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

[galaxyproject/galaxy] aad5d9: Bump 15.10 version to 15.10.1 (and apparently it h...
by GitHub 18 Feb '16

18 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aad5d9a2e557e935bd88f725deb10d0ed82468d8 https://github.com/galaxyproject/galaxy/commit/aad5d9a2e557e935bd88f725deb1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Bump 15.10 version to 15.10.1 (and apparently it has been incorrectly set to 15.10.dev all this time). Commit: 868acc362f6ce8a8b3559fcb88ebb4c060321905 https://github.com/galaxyproject/galaxy/commit/868acc362f6ce8a8b3559fcb88eb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #1555 from natefoo/release_15.10 [15.10] Bump 15.10 version to 15.10.1 Commit: 37b98b773ea378bdd4a7845d60f589f7454f2291 https://github.com/galaxyproject/galaxy/commit/37b98b773ea378bdd4a7845d60f5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Load whitelist regardless of whether the setting is explicit in config. This is a sensible enough default, and requiring the option to be set in galaxy.ini is cumbersome and unnecessary since it's admin-only functionality. Commit: aabc916ed20ac7f25174ce4d552b735253697081 https://github.com/galaxyproject/galaxy/commit/aabc916ed20ac7f25174ce4d552b… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #1749 from dannon/whitelist_loading Load whitelist regardless of whether the setting is explicit in config. Commit: 84de6b4ed31906756c3c219eda3f4462773d0a21 https://github.com/galaxyproject/galaxy/commit/84de6b4ed31906756c3c219eda3f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/ui/popup-menu.js M static/maps/mvc/ui/popup-menu.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/popup-menu.js M templates/webapps/galaxy/history/display.mako Log Message: ----------- Fix target or window.location when importing histories from display.mako (shared with me->view) to allow for iframes; silence popup-menu.js when menu is closed due to location change Commit: 80a858a3afd970ca086992744b46725eb829b94e https://github.com/galaxyproject/galaxy/commit/80a858a3afd970ca086992744b46… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/ui/popup-menu.js M static/maps/mvc/ui/popup-menu.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/popup-menu.js M templates/webapps/galaxy/history/display.mako Log Message: ----------- Merge pull request #1753 from carlfeberhard/release_16.01 [16.01] Fix target or window.location when importing histories from display.m… Commit: 587d450402f8b618e4922a04aa87fc5625edce82 https://github.com/galaxyproject/galaxy/commit/587d450402f8b618e4922a04aa87… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/tool_shed/util/encoding_util.py Log Message: ----------- Fix installation of Tool Shed repositories containing non-ASCII characters in the description. Fix #1702. Commit: 476734d8651009e38505408be2e5f7331800680b https://github.com/galaxyproject/galaxy/commit/476734d8651009e38505408be2e5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/tool_shed/util/encoding_util.py Log Message: ----------- Merge pull request #1759 from nsoranzo/release_15.10_fix_for_1702 [15.10] Fix installation of Tool Shed repositories containing non-ASCII characters in the description. Commit: 3f34131ff506836d400f8d55b696d8044546b162 https://github.com/galaxyproject/galaxy/commit/3f34131ff506836d400f8d55b696… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/tool_shed/util/encoding_util.py Log Message: ----------- Merge branch 'release_15.10' into release_16.01 Conflicts: lib/galaxy/version.py Commit: a0537762f2861247109ead028c33eaca2bd42dbc https://github.com/galaxyproject/galaxy/commit/a0537762f2861247109ead028c33… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/ui/popup-menu.js M lib/galaxy/config.py M lib/tool_shed/util/encoding_util.py M static/maps/mvc/ui/popup-menu.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/popup-menu.js M templates/webapps/galaxy/history/display.mako Log Message: ----------- Merge branch 'release_16.01' into 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/68e6312a6410...a0537762f286

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[galaxyproject/galaxy] aad5d9: Bump 15.10 version to 15.10.1 (and apparently it h...
by GitHub 18 Feb '16

