Commit: 932e686ff6f8cff4ba1ab4c710bcf55a679d9685 https://github.com/galaxyproject/galaxy/commit/932e686ff6f8cff4ba1ab4c710bc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-19 (Tue, 19 Jan 2016) Changed paths: M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js A client/galaxy/scripts/libs/handlebars.runtime.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/onload.js A client/galaxy/scripts/templates/compiled/panel_section.js A client/galaxy/scripts/templates/compiled/tool_form.js A client/galaxy/scripts/templates/compiled/tool_link.js A client/galaxy/scripts/templates/compiled/tool_search.js A client/galaxy/scripts/templates/panel_section.handlebars A client/galaxy/scripts/templates/tool_form.handlebars A client/galaxy/scripts/templates/tool_link.handlebars A client/galaxy/scripts/templates/tool_search.handlebars M client/galaxy/style/less/base.less M client/grunt-tasks/install-libs.js M client/grunt-tasks/style.js A client/grunt-tasks/templates.js M client/package.json M client/webpack.config.js M config/plugins/visualizations/scatterplot/Gruntfile.js M config/plugins/visualizations/scatterplot/package.json A config/plugins/visualizations/scatterplot/src/handlebars/chartcontrol.handlebars A config/plugins/visualizations/scatterplot/src/handlebars/datacontrol.handlebars A config/plugins/visualizations/scatterplot/src/handlebars/editor.handlebars M config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js M config/plugins/visualizations/scatterplot/static/scatterplot-edit.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M lib/galaxy/webapps/galaxy/controllers/root.py A static/maps/libs/handlebars.runtime.js.map M static/maps/mvc/tool/tools.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map A static/scripts/libs/handlebars.runtime.js M static/scripts/mvc/tool/tools.js M static/scripts/onload.js A static/scripts/templates/compiled/panel_section.js A static/scripts/templates/compiled/tool_form.js A static/scripts/templates/compiled/tool_link.js A static/scripts/templates/compiled/tool_search.js M static/style/blue/base.css M templates/base/base_panels.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/visualization/sweepster.mako Log Message: ----------- Revert "Remove handlebars and rely solely on underscore templates"

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[galaxyproject/galaxy] cf1bca: UI, Tools: convert handlebars templates for tool p...
by GitHub 19 Jan '16

