Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0c03f69c3952ab4dda8c09b39bf5caea97cd10d6 https://github.com/galaxyproject/galaxy/commit/0c03f69c3952ab4dda8c09b39bf5c... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: A client/galaxy/scripts/apps/history-app.js A client/galaxy/scripts/apps/libs.js A client/galaxy/scripts/galaxy-app-webpack.js A client/galaxy/scripts/libs/common-libs.js A client/galaxy/scripts/utils/webpack-localization.js A client/webpack.config.js M lib/galaxy/web/base/controller.py A static/maps/apps/history-app.js.map A static/maps/apps/libs.js.map A static/maps/galaxy-app-webpack.js.map A static/maps/libs/common-libs.js.map A static/maps/utils/webpack-localization.js.map A static/scripts/apps/history-app.js A static/scripts/apps/libs.js A static/scripts/bundled/common.js A static/scripts/bundled/history.bundled.js A static/scripts/bundled/libs.bundled.js A static/scripts/galaxy-app-webpack.js A static/scripts/libs/common-libs.js A static/scripts/utils/webpack-localization.js A templates/js-app.mako Log Message: ----------- Client build, webpack: prototype commit Commit: 25770f4c7cf8c7dfb4f50692fbe2154b4053a484 https://github.com/galaxyproject/galaxy/commit/25770f4c7cf8c7dfb4f50692fbe21... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/galaxy-app-webpack.js M lib/galaxy/managers/configuration.py M lib/galaxy/web/base/controller.py M static/maps/galaxy-app-base.js.map M static/maps/galaxy-app-webpack.js.map M static/scripts/bundled/history.bundled.js M static/scripts/galaxy-app-base.js M static/scripts/galaxy-app-webpack.js Log Message: ----------- Client build, webpack: move app-webpack closer to app-base for replacement/inheritance, fix bootstrapping of configuration and use managers Commit: 1fd38fb3ee467473d5326ef8c197cedcd9472d53 https://github.com/galaxyproject/galaxy/commit/1fd38fb3ee467473d5326ef8c197c... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-07-21 (Tue, 21 Jul 2015) Changed paths: M client/package.json M static/scripts/bundled/history.bundled.js Log Message: ----------- Client build: update webpack versions in package.json; recompile Commit: 0235eceb57101d03f6027a28980535a4accd02a6 https://github.com/galaxyproject/galaxy/commit/0235eceb57101d03f6027a2898053... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-10-23 (Fri, 23 Oct 2015) Changed paths: A .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh R .ci/pep8_sources.txt M .gitignore A CODE_OF_CONDUCT.md M CONTRIBUTING.md M README.rst M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/galaxy.panels.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/farbtastic.js M client/galaxy/scripts/libs/handlebars.runtime.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/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/libs/tracekit.js A client/galaxy/scripts/mvc/app/app-analysis.js A client/galaxy/scripts/mvc/app/app-view.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/list-of-pairs-collection-creator.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/form/form-input.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-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/hdca-li.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-panel-edit-current.js M 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tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/sr_mapping/bfast_wrapper.xml M tools/sr_mapping/fastq_statistics.xml M tools/sr_mapping/mosaik.xml M tools/sr_mapping/srma_wrapper.xml M tools/stats/grouping.py M tools/visualization/LAJ.xml M tox.ini Log Message: ----------- (merge dev) Commit: 5dfb3ffbecf18c9bc1275a4aae7024f69e5ef303 https://github.com/galaxyproject/galaxy/commit/5dfb3ffbecf18c9bc1275a4aae702... 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Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M client/grunt-tasks/scripts.js M static/maps/libs/common-libs.js.map M static/maps/mvc/tools.js.map M static/scripts/libs/common-libs.js M static/scripts/mvc/tools.js M static/scripts/templates/compiled/tool_form.js Log Message: ----------- Webpack: restore original page scripts Commit: 7bfbb71b27af3147a18beaf2fdd889c7e1c7455d https://github.com/galaxyproject/galaxy/commit/7bfbb71b27af3147a18beaf2fdd88... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M .gitignore A lib/galaxy/webapps/galaxy/controllers/test.py Log Message: ----------- Webpack: temp add test controller, add bundled webpack directory to gitignore Commit: 2513e766be2ac2a37b87ff7682dff83688bed815 https://github.com/galaxyproject/galaxy/commit/2513e766be2ac2a37b87ff7682dff... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: A static/scripts/bundled/analysis.bundled.js A static/scripts/bundled/analysis.bundled.js.map A static/scripts/bundled/common.js A static/scripts/bundled/common.js.map A static/scripts/bundled/galaxy.bundled.js A static/scripts/bundled/galaxy.bundled.js.map A static/scripts/bundled/history.bundled.js A static/scripts/bundled/history.bundled.js.map A static/scripts/bundled/libs.bundled.js A static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Webpack: adding production bundles Commit: 4ce8b3d96a0922483de24afe8c02e221ef142f57 https://github.com/galaxyproject/galaxy/commit/4ce8b3d96a0922483de24afe8c02e... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M lib/galaxy/managers/users.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/test.py M templates/js-app.mako Log Message: ----------- Managers, users: change serialize_current_anonymous_user to return None when no history present; Webpack: move jsAppLauncher test controller into root controller, replace index method Commit: 790c2f5954fbb30ad4c3c0362bbd01ab85de9e3a https://github.com/galaxyproject/galaxy/commit/790c2f5954fbb30ad4c3c0362bbd0... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: R lib/galaxy/webapps/galaxy/controllers/test.py Log Message: ----------- Webpack: remove test controller Commit: 1b89d839aed4c14c5cf62e4b6f3c9b4816f419d2 https://github.com/galaxyproject/galaxy/commit/1b89d839aed4c14c5cf62e4b6f3c9... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M templates/base/base_panels.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Webpack: fix newlibs jquery Commit: 9a659d85d6896dffa280005e66cc72abc0dcbab1 https://github.com/galaxyproject/galaxy/commit/9a659d85d6896dffa280005e66cc7... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-03 (Tue, 03 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/common.js M static/scripts/bundled/common.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/bundled/history.bundled.js M static/scripts/bundled/history.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 templates/base.mako M templates/base/base_panels.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Webpack: use bundled libs in base templates Commit: 84b40650ec1adc98879457fe087c5d802838b421 https://github.com/galaxyproject/galaxy/commit/84b40650ec1adc98879457fe087c5... 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client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/templates/compiled/tool_link.js M client/galaxy/scripts/templates/tool_link.handlebars M client/galaxy/scripts/utils/add-logging.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/metrics-logger.js M client/galaxy/style/less/base.less M client/galaxy/style/less/bootstrap.less 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/views/group.js M config/plugins/visualizations/charts/static/views/viewport.js M doc/source/lib/galaxy.auth.providers.rst M doc/source/lib/galaxy.datatypes.rst A doc/source/lib/galaxy.dependencies.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.jobs.runners.