18 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: aad5d9a2e557e935bd88f725deb10d0ed82468d8 https://github.com/galaxyproject/galaxy/commit/aad5d9a2e557e935bd88f725deb1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Bump 15.10 version to 15.10.1 (and apparently it has been incorrectly set to 15.10.dev all this time). Commit: 868acc362f6ce8a8b3559fcb88ebb4c060321905 https://github.com/galaxyproject/galaxy/commit/868acc362f6ce8a8b3559fcb88eb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #1555 from natefoo/release_15.10 [15.10] Bump 15.10 version to 15.10.1 Commit: 587d450402f8b618e4922a04aa87fc5625edce82 https://github.com/galaxyproject/galaxy/commit/587d450402f8b618e4922a04aa87… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/tool_shed/util/encoding_util.py Log Message: ----------- Fix installation of Tool Shed repositories containing non-ASCII characters in the description. Fix #1702. Commit: 476734d8651009e38505408be2e5f7331800680b https://github.com/galaxyproject/galaxy/commit/476734d8651009e38505408be2e5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/tool_shed/util/encoding_util.py Log Message: ----------- Merge pull request #1759 from nsoranzo/release_15.10_fix_for_1702 [15.10] Fix installation of Tool Shed repositories containing non-ASCII characters in the description. Commit: 3f34131ff506836d400f8d55b696d8044546b162 https://github.com/galaxyproject/galaxy/commit/3f34131ff506836d400f8d55b696… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/tool_shed/util/encoding_util.py Log Message: ----------- Merge branch 'release_15.10' into release_16.01 Conflicts: lib/galaxy/version.py Compare: https://github.com/galaxyproject/galaxy/compare/80a858a3afd9...3f34131ff506

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[galaxyproject/galaxy] 587d45: Fix installation of Tool Shed repositories contain...
by GitHub 18 Feb '16

18 Feb '16

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 587d450402f8b618e4922a04aa87fc5625edce82 https://github.com/galaxyproject/galaxy/commit/587d450402f8b618e4922a04aa87… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/tool_shed/util/encoding_util.py Log Message: ----------- Fix installation of Tool Shed repositories containing non-ASCII characters in the description. Fix #1702. Commit: 476734d8651009e38505408be2e5f7331800680b https://github.com/galaxyproject/galaxy/commit/476734d8651009e38505408be2e5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/tool_shed/util/encoding_util.py Log Message: ----------- Merge pull request #1759 from nsoranzo/release_15.10_fix_for_1702 [15.10] Fix installation of Tool Shed repositories containing non-ASCII characters in the description. Compare: https://github.com/galaxyproject/galaxy/compare/868acc362f6c...476734d86510

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[galaxyproject/usegalaxy-playbook] c9696f: install new MEME and bwa on Main
by GitHub 18 Feb '16

18 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c9696f8218c4e21051ae7e59daec2140dddd161e https://github.com/galaxyproject/usegalaxy-playbook/commit/c9696f8218c4e210… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- install new MEME and bwa on Main update Main mutable confs

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[galaxyproject/galaxy] afb2ea: Clean up some twilltestcase methods.
by GitHub 18 Feb '16