19 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cf1bcaa0a6b6fa55f922a352a614d52be86c6c60 https://github.com/galaxyproject/galaxy/commit/cf1bcaa0a6b6fa55f922a352a614… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-19 (Tue, 19 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M static/maps/mvc/tool/tools.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/tool/tools.js Log Message: ----------- UI, Tools: convert handlebars templates for tool panel to underscore tempaltes Commit: 250ad3773792a6156d872684d0680a684a4c9908 https://github.com/galaxyproject/galaxy/commit/250ad3773792a6156d872684d068… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-19 (Tue, 19 Jan 2016) Changed paths: R client/galaxy/scripts/templates/compiled/panel_section.js R client/galaxy/scripts/templates/compiled/tool_form.js R client/galaxy/scripts/templates/compiled/tool_link.js R client/galaxy/scripts/templates/compiled/tool_search.js R client/galaxy/scripts/templates/panel_section.handlebars R client/galaxy/scripts/templates/tool_form.handlebars R client/galaxy/scripts/templates/tool_link.handlebars R client/galaxy/scripts/templates/tool_search.handlebars R static/scripts/templates/compiled/panel_section.js R static/scripts/templates/compiled/tool_form.js R static/scripts/templates/compiled/tool_link.js R static/scripts/templates/compiled/tool_search.js Log Message: ----------- UI, Tools: remove handlebars templates Commit: ea304e2f588201c9145317ea664209e2b48b81e5 https://github.com/galaxyproject/galaxy/commit/ea304e2f588201c9145317ea6642… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-19 (Tue, 19 Jan 2016) Changed paths: M templates/base/base_panels.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- UI, Tools: remove handlebars path alias for requirejs from mako templates Commit: 3327bb9316a6c3dcebacdc3b87cf97e9dd789515 https://github.com/galaxyproject/galaxy/commit/3327bb9316a6c3dcebacdc3b87cf… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-19 (Tue, 19 Jan 2016) Changed paths: M client/GruntFile.js M client/README.md M client/bower.json R client/grunt-tasks/templates.js M client/package.json M client/webpack.config.js Log Message: ----------- Client build: remove handlebars infrastructure Commit: 4ea5f15edde00b0b5ca467d870cc14cf581447a8 https://github.com/galaxyproject/galaxy/commit/4ea5f15edde00b0b5ca467d870cc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-19 (Tue, 19 Jan 2016) Changed paths: M config/plugins/visualizations/scatterplot/Gruntfile.js M config/plugins/visualizations/scatterplot/package.json R config/plugins/visualizations/scatterplot/src/handlebars/chartcontrol.handlebars R config/plugins/visualizations/scatterplot/src/handlebars/datacontrol.handlebars R config/plugins/visualizations/scatterplot/src/handlebars/editor.handlebars M config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js M config/plugins/visualizations/scatterplot/static/scatterplot-edit.js Log Message: ----------- Scatterplot: remove handlebars by converting to underscore, remove grunt handlebars task Commit: 3b63341461d19b6afc4987d4fbe94142cd8bcc2a https://github.com/galaxyproject/galaxy/commit/3b63341461d19b6afc4987d4fbe9… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-19 (Tue, 19 Jan 2016) Changed paths: R client/galaxy/scripts/libs/handlebars.runtime.js M client/grunt-tasks/install-libs.js Log Message: ----------- UI: remove handlebars library Commit: bf459c8d55ba7c3c895fbf169b203b37a8c829fd https://github.com/galaxyproject/galaxy/commit/bf459c8d55ba7c3c895fbf169b20… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-19 (Tue, 19 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/onload.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako R static/maps/libs/handlebars.runtime.js.map R static/scripts/libs/handlebars.runtime.js M templates/webapps/galaxy/visualization/sweepster.mako Log Message: ----------- UI: (cleaning up) remove handlebars compiled/map and remaining references Commit: 7dba828632cb6cec10066eb9f6a4c8e41a811948 https://github.com/galaxyproject/galaxy/commit/7dba828632cb6cec10066eb9f6a4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-19 (Tue, 19 Jan 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/style/less/base.less M client/grunt-tasks/style.js M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/mvc/tool/tools.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/tool/tools.js M static/scripts/onload.js M static/style/blue/base.css Log Message: ----------- UI, Tool form: replace spinner gif with font awesome icon Commit: fe6d22e1a7e4e6d38b15f4128554783765bc69a1 https://github.com/galaxyproject/galaxy/commit/fe6d22e1a7e4e6d38b15f4128554… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-19 (Tue, 19 Jan 2016) Changed paths: M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js R client/galaxy/scripts/libs/handlebars.runtime.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/onload.js R client/galaxy/scripts/templates/compiled/panel_section.js R client/galaxy/scripts/templates/compiled/tool_form.js R client/galaxy/scripts/templates/compiled/tool_link.js R client/galaxy/scripts/templates/compiled/tool_search.js R client/galaxy/scripts/templates/panel_section.handlebars R client/galaxy/scripts/templates/tool_form.handlebars R client/galaxy/scripts/templates/tool_link.handlebars R client/galaxy/scripts/templates/tool_search.handlebars M client/galaxy/style/less/base.less M client/grunt-tasks/install-libs.js M client/grunt-tasks/style.js R client/grunt-tasks/templates.js M client/package.json M client/webpack.config.js M config/plugins/visualizations/scatterplot/Gruntfile.js M config/plugins/visualizations/scatterplot/package.json R config/plugins/visualizations/scatterplot/src/handlebars/chartcontrol.handlebars R config/plugins/visualizations/scatterplot/src/handlebars/datacontrol.handlebars R config/plugins/visualizations/scatterplot/src/handlebars/editor.handlebars M config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js M config/plugins/visualizations/scatterplot/static/scatterplot-edit.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M lib/galaxy/webapps/galaxy/controllers/root.py R static/maps/libs/handlebars.runtime.js.map M static/maps/mvc/tool/tools.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map R static/scripts/libs/handlebars.runtime.js M static/scripts/mvc/tool/tools.js M static/scripts/onload.js R static/scripts/templates/compiled/panel_section.js R static/scripts/templates/compiled/tool_form.js R static/scripts/templates/compiled/tool_link.js R static/scripts/templates/compiled/tool_search.js M static/style/blue/base.css M templates/base/base_panels.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/visualization/sweepster.mako Log Message: ----------- Merge pull request #1537 from carlfeberhard/handlebars.removal Remove handlebars and rely solely on underscore templates Compare: https://github.com/galaxyproject/galaxy/compare/f0cdb52f6416...fe6d22e1a7e4

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[galaxyproject/usegalaxy-playbook] 9eba35: rename duplex novo to du novo
by GitHub 19 Jan '16

