galaxy-commits May 2016

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[galaxyproject/galaxy] ad3a65: remove the comment that breaks toc generation
by GitHub 18 May '16

18 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: ad3a65a6881712b7dcd7e44ca55a6529144e4080 https://github.com/galaxyproject/galaxy/commit/ad3a65a6881712b7dcd7e44ca55a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M doc/source/releases/index.rst Log Message: ----------- remove the comment that breaks toc generation Commit: d926b3f5099cb0f3153126a59d3a07374e486c80 https://github.com/galaxyproject/galaxy/commit/d926b3f5099cb0f3153126a59d3a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M doc/source/releases/index.rst Log Message: ----------- Merge pull request #2373 from martenson/fix=release-docs [16.04] remove the comment that breaks toc generation Compare: https://github.com/galaxyproject/galaxy/compare/99c8f54a77c4...d926b3f5099c

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[galaxyproject/galaxy] 2ddf4e: Upgrade shared ui libraries, add test cases
by GitHub 18 May '16

18 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2ddf4e02fc6e8ee1cb28b1cf78146efe0a8e16ab https://github.com/galaxyproject/galaxy/commit/2ddf4e02fc6e8ee1cb28b1cf7814… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js R client/galaxy/scripts/mvc/tool/tool-template.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/utils/utils.js M static/style/blue/base.css M test/qunit/test-app.js M test/qunit/test-data/fakeserver.js M test/qunit/tests/form_tests.js M test/qunit/tests/modal_tests.js M test/qunit/tests/ui_tests.js Log Message: ----------- Upgrade shared ui libraries, add test cases Commit: 8cdc1244ef3470df5c53cc8c1147575a56388216 https://github.com/galaxyproject/galaxy/commit/8cdc1244ef3470df5c53cc8c1147… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js R client/galaxy/scripts/mvc/tool/tool-template.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/utils/utils.js M static/style/blue/base.css M test/qunit/test-app.js M test/qunit/test-data/fakeserver.js M test/qunit/tests/form_tests.js M test/qunit/tests/modal_tests.js M test/qunit/tests/ui_tests.js Log Message: ----------- Merge pull request #2368 from guerler/revise_ui_001 Upgrade shared ui libraries, add test cases Compare: https://github.com/galaxyproject/galaxy/compare/702fe3c11218...8cdc1244ef34

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[galaxyproject/galaxy] 5a8d2a: More clarification of release process.
by GitHub 18 May '16

18 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5a8d2a1ad8b70c86f6fd57fd31337e82c0e7ee3f https://github.com/galaxyproject/galaxy/commit/5a8d2a1ad8b70c86f6fd57fd3133… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M Makefile M scripts/bootstrap_history.py Log Message: ----------- More clarification of release process. Commit: 702fe3c11218d6a44b8b07379e9e980a672c9c12 https://github.com/galaxyproject/galaxy/commit/702fe3c11218d6a44b8b07379e9e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M Makefile M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #2372 from jmchilton/release_process_revise_again More clarification of release process. Compare: https://github.com/galaxyproject/galaxy/compare/978fec055ef8...702fe3c11218

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[galaxyproject/galaxy] ed4132: Python3: Use open() instead of file()
by GitHub 18 May '16

