[galaxy-commits] [galaxyproject/galaxy] fa80b4: Merge pull request #1 from galaxyproject/dev

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fa80b4961182ab7391fdd99624652288669851d5 https://github.com/galaxyproject/galaxy/commit/fa80b4961182ab7391fdd99624652... Author: pvanheus <pvh@webbedfeet.co.za> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M .ci/flake8_blacklist.txt A .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper.sh A .ci/flake8_wrapper_docstrings.sh A .ci/jenkins/api/run_tests.sh A .ci/jenkins/framework/run_tests.sh A .ci/jenkins/integration/run_tests.sh A .ci/jenkins/selenium/Dockerfile A .ci/jenkins/selenium/docker-compose.yml A .ci/jenkins/selenium/galaxy.ini A .ci/jenkins/selenium/run_galaxy.bash A .ci/jenkins/selenium/run_tests.sh A .ci/jenkins/toolshed/run_tests.sh M .ci/py3_sources.txt A .ci/validate_test_tools.sh M .gitignore M .travis.yml M CONTRIBUTORS.md M LICENSE.txt M Makefile M client/galaxy/scripts/apps/analysis.js 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/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js A 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tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge pull request #1 from galaxyproject/dev Merge from upstream Commit: 0db0d7b367c4435c44c3f47b512d128735a78ad0 https://github.com/galaxyproject/galaxy/commit/0db0d7b367c4435c44c3f47b512d1... Author: pvanheus <pvh@webbedfeet.co.za> Date: 2017-06-02 (Fri, 02 Jun 2017) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M .gitignore M .travis.yml M CITATION M CONTRIBUTING.md M CONTRIBUTORS.md M Makefile M README.rst A client/galaxy/scripts/admin.toolshed.js A client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/apps/panels/history-panel.js A client/galaxy/scripts/apps/panels/tool-panel.js R client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M 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M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_gen_conv.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tox.ini Log Message: ----------- Merge pull request #2 from galaxyproject/dev Merge from upstream #2 Commit: 7dab2aac26a59af1bdf2d6314edf625636987d2f https://github.com/galaxyproject/galaxy/commit/7dab2aac26a59af1bdf2d6314edf6... Author: pvanheus <pvh@webbedfeet.co.za> Date: 2017-06-20 (Tue, 20 Jun 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .gitignore M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js A client/galaxy/scripts/mvc/page/page-list.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js M client/galaxy/style/less/ui.less M client/webpack.config.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml A config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/static/script.js A config/plugins/webhooks/demo/tour_generator/static/styles.css M cron/updateucsc.sh.sample M doc/Makefile R doc/patch.py R doc/source/api/api.rst R doc/source/api/ts_api.rst M doc/source/lib/galaxy.actions.rst M doc/source/lib/galaxy.auth.providers.rst M doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.containers.rst M doc/source/lib/galaxy.dataset_collections.rst M doc/source/lib/galaxy.dataset_collections.types.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.datatypes.dataproviders.rst M 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lib/galaxy/datatypes/data.py A lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/managers/collections_util.py A lib/galaxy/tools/cache.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.py M lib/galaxy/tools/deps/mulled/mulled_search.py M lib/galaxy/tools/deps/mulled/util.py A lib/galaxy/tools/deps/singularity_util.py R lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/page.py M scripts/api/library_upload_dir.py M static/maps/layout/menu.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map A static/maps/mvc/page/page-list.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-slider.js.map M static/maps/mvc/webhooks.js.map M static/maps/onload.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js A static/scripts/mvc/page/page-list.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/mvc/webhooks.js M static/scripts/onload.js M static/style/blue/base.css M templates/grid_base.mako M templates/js-app.mako M templates/sharing_base.mako R templates/webapps/galaxy/dataset/grid.mako M templates/webapps/galaxy/page/editor.mako R templates/webapps/galaxy/page/index.mako R templates/webapps/galaxy/page/list_published.mako M test/api/test_dataset_collections.py M test/base/populators.py A test/functional/tools/mulled_example_multi_versionless.xml M test/functional/tools/samples_tool_conf.xml M test/functional/webhooks/phdcomics/helper/__init__.py M test/functional/webhooks/trans_object/config/trans_object.yaml M test/functional/webhooks/trans_object/helper/__init__.py M test/qunit/tests/ui_tests.html M test/qunit/tests/ui_tests.js A test/unit/jobs/conditional_runners_job_conf.xml M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #3 from galaxyproject/dev Merge from upstream Commit: b1477a8b87198e5e47ab508633d9999edf047dc3 https://github.com/galaxyproject/galaxy/commit/b1477a8b87198e5e47ab508633d99... Author: pvanheus <pvh@webbedfeet.co.za> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M .gitignore M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/grid/grid-view.js A client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/base.less M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/neo/config/neo.xml M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/search/static/script.js M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/layout/panel.js.map M static/maps/mvc/grid/grid-view.js.map A static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow-configure-menu.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/mvc/grid/grid-view.js A static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow.js M static/scripts/utils/utils.js M static/style/blue/base.css R templates/webapps/galaxy/history/grid.mako R templates/webapps/galaxy/history/grid_js.mako R templates/webapps/galaxy/visualization/list_published.mako R templates/webapps/galaxy/workflow/import.mako R templates/webapps/galaxy/workflow/list_published.mako R templates/webapps/galaxy/workflow/run.mako M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge pull request #4 from galaxyproject/dev Merge just before GCC2017 Commit: e63ababa79ed79cce8f999199578005a18d27d5c https://github.com/galaxyproject/galaxy/commit/e63ababa79ed79cce8f9991995780... Author: Peter van Heusden <pvh@sanbi.ac.za> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- add public-only filter for data libraries Commit: c41b2849998250af2abc4d4655c0d6aaee27fc77 https://github.com/galaxyproject/galaxy/commit/c41b2849998250af2abc4d4655c0d... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M static/maps/galaxy.library.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/galaxy.library.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- adjust logic to match the include deleted checkbox also make client and set default user preference Commit: 6a43fad892d870caf7f9fa12adb4c532a16e56c9 https://github.com/galaxyproject/galaxy/commit/6a43fad892d870caf7f9fa12adb4c... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/managers/workflows.py M static/maps/mvc/tool/tool-form-base.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/mvc/tool/tool-form-base.js A test-data/5_Ig-like.gff M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/wc_gnu.xml Log Message: ----------- Merge branch 'dev' into lib_exclude_restricted Conflicts: static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map Commit: e98378160a46c97979daec4f6e1183cd6214fe79 https://github.com/galaxyproject/galaxy/commit/e98378160a46c97979daec4f6e118... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M static/maps/galaxy.library.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/galaxy.library.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- Merge pull request #4232 from pvanheus/dev add public-only filter for data libraries Compare: https://github.com/galaxyproject/galaxy/compare/153b8d4dca04...e98378160a46