19 Jan '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9eba3573c0df6ac6ea20db6de8ae6acf28f60883 https://github.com/galaxyproject/usegalaxy-playbook/commit/9eba3573c0df6ac6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-19 (Tue, 19 Jan 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml Log Message: ----------- rename duplex novo to du novo

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[galaxyproject/galaxy] 27ee03: Add js for mako based masthead
by GitHub 19 Jan '16

19 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 27ee036c69c3212743690c2d03699dc68f002388 https://github.com/galaxyproject/galaxy/commit/27ee036c69c3212743690c2d0369… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-19 (Tue, 19 Jan 2016) Changed paths: M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Add js for mako based masthead Commit: f0cdb52f641666afe2d2721493a6c0b7098106e3 https://github.com/galaxyproject/galaxy/commit/f0cdb52f641666afe2d2721493a6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-19 (Tue, 19 Jan 2016) Changed paths: M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Merge pull request #1533 from guerler/fix_toolshed_000 Add js for mako based masthead Compare: https://github.com/galaxyproject/galaxy/compare/10f7c9016445...f0cdb52f6416

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[galaxyproject/usegalaxy-playbook] 779075: Increase memory/cores for align families tool
by GitHub 19 Jan '16

19 Jan '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 779075f34dc649df6b8c8f472fb758d0c3fb4f5d https://github.com/galaxyproject/usegalaxy-playbook/commit/779075f34dc649df… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-19 (Tue, 19 Jan 2016) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Increase memory/cores for align families tool

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[galaxyproject/galaxy] 313c6a: Client-build, Webpack: add tasks to grunt for the ...
by GitHub 18 Jan '16

18 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 313c6a7247cedad288eab7879bc4ba162eff12ac https://github.com/galaxyproject/galaxy/commit/313c6a7247cedad288eab7879bc4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M client/GruntFile.js M client/README.md M client/grunt-tasks/install-libs.js M client/package.json M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Client-build, Webpack: add tasks to grunt for the common webpack tasks, update readme Commit: 9f8cc9a13fa09390fb92291a33469f79ee49f889 https://github.com/galaxyproject/galaxy/commit/9f8cc9a13fa09390fb92291a3346… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M .gitignore M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/base-mvc.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 M client/galaxy/scripts/mvc/collection/collection-view-edit.js M 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 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/dataset/states.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-view.js M 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-li.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/hdca-model.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 M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less A client/grunt-tasks/webpack.js M config/galaxy.ini.sample R config/plugins/interactive_environments/ipython/config/ipython.ini.sample R config/plugins/interactive_environments/ipython/config/ipython.xml R config/plugins/interactive_environments/ipython/static/js/ipython.js R config/plugins/interactive_environments/ipython/templates/ipython.mako R config/plugins/interactive_environments/ipython/templates/notebook.ipynb M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml A config/plugins/tours/core.scratchbook.yaml R config/plugins/visualizations/charts/static/build-app.js M lib/galaxy/config.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt 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/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/output_actions.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/tools/toolbox/panel.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/visualization/genomes.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/extract.py M lib/pulsar/client/amqp_exchange.py M requirements.txt M run.sh M run_tests.sh M scripts/binary_compatibility.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/common_startup.sh M static/maps/layout/menu.js.map M static/maps/mvc/base-mvc.js.map M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-list.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/dataset/states.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hda-model.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-structure-view.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/job-dag.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/workflow/workflow-view.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/layout/menu.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/dataset/states.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/hda-li-edit.js M 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static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako M test/api/helpers.py M test/api/test_tools.py M test/casperjs/casperjs_runner.py M test/casperjs/modules/user.js M test/functional/test_toolbox.py M 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: ----------- Client-build: add the webpack task file, merge dev Commit: 10f7c901644519d2968b21bf843cb08acc9b489b https://github.com/galaxyproject/galaxy/commit/10f7c901644519d2968b21bf843c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-18 (Mon, 18 Jan 2016) Changed paths: M client/GruntFile.js M client/README.md M client/grunt-tasks/install-libs.js A client/grunt-tasks/webpack.js M client/package.json M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #1523 from carlfeberhard/grunt-webpack Client-build, Webpack: add tasks to grunt for the common webpack tasks, update readme Compare: https://github.com/galaxyproject/galaxy/compare/91f1a65cb149...10f7c9016445

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[galaxyproject/usegalaxy-playbook] 445a57: Swapped in PIA as the featured public Galaxy serve...
by GitHub 18 Jan '16

18 Jan '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 445a57258649167b0cba42ecdb6d5a914b9e5409 https://github.com/galaxyproject/usegalaxy-playbook/commit/445a57258649167b… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2016-01-18 (Mon, 18 Jan 2016) Changed paths: A files/galaxy/common/static/welcome_img/PIAGalaxy.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Swapped in PIA as the featured public Galaxy server.

