Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 39045677d029c60e1ad3712f6cd7bef480ecceba
https://github.com/galaxyproject/galaxy/commit/39045677d029c60e1ad3712f6cd7…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-04 (Thu, 04 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M static/maps/mvc/dataset/dataset-li.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/dataset/dataset-li.js
Log Message:
-----------
Scratchbook enhancment to include info/view details for datasets
Commit: 5b905fece8d3d6ea84e6cece45ed42f6a566a10c
https://github.com/galaxyproject/galaxy/commit/5b905fece8d3d6ea84e6cece45ed…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-05 (Fri, 05 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M static/maps/mvc/dataset/dataset-li.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/dataset/dataset-li.js
Log Message:
-----------
Merge pull request #2733 from guerler/add_dataset_info_to_frames
Scratchbook enhancement to include info/view details for datasets
Compare: https://github.com/galaxyproject/galaxy/compare/96457353d94a...5b905fece8d3
Branch: refs/heads/release_16.07
Home: https://github.com/galaxyproject/galaxy
Commit: 786da21a3bd97da1c2f349f77515fed2b3713d6c
https://github.com/galaxyproject/galaxy/commit/786da21a3bd97da1c2f349f77515…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-05 (Fri, 05 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form.js
M static/maps/mvc/tool/tool-form.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form.js
Log Message:
-----------
Hide form instead of removing it to preserve attached listento events
Commit: 3f8f9b7bbb0c565a07de43820dcfa5ed6e4d03e1
https://github.com/galaxyproject/galaxy/commit/3f8f9b7bbb0c565a07de43820dcf…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-05 (Fri, 05 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form.js
M static/maps/mvc/tool/tool-form.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form.js
Log Message:
-----------
Merge pull request #2737 from guerler/hide_form_on_success
[16.07] Hide form instead of removing it to preserve attached listenTo events
Compare: https://github.com/galaxyproject/galaxy/compare/8c57ed7e5432...3f8f9b7bbb0c
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: de3c50a5ef7731961d6902a592333092a2fe85e1
https://github.com/galaxyproject/galaxy/commit/de3c50a5ef7731961d6902a59233…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-08-04 (Thu, 04 Aug 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/repository/relation_builder.py
M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/installed_repository_manager.py
M lib/tool_shed/galaxy_install/migrate/common.py
M lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py
M lib/tool_shed/galaxy_install/repair_repository_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M lib/tool_shed/grids/admin_grids.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/repository_review_grids.py
M lib/tool_shed/managers/repositories.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_types/registry.py
M lib/tool_shed/tool_shed_registry.py
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_content_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/util/web_util.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M scripts/tool_shed/api/common.py
M setup.cfg
Log Message:
-----------
Python3 support and import order fixes for lib/tool_shed/
Commit: 2efec4e062afbd2281271e8d30a8b1fdd627b9be
https://github.com/galaxyproject/galaxy/commit/2efec4e062afbd2281271e8d30a8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-05 (Fri, 05 Aug 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/repository/relation_builder.py
M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/installed_repository_manager.py
M lib/tool_shed/galaxy_install/migrate/common.py
M lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py
M lib/tool_shed/galaxy_install/repair_repository_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M lib/tool_shed/grids/admin_grids.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/repository_review_grids.py
M lib/tool_shed/managers/repositories.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_types/registry.py
M lib/tool_shed/tool_shed_registry.py
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_content_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/util/web_util.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M scripts/tool_shed/api/common.py
M setup.cfg
Log Message:
-----------
Merge pull request #2731 from nsoranzo/python3
Python3 support and import order fixes for lib/tool_shed/
Compare: https://github.com/galaxyproject/galaxy/compare/2ebef640cb63...2efec4e062af
Branch: refs/heads/release_16.07
Home: https://github.com/galaxyproject/galaxy
Commit: 5c79aa8fbc727feec6fa2041881645acdaed75f4
https://github.com/galaxyproject/galaxy/commit/5c79aa8fbc727feec6fa20418816…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-05 (Fri, 05 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M static/maps/mvc/ui/ui-buttons.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-buttons.js
Log Message:
-----------
Allow link buttons to trigger regular click events
Commit: fe3db95eec8fd942a9a46ad05c579c41eda9705e
https://github.com/galaxyproject/galaxy/commit/fe3db95eec8fd942a9a46ad05c57…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-05 (Fri, 05 Aug 2016)
Changed paths:
M client/galaxy/scripts/layout/scratchbook.js
M static/maps/layout/scratchbook.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/scratchbook.js
Log Message:
-----------
Merge branch 'release_16.07' into fix_history_refresh
Commit: 8c57ed7e5432e4f92b95bc41fc657b562db18430
https://github.com/galaxyproject/galaxy/commit/8c57ed7e5432e4f92b95bc41fc65…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-05 (Fri, 05 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M static/maps/mvc/ui/ui-buttons.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-buttons.js
Log Message:
-----------
Merge pull request #2743 from guerler/fix_history_refresh
[16.07] Allow link buttons to trigger regular click events
Compare: https://github.com/galaxyproject/galaxy/compare/258e4a7b669e...8c57ed7e5432
Branch: refs/heads/release_16.07
Home: https://github.com/galaxyproject/galaxy
Commit: 83d4ebd0348cae7c9d0056e37b269c96768d0312
https://github.com/galaxyproject/galaxy/commit/83d4ebd0348cae7c9d0056e37b26…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-05 (Fri, 05 Aug 2016)
Changed paths:
M client/galaxy/scripts/layout/scratchbook.js
M static/maps/layout/scratchbook.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/scratchbook.js
Log Message:
-----------
Fix unused href parameter when adding scratchbook frames
Commit: 258e4a7b669edb2aca15e295353db384bc72575a
https://github.com/galaxyproject/galaxy/commit/258e4a7b669edb2aca15e295353d…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-05 (Fri, 05 Aug 2016)
Changed paths:
M client/galaxy/scripts/layout/scratchbook.js
M static/maps/layout/scratchbook.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/scratchbook.js
Log Message:
-----------
Merge pull request #2744 from guerler/fix_scratchbook_href
[16.07] Fix unused href parameter when adding scratchbook frames
Compare: https://github.com/galaxyproject/galaxy/compare/8b0d88b30e62...258e4a7b669e
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 50b6897fec475d62f7e8cf0e640000d088a958ac
https://github.com/galaxyproject/galaxy/commit/50b6897fec475d62f7e8cf0e6400…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-04 (Thu, 04 Aug 2016)
Changed paths:
M config/tool_shed.ini.sample
M lib/galaxy/webapps/tool_shed/config.py
Log Message:
-----------
Make tool shed logging like Galaxy logging.