18 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: afb2ea387d5a8c5b6794f3bf95940cce842aea2b https://github.com/galaxyproject/galaxy/commit/afb2ea387d5a8c5b6794f3bf9594… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-16 (Tue, 16 Feb 2016) Changed paths: M test/base/twilltestcase.py M test/functional/test_admin_features.py M test/functional/test_data_security.py M test/functional/test_dataset_features.py M test/functional/test_get_data.py M test/functional/test_library_features.py M test/functional/test_library_security.py M test/functional/test_library_templates.py M test/functional/test_metadata_editing.py M test/functional/test_sample_tracking.py M test/functional/test_tags.py M test/functional/test_ucsc_table_browser.py M test/functional/test_user_info.py M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0000_basic_repository_features.py M test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py M test/tool_shed/functional/test_0020_basic_repository_dependencies.py M test/tool_shed/functional/test_0030_repository_dependency_revisions.py M test/tool_shed/functional/test_0040_repository_circular_dependencies.py M test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_0060_workflows.py M test/tool_shed/functional/test_0070_invalid_tool.py M test/tool_shed/functional/test_0080_advanced_circular_dependencies.py M test/tool_shed/functional/test_0090_tool_search.py M test/tool_shed/functional/test_0100_complex_repository_dependencies.py M test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_0130_datatype_converters.py M test/tool_shed/functional/test_0140_tool_help_images.py M test/tool_shed/functional/test_0150_prior_installation_required.py M test/tool_shed/functional/test_0160_circular_prior_installation_required.py M test/tool_shed/functional/test_0170_complex_prior_installation_required.py M test/tool_shed/functional/test_0300_reset_all_metadata.py M test/tool_shed/functional/test_0310_hg_push_from_api.py M test/tool_shed/functional/test_0400_repository_component_reviews.py M test/tool_shed/functional/test_0410_repository_component_review_access_control.py M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py M test/tool_shed/functional/test_0430_browse_utilities.py M test/tool_shed/functional/test_0440_deleting_dependency_definitions.py M test/tool_shed/functional/test_0450_skip_tool_tests.py M test/tool_shed/functional/test_0460_upload_to_repository.py M test/tool_shed/functional/test_0470_tool_dependency_repository_type.py M test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py M test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py M test/tool_shed/functional/test_0520_import_export_circular_dependencies.py M test/tool_shed/functional/test_0530_repository_admin_feature.py M test/tool_shed/functional/test_1000_install_basic_repository.py M test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py M test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_1060_install_repository_with_workflow.py M test/tool_shed/functional/test_1070_invalid_tool.py M test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py M test/tool_shed/functional/test_1085_repository_dependency_handling.py M test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py M test/tool_shed/functional/test_1090_install_tool_from_tool_search.py M test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py M test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py M test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_1130_datatype_converters.py M test/tool_shed/functional/test_1140_tool_help_images.py M test/tool_shed/functional/test_1150_prior_installation_required.py M test/tool_shed/functional/test_1160_circular_prior_installation_required.py M test/tool_shed/functional/test_1170_complex_prior_installation_required.py M test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py M test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1300_reset_all_metadata.py M test/tool_shed/functional/test_1400_review_migration_stages.py M test/tool_shed/functional/test_1410_update_manager.py M test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py M test/tool_shed/functional/test_1430_repair_installed_repository.py M test/tool_shed/functional/test_1440_missing_env_sh_files.py M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py M test/tool_shed/functional/test_1460_data_managers.py M test/tool_shed/functional/test_1470_updating_installed_repositories.py Log Message: ----------- Clean up some twilltestcase methods. Commit: b96bc82db610a58f2c3fabdd65fc2e99a42b6e45 https://github.com/galaxyproject/galaxy/commit/b96bc82db610a58f2c3fabdd65fc… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-16 (Tue, 16 Feb 2016) Changed paths: M test/functional/test_get_data.py M test/tool_shed/functional/test_1170_complex_prior_installation_required.py Log Message: ----------- Fix overly enthusiastic s///g. Commit: a941e88b04005f8f44338af65ee2212447181da7 https://github.com/galaxyproject/galaxy/commit/a941e88b04005f8f44338af65ee2… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: R test/tool_shed/functional/test_1085_repository_dependency_handling.py R test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py R test/tool_shed/functional/test_1090_install_tool_from_tool_search.py A test/tool_shed/functional/test_1090_repository_dependency_handling.py R test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py A test/tool_shed/functional/test_1100_install_updated_repository_dependencies.py R test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py A test/tool_shed/functional/test_1110_install_tool_from_tool_search.py A test/tool_shed/functional/test_1120_install_repository_with_complex_dependencies.py R test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_1130_datatype_converters.py A test/tool_shed/functional/test_1130_install_repository_with_invalid_repository_dependency.py A test/tool_shed/functional/test_1140_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_1140_tool_help_images.py A test/tool_shed/functional/test_1150_datatype_converters.py R