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[galaxyproject/galaxy] fc434d: Handle unvalidated values in depth
by GitHub 15 Jan '16

15 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: fc434d62e971df92bc51b296d119030ca85af303 https://github.com/galaxyproject/galaxy/commit/fc434d62e971df92bc51b296d119… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Handle unvalidated values in depth Commit: 16e0bc08c8333c75c05a1a47de57eed8196bf9d9 https://github.com/galaxyproject/galaxy/commit/16e0bc08c8333c75c05a1a47de57… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1526 from guerler/fix_unvalidated_001 [16.01] Handle unvalidated values in depth Compare: https://github.com/galaxyproject/galaxy/compare/a77403cc9e6e...16e0bc08c833

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[galaxyproject/galaxy] 0e9302: sourcing Conda will write to stderr, we need to re...
by GitHub 15 Jan '16

15 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 0e9302127f4478611170dee237d811e072100e99 https://github.com/galaxyproject/galaxy/commit/0e9302127f4478611170dee237d8… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-01-16 (Sat, 16 Jan 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- sourcing Conda will write to stderr, we need to redirect it to stdout Commit: a77403cc9e6ef2d90ba78822afca601eed09e6ec https://github.com/galaxyproject/galaxy/commit/a77403cc9e6ef2d90ba78822afca… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #1527 from bgruening/release_16.01 Sourcing Conda will write to stderr Compare: https://github.com/galaxyproject/galaxy/compare/817f36626d7e...a77403cc9e6e

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[galaxyproject/galaxy] adb577: UI: use strict and replace leaky uses of Backbone....
by GitHub 15 Jan '16

15 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: adb577e7f85d981c2877452e0915eb0ed509655e https://github.com/galaxyproject/galaxy/commit/adb577e7f85d981c2877452e0915… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-12 (Tue, 12 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/base-mvc.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 M client/galaxy/scripts/mvc/collection/collection-view-edit.js M 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 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 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static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/dataset/states.js M static/scripts/mvc/history/hda-li-edit.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hda-model.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/job-dag.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- UI: use strict and replace leaky uses of Backbone.Events.on with listenTo Commit: d5d39ed85cb96a70ae739cd5210859ee2153dcc5 https://github.com/galaxyproject/galaxy/commit/d5d39ed85cb96a70ae739cd52108… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M .gitignore M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/collection/list-collection-creator.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-view.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M config/galaxy.ini.sample R config/plugins/interactive_environments/ipython/config/ipython.ini.sample R config/plugins/interactive_environments/ipython/config/ipython.xml R config/plugins/interactive_environments/ipython/static/js/ipython.js R config/plugins/interactive_environments/ipython/templates/ipython.mako R config/plugins/interactive_environments/ipython/templates/notebook.ipynb M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml A config/plugins/tours/core.scratchbook.yaml R config/plugins/visualizations/charts/static/build-app.js M lib/galaxy/config.py M lib/galaxy/datatypes/tabular.py A 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scripts/binary_compatibility.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/common_startup.sh M static/maps/layout/menu.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/workflow/workflow-view.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/layout/menu.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako M test/api/helpers.py M test/api/test_tools.py M test/casperjs/casperjs_runner.py M test/casperjs/modules/user.js M test/functional/test_toolbox.py M 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 dev) Commit: 91f1a65cb1495993355c473e858195ae07a6f3b7 https://github.com/galaxyproject/galaxy/commit/91f1a65cb1495993355c473e8581… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/base-mvc.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 M client/galaxy/scripts/mvc/collection/collection-view-edit.js M 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 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/dataset/states.js M 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-li.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/hdca-model.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 M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-quotameter.js M static/maps/mvc/base-mvc.js.map M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-list.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/dataset/states.js.map M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hda-model.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-structure-view.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/job-dag.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/user/user-quotameter.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/base-mvc.js M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/dataset/states.js M static/scripts/mvc/history/hda-li-edit.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hda-model.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/job-dag.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Merge pull request #1522 from carlfeberhard/history.iteration History UI: clean up. Compare: https://github.com/galaxyproject/galaxy/compare/49a72dacc678...91f1a65cb149

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