18 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ed4132d9c0c94baa38e289b43aa08c1c42b81083 https://github.com/galaxyproject/galaxy/commit/ed4132d9c0c94baa38e289b43aa0… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/runners/__init__.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py M lib/tool_shed/util/tool_util.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M test/base/twilltestcase.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_0060_workflows.py M test/shed_functional/functional/test_0100_complex_repository_dependencies.py M test/shed_functional/functional/test_0170_complex_prior_installation_required.py M test/shed_functional/functional/test_0300_reset_all_metadata.py M test/shed_functional/functional/test_0310_hg_api_features.py M test/shed_functional/functional/test_1060_install_repository_with_workflow.py M test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py M test/shed_functional/functional/test_1190_complex_prior_installation_required.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py M test/shed_functional/functional_tests.py M tools/data_source/microbial_import.py M tools/extract/extract_genomic_dna.py M tools/filters/axt_to_lav.py M tools/filters/bed_to_gff_converter.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff_to_bed_converter.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/joinWrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/filtering.py M tools/stats/gsummary.py Log Message: ----------- Python3: Use open() instead of file() Commit: 8a43b2b492e6282a67cc7e8279cc727d5de26dc2 https://github.com/galaxyproject/galaxy/commit/8a43b2b492e6282a67cc7e8279cc… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M contrib/nagios/check_galaxy.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0057_request_notify.py M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M scripts/api/upload_to_history.py M scripts/check_galaxy.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/data_libraries/build_whoosh_index.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py M scripts/extract_dataset_part.py M scripts/microbes/harvest_bacteria.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/tool_shed/api/common.py M scripts/tool_shed/api/create_categories.py M scripts/tool_shed/api/create_users.py M scripts/tool_shed/api/import_capsule.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tools/maf/check_loc_file.py M scripts/transfer.py M test/base/asserts/__init__.py M test/base/asserts/xml.py M test/base/driver_util.py M test/base/twilltestcase.py M test/casperjs/casperjs_runner.py M test/casperjs/server_env.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/shed_functional/base/twilltestcase.py M test/unit/tools/test_execution.py M test/unit/tools/test_select_parameters.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/hbvar_filter.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/gff/gff_filter_by_attribute.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/sff_extract.py M tools/filters/sorter.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_split_by_species.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.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: ----------- Python 3: use "as" instead of comma in except clause Commit: 6ba6f798ecfae5d7a30d50de785075ffa7bfb844 https://github.com/galaxyproject/galaxy/commit/6ba6f798ecfae5d7a30d50de7850… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M contrib/nagios/check_galaxy.py M cron/build_chrom_db.py M lib/galaxy/security/__init__.py M lib/galaxy/util/directory_hash.py M lib/galaxy_utils/sequence/vcf.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/migrate/common.py M lib/tool_shed/metadata/metadata_generator.py M scripts/api/data_manager_example_execute.py M scripts/api/search.py M scripts/api/upload_to_history.py M scripts/check_galaxy.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M scripts/runtime_stats.py M scripts/tool_shed/build_ts_whoosh_index.py M test/api/test_datasets.py M test/base/driver_util.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HistoryManager.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 tools/extract/extract_genomic_dna.py M tools/filters/join.py M tools/filters/mergeCols.py M tools/filters/sff_extract.py M tools/genomespace/genomespace_file_browser.py M tools/metag_tools/shrimp_wrapper.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/stats/gsummary.py Log Message: ----------- Fix more E203 flake8 errors Commit: 978fec055ef817e008252002ea956f9d304d51c3 https://github.com/galaxyproject/galaxy/commit/978fec055ef817e008252002ea95… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M contrib/nagios/check_galaxy.py M cron/build_chrom_db.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0057_request_notify.py M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/security/__init__.py M lib/galaxy/util/directory_hash.py M lib/galaxy_utils/sequence/vcf.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/migrate/common.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/tool_util.py M scripts/api/data_manager_example_execute.py M scripts/api/search.py M scripts/api/upload_to_history.py M scripts/check_galaxy.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py M scripts/extract_dataset_part.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/runtime_stats.py M scripts/tool_shed/api/common.py M scripts/tool_shed/api/create_categories.py M scripts/tool_shed/api/create_users.py M scripts/tool_shed/api/import_capsule.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tools/maf/check_loc_file.py M scripts/transfer.py M test/api/test_datasets.py M test/base/asserts/__init__.py M test/base/asserts/xml.py M test/base/driver_util.py M test/base/twilltestcase.py M test/casperjs/casperjs_runner.py M test/casperjs/server_env.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_0060_workflows.py M test/shed_functional/functional/test_0100_complex_repository_dependencies.py M test/shed_functional/functional/test_0170_complex_prior_installation_required.py M test/shed_functional/functional/test_0300_reset_all_metadata.py M test/shed_functional/functional/test_0310_hg_api_features.py M test/shed_functional/functional/test_1060_install_repository_with_workflow.py M test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py M test/shed_functional/functional/test_1190_complex_prior_installation_required.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py M test/shed_functional/functional_tests.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HistoryManager.py M test/unit/tools/test_execution.py M test/unit/tools/test_select_parameters.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 tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/hbvar_filter.py M tools/data_source/microbial_import.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_lav.py M tools/filters/bed_to_gff_converter.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff_to_bed_converter.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/sff_extract.py M tools/filters/sorter.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_split_by_species.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.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 pull request #2370 from nsoranzo/python3 Python3: use open() instead of file() Compare: https://github.com/galaxyproject/galaxy/compare/5a15bd0a00a6...978fec055ef8