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst M doc/source/lib/galaxy.webapps.rst M doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/lib/modules.rst R doc/source/lib/pkg_resources.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/runners/drmaa.py A lib/galaxy/jobs/runners/util/drmaa/__init__.py A lib/galaxy/jobs/runners/util/retry.py A lib/galaxy/jobs/runners/util/sudo.py M lib/galaxy/main.py M lib/galaxy/managers/configuration.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0130_change_pref_datatype.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/deps/commands.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/dockerfiles.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/lint.py A lib/galaxy/tools/lint_util.py M lib/galaxy/tools/linters/command.py M lib/galaxy/tools/linters/help.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/outputs.py A lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/linters/top_level.py A lib/galaxy/tools/linters/xml_order.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/xml_macros.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/pulsar/client/transport/curl.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/hg_util.py M run.sh M run_tests.sh A scripts/binary_compatibility.py M scripts/common_startup.sh A scripts/galaxy-main M scripts/tools/maf/check_loc_file.py M static/maps/galaxy-app-base.js.map M static/maps/galaxy.library.js.map M static/maps/mvc/app/app-analysis.js.map A static/maps/mvc/app/app-login.js.map M static/maps/mvc/app/app-view.js.map M static/maps/mvc/base-mvc.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-panel.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/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-panel.js.map M static/maps/mvc/history/history-structure-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tags.js.map M static/maps/mvc/tools.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/reports_webapp/run_stats.js.map M static/maps/templates/compiled/tool_link.js.map M static/maps/utils/add-logging.js.map M static/maps/utils/deferred.js.map M static/maps/utils/metrics-logger.js.map M static/scripts/galaxy-app-base.js M static/scripts/galaxy.library.js M static/scripts/mvc/app/app-analysis.js A static/scripts/mvc/app/app-login.js M static/scripts/mvc/app/app-view.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-panel.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/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-panel.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/reports_webapp/run_stats.js M static/scripts/templates/compiled/tool_link.js M static/scripts/utils/add-logging.js M static/scripts/utils/deferred.js M static/scripts/utils/metrics-logger.js M static/style/blue/base.css M static/welcome.html.sample M test/qunit/tests/galaxy-app-base.js M tools/data_source/data_source.py M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_concat_fasta.py M tools/filters/axt_to_fasta.py M tools/filters/axt_to_lav.py M tools/filters/catWrapper.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/sort_gtf.py M tools/filters/gff_to_bed_converter.py M tools/filters/lav_to_bed.py M tools/filters/secure_hash_message_digest.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/maf/interval2maf.py M tools/maf/interval2maf.xml M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- (merge dev) Commit: d80d74c8880c8194dc2c727b7fc9dbf2297483f0 https://github.com/galaxyproject/galaxy/commit/d80d74c8880c8194dc2c727b7fc9d... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-05 (Thu, 05 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/galaxy.base.js M client/galaxy/scripts/galaxy.panels.js A client/galaxy/scripts/libs/backbone.js R client/galaxy/scripts/libs/backbone/backbone.js M client/galaxy/scripts/libs/common-libs.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/user/user-model.js M client/grunt-tasks/install-libs.js M client/webpack.config.js M static/maps/galaxy-app-base.js.map M static/maps/galaxy.panels.js.map A static/maps/libs/backbone.js.map M static/maps/libs/common-libs.js.map M static/maps/mvc/base-mvc.js.map M static/maps/mvc/user/user-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map R static/scripts/bundled/common.js R static/scripts/bundled/common.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map R static/scripts/bundled/history.bundled.js R static/scripts/bundled/history.bundled.js.map R static/scripts/bundled/libs.bundled.js R static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy-app-base.js M static/scripts/galaxy.base.js M static/scripts/galaxy.panels.js A static/scripts/libs/backbone.js M static/scripts/libs/common-libs.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/user/user-model.js M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/sweepster.mako Log Message: ----------- Client libs: move backbone down into /libs (not backbone/backbone); Webpack: move to non-entry vendor bundling for libraries, clean up assoc. Commit: 4f242151e7f6519e27ecae04632bdbbccddb2879 https://github.com/galaxyproject/galaxy/commit/4f242151e7f6519e27ecae04632bd... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-05 (Thu, 05 Nov 2015) Changed paths: R client/galaxy/scripts/apps/history-app.js R client/galaxy/scripts/apps/libs.js R client/galaxy/scripts/libs/common-libs.js R static/maps/apps/history-app.js.map R static/maps/apps/libs.js.map M static/maps/galaxy-app-base.js.map M static/maps/galaxy.base.js.map R static/scripts/apps/history-app.js R static/scripts/apps/libs.js M static/scripts/galaxy-app-base.js M static/scripts/galaxy.base.js M static/scripts/mvc/base-mvc.js Log Message: ----------- Webpack: remove libs and history apps, grunt:pack scripts Commit: e59d08f85631eacb83eada88c3351e4c19bcd667 https://github.com/galaxyproject/galaxy/commit/e59d08f85631eacb83eada88c3351... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-06 (Fri, 06 Nov 2015) Changed paths: R client/galaxy/scripts/galaxy-app-webpack.js A client/galaxy/scripts/galaxy-async.js R client/galaxy/scripts/galaxy.autocom_tagging.js M client/galaxy/scripts/galaxy.base.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/galaxy.panels.js A client/galaxy/scripts/modal.js M client/galaxy/scripts/mvc/annotations.js M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/collection/collection-panel-edit.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-panel-edit.js M client/galaxy/scripts/mvc/workflow/workflow-view.js A client/galaxy/scripts/polyfills.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/utils/async-save-text.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/webpack.config.js R static/maps/galaxy-app-webpack.js.map A static/maps/galaxy-async.js.map R static/maps/galaxy.autocom_tagging.js.map M static/maps/galaxy.base.js.map M static/maps/galaxy.pages.js.map M static/maps/galaxy.panels.js.map A static/maps/modal.js.map M static/maps/mvc/annotations.js.map M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/app/app-view.js.map M static/maps/mvc/collection/collection-panel-edit.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/history-panel-edit.js.map M static/maps/mvc/workflow/workflow-view.js.map A static/maps/polyfills.js.map A static/maps/ui/autocom_tagging.js.map A static/maps/ui/editable-text.js.map A static/maps/ui/popupmenu.js.map A static/maps/utils/async-save-text.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/trackster/util.