Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: d10f740cff8e3520383c004a16830700b2789c9f https://github.com/galaxyproject/galaxy/commit/d10f740cff8e3520383c004a16830... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py A templates/webapps/galaxy/user/manage_info.mako
Log Message: ----------- The user controller functions for changing information were ripped out before providing a way for admin functionality to use the new javascript stuff. Seems nontrivial, so this puts the endpoint back temporarily until the adminjs rewrite which can include the new functionality.
Commit: 6f3c8c7447e9a71c580ef9307395cd5dcd314915 https://github.com/galaxyproject/galaxy/commit/6f3c8c7447e9a71c580ef9307395c... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message: ----------- This template inherited field never worked apparently, but nobody noticed. This correctly sets the is_admin flag here.
Commit: 4be00d3058396ed30da4f6f0958ad6fa989249cb https://github.com/galaxyproject/galaxy/commit/4be00d3058396ed30da4f6f0958ad... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths: M templates/webapps/galaxy/user/manage_info.mako
Log Message: ----------- Strip out unnecessary user address editing.
Commit: 456acf0b84004c85c94d3129f0a89af9be2d5452 https://github.com/galaxyproject/galaxy/commit/456acf0b84004c85c94d3129f0a89... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message: ----------- Update docstring to explicitly mention this as a temporary endpoint.
Commit: b46ac475a93fbf0da71272861677a00a3877b91b https://github.com/galaxyproject/galaxy/commit/b46ac475a93fbf0da71272861677a... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message: ----------- Fix verbiage in temporary method.
Commit: 64036a441284151e1b1a3e9305537d526005ff3a https://github.com/galaxyproject/galaxy/commit/64036a441284151e1b1a3e9305537... Author: Martin Cech cech.marten@gmail.com Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py A templates/webapps/galaxy/user/manage_info.mako
Log Message: ----------- Merge pull request #3656 from dannon/admin-userinfo-edit-fix
[17.01] Admin user information editing
Commit: 0636053901545a26662ed8f42a15bb67407f2231 https://github.com/galaxyproject/galaxy/commit/0636053901545a26662ed8f42a15b... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message: ----------- Use pgcalc when possible
Commit: 895351cdf8e8867452d28dffb89a2067eabfadb3 https://github.com/galaxyproject/galaxy/commit/895351cdf8e8867452d28dffb89a2... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message: ----------- initial working async recalc
Commit: 45d75e3da55e43a4444c1a7982e1ea31e1aa5cb7 https://github.com/galaxyproject/galaxy/commit/45d75e3da55e43a4444c1a7982e1e... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message: ----------- Encode userid in messages.
Commit: c373bf27e79e48bc2e8ba983e9f08abde16db4df https://github.com/galaxyproject/galaxy/commit/c373bf27e79e48bc2e8ba983e9f08... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths: M lib/galaxy/queue_worker.py
Log Message: ----------- Change handling of declare in queue_async_task
Commit: 00b1591f05af4743d8b16b7d1bbbbc99a3974adb https://github.com/galaxyproject/galaxy/commit/00b1591f05af4743d8b16b7d1bbbb... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message: ----------- Fix inline doc
Commit: 5a5dbb97f1e04dfe15fbf71c441eb50ae4b70b11 https://github.com/galaxyproject/galaxy/commit/5a5dbb97f1e04dfe15fbf71c441eb... Author: Martin Cech cech.marten@gmail.com Date: 2017-02-25 (Sat, 25 Feb 2017)
Changed paths: M doc/source/releases/17.01_announce.rst
Log Message: ----------- improve 17.01 get galaxy release notes
Commit: 53c00df805e7ae7e509c08374bc941d31d20000d https://github.com/galaxyproject/galaxy/commit/53c00df805e7ae7e509c08374bc94... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-02-25 (Sat, 25 Feb 2017)
Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message: ----------- Rename send_local_controL_task, add at least a tiny bit of documentation.