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[galaxyproject/galaxy] 35a716: Not all objects added to the runner work queue are
by GitHub 18 May '16

18 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 35a716b8549bd575c96ef9cafe0e78a7e2048139 https://github.com/galaxyproject/galaxy/commit/35a716b8549bd575c96ef9cafe0e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Not all objects added to the runner work queue are JobWrappers/TaskWrappers as claimed in the comment. AsynchronousJobStates could also be added, and if the fail method was called this would result in the AttributeError of attempting to access an AJS' non-existent `get_id_tag` being logged in job.exeception as a red herring. Commit: d8430e5c4b6c5d8dd18fed6846f6f30d4a97e0eb https://github.com/galaxyproject/galaxy/commit/d8430e5c4b6c5d8dd18fed6846f6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: A doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst A doc/source/releases/16.07_announce.rst M doc/source/releases/index.rst Log Message: ----------- generated notes with basic manual curation Commit: 93d1d5611e3d62f928af49edd884dfea5fcf4c11 https://github.com/galaxyproject/galaxy/commit/93d1d5611e3d62f928af49edd884… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- add deprecation notices Commit: 40e596f26479e14b66b71842cee779e46a882047 https://github.com/galaxyproject/galaxy/commit/40e596f26479e14b66b71842cee7… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- Update 16.04_announce.rst Added more deprecations from #1757 Commit: 86127cdfdd7140e167a54622b83e09e616dbbe9a https://github.com/galaxyproject/galaxy/commit/86127cdfdd7140e167a54622b83e… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- Update 16.04_announce.rst Fix my rst syntax. Commit: e0a9efc307ac9f3a7a36c724684b16802cd6d31b https://github.com/galaxyproject/galaxy/commit/e0a9efc307ac9f3a7a36c724684b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst Log Message: ----------- include security note for hg upgrade; some reordering Commit: edbc82c215e87a5962ed740d97c352931b9402c0 https://github.com/galaxyproject/galaxy/commit/edbc82c215e87a5962ed740d97c3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- Merge branch '16.04_release_notes' of https://github.com/martenson/galaxy into 16.04_release_notes Conflicts: doc/source/releases/16.04_announce.rst Commit: 633162c7f558f1bc3bfaaa54dde3c7fc4156c190 https://github.com/galaxyproject/galaxy/commit/633162c7f558f1bc3bfaaa54dde3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- fix wrong merge Commit: 65e1d68efd2a1bc83e340a8419f55f95a440c6c3 https://github.com/galaxyproject/galaxy/commit/65e1d68efd2a1bc83e340a8419f5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- typo Commit: db5c0d95f6e10a5a723bc4bb54c11597ed629e9c https://github.com/galaxyproject/galaxy/commit/db5c0d95f6e10a5a723bc4bb54c1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04.rst Log Message: ----------- reorde notes a bit more based on impact/importance Commit: b85d604e30809d7e6b73f4762189182e7e82416b https://github.com/galaxyproject/galaxy/commit/b85d604e30809d7e6b73f4762189… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-13 (Fri, 13 May 2016) Changed paths: M doc/source/releases/16.01.rst M doc/source/releases/16.04.rst Log Message: ----------- Move some PRs that were merged in 16.01 before its release Galaxy 16.01 was officially released on 2016/02/24. Commit: c516c9fd45ffda5d4d74497bc96efc51966fdd22 https://github.com/galaxyproject/galaxy/commit/c516c9fd45ffda5d4d74497bc96e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-13 (Fri, 13 May 2016) Changed paths: M doc/source/releases/16.04.rst Log Message: ----------- Fix truncated PR titles and some acknowledgements Commit: dc5a5eb2eb1af48e14234d42aa8cacd3fd1aba1e https://github.com/galaxyproject/galaxy/commit/dc5a5eb2eb1af48e14234d42aa8c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-13 (Fri, 13 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- Add Bitbucket deprecation details Commit: 76fb9b72c34ecd6bead61b372a32dc0bd24375eb https://github.com/galaxyproject/galaxy/commit/76fb9b72c34ecd6bead61b372a32… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-13 (Fri, 13 May 2016) Changed paths: M doc/source/releases/16.04.rst Log Message: ----------- Add some missing PRs and merge some entries Commit: 