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map R static/scripts/galaxy-app-webpack.js A static/scripts/galaxy-async.js R static/scripts/galaxy.autocom_tagging.js M static/scripts/galaxy.base.js M static/scripts/galaxy.pages.js M static/scripts/galaxy.panels.js A static/scripts/modal.js M static/scripts/mvc/annotations.js M static/scripts/mvc/app/app-view.js M static/scripts/mvc/collection/collection-panel-edit.js M static/scripts/mvc/history/history-panel-edit.js M static/scripts/mvc/workflow/workflow-view.js A static/scripts/polyfills.js A static/scripts/ui/autocom_tagging.js A static/scripts/ui/editable-text.js A static/scripts/ui/popupmenu.js A static/scripts/utils/async-save-text.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/tracks.js M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako M templates/refresh_frames.mako M templates/tagging_common.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Webpack: move vendor to libs; break up galaxy.panels to panels and modal; break up galaxy.base to polyfills, galaxy-async, ui/popupmenu, ui/editable-text, and utils/async-save-text; move reset_tool_search into workflow-view; move commatize into trackster/util; move galaxy.autocom_tagging to ui/autocom_tagging Commit: 9c35d35c52eca6638e25459293ac9a28e40f9d63 https://github.com/galaxyproject/galaxy/commit/9c35d35c52eca6638e25459293ac9... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: R client/galaxy/scripts/galaxy.base.js M client/galaxy/scripts/galaxy.masthead.js R client/galaxy/scripts/galaxy.panels.js M client/galaxy/scripts/mvc/app/app-view.js A client/galaxy/scripts/onload.js A client/galaxy/scripts/panel.js M client/galaxy/scripts/ui/autocom_tagging.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/trackster/util.js M client/webpack.config.js R static/maps/galaxy.base.js.map R static/maps/galaxy.panels.js.map M static/maps/mvc/app/app-view.js.map A static/maps/onload.js.map A static/maps/panel.js.map M static/maps/ui/autocom_tagging.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/trackster/util.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map R static/scripts/galaxy.base.js R static/scripts/galaxy.panels.js M static/scripts/mvc/app/app-view.js A static/scripts/onload.js A static/scripts/panel.js M static/scripts/ui/autocom_tagging.js M static/scripts/viz/trackster/util.js Log Message: ----------- Webpack: make autocom_tagging into a module, export commatize, rename galaxy.base to onload and galaxy.panels to panels Commit: 649a83c1aa8026160f8d77cb423547ecb76cda28 https://github.com/galaxyproject/galaxy/commit/649a83c1aa8026160f8d77cb42354... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.frame.js M client/galaxy/scripts/galaxy.masthead.js M client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/style/less/base.less M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/galaxy.frame.js.map M static/maps/galaxy.masthead.js.map M static/maps/galaxy.menu.js.map M static/maps/mvc/app/app-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/galaxy.frame.js M static/scripts/galaxy.masthead.js M static/scripts/galaxy.menu.js M static/scripts/mvc/app/app-view.js M static/style/blue/base.css M templates/js-app.mako M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Webpack: (shoulda been 2 sep. commits) re-add minimal DOM for 1,2,3 panel layouts via server-side/js-app.mako, correct noscript tag styling; Instantiate galaxy.frame and galaxy.menu from galaxy.masthead (currently the only user), reverse dependencies in them (masthead imports them), and move GalaxyMastheadTab into galaxy.menu and GalaxyMastheadIcon into galaxy.frame - allowing a single import of galaxy.masthead Commit: a639b0c996b13d45412115009615af826ca38ed8 https://github.com/galaxyproject/galaxy/commit/a639b0c996b13d45412115009615a... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: R client/galaxy/scripts/galaxy.frame.js R client/galaxy/scripts/galaxy.masthead.js R client/galaxy/scripts/galaxy.menu.js A client/galaxy/scripts/layout/masthead.js A client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/layout/panel.js A client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/app/app-view.js R client/galaxy/scripts/panel.js M client/webpack.config.js R static/maps/galaxy.frame.js.map R static/maps/galaxy.masthead.js.map R static/maps/galaxy.menu.js.map A static/maps/layout/masthead.js.map A static/maps/layout/menu.js.map A static/maps/layout/panel.js.map A static/maps/layout/scratchbook.js.map M static/maps/mvc/app/app-view.js.map R static/maps/panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map R static/scripts/galaxy.frame.js R static/scripts/galaxy.masthead.js R static/scripts/galaxy.menu.js A static/scripts/layout/masthead.js A static/scripts/layout/menu.js A static/scripts/layout/panel.js A static/scripts/layout/scratchbook.js M static/scripts/mvc/app/app-view.js R static/scripts/panel.js M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Webpack: move galaxy.masthead and galaxy.menu to layout/masthead and layout/menu, panel to layout/panel, and rename galaxy.frame to layout/scratchbook Commit: b1266b45dc4ddd63a2b2ae1cc9c28ba9d43a2bc0 https://github.com/galaxyproject/galaxy/commit/b1266b45dc4ddd63a2b2ae1cc9c28... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/galaxy.js A client/galaxy/scripts/apps/history-panel.js A client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/galaxy-app-base.js A client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/onload.js M client/webpack.config.js M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/galaxy-app-base.js.map A static/maps/layout/page.js.map M static/maps/layout/panel.js.map M static/maps/mvc/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/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/galaxy-app-base.js A static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/mvc/tools.js M static/scripts/onload.js M templates/base/base_panels.mako M templates/js-app.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Webpack: move panel to Backbone, implement ToolPanel and HistoryPanel; simplify js-app.mako (by removing alternate layouts); clean up debugging info, make Galaxy less chatty before logging setup Commit: c1cc3bd483fc2197b43048f467be6e80f80babea https://github.com/galaxyproject/galaxy/commit/c1cc3bd483fc2197b43048f467be6... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.library.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-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M static/scripts/galaxy.library.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-libraryrow-view.js M templates/base/base_panels.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Webpack: fix masthead in libraries; update Panel usage in base_panels.mako, galaxy.panels.mako Commit: a4edf159be9996d09bb029d2098d9c0d39fb2975 https://github.com/galaxyproject/galaxy/commit/a4edf159be9996d09bb029d2098d9... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M .gitignore M CONTRIBUTORS.md M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/libs/jquery/select2.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.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-select-content.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M config/plugins/visualizations/charts/static/build-app.js M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/users.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/users.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M run.sh A scripts/check_eggs.py A scripts/fetch_eggs.py M static/maps/galaxy-app-base.js.map M static/maps/libs/jquery/select2.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.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-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/utils/deferred.js.map M static/maps/utils/uploadbox.js.map M static/scripts/galaxy-app-base.js M static/scripts/libs/jquery/select2.