- Reduces duplicated code.
- Enables best practice of commenting out defaults in shed sample config.
- Add auto_configure_logging option to tool shed to match Galaxy.
Commit: 2116f97a2f04b78f75c4a83cc1bf3ecad0a75cd6
https://github.com/galaxyproject/galaxy/commit/2116f97a2f04b78f75c4a83cc1bf…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-04 (Thu, 04 Aug 2016)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
Add routes middleware to chatty loggers disabled at debug level.
Also add option to skip disabling the chatty loggers.
Commit: 41acdadbae8aab6d4fe38d1de354404819f7851d
https://github.com/galaxyproject/galaxy/commit/41acdadbae8aab6d4fe38d1de354…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-05 (Fri, 05 Aug 2016)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/webapps/tool_shed/app.py
M lib/galaxy/webapps/tool_shed/config.py
Log Message:
-----------
move the configure_logging import to the app.py where it is used
remove routes.middleware chatty logging as the PR is independent on this
Commit: 9b86eae99569cfb6e8884afd7324e96b1b5d7028
https://github.com/galaxyproject/galaxy/commit/9b86eae99569cfb6e8884afd7324…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-05 (Fri, 05 Aug 2016)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/webapps/tool_shed/app.py
M lib/galaxy/webapps/tool_shed/config.py
Log Message:
-----------
Merge pull request #49 from martenson/conf-logging
move the configure_logging import to the app.py where it is used
Commit: 2ebef640cb639f12012da52361891065e8d13570
https://github.com/galaxyproject/galaxy/commit/2ebef640cb639f12012da5236189…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-05 (Fri, 05 Aug 2016)
Changed paths:
M config/tool_shed.ini.sample
M lib/galaxy/config.py
M lib/galaxy/webapps/tool_shed/app.py
M lib/galaxy/webapps/tool_shed/config.py
Log Message:
-----------
Merge pull request #2735 from jmchilton/logging_dedup
Slightly revise auto configuration of loggers
Compare: https://github.com/galaxyproject/galaxy/compare/08d20b26784a...2ebef640cb63
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: e13095d3d2dc802143da69b94bc87390a6ea9699
https://github.com/galaxyproject/galaxy/commit/e13095d3d2dc802143da69b94bc8…
Author: galaxy <galaxy(a)galaxy.development>
Date: 2016-08-04 (Thu, 04 Aug 2016)
Changed paths:
M client/galaxy/style/less/base.less
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/style/blue/base.css
Log Message:
-----------
Changed css in base.less to allow tool search input field to
remain fixed when a long list is being scroll. Issue 2375.
Commit: c28f7e6b4e08624f6d690cf7899a41812ed68534
https://github.com/galaxyproject/galaxy/commit/c28f7e6b4e08624f6d690cf7899a…
Author: Scott Szakonyi <sszakony(a)nd.edu>
Date: 2016-08-04 (Thu, 04 Aug 2016)
Changed paths:
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Updating to latest from project
Commit: bf54f08fc2bca68c5e158e5e88f8e70e9a84f83c
https://github.com/galaxyproject/galaxy/commit/bf54f08fc2bca68c5e158e5e88f8…
Author: Scott Szakonyi <sszakony(a)nd.edu>
Date: 2016-08-04 (Thu, 04 Aug 2016)
Changed paths:
M client/galaxy/style/less/base.less
M static/style/blue/base.css
Log Message:
-----------
Merge branch 'Gal2375' into dev
Conflicts:
static/scripts/bundled/analysis.bundled.js
static/scripts/bundled/analysis.bundled.js.map
static/scripts/bundled/libs.bundled.js.map
static/style/blue/base.css
Commit: ae5b844388ddd0ded9816814abc8c46398d50511
https://github.com/galaxyproject/galaxy/commit/ae5b844388ddd0ded9816814abc8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-04 (Thu, 04 Aug 2016)
Changed paths:
M client/galaxy/style/less/base.less
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/style/blue/base.css
Log Message:
-----------
Merge remote-tracking branch 'sszakony/dev' into dev
Commit: 08d20b26784aca80c54ef7be8a8422dbb9328d93
https://github.com/galaxyproject/galaxy/commit/08d20b26784aca80c54ef7be8a84…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-04 (Thu, 04 Aug 2016)
Changed paths:
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Repack w/ merge, not sure how the bundled libs got out of sync here.
Compare: https://github.com/galaxyproject/galaxy/compare/3206a5405562...08d20b26784a