38209bbbac705612c11f7f3083e357e046cb5c64 https://github.com/galaxyproject/galaxy/commit/38209bbbac705612c11f7f3083e3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-14 (Sat, 14 May 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Merge pull request #2350 from natefoo/fix-ajs-red-herring [16.04] Properly handle AsynchronousJobState objects in the job runner work queue Commit: 2390da54aec143358767e7977cffc70d040b04b5 https://github.com/galaxyproject/galaxy/commit/2390da54aec143358767e7977cff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Fix for slurm's complete_terminal_job where if unable to inspect the failed job with scontrol drmaajobrunner's _complete_terminal_job was called twice. Commit: 3b7f6cb7777cf2a92d17928b38abe13bd3cdb338 https://github.com/galaxyproject/galaxy/commit/3b7f6cb7777cf2a92d17928b38ab… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- add some highlights, seems tough for this release Commit: 62b6eaa92aac9520f12968cb41690692c8c3fa4f https://github.com/galaxyproject/galaxy/commit/62b6eaa92aac9520f12968cb4169… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M doc/source/releases/16.01.rst M doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst Log Message: ----------- Merge branch '16.04_release_notes' of https://github.com/martenson/galaxy into 16.04_release_notes Commit: cc86096c83b5835e40e034611ad64bf3827e5c6d https://github.com/galaxyproject/galaxy/commit/cc86096c83b5835e40e034611ad6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2362 from dannon/slurm_complete_job_fix [16.04] Fix for slurm's complete_terminal_job where if unable to inspect the … Commit: afb9027482f3a98a2b6d9e9fd049ded1da78c666 https://github.com/galaxyproject/galaxy/commit/afb9027482f3a98a2b6d9e9fd049… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- final touch of release notes from my side Commit: 50e596fb1b540a69f785296921a2611566a5b12b https://github.com/galaxyproject/galaxy/commit/50e596fb1b540a69f785296921a2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- reorder sections, un-quote bitbucket paragraph Commit: 9d5bf7b62d8f9a58e35e0317acb9dd5d88311b6f https://github.com/galaxyproject/galaxy/commit/9d5bf7b62d8f9a58e35e0317acb9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- minor release notes touch Commit: f887c059a2aff33a7c449d8ea234c4bbd9d09dd7 https://github.com/galaxyproject/galaxy/commit/f887c059a2aff33a7c449d8ea234… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- Expand 16.04 highlights... Commit: 8195d81739540ba489828616baa28a7b1c9d7711 https://github.com/galaxyproject/galaxy/commit/8195d81739540ba489828616baa2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M doc/source/releases/16.01.rst A doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst A doc/source/releases/16.07_announce.rst M doc/source/releases/index.rst Log Message: ----------- Merge pull request #2353 from martenson/16.04_release_notes [16.04] Release notes for 16.04 Commit: 938e0c022063db0bc999d7699ae122e415452f34 https://github.com/galaxyproject/galaxy/commit/938e0c022063db0bc999d7699ae1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M doc/source/releases/16.01.rst A doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst A doc/source/releases/16.07_announce.rst M doc/source/releases/index.rst M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge branch 'release_16.04' into dev Commit: 99c8f54a77c436125359f17a8d681f115e157742 https://github.com/galaxyproject/galaxy/commit/99c8f54a77c436125359f17a8d68… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.04 Commit: d03ba68ecf02ce7c352e43dedade111fed588bf6 https://github.com/galaxyproject/galaxy/commit/d03ba68ecf02ce7c352e43dedade… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Log Message: ----------- Merge branch 'release_16.04' into dev Commit: 5a15bd0a00a634d0856dca8bec8c7b78a6034dd4 https://github.com/galaxyproject/galaxy/commit/5a15bd0a00a634d0856dca8bec8c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M doc/source/releases/16.01.rst A doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst A doc/source/releases/16.07_announce.rst M doc/source/releases/index.rst M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2371 from jmchilton/dev Merge v16.04 into dev Compare: https://github.com/galaxyproject/galaxy/compare/a144a32f403b...5a15bd0a00a6