test/tool_shed/functional/test_1150_prior_installation_required.py R test/tool_shed/functional/test_1160_circular_prior_installation_required.py A test/tool_shed/functional/test_1160_tool_help_images.py R test/tool_shed/functional/test_1170_complex_prior_installation_required.py A test/tool_shed/functional/test_1170_prior_installation_required.py A test/tool_shed/functional/test_1180_circular_prior_installation_required.py A test/tool_shed/functional/test_1190_complex_prior_installation_required.py M test/tool_shed/functional/test_1410_update_manager.py M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py M test/tool_shed/functional/test_1470_updating_installed_repositories.py Log Message: ----------- Ensure that a valid login exists after cookies are cleared. Commit: 68e6312a6410b44edd7f52d629f422a62d2818ce https://github.com/galaxyproject/galaxy/commit/68e6312a6410b44edd7f52d629f4… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M test/base/twilltestcase.py M test/functional/test_admin_features.py M test/functional/test_data_security.py M test/functional/test_dataset_features.py M test/functional/test_get_data.py M test/functional/test_library_features.py M test/functional/test_library_security.py M test/functional/test_library_templates.py M test/functional/test_metadata_editing.py M test/functional/test_sample_tracking.py M test/functional/test_tags.py M test/functional/test_ucsc_table_browser.py M test/functional/test_user_info.py M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0000_basic_repository_features.py M test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py M test/tool_shed/functional/test_0020_basic_repository_dependencies.py M test/tool_shed/functional/test_0030_repository_dependency_revisions.py M test/tool_shed/functional/test_0040_repository_circular_dependencies.py M test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_0060_workflows.py M test/tool_shed/functional/test_0070_invalid_tool.py M test/tool_shed/functional/test_0080_advanced_circular_dependencies.py M test/tool_shed/functional/test_0090_tool_search.py M test/tool_shed/functional/test_0100_complex_repository_dependencies.py M test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_0130_datatype_converters.py M test/tool_shed/functional/test_0140_tool_help_images.py M test/tool_shed/functional/test_0150_prior_installation_required.py M test/tool_shed/functional/test_0160_circular_prior_installation_required.py M test/tool_shed/functional/test_0170_complex_prior_installation_required.py M test/tool_shed/functional/test_0300_reset_all_metadata.py M test/tool_shed/functional/test_0310_hg_push_from_api.py M test/tool_shed/functional/test_0400_repository_component_reviews.py M test/tool_shed/functional/test_0410_repository_component_review_access_control.py M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py M test/tool_shed/functional/test_0430_browse_utilities.py M test/tool_shed/functional/test_0440_deleting_dependency_definitions.py M test/tool_shed/functional/test_0450_skip_tool_tests.py M test/tool_shed/functional/test_0460_upload_to_repository.py M test/tool_shed/functional/test_0470_tool_dependency_repository_type.py M test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py M test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py M test/tool_shed/functional/test_0520_import_export_circular_dependencies.py M test/tool_shed/functional/test_0530_repository_admin_feature.py M test/tool_shed/functional/test_1000_install_basic_repository.py M test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py M test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_1060_install_repository_with_workflow.py M test/tool_shed/functional/test_1070_invalid_tool.py M test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py R test/tool_shed/functional/test_1085_repository_dependency_handling.py R test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py R test/tool_shed/functional/test_1090_install_tool_from_tool_search.py A test/tool_shed/functional/test_1090_repository_dependency_handling.py R test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py A test/tool_shed/functional/test_1100_install_updated_repository_dependencies.py R test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py A test/tool_shed/functional/test_1110_install_tool_from_tool_search.py A test/tool_shed/functional/test_1120_install_repository_with_complex_dependencies.py R test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_1130_datatype_converters.py A test/tool_shed/functional/test_1130_install_repository_with_invalid_repository_dependency.py A test/tool_shed/functional/test_1140_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_1140_tool_help_images.py A test/tool_shed/functional/test_1150_datatype_converters.py R test/tool_shed/functional/test_1150_prior_installation_required.py R test/tool_shed/functional/test_1160_circular_prior_installation_required.py A test/tool_shed/functional/test_1160_tool_help_images.py R test/tool_shed/functional/test_1170_complex_prior_installation_required.py A test/tool_shed/functional/test_1170_prior_installation_required.py A test/tool_shed/functional/test_1180_circular_prior_installation_required.py A test/tool_shed/functional/test_1190_complex_prior_installation_required.py M test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py M test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1300_reset_all_metadata.py M test/tool_shed/functional/test_1400_review_migration_stages.py M test/tool_shed/functional/test_1410_update_manager.py M test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py M test/tool_shed/functional/test_1430_repair_installed_repository.py M test/tool_shed/functional/test_1440_missing_env_sh_files.py M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py M test/tool_shed/functional/test_1460_data_managers.py M test/tool_shed/functional/test_1470_updating_installed_repositories.py Log Message: ----------- Merge pull request #1742 from davebx/ttc_cleanup Clean up some twilltestcase methods. Compare: https://github.com/galaxyproject/galaxy/compare/f5277a654a04...68e6312a6410