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-button.js M static/scripts/utils/deferred.js M static/scripts/utils/uploadbox.js M static/style/blue/base.css M test/api/helpers.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/unicode_stream.xml M test/unit/jobs/test_job_output_checker.py M tools/filters/wig_to_bigwig.xml M tools/stats/gsummary.py Log Message: ----------- (merge dev) Commit: dc0b960ea1242ae3ec34e7d00c5f8619e06f7b59 https://github.com/galaxyproject/galaxy/commit/dc0b960ea1242ae3ec34e7d00c5f8... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/onload.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/onload.js M templates/base/base_panels.mako M templates/js-app.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Webpack: lowercase DD-helper throughout project to reflect changes in 7717659 Commit: 78e6253178b51afa77346b259801f221eb9c201e https://github.com/galaxyproject/galaxy/commit/78e6253178b51afa77346b259801f... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: A client/galaxy/scripts/layout/modal.js R client/galaxy/scripts/modal.js M client/galaxy/scripts/onload.js M client/webpack.config.js A static/maps/layout/modal.js.map R static/maps/modal.js.map A static/scripts/layout/modal.js R static/scripts/modal.js Log Message: ----------- Webpack: move old school modal into layout/ Commit: 215391f571f72725a87f45b556be10e8446db8a9 https://github.com/galaxyproject/galaxy/commit/215391f571f72725a87f45b556be1... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: R client/galaxy/scripts/galaxy-async.js R static/maps/galaxy-async.js.map R static/scripts/galaxy-async.js Log Message: ----------- Webpack: remove galaxy-async Commit: 350a53f1ef9c686ad3617cc37f037251a79a28ef https://github.com/galaxyproject/galaxy/commit/350a53f1ef9c686ad3617cc37f037... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: R client/galaxy/scripts/base.js M client/galaxy/scripts/viz/trackster.js R static/maps/base.js.map M static/maps/viz/trackster.js.map R static/scripts/base.js M static/scripts/viz/trackster.js Log Message: ----------- Webpack: move base.Base to trackster (which uses it) Commit: f971e17f95d62662eaec47a96da88f1b45d823ce https://github.com/galaxyproject/galaxy/commit/f971e17f95d62662eaec47a96da88... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: R client/galaxy/scripts/galaxy.ui.scrollPanel.js A client/galaxy/scripts/ui/scroll-panel.js R static/maps/galaxy.ui.scrollPanel.js.map A static/maps/ui/scroll-panel.js.map R static/scripts/galaxy.ui.scrollPanel.js A static/scripts/ui/scroll-panel.js Log Message: ----------- Webpack: move galaxy.ui.scrollPanel into ui/scroll-panel Commit: 93629bb29e35340618aca2d1b420d948b56c695b https://github.com/galaxyproject/galaxy/commit/93629bb29e35340618aca2d1b420d... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M client/package.json M client/webpack.config.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map Log Message: ----------- Webpack: add handlebars loader, update tools.js Commit: 2f0b64613770c8e59613bb46218e12565d260038 https://github.com/galaxyproject/galaxy/commit/2f0b64613770c8e59613bb46218e1... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/galaxy.tools.js M client/galaxy/scripts/mvc/app/app-analysis.js R client/galaxy/scripts/mvc/tools.js A client/galaxy/scripts/mvc/tools/tools.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster/tracks.js R static/maps/mvc/tools.js.map A static/maps/mvc/tools/tools.js.map R static/scripts/mvc/tools.js A static/scripts/mvc/tools/tools.js Log Message: ----------- Webpack: move tools.js into mvc/tools/ Commit: 372c2e9e43854b0e5e576abcead50e22f00923d9 https://github.com/galaxyproject/galaxy/commit/372c2e9e43854b0e5e576abcead50... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/mvc/data.js A client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/tools/tools.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M static/maps/galaxy.tools.js.map M static/maps/layout/scratchbook.js.map M static/maps/mvc/app/app-analysis.js.map R static/maps/mvc/data.js.map A static/maps/mvc/dataset/data.js.map M static/maps/mvc/tools/tools.js.map M static/maps/onload.js.map M static/maps/ui/scroll-panel.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/sweepster.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.tools.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/app/app-analysis.js R static/scripts/mvc/data.js A static/scripts/mvc/dataset/data.js M static/scripts/mvc/tools/tools.js M static/scripts/onload.js M static/scripts/ui/scroll-panel.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako Log Message: ----------- Webpack: move data.js into dataset/data.js; pack scripts Commit: 6d0ab669ecbd12e75cf38f8c914bbf5954caac20 https://github.com/galaxyproject/galaxy/commit/6d0ab669ecbd12e75cf38f8c914bb... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M client/webpack.config.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Webpack: correctly load jQuery-ui, require bibtex in citations, and move polyfills to first loaded Commit: c66bc7ab766e2af197a668a76e15e1dc21cfb9fa https://github.com/galaxyproject/galaxy/commit/c66bc7ab766e2af197a668a76e15e... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: 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 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 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/webpack.config.js R static/maps/mvc/collection/collection-panel-edit.js.map R static/maps/mvc/collection/collection-panel.js.map A static/maps/mvc/collection/collection-view-edit.js.map A static/maps/mvc/collection/collection-view.js.map R static/maps/mvc/history/history-panel-annotated.js.map R static/maps/mvc/history/history-panel-edit-current.js.map R static/maps/mvc/history/history-panel-edit.js.map R static/maps/mvc/history/history-panel.js.map A static/maps/mvc/history/history-view-annotated.js.map A static/maps/mvc/history/history-view-edit-current.js.map A static/maps/mvc/history/history-view-edit.js.map A static/maps/mvc/history/history-view.js.map R static/scripts/mvc/collection/collection-panel-edit.js R static/scripts/mvc/collection/collection-panel.js A static/scripts/mvc/collection/collection-view-edit.js A static/scripts/mvc/collection/collection-view.js R static/scripts/mvc/history/history-panel-annotated.js R static/scripts/mvc/history/history-panel-edit-current.js R static/scripts/mvc/history/history-panel-edit.js R static/scripts/mvc/history/history-panel.js A static/scripts/mvc/history/history-view-annotated.js A static/scripts/mvc/history/history-view-edit-current.js A static/scripts/mvc/history/history-view-edit.js A static/scripts/mvc/history/history-view.js Log Message: ----------- Webpack: normalize history and panel module names with other mvc modules (history-panel is not a panel - just a view) Commit: 55068dea285c82232bd9dbf024de580013c5f3d8 https://github.com/galaxyproject/galaxy/commit/55068dea285c82232bd9dbf024de5... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/base-mvc.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/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.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/multi-panel.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/nls/zh/locale.js M static/maps/mvc/app/app-analysis.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/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.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/multi-panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.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/multi-panel.js M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- Webpack: normalize 'panel' names part-2: history and collection modules Commit: 8efabbbcd5546441182cbff1cc66e525cf6abf48 https://github.com/galaxyproject/galaxy/commit/8efabbbcd5546441182cbff1cc66e... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M templates/grid_base.mako M templates/webapps/galaxy/dataset/edit_attributes.mako M templates/webapps/galaxy/library/common/ldda_edit_info.mako M templates/webapps/galaxy/library/common/move_library_item.mako M templates/webapps/galaxy/library/common/upload.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/requests/common/create_request.mako M templates/webapps/galaxy/requests/common/find_samples.mako M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Webpack: fix load order in embedded grids by removing autocom_tagging script tag (it's in the libs.bundle), remove it from other mako templates as well; remove bibtex script from workflow/editor.mako (unused) Commit: c3f4b54b686ba93b3bb8f65d17f3961d344b9d7c https://github.com/galaxyproject/galaxy/commit/c3f4b54b686ba93b3bb8f65d17f39... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/utils/localization.js R client/galaxy/scripts/utils/webpack-localization.js M client/package.json M client/webpack.config.js M static/maps/galaxy-app-base.js.map M static/maps/utils/localization.js.map R static/maps/utils/webpack-localization.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/utils/localization.js R static/scripts/utils/webpack-localization.js Log Message: ----------- Webpack, localization: support both requirejs and webpack i18n by including the amdi18n-loader (both now share the utils/localization file) Commit: 6f754216a4100969b18185aa705065b03a215628 https://github.com/galaxyproject/galaxy/commit/6f754216a4100969b18185aa70506... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js R client/galaxy/scripts/mvc/list/list-panel.js A client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-list.js.map M static/maps/mvc/history/history-view.js.map R static/maps/mvc/list/list-panel.js.map A 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/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/history/history-view.js R static/scripts/mvc/list/list-panel.js A static/scripts/mvc/list/list-view.js Log Message: ----------- Webpack: normalize list-panel to list-view Commit: d285c01108f59d1b054955f312b16c3b978aa97a https://github.com/galaxyproject/galaxy/commit/d285c01108f59d1b054955f312b16... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: A client/galaxy/scripts/mvc/annotation.js R client/galaxy/scripts/mvc/annotations.js A client/galaxy/scripts/mvc/tag.js R client/galaxy/scripts/mvc/tags.js A client/galaxy/scripts/mvc/tool/tools-form-base.js A client/galaxy/scripts/mvc/tool/tools-form-workflow.js A client/galaxy/scripts/mvc/tool/tools-form.js A client/galaxy/scripts/mvc/tool/tools-jobs.js A client/galaxy/scripts/mvc/tool/tools-template.js A client/galaxy/scripts/mvc/tool/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 R client/galaxy/scripts/mvc/tools/tools.js Log Message: ----------- Webpack: normalize tags, annotations, and tools (the names of) Commit: 894af4c5deadc75d2f1a5e11e26abc9c3f4f7256 https://github.com/galaxyproject/galaxy/commit/894af4c5deadc75d2f1a5e11e26ab... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: A static/maps/mvc/annotation.js.map R static/maps/mvc/annotations.js.map A static/maps/mvc/tag.js.map R static/maps/mvc/tags.js.map A static/maps/mvc/tool/tools-form-base.js.map A static/maps/mvc/tool/tools-form-workflow.js.map A static/maps/mvc/tool/tools-form.js.map A static/maps/mvc/tool/tools-jobs.js.map A static/maps/mvc/tool/tools-template.js.map A static/maps/mvc/tool/tools.js.map R static/maps/mvc/tools/tools-form-base.js.map R static/maps/mvc/tools/tools-form-workflow.js.map R static/maps/mvc/tools/tools-form.js.map R static/maps/mvc/tools/tools-jobs.js.map R static/maps/mvc/tools/tools-template.js.map R static/maps/mvc/tools/tools.js.map A static/scripts/mvc/annotation.js R static/scripts/mvc/annotations.js A static/scripts/mvc/tag.js R static/scripts/mvc/tags.js A static/scripts/mvc/tool/tools-form-base.js A static/scripts/mvc/tool/tools-form-workflow.js A static/scripts/mvc/tool/tools-form.js A static/scripts/mvc/tool/tools-jobs.js A static/scripts/mvc/tool/tools-template.js A static/scripts/mvc/tool/tools.js R static/scripts/mvc/tools/tools-form-base.js R static/scripts/mvc/tools/tools-form-workflow.js R static/scripts/mvc/tools/tools-form.js R static/scripts/mvc/tools/tools-jobs.js R static/scripts/mvc/tools/tools-template.js R static/scripts/mvc/tools/tools.js Log Message: ----------- Webpack: normalize tags, annotations, and tools (2 of 3) Commit: cc6c15f3b102afd22c3a9f1c7d1a5d92daad03bc https://github.com/galaxyproject/galaxy/commit/cc6c15f3b102afd22c3a9f1c7d1a5... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/tool/tools-form-base.js M client/galaxy/scripts/mvc/tool/tools-form-workflow.js M client/galaxy/scripts/mvc/tool/tools-form.js M client/galaxy/scripts/mvc/tool/tools-jobs.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/viz/trackster/tracks.js M static/maps/mvc/annotation.js.map M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/tag.js.map M static/maps/mvc/tool/tools-form-base.js.map M static/maps/mvc/tool/tools-form-workflow.js.map M static/maps/mvc/tool/tools-form.js.map M static/maps/mvc/tool/tools-jobs.js.map M static/maps/mvc/tool/tools-template.js.map M static/maps/mvc/tool/tools.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/mvc/annotation.js M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/tag.js M static/scripts/mvc/tool/tools-form-base.js M static/scripts/mvc/tool/tools-form-workflow.js M static/scripts/mvc/tool/tools-form.js M static/scripts/mvc/tool/tools-jobs.js M static/scripts/mvc/tool/tools-template.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/viz/trackster/tracks.js Log Message: ----------- Webpack: normalize tags, annotations, and tools (change refs - 3 of 3) Commit: 2956b12e9b292e42dfd2e2309b5c7d29b5b0d48b https://github.com/galaxyproject/galaxy/commit/2956b12e9b292e42dfd2e2309b5c7... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js 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/citation/citation-model.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/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-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-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/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.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-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-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/tag.js M client/galaxy/scripts/mvc/tool/tools-form-workflow.js M client/galaxy/scripts/mvc/tool/tools-jobs.js M client/galaxy/scripts/mvc/tool/tools.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/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/circster.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/visualization.js M static/maps/galaxy-app-base.js.map M static/maps/galaxy.library.js.map M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.js.map M static/maps/mvc/citation/citation-model.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/list-of-pairs-collection-creator.js.map M static/maps/mvc/dataset/data.js.map M static/maps/mvc/dataset/dataset-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-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/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/job/job-model.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/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/tag.js.map M static/maps/mvc/tool/tools-form-workflow.js.map M static/maps/mvc/tool/tools-jobs.js.map M static/maps/mvc/tool/tools.js.map M static/maps/mvc/ui/ui-select-ftp.