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[galaxyproject/galaxy]
by GitHub 18 May '16

18 May '16

Branch: refs/tags/v16.04 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] 99c8f5: Update version to 16.04
by GitHub 18 May '16

18 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 99c8f54a77c436125359f17a8d681f115e157742 https://github.com/galaxyproject/galaxy/commit/99c8f54a77c436125359f17a8d68… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.04

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[galaxyproject/galaxy] d8430e: generated notes with basic manual curation
by GitHub 18 May '16

18 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: d8430e5c4b6c5d8dd18fed6846f6f30d4a97e0eb https://github.com/galaxyproject/galaxy/commit/d8430e5c4b6c5d8dd18fed6846f6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: A doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst A doc/source/releases/16.07_announce.rst M doc/source/releases/index.rst Log Message: ----------- generated notes with basic manual curation Commit: 93d1d5611e3d62f928af49edd884dfea5fcf4c11 https://github.com/galaxyproject/galaxy/commit/93d1d5611e3d62f928af49edd884… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- add deprecation notices Commit: 40e596f26479e14b66b71842cee779e46a882047 https://github.com/galaxyproject/galaxy/commit/40e596f26479e14b66b71842cee7… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- Update 16.04_announce.rst Added more deprecations from #1757 Commit: 86127cdfdd7140e167a54622b83e09e616dbbe9a https://github.com/galaxyproject/galaxy/commit/86127cdfdd7140e167a54622b83e… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- Update 16.04_announce.rst Fix my rst syntax. Commit: e0a9efc307ac9f3a7a36c724684b16802cd6d31b https://github.com/galaxyproject/galaxy/commit/e0a9efc307ac9f3a7a36c724684b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst Log Message: ----------- include security note for hg upgrade; some reordering Commit: edbc82c215e87a5962ed740d97c352931b9402c0 https://github.com/galaxyproject/galaxy/commit/edbc82c215e87a5962ed740d97c3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- Merge branch '16.04_release_notes' of https://github.com/martenson/galaxy into 16.04_release_notes Conflicts: doc/source/releases/16.04_announce.rst Commit: 633162c7f558f1bc3bfaaa54dde3c7fc4156c190 https://github.com/galaxyproject/galaxy/commit/633162c7f558f1bc3bfaaa54dde3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- fix wrong merge Commit: 65e1d68efd2a1bc83e340a8419f55f95a440c6c3 https://github.com/galaxyproject/galaxy/commit/65e1d68efd2a1bc83e340a8419f5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- typo Commit: db5c0d95f6e10a5a723bc4bb54c11597ed629e9c https://github.com/galaxyproject/galaxy/commit/db5c0d95f6e10a5a723bc4bb54c1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04.rst Log Message: ----------- reorde notes a bit more based on impact/importance Commit: b85d604e30809d7e6b73f4762189182e7e82416b https://github.com/galaxyproject/galaxy/commit/b85d604e30809d7e6b73f4762189… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-13 (Fri, 13 May 2016) Changed paths: M doc/source/releases/16.01.rst M doc/source/releases/16.04.rst Log Message: ----------- Move some PRs that were merged in 16.01 before its release Galaxy 16.01 was officially released on 2016/02/24. Commit: c516c9fd45ffda5d4d74497bc96efc51966fdd22 https://github.com/galaxyproject/galaxy/commit/c516c9fd45ffda5d4d74497bc96e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-13 (Fri, 13 May 2016) Changed paths: M doc/source/releases/16.04.rst Log Message: ----------- Fix truncated PR titles and some acknowledgements Commit: dc5a5eb2eb1af48e14234d42aa8cacd3fd1aba1e https://github.com/galaxyproject/galaxy/commit/dc5a5eb2eb1af48e14234d42aa8c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-13 (Fri, 13 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- Add Bitbucket deprecation details Commit: 76fb9b72c34ecd6bead61b372a32dc0bd24375eb https://github.com/galaxyproject/galaxy/commit/76fb9b72c34ecd6bead61b372a32… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-13 (Fri, 13 May 2016) Changed paths: M doc/source/releases/16.04.rst Log Message: ----------- Add some missing PRs and merge some entries Commit: 3b7f6cb7777cf2a92d17928b38abe13bd3cdb338 https://github.com/galaxyproject/galaxy/commit/3b7f6cb7777cf2a92d17928b38ab… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- add some highlights, seems tough for this release Commit: 62b6eaa92aac9520f12968cb41690692c8c3fa4f https://github.com/galaxyproject/galaxy/commit/62b6eaa92aac9520f12968cb4169… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M doc/source/releases/16.01.rst M doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst Log Message: ----------- Merge branch '16.04_release_notes' of https://github.com/martenson/galaxy into 16.04_release_notes Commit: afb9027482f3a98a2b6d9e9fd049ded1da78c666 https://github.com/galaxyproject/galaxy/commit/afb9027482f3a98a2b6d9e9fd049… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- final touch of release notes from my side Commit: 50e596fb1b540a69f785296921a2611566a5b12b https://github.com/galaxyproject/galaxy/commit/50e596fb1b540a69f785296921a2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- reorder sections, un-quote bitbucket paragraph Commit: 9d5bf7b62d8f9a58e35e0317acb9dd5d88311b6f https://github.com/galaxyproject/galaxy/commit/9d5bf7b62d8f9a58e35e0317acb9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- minor release notes touch Commit: f887c059a2aff33a7c449d8ea234c4bbd9d09dd7 https://github.com/galaxyproject/galaxy/commit/f887c059a2aff33a7c449d8ea234… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- Expand 16.04 highlights... Commit: 8195d81739540ba489828616baa28a7b1c9d7711 https://github.com/galaxyproject/galaxy/commit/8195d81739540ba489828616baa2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M doc/source/releases/16.01.rst A doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst A doc/source/releases/16.07_announce.rst M doc/source/releases/index.rst Log Message: ----------- Merge pull request #2353 from martenson/16.04_release_notes [16.04] Release notes for 16.04 Compare: https://github.com/galaxyproject/galaxy/compare/cc86096c83b5...8195d8173954