Commit: d4b677bc38b221678bc991e0fddc43622accb928 https://github.com/galaxyproject/galaxy/commit/d4b677bc38b221678bc991e0fddc4... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-02-27 (Mon, 27 Feb 2017)
Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message: ----------- Merge pull request #3669 from dannon/logout-recalc-improvements
[17.01] Logout recalc improvements
Commit: 28875de584ac1967a8f2c0cdc8f5fa7b37e70f21 https://github.com/galaxyproject/galaxy/commit/28875de584ac1967a8f2c0cdc8f5f... Author: Daniel Blankenberg dan.blankenberg@gmail.com Date: 2017-02-28 (Tue, 28 Feb 2017)
Changed paths: M doc/source/releases/17.01_announce.rst
Log Message: ----------- Merge pull request #3670 from martenson/fix-RN1701
[17.01] improve 17.01 get galaxy release notes
Commit: 0997348a1c0a450986d376a96af024c73d4c7f37 https://github.com/galaxyproject/galaxy/commit/0997348a1c0a450986d376a96af02... Author: Martin Cech cech.marten@gmail.com Date: 2017-02-28 (Tue, 28 Feb 2017)
Changed paths: M lib/galaxy/tools/search/__init__.py
Log Message: ----------- fix tool search idnex building for tools with / in id and not from TS
Commit: c11cb3dd4572e7a4f1f814a31a45477f9ecd5ae9 https://github.com/galaxyproject/galaxy/commit/c11cb3dd4572e7a4f1f814a31a454... Author: Martin Cech cech.marten@gmail.com Date: 2017-02-28 (Tue, 28 Feb 2017)
Changed paths: M lib/galaxy/tools/search/__init__.py
Log Message: ----------- fix typo spotted by :beer: :eyes:
Commit: 169b45b138685164010043be95cefe8148c6f713 https://github.com/galaxyproject/galaxy/commit/169b45b138685164010043be95cef... Author: guerler aysam.guerler@gmail.com Date: 2017-02-28 (Tue, 28 Feb 2017)
Changed paths: M lib/galaxy/managers/workflows.py
Log Message: ----------- Fix step name display for 17.01
Commit: e23facb966c9962bb5bd1fdd07bf6ee28d7d5930 https://github.com/galaxyproject/galaxy/commit/e23facb966c9962bb5bd1fdd07bf6... Author: John Chilton jmchilton@gmail.com Date: 2017-02-28 (Tue, 28 Feb 2017)
Changed paths: M lib/galaxy/tools/search/__init__.py
Log Message: ----------- Merge pull request #3680 from martenson/fix-id-indexing
[17.01] fix tool search index building for tools with slash in id and not from TS
Commit: 7824cd31fd7b9351efa1cf8274b89b2b9a0d811d https://github.com/galaxyproject/galaxy/commit/7824cd31fd7b9351efa1cf8274b89... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-03-01 (Wed, 01 Mar 2017)
Changed paths: M lib/galaxy/managers/workflows.py
Log Message: ----------- Merge pull request #3681 from guerler/fix_name_display
[17.01] Fix step name display for 17.01
Commit: dda11d21c2e88f6b935f9f90f270a7aeccd929da https://github.com/galaxyproject/galaxy/commit/dda11d21c2e88f6b935f9f90f270a... Author: John Chilton jmchilton@gmail.com Date: 2017-03-01 (Wed, 01 Mar 2017)
Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/requirements.py
Log Message: ----------- [17.01] Fix container resolver log statements exposing pointers.