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-view-data.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/utils/utils.js.map M static/maps/viz/circster.js.map M static/maps/viz/sweepster.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/visualization.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/galaxy-app-base.js M static/scripts/galaxy.library.js M static/scripts/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-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-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/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/tag.js M static/scripts/mvc/tool/tools-form-workflow.js M static/scripts/mvc/tool/tools-jobs.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/ui/ui-select-ftp.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/utils/utils.js M static/scripts/viz/circster.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako M templates/user/logout.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Webpack: correct tool menu template loading in requirejs/galaxy.panels.mako by using require.config.map; normalize galaxy_config.root and Galaxy.options.root to Galaxy.root across the templates and js Commit: b8870bfedc008d378481bd6740f31ff516271c16 https://github.com/galaxyproject/galaxy/commit/b8870bfedc008d378481bd6740f31... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/trackster.less M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.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 static/maps/mvc/tool/tools.js.map A static/maps/mvc/tools.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/mvc/tool/tools.js A static/scripts/mvc/tools.js M static/scripts/viz/trackster/tracks.js M static/style/blue/trackster.css M templates/admin/reload_tool.mako M templates/show_params.mako M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/provision.yml M test/docker/base/run_test_wrapper.sh M test/docker/base/start_mysql.sh M tools/data_source/upload.py Log Message: ----------- (merge dev) Commit: bb089dfa424cefc64e65f1dd2aab5fe8fe1dad16 https://github.com/galaxyproject/galaxy/commit/bb089dfa424cefc64e65f1dd2aab5... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M static/maps/galaxy-app-base.js.map M test/qunit/test-common.js M test/qunit/tests/galaxy-app-base.js Log Message: ----------- Tests, qunit: fix import of underscore from libs, fix galaxy-app-base to not require config but have it passed in Commit: 474a454958398bc3e70d16f7eaab5805aa89cf19 https://github.com/galaxyproject/galaxy/commit/474a454958398bc3e70d16f7eaab5... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/history/hda-model.js M test/qunit/test-app.js M test/qunit/test-common.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Tests, qunit: galaxy_config.root->Galaxy.root, correct locations and shims of underscore and backbone in qunit tests Commit: 7b93a53a4cbe671c40bb39849ae354938fffa284 https://github.com/galaxyproject/galaxy/commit/7b93a53a4cbe671c40bb39849ae35... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/polyfills.js M client/galaxy/scripts/utils/localization.js M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/layout/masthead.js.map M static/maps/layout/page.js.map M static/maps/polyfills.js.map M static/maps/utils/localization.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/layout/masthead.js M static/scripts/layout/page.js M static/scripts/polyfills.js M static/scripts/utils/localization.js R static/style/blue/galaxy.frame.masthead.css M templates/base/base_panels.mako M templates/js-app.mako M templates/webapps/galaxy/galaxy.masthead.mako M test/casperjs/api-history-permission-tests.js Log Message: ----------- Webpack: polyfill object.assign for phantomjs; remove galaxy.frame.masthead.css in favor of adding styles locally; change css load order to prevent 'ui-button' name collision between base and jquery-ui Commit: d1d2f8388a4bc077275f535e41841158076a56de https://github.com/galaxyproject/galaxy/commit/d1d2f8388a4bc077275f535e41841... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/utils/query-string-parsing.js M client/webpack.config.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/layout/masthead.js.map M static/maps/layout/page.js.map M static/maps/utils/query-string-parsing.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/layout/masthead.js M static/scripts/layout/page.js M static/scripts/utils/query-string-parsing.js M templates/js-app.mako Log Message: ----------- Webpack: allow extending options from template call, add /login as app entry point for login app (still allowing user/login), add root/welcome and /login to allowed paths when require_login, fix None type error for redirect when visiting user/login directly, fix rendering of masthead, add query string to object util, correct job_id loading from index Commit: 5eb9b206e798522fff1a9332e5d1a58c83528523 https://github.com/galaxyproject/galaxy/commit/5eb9b206e798522fff1a9332e5d1a... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: A client/galaxy/scripts/apps/login.js A static/scripts/bundled/login.bundled.js A static/scripts/bundled/login.bundled.js.map Log Message: ----------- Webpack: properly add login app to the repo Commit: 17ec1b08fbc88c4960b94fbd19252c40e8a4e579 https://github.com/galaxyproject/galaxy/commit/17ec1b08fbc88c4960b94fbd19252... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Webpack: add masthead div to galaxy.panels.mako as a target for replacement and becauseiamgoingcrazyfromtheeightdifferentwayswehavetorenderwebpages Commit: 7cd5713dbb3acc82ee7c01f5110d37cb413392c8 https://github.com/galaxyproject/galaxy/commit/7cd5713dbb3acc82ee7c01f5110d3... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.panels.mako M test/casperjs/spaceghost.js Log Message: ----------- Webpack: simplify query routes in analysis, remove duplicate js in display.mako and tabular_chunked.mako, change order of requirejs import; testing, casperjs: quiet requirejs scripterrors when navigating away from pages Commit: 9c5d4cfc0e95966f8a41e8dedf83ea4b4793868e https://github.com/galaxyproject/galaxy/commit/9c5d4cfc0e95966f8a41e8dedf83e... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/app/app-login.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/history/copy-dialog.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-listrow-view.js M config/datatypes_conf.xml.sample 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/static/js/rstudio.js M cron/build_chrom_db.py M doc/source/admin/interactive_environments.rst M doc/source/project/organization.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/configuration.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/test.py M lib/galaxy/util/xml_macros.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/request_type.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/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M run_tests.sh M static/maps/galaxy-app-base.js.map A static/maps/galaxy.menu.js.map M static/maps/layout/menu.js.map M static/maps/mvc/app/app-login.js.map M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/ui/ui-select-default.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/galaxy.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map A static/scripts/galaxy.menu.js M static/scripts/layout/menu.js M static/scripts/mvc/app/app-login.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/history/copy-dialog.js A static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/utils/utils.js M test/api/helpers.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_workflow_extraction.py M test/base/api.py M test/base/interactor.py M test/base/twilltestcase.py A test/functional/tools/cheetah_problem_syntax_error.xml A test/functional/tools/cheetah_problem_unbound_var.xml A test/functional/tools/cheetah_problem_unbound_var_input.xml A test/functional/tools/maxseconds.