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[galaxyproject/galaxy] 84de6b: Fix target or window.location when importing histo...
by GitHub 17 Feb '16

17 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 84de6b4ed31906756c3c219eda3f4462773d0a21 https://github.com/galaxyproject/galaxy/commit/84de6b4ed31906756c3c219eda3f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/ui/popup-menu.js M static/maps/mvc/ui/popup-menu.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/popup-menu.js M templates/webapps/galaxy/history/display.mako Log Message: ----------- Fix target or window.location when importing histories from display.mako (shared with me->view) to allow for iframes; silence popup-menu.js when menu is closed due to location change Commit: 80a858a3afd970ca086992744b46725eb829b94e https://github.com/galaxyproject/galaxy/commit/80a858a3afd970ca086992744b46… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/ui/popup-menu.js M static/maps/mvc/ui/popup-menu.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/popup-menu.js M templates/webapps/galaxy/history/display.mako Log Message: ----------- Merge pull request #1753 from carlfeberhard/release_16.01 [16.01] Fix target or window.location when importing histories from display.m… Compare: https://github.com/galaxyproject/galaxy/compare/aabc916ed20a...80a858a3afd9

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[galaxyproject/galaxy] c56635: Make api/tools return tool_shed_repository informa...
by GitHub 17 Feb '16

17 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c56635ad2883df92575c85a5946726037ceef600 https://github.com/galaxyproject/galaxy/commit/c56635ad2883df92575c85a59467… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Make api/tools return tool_shed_repository information. Commit: f5277a654a048869d213f4941198ef43c03a46b6 https://github.com/galaxyproject/galaxy/commit/f5277a654a048869d213f4941198… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1752 from mvdbeek/return_tsr_info_on_tools_api Make api/tools return tool_shed_repository information. Compare: https://github.com/galaxyproject/galaxy/compare/e3b1fc1bef99...f5277a654a04

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[galaxyproject/galaxy] 80f4a5: [PROCEDURES] Drop Ross from the committers group.
by GitHub 17 Feb '16

17 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 80f4a5eaed2ec17e5ef97dc800707ea56a60d6dd https://github.com/galaxyproject/galaxy/commit/80f4a5eaed2ec17e5ef97dc80070… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- [PROCEDURES] Drop Ross from the committers group. Ross Lazarus has done a lot for Galaxy for a long time and has been a fantastic presence in the community. He is now retired and has no intention of touching the code or reviewing pull requests so I think it is best to remove him from the committers list. I have contacted him to confirm this and he has no problem with his removal from this group. Just to reiterate, this isn't a condemnation of any kind, from the organization policies - "Periodically, active members may review this group and request inactive members are removed - this should not be interpreted as a condemnation of these inactive members but merely as a reflection of a desire to keep this group focused enough to remain effective." Commit: e3b1fc1bef99bca281e6a86f927b44bbfa7fdaae https://github.com/galaxyproject/galaxy/commit/e3b1fc1bef99bca281e6a86f927b… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Merge pull request #1698 from jmchilton/ross [PROCEDURES] Drop Ross from the committers group. Compare: https://github.com/galaxyproject/galaxy/compare/b3296526da94...e3b1fc1bef99

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[galaxyproject/galaxy] b2da13: [PROCEDURES] Add Marius van den Beek to Galaxy com...
by GitHub 17 Feb '16

17 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b2da133e07c971afd35963c50b9b36eb5b24a358 https://github.com/galaxyproject/galaxy/commit/b2da133e07c971afd35963c50b9b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- [PROCEDURES] Add Marius van den Beek to Galaxy committer group. Marius has been an indispensable member of the Galaxy community for a while - his contributions to tools, planemo, and ansible roles have been signficant and invaluable. However over the last several months he has taken a very active role on the Galaxy central code base itself. He has worked through a number of very intricate bugs to tool shed, tooling, and workflow code - consistently providing high quality and important bug fixes. Beyond that he has made signficant enhancements to the testing of Galaxy and workflow available to tool developers leveraging local tool sheds. He also is very active in the review of issues and pull requests, perhaps the most important role of Galaxy committer group members. Commit: b3296526da94cee8ffd1acdf3186548d967f075f https://github.com/galaxyproject/galaxy/commit/b3296526da94cee8ffd1acdf3186… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Merge pull request #1699 from jmchilton/mvdbeek [PROCEDURES] Add Marius van den Beek to Galaxy committer group. Compare: https://github.com/galaxyproject/galaxy/compare/8e5aa4ac6774...b3296526da94

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[galaxyproject/infrastructure-playbook] 1bd157: Change access lists for orval
by GitHub 17 Feb '16

17 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1bd1570dcd2376995d29468e5c67ea630ec8ef09 https://github.com/galaxyproject/infrastructure-playbook/commit/1bd1570dcd2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M galaxyenv/secret_host_vars/orval.galaxyproject.org.yml Log Message: ----------- Change access lists for orval

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