These log statements:
``` 2017-02-27 12:11:50,959 INFO [galaxy.tools.deps.containers] Checking with container resolver [<galaxy.tools.deps.container_resolvers.explicit.ExplicitContainerResolver object at 0x10b211590>] found description [None] 2017-02-27 12:11:51,062 INFO [galaxy.tools.deps.containers] Checking with container resolver [<galaxy.tools.deps.container_resolvers.mulled.CachedMulledContainerResolver object at 0x10b2115d0>] found description [None] 2017-02-27 12:11:51,490 INFO [galaxy.tools.deps.containers] Checking with container resolver [<galaxy.tools.deps.container_resolvers.mulled.MulledContainerResolver object at 0x10b211610>] found description [<galaxy.tools.deps.requirements.ContainerDescription object at 0x10d6f1550>] ```
Become:
``` 2017-02-27 13:19:06,201 INFO [galaxy.tools.deps.containers] Checking with container resolver [ExplicitContainerResolver[]] found description [None] 2017-02-27 13:19:06,251 INFO [galaxy.tools.deps.containers] Checking with container resolver [CachedMulledContainerResolver[namespace=None]] found description [None] 2017-02-27 13:19:06,679 INFO [galaxy.tools.deps.containers] Checking with container resolver [MulledContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/seqtk:1.2--0,type=docker]] ```
Rebased with suggestion from @nsoranzo :eagle::eyes:
Commit: ca5bb99ee043587fe37cc9354885d3de6fbd5ce3 https://github.com/galaxyproject/galaxy/commit/ca5bb99ee043587fe37cc9354885d... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-03-01 (Wed, 01 Mar 2017)
Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/requirements.py
Log Message: ----------- Merge pull request #3679 from jmchilton/fix_logs
[17.01] Fix container resolver log statements exposing pointers.
Commit: ce7f9e91ca8893ce290aeeac4836e18db07af3a5 https://github.com/galaxyproject/galaxy/commit/ce7f9e91ca8893ce290aeeac4836e... Author: John Chilton jmchilton@gmail.com Date: 2017-03-01 (Wed, 01 Mar 2017)
Changed paths: M lib/galaxy/tools/__init__.py
Log Message: ----------- Annotate converters that appear to need galaxy on PYTHONPATH.
Should fix #3499 (thanks for the explicit heads up @mvdbeek).
Commit: 93a802bd450658f0c66d4226c626112e8163d5a6 https://github.com/galaxyproject/galaxy/commit/93a802bd450658f0c66d4226c6261... Author: Martin Cech cech.marten@gmail.com Date: 2017-03-02 (Thu, 02 Mar 2017)
Changed paths: M lib/galaxy/tools/__init__.py
Log Message: ----------- Merge pull request #3690 from jmchilton/converter_galaxy_lib_fixes
[17.01] Annotate converters that appear to need galaxy on PYTHONPATH.
Commit: 02f3a2737dd1c48574df9bf8e51ce43e6789bf1e https://github.com/galaxyproject/galaxy/commit/02f3a2737dd1c48574df9bf8e51ce... Author: anuprulez anup.rulez@gmail.com Date: 2017-03-08 (Wed, 08 Mar 2017)
Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js
Log Message: ----------- Bug fix for masthead webhook if Galaxy.page is undefined for workflow, data libraries etc pages
Commit: 7988ae59f5b94b952bd1965b76250ad3f21525d6 https://github.com/galaxyproject/galaxy/commit/7988ae59f5b94b952bd1965b76250... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako
Log Message: ----------- Allow display of install_resolver_checkbox when installing data manager tools
by merging select_shed_tool_panel_config.mako functionality into select_tool_panel_section.mako (thx @nsoranzo for this suggestion).
Commit: e8922295bd5753e0be262f141b25a05622972ee6 https://github.com/galaxyproject/galaxy/commit/e8922295bd5753e0be262f141b25a... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
Log Message: ----------- Remove checks
for `includes_tools_for_display_in_tool_panel` and `includes_tools_for_display_in_tool_panel` when determining if initiate_repository_installation.mako should be posted to. It is sufficient to check that select_tool_panel_section_button has been clicked.
Commit: 2df727cb05d8d15e14a23a4f8c1da920bfde999d https://github.com/galaxyproject/galaxy/commit/2df727cb05d8d15e14a23a4f8c1da... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths: M test/shed_functional/functional/test_1150_datatype_converters.py
Log Message: ----------- Adjust wording of datatype converter install test.