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_tool_loader.py Log Message: ----------- (merge dev) Commit: dba7e6640f816325c853fcc320e97c454a465bae https://github.com/galaxyproject/galaxy/commit/dba7e6640f816325c853fcc320e97... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/tool/tools.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/viz/sweepster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/grunt-tasks/templates.js M static/maps/layout/panel.js.map M static/maps/mvc/tool/tools.js.map M static/maps/templates/compiled/panel_section.js.map M static/maps/templates/compiled/tool_form.js.map M static/maps/templates/compiled/tool_link.js.map M static/maps/templates/compiled/tool_search.js.map M static/maps/viz/sweepster.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/layout/panel.js M static/scripts/templates/compiled/panel_section.js M static/scripts/templates/compiled/tool_form.js M static/scripts/templates/compiled/tool_link.js M static/scripts/templates/compiled/tool_search.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster/tracks.js M templates/base/base_panels.mako M templates/webapps/galaxy/visualization/sweepster.mako Log Message: ----------- Webpack: correct handlebars template generation to return an AMD function - this normalizes import of templates between webpack and require, fix sweepster tools import and templates Commit: 51e098649070435570f9b68bf17ecc005da65bc2 https://github.com/galaxyproject/galaxy/commit/51e098649070435570f9b68bf17ec... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: A static/scripts/bundled/libs.bundled.js A static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Webpack: add in the libs bundles, Carl. They're kinda important. Commit: baeaae99059fc94ae2a0dc059cfd448d05bdcbbe https://github.com/galaxyproject/galaxy/commit/baeaae99059fc94ae2a0dc059cfd4... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.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: ----------- Webpack: rebuild bundles using webpack 1.12.8 as defined in the package.json Commit: f3f8fef28a55c7b4e6994b08e3125a0d66a36140 https://github.com/galaxyproject/galaxy/commit/f3f8fef28a55c7b4e6994b08e3125... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/apps/galaxy.js M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/apps/login.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/galaxy-app-base.js M client/grunt-tasks/scripts.js M client/webpack.config.js M lib/galaxy/web/base/controller.py M static/maps/galaxy-app-base.js.map R static/maps/galaxy.menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map R static/scripts/bundled/galaxy.bundled.js R static/scripts/bundled/galaxy.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/galaxy-app-base.js R static/scripts/galaxy.menu.js M templates/js-app.mako Log Message: ----------- Webpack: move Galaxy object creation from mako to app js, clean up and localize page, panels, and app Commit: b15a4082939be8b533dddf9a6a63efec9be6b817 https://github.com/galaxyproject/galaxy/commit/b15a4082939be8b533dddf9a6a63e... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: 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 R static/maps/tools/rgenetics/checkbox_and_radiobutton.js.map R static/maps/tools/rgenetics/helper_functions.js.map R static/maps/tools/rgenetics/timer.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map 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/tools/rgenetics/checkbox_and_radiobutton.js R static/scripts/tools/rgenetics/helper_functions.js R static/scripts/tools/rgenetics/timer.js Log Message: ----------- Client: remove duplicate rgenetics directory tools/rgenetics Commit: d921b4243101130d7de5517167eb38fa1aa6b1d3 https://github.com/galaxyproject/galaxy/commit/d921b4243101130d7de5517167eb3... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: R client/galaxy/scripts/mvc/app/app-analysis.js R client/galaxy/scripts/mvc/app/app-login.js R client/galaxy/scripts/mvc/app/app-view.js R static/maps/mvc/app/app-analysis.js.map R static/maps/mvc/app/app-login.js.map R static/maps/mvc/app/app-view.js.map R static/scripts/mvc/app/app-analysis.js R static/scripts/mvc/app/app-login.js R static/scripts/mvc/app/app-view.js Log Message: ----------- Webpack: remove mvc/app Commit: 9f91b82245fc3ba467e8bef7b57bfc58ef02e9f0 https://github.com/galaxyproject/galaxy/commit/9f91b82245fc3ba467e8bef7b57bf... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: 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 M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/polyfills.js M client/galaxy/scripts/viz/visualization.js A static/incompatible-browser.html R static/maps/libs/IE/IE7.js.map R static/maps/libs/IE/IE8.js.map R static/maps/libs/IE/excanvas.js.map R static/maps/libs/IE/ie7-recalc.js.map M static/maps/mvc/workflow/workflow-connector.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/polyfills.js.map M static/maps/viz/visualization.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/IE/IE7.js R static/scripts/libs/IE/IE8.js R static/scripts/libs/IE/blank.gif R static/scripts/libs/IE/excanvas.js R static/scripts/libs/IE/ie7-recalc.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/polyfills.js M static/scripts/viz/visualization.js M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Client: remove IE7/8 and excanvas polyfills Commit: e3e9579a812c468fba3f8a64fae7c7455e4b5a9e https://github.com/galaxyproject/galaxy/commit/e3e9579a812c468fba3f8a64fae7c... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/login.js R client/galaxy/scripts/galaxy-app-base.js A client/galaxy/scripts/galaxy.js R static/maps/galaxy-app-base.js.map A static/maps/galaxy.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/galaxy-app-base.js A static/scripts/galaxy.js M templates/galaxy_client_app.mako Log Message: ----------- Webpack: pack scripts, move galaxy-app-base.js to galaxy.js Commit: 68da0004709e88ed8a856d39e9fa4e64aa3bc653 https://github.com/galaxyproject/galaxy/commit/68da0004709e88ed8a856d39e9fa4... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: R client/galaxy/scripts/rgenetics/checkbox_and_radiobutton.js R client/galaxy/scripts/rgenetics/helper_functions.js R client/galaxy/scripts/rgenetics/timer.js R static/maps/rgenetics/checkbox_and_radiobutton.js.map R static/maps/rgenetics/helper_functions.js.map R static/maps/rgenetics/timer.js.map R static/scripts/rgenetics/checkbox_and_radiobutton.js R static/scripts/rgenetics/helper_functions.js R static/scripts/rgenetics/timer.js Log Message: ----------- Client, rgenetics: 'Nuke 'em all' - R.Lazarus Commit: f397584538f59d03d9c37d3f9366b455022e97b2 https://github.com/galaxyproject/galaxy/commit/f397584538f59d03d9c37d3f9366b... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M client/galaxy/scripts/polyfills.js M static/maps/polyfills.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/polyfills.js M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako Log Message: ----------- Webpack: add link rel='index' with href to Galaxy.root, rework browser testing to use the same when redirecting to error pages Commit: 002bc6b40a4314fc5f35f6156a73cad91532484d https://github.com/galaxyproject/galaxy/commit/002bc6b40a4314fc5f35f6156a73c... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M .gitignore M client/GruntFile.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/dataset/dataset-li.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/list/list-view.js M client/galaxy/scripts/mvc/tool/tools-form-base.