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[galaxyproject/galaxy] 365f4b: modifying getIndex method
by GitHub 17 May '16

17 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 365f4b374e3af4134b57144e9340676ac4f903a5 https://github.com/galaxyproject/galaxy/commit/365f4b374e3af4134b57144e9340… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select.js Log Message: ----------- modifying getIndex method Commit: b361ffa1c217a7e2c57a4d770b100ec718ca22b8 https://github.com/galaxyproject/galaxy/commit/b361ffa1c217a7e2c57a4d770b10… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select.js M static/maps/mvc/ui/ui-select.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select.js Log Message: ----------- removing old code from _getIndex method Commit: 7f95786aef314a9484a5dab78d2883d9d42a8a43 https://github.com/galaxyproject/galaxy/commit/7f95786aef314a9484a5dab78d28… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M client/bower.json M client/galaxy/scripts/mvc/ui/ui-select.js M static/maps/mvc/ui/ui-select.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/ui/ui-select.js Log Message: ----------- Adding latest Underscore.js dependency Commit: e96b8bbf7afcfc58162b599a0e3d4e3d1fd0755a https://github.com/galaxyproject/galaxy/commit/e96b8bbf7afcfc58162b599a0e3d… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M CONTRIBUTORS.md M Makefile M client/README.md M client/bower.json M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/libs/backbone.js M client/galaxy/scripts/libs/bootstrap-tour.js M 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lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py M static/maps/layout/page.js.map M static/maps/libs/backbone.js.map M static/maps/libs/bootstrap-tour.js.map M static/maps/libs/d3.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/jquery/jquery.migrate.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M static/maps/libs/tracekit.js.map M static/maps/libs/underscore.js.map M static/maps/mvc/citation/citation-model.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/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/history/history-model.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.js.map M static/maps/mvc/history/multi-panel.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-library-view.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/popup-menu.js.map M static/maps/mvc/ui/ui-drilldown.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/ui/hoverhighlight.js.map M static/maps/ui/loading-indicator.js.map M static/maps/ui/mode-button.js.map M static/maps/ui/pagination.js.map M static/maps/ui/peek-column-selector.js.map M static/maps/utils/localization.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js M static/scripts/libs/backbone.js M static/scripts/libs/bootstrap-tour.js M static/scripts/libs/d3.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/jquery/jquery.migrate.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/libs/tracekit.js M static/scripts/libs/underscore.js M static/scripts/mvc/citation/citation-model.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/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/history/history-model.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.js M static/scripts/mvc/history/multi-panel.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-library-view.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/base/base_panels.mako M templates/display_base.mako M templates/sharing_base.mako M templates/show_params.mako A templates/slug_editing_js.mako M templates/webapps/galaxy/data_manager/view_job.