Commit: 1b9a2868a17899787bf65181f96892596b16b51b https://github.com/galaxyproject/galaxy/commit/1b9a2868a17899787bf65181f9689... Author: John Chilton jmchilton@gmail.com Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js
Log Message: ----------- Merge pull request #3728 from martenson/backport-masthead-fix
[16.10] backport of webhook masthead fix for datalibs and workflows
Commit: 376212eff900d28450165ddf715f3d9a29870ca9 https://github.com/galaxyproject/galaxy/commit/376212eff900d28450165ddf715f3... Author: Daniel Blankenberg dan.blankenberg@gmail.com Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py
Log Message: ----------- Fix for uploading rdata datasets when explicitly declaring datatype.
Now that ext's are forced to be all lowercase, you cannot upload a dataset with any uppercase characters in the extension.
TODO: An additional fix directly for the upload tool/datatype widget should be pursued that will prevent these issues.
Commit: fa37f67786b88b5d1c4138a142efccf3cc42d219 https://github.com/galaxyproject/galaxy/commit/fa37f67786b88b5d1c4138a142efc... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map
Log Message: ----------- Merge branch 'release_16.10' into release_17.01
Conflicts: static/maps/layout/menu.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map static/scripts/layout/menu.js
Commit: 7429ded33e1af8214f2ca20563698f73dd3869d3 https://github.com/galaxyproject/galaxy/commit/7429ded33e1af8214f2ca20563698... Author: Martin Cech marten@bx.psu.edu Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths: M lib/galaxy/webapps/galaxy/api/users.py
Log Message: ----------- fix datetime import
Commit: aaafbe956f343eb6d34dbdcec0b8b937e439334a https://github.com/galaxyproject/galaxy/commit/aaafbe956f343eb6d34dbdcec0b8b... Author: Martin Cech marten@bx.psu.edu Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths: M lib/galaxy/webapps/galaxy/api/users.py
Log Message: ----------- add the activation functionality to API users controller it was invoked but not included resulting in errors
Commit: 642956a899ea2b97348be698bd81dd11a85d113e https://github.com/galaxyproject/galaxy/commit/642956a899ea2b97348be698bd81d... Author: Martin Cech marten@bx.psu.edu Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths: M lib/galaxy/webapps/galaxy/api/users.py
Log Message: ----------- remove unused import
Commit: 54fb1a433d061d398d67a0cb3e80ea1406226898 https://github.com/galaxyproject/galaxy/commit/54fb1a433d061d398d67a0cb3e80e... Author: Martin Cech marten@bx.psu.edu Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths: M lib/galaxy/webapps/galaxy/api/users.py
Log Message: ----------- only request verificaion when needed thanks @nsoranzo
Commit: 56c710adbc1f10579511c506503493241df4176c https://github.com/galaxyproject/galaxy/commit/56c710adbc1f10579511c50650349... Author: Martin Cech marten@bx.psu.edu Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths: M lib/galaxy/webapps/galaxy/api/users.py
Log Message: ----------- reqork the activation logic when email is changed thanks to @nsoranzo for help
Commit: cfa3e29cadf0960f01735a2ad43b64ac9c17e031 https://github.com/galaxyproject/galaxy/commit/cfa3e29cadf0960f01735a2ad43b6... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/shed_functional/functional/test_1150_datatype_converters.py
Log Message: ----------- Merge pull request #3686 from mvdbeek/datamanager_conda_install
[17.01] Allow display of install_resolver_checkbox when installing data manag…
Commit: 6ab5cc1caf8c9fc0d4ce311c43988d12ea2ae6bb https://github.com/galaxyproject/galaxy/commit/6ab5cc1caf8c9fc0d4ce311c43988... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-03-18 (Sat, 18 Mar 2017)
Changed paths: M lib/galaxy/webapps/galaxy/api/users.py
Log Message: ----------- Merge pull request #3771 from martenson/fix-users-api
[17.01] Fixes for users API
Commit: e3e24facc72103dadeca2dc72c9d038f907eb10e https://github.com/galaxyproject/galaxy/commit/e3e24facc72103dadeca2dc72c9d0... Author: Martin Cech marten@bx.psu.edu Date: 2017-03-20 (Mon, 20 Mar 2017)
Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py
Log Message: ----------- Merge pull request #3766 from blankenberg/17.01-rdata-upload-fix
[17.01] Fix for uploading rdata datasets when explicitly declaring datatype.