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/grunt-tasks/style.js M client/package.json M config/datatypes_conf.xml.sample M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/visualizations/charts/templates/charts.mako A config/reports.ini.sample R config/reports_wsgi.ini.sample M config/tool_shed.ini.sample A doc/source/releases/15.10.rst M doc/source/releases/15.10_announce.rst A doc/source/releases/16.01_announce.rst M lib/galaxy/datatypes/interval.py M lib/galaxy/dependencies/requirements.txt M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/shed_util_common.py M run_reports.sh M scripts/bootstrap_history.py M scripts/functional_tests.py M scripts/sync_reports_config.py M static/maps/layout/masthead.js.map M static/maps/layout/panel.js.map M static/maps/layout/scratchbook.js.map M static/maps/mvc/base-mvc.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map A static/maps/mvc/list/list-panel.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/tool/tools-form-base.js.map A static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/ui/ui-buttons.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/masthead.js M static/scripts/layout/panel.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/tool/tools-form-base.js A static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/ui/ui-buttons.js M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/trackster.css M templates/webapps/galaxy/root/index.mako M templates/webapps/galaxy/workflow/run.mako M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py A test/api/workflows_format_2/README.txt A test/api/workflows_format_2/__init__.py A test/api/workflows_format_2/converter.py A test/api/workflows_format_2/interface.py A test/api/workflows_format_2/main.py R test/api/yaml_to_workflow.py A test/functional/tools/collection_type_source.xml A test/functional/tools/output_format_collection.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/simple_constructs.yml M test/qunit/package.json M test/unit/tools/test_actions.py M test/unit/tools/test_parsing.py Log Message: ----------- (merge dev) Commit: cfdbf8c0e71c5cdfa0ae47f6da7cc4553efd8429 https://github.com/galaxyproject/galaxy/commit/cfdbf8c0e71c5cdfa0ae47f6da7cc... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M test/qunit/test-app.js M test/qunit/test-data/bootstrapped.js M test/qunit/tests/galaxy-app-base.js Log Message: ----------- Testing, webpack: correct name of Galaxy module in qunit, properly call require, pass GalaxyApp data Commit: 963d8637e869a214ee0e2c352a8184feb980a40e https://github.com/galaxyproject/galaxy/commit/963d8637e869a214ee0e2c352a818... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: R client/galaxy/scripts/galaxy.tools.js R static/maps/galaxy.tools.js.map R static/maps/galaxy.workflows.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map R static/scripts/galaxy.tools.js R static/scripts/galaxy.workflows.js Log Message: ----------- Webpack: remove cruft galaxy.tools.js and (remnants of) galaxy.workflows.js Commit: a3e3bde6a2b5c2fc9433336526ec32badfc8ce9d https://github.com/galaxyproject/galaxy/commit/a3e3bde6a2b5c2fc9433336526ec3... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M client/galaxy/scripts/apps/login.js M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/root.py M static/scripts/bundled/analysis.bundled.js.map 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: ----------- Webpack: restore redirect for after login when require_login; remove allowed_paths for require_login: /index, /tool_menu, /masthead, library/browse, history/list, dataset/list Commit: b72035c9fc4136af5f3db464fd5b2a9c5e330cca https://github.com/galaxyproject/galaxy/commit/b72035c9fc4136af5f3db464fd5b2... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M static/maps/layout/masthead.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit-current.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/masthead.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Webpack: fix/re-work the pub-sub connection between the quotameter and the history panel so that the meter updates properly when a new dataset is added Commit: f40d4fc178cbf3a3266a56ce0108b87e21bd5be0 https://github.com/galaxyproject/galaxy/commit/f40d4fc178cbf3a3266a56ce0108b... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M config/galaxy.ini.sample R templates/webapps/galaxy/root/index.mako Log Message: ----------- Webpack: re-add show_welcome_with_login config option (lost due to merge/gitignore?); remove root/index.mako Commit: 9e8068f3671cdef499ed51aca3869f91e2e5b69d https://github.com/galaxyproject/galaxy/commit/9e8068f3671cdef499ed51aca3869... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M README.rst M client/galaxy/scripts/mvc/history/options-menu.js M config/datatypes_conf.xml.sample A config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/test.idpDB A lib/galaxy/datatypes/test/test.mz5 A lib/galaxy/datatypes/triples.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/execute.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/galaxy_install/migrate/check.py M run_tests.sh M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/options-menu.js M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M test/api/helpers.py M test/api/test_jobs.py M test/api/test_workflows.py A test/functional/tools/create_10.xml M test/functional/tools/samples_tool_conf.xml M test/qunit/test-common.js M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml M test/unit/test_galaxy_mapping.py M test/unit/workflows/test_render.py A test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py Log Message: ----------- (merge dev) Commit: 9f8eb465e718d4b643120e8554d119702c264135 https://github.com/galaxyproject/galaxy/commit/9f8eb465e718d4b643120e8554d11... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M .gitignore 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 A client/galaxy/scripts/mvc/annotation.js R client/galaxy/scripts/mvc/annotations.js R client/galaxy/scripts/mvc/app/app-analysis.js R client/galaxy/scripts/mvc/app/app-login.js R client/galaxy/scripts/mvc/app/app-view.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-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 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client/galaxy/scripts/mvc/history/history-panel.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-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 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static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/style/blue/base.css R static/style/blue/galaxy.frame.masthead.css M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/galaxy_client_app.mako M templates/grid_base.mako A templates/js-app.mako M templates/refresh_frames.mako M templates/tagging_common.mako M templates/user/logout.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/edit_attributes.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/library/common/ldda_edit_info.mako M templates/webapps/galaxy/library/common/move_library_item.mako M templates/webapps/galaxy/library/common/upload.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/requests/common/create_request.mako M templates/webapps/galaxy/requests/common/find_samples.mako R templates/webapps/galaxy/root/index.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/run.mako M test/casperjs/api-history-permission-tests.js M test/casperjs/spaceghost.js M test/qunit/test-app.js M test/qunit/test-common.js M test/qunit/test-data/bootstrapped.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge pull request #1144 from carlfeberhard/webpack Webpack Compare: https://github.com/galaxyproject/galaxy/compare/3e8b58c5aa66...9f8eb465e718