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/library/common/browse_library.mako M templates/webapps/galaxy/library/common/ldda_info.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/galaxy/workflow/sharing.mako M templates/webapps/tool_shed/index.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/manage_repository.mako M test/api/test_tools.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py M test/base/interactor.py A test/functional/tools/multi_data_repeat.xml M test/functional/tools/samples_tool_conf.xml M test/integration/test_pulsar_embedded.py M test/qunit/test-common.js R test/qunit/test-libs/qunit-1.14.0.css R test/qunit/test-libs/qunit-1.14.0.js A test/qunit/test-libs/qunit-1.23.1.css A test/qunit/test-libs/qunit-1.23.1.js A test/qunit/test-libs/sinon-1.17.3.js R test/qunit/test-libs/sinon-1.9.1.js M test/qunit/tests/form_tests.js M test/qunit/tests/list-of-pairs-collection-creator.js M test/qunit/tests/metrics-logger.js M test/qunit/tests/page_tests.js M test/qunit/tests/ui_tests.html M test/qunit/tests/ui_tests.js A test/qunit/tests/utils_test.html A test/qunit/tests/utils_test.js M test/qunit/tests/workflow_editor_tests.js R test/shed_functional/functional/test_0450_skip_tool_tests.py M test/shed_functional/functional/test_0540_get_all_metadata_from_api.py A test/shed_functional/functional/test_0550_metadata_updated_dependencies.py A test/shed_functional/test_data/0550_files/filtering_1.0.tgz A test/shed_functional/test_data/0550_files/package_freebayes_1_0550.tgz A test/shed_functional/test_data/0550_files/package_freebayes_2_0550.tgz A test/shed_functional/test_data/0550_files/package_samtools_1_0550.tgz A test/shed_functional/test_data/0550_files/package_samtools_2_0550.tgz A test/shed_functional/test_data/0550_files/temp/tool_dependencies.xml M test/unit/test_objectstore.py M tools/data_source/biomart.xml M tools/data_source/upload.py M tools/filters/trimmer.xml M tools/stats/grouping.py M tools/stats/grouping.xml Log Message: ----------- Adding changes for latest Underscore JS library Commit: 4d6b8bf2b44a96d97b98fbc992ffc8518acb6a82 https://github.com/galaxyproject/galaxy/commit/4d6b8bf2b44a96d97b98fbc992ff… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M client/bower.json Log Message: ----------- reverting the version of underscore as it is already updated in the galaxy main Commit: a144a32f403bad299793a494e0547483c5cb1322 https://github.com/galaxyproject/galaxy/commit/a144a32f403bad299793a494e054… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select.js M static/maps/mvc/ui/ui-select.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/ui/ui-select.js Log Message: ----------- Merge branch 'dev' of https://github.com/anuprulez/galaxy into anuprulez-dev Conflicts: static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map Compare: https://github.com/galaxyproject/galaxy/compare/c2ea4ee52663...a144a32f403b

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[galaxyproject/infrastructure-playbook] 5763b3: Modify Jetstream access lists
by GitHub 17 May '16

17 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 5763b32749635d5db46e8d61ae9afac7bb1347cb https://github.com/galaxyproject/infrastructure-playbook/commit/5763b327496… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: A common_env/secret_group_vars/baseenv.yml A jetstreamiuenv/secret_group_vars/baseenv.yml A jetstreamiuenv/secret_group_vars/controllers.yml A jetstreamtaccenv/secret_group_vars/baseenv.yml A jetstreamtaccenv/secret_group_vars/controllers.yml Log Message: ----------- Modify Jetstream access lists

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