Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: db63b131c1728493a87901764c102dbc47f74f3f https://github.com/galaxyproject/galaxy/commit/db63b131c1728493a87901764c102... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-15 (Tue, 15 Nov 2016) 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/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Fix styling, we don't need to force rounded edges here. Commit: ca24098883fda1c35241d4c380f8b0765de7bb95 https://github.com/galaxyproject/galaxy/commit/ca24098883fda1c35241d4c380f8b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-15 (Tue, 15 Nov 2016) Changed paths: M client/galaxy/style/less/dataset.less M static/style/blue/base.css Log Message: ----------- Remove unused style, we can rely on the :last pseudoclasses for this. Commit: f8974acba2884dc2fc1728aaa81021708ad05493 https://github.com/galaxyproject/galaxy/commit/f8974acba2884dc2fc1728aaa8102... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-15 (Tue, 15 Nov 2016) 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/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Fix styling when only one visualization type exists Commit: ce320b66ea1de3c15f4f080f19a729b1ff2087cb https://github.com/galaxyproject/galaxy/commit/ce320b66ea1de3c15f4f080f19a72... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) 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/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- A bit of refactoring, handling of unavailable tools or tools with no help. Slight style changes. Commit: 29cf7187233bbd031f07df4584f1bef55de612e4 https://github.com/galaxyproject/galaxy/commit/29cf7187233bbd031f07df4584f1b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) 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/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Minor styling tweaks -- todo: swap from inline to class-based. Commit: 83e1392cf8d875109d121eb9cf13c274659c02b7 https://github.com/galaxyproject/galaxy/commit/83e1392cf8d875109d121eb9cf13c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/style/less/dataset.less 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/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js M static/style/blue/base.css Log Message: ----------- Standard styles inclusion in .less, more styling to match rounded edges and spacing. Commit: be6a2f8132f3002e0570488a4ad5f80e07b6c2a8 https://github.com/galaxyproject/galaxy/commit/be6a2f8132f3002e0570488a4ad5f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M client/galaxy/style/source_material/circle.py M config/galaxy.ini.sample M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/tours/core.galaxy_ui.yaml M contrib/galaxy_config_merger.py M contrib/nagios/check_galaxy.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds.py M 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M scripts/tool_shed/api/create_categories.py M scripts/tool_shed/api/create_users.py M scripts/tool_shed/api/export.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/api/import_capsule.py M scripts/tool_shed/api/remove_repository_registry_entry.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/clean_up_tool_dependency_directory.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M scripts/tools/maf/check_loc_file.py M 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test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_fabric_util.py M test/unit/shed_unit/test_td_common_util.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_galaxy_transactions.py M test/unit/test_routes.py M test/unit/tools/test_actions.py M test/unit/tools/test_citations.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_external_files.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_wrappers.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py M tools/data_source/data_source.py M tools/data_source/genbank.py M tools/data_source/upload.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_fasta.py M tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.py M tools/filters/convert_characters.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/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/secure_hash_message_digest.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M 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tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.10' into fix_help_history Commit: 9c435685cded86c36b605bf81eb9bec7f112cce3 https://github.com/galaxyproject/galaxy/commit/9c435685cded86c36b605bf81eb9b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) 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/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Don't rely on complex, absolute selector, use local element.find() Commit: 3ab4e1d742fe08701c1b997bf87f8406d1ccdecb https://github.com/galaxyproject/galaxy/commit/3ab4e1d742fe08701c1b997bf87f8... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) 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/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- The jobs API, which this functionality is based on, requires a logged in user, so prevent anonymous access here. Also shifts to using Galaxy.root correctly, instead of assuming / Commit: d2ab7e701c87f4292b655893103c7842900a47b5 https://github.com/galaxyproject/galaxy/commit/d2ab7e701c87f4292b655893103c7... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/style/less/dataset.less M static/maps/mvc/dataset/dataset-li-edit.js.map A static/maps/mvc/user/change-password.js.map A static/maps/mvc/user/extra-information.js.map A static/maps/mvc/user/manage-user-information.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.map M static/scripts/mvc/dataset/dataset-li-edit.js A static/scripts/mvc/user/change-password.js A static/scripts/mvc/user/extra-information.js A static/scripts/mvc/user/manage-user-information.js M static/style/blue/base.css Log Message: ----------- build the client Compare: https://github.com/galaxyproject/galaxy/compare/329108f81021...d2ab7e701c87