Commit: 12eb3838496f373e429235cd8e75117baf682005 https://github.com/galaxyproject/galaxy/commit/12eb3838496f373e429235cd8e751... Author: Martin Cech marten@bx.psu.edu Date: 2017-03-20 (Mon, 20 Mar 2017)
Changed paths: M lib/galaxy/web/framework/helpers/grids.py
Log Message: ----------- fix xss thanks to @erasche
Commit: 2528a89bd087786c458c86d6ac78c24e8fb7f51d https://github.com/galaxyproject/galaxy/commit/2528a89bd087786c458c86d6ac78c... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-03-20 (Mon, 20 Mar 2017)
Changed paths: M lib/galaxy/web/framework/helpers/grids.py
Log Message: ----------- Merge pull request #3776 from martenson/xss-fix
[16.04] fix xss vuln in grids
Commit: e3255fd3cb7c1b0cf9ce9fa82f0a4a9c39719f19 https://github.com/galaxyproject/galaxy/commit/e3255fd3cb7c1b0cf9ce9fa82f0a4... Author: nekrut anton@nekrut.org Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths: M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/unzip_collection.xml M lib/galaxy/tools/zip_collection.xml
Log Message: ----------- made collection ops help sections slightly more readable
Commit: d9c3a0bb57e63a1849bb3f55c056ae0384a2279a https://github.com/galaxyproject/galaxy/commit/d9c3a0bb57e63a1849bb3f55c056a... Author: Anton Nekrutenko anekrut@gmail.com Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths: M lib/galaxy/tools/unzip_collection.xml
Log Message: ----------- Update unzip_collection.xml
fixed typos identified by @mvdbeek
Commit: 80ecc79a4cb8fa3dbaf9b3348216df6f9387a91c https://github.com/galaxyproject/galaxy/commit/80ecc79a4cb8fa3dbaf9b3348216d... Author: Martin Cech marten@bx.psu.edu Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths: M lib/galaxy/web/framework/helpers/grids.py
Log Message: ----------- Merge pull request #3789 from galaxyproject/release_16.04
merge 16.04 into 16.07
Commit: 490e565611b5e3a22124d937e22cf0363afb62f6 https://github.com/galaxyproject/galaxy/commit/490e565611b5e3a22124d937e22cf... Author: Martin Cech marten@bx.psu.edu Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths: M lib/galaxy/web/framework/helpers/grids.py
Log Message: ----------- Merge pull request #3790 from galaxyproject/release_16.07
merge 16.07 into 16.10
Commit: ec88dda1e9c926341b87bc7e19b7b5842eb92ddb https://github.com/galaxyproject/galaxy/commit/ec88dda1e9c926341b87bc7e19b7b... Author: Martin Cech marten@bx.psu.edu Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths: M lib/galaxy/web/framework/helpers/grids.py
Log Message: ----------- Merge pull request #3791 from galaxyproject/release_16.10
merge 16.10 into 17.01
Commit: c84b3ba0b8f9de983d43ea17c165856d23960911 https://github.com/galaxyproject/galaxy/commit/c84b3ba0b8f9de983d43ea17c1658... Author: Daniel Blankenberg dan.blankenberg@gmail.com Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths: M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/unzip_collection.xml M lib/galaxy/tools/zip_collection.xml
Log Message: ----------- Merge pull request #3788 from jmchilton/backport_collection_option_help_fixes
[17.01] Backport collection operation help fixes
Commit: 15aa0bd615726ed46fa7beec9a364bb3c11df9f2 https://github.com/galaxyproject/galaxy/commit/15aa0bd615726ed46fa7beec9a364... Author: John Chilton jmchilton@gmail.com Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths: M lib/galaxy/jobs/runners/__init__.py
Log Message: ----------- Fix problem with cleaning up jobs in local runner.
Fixes #3801 (broken in b78287f as part of #3291).
Commit: 65cbddee7c3bc2d772686b261aaf853f84f76235 https://github.com/galaxyproject/galaxy/commit/65cbddee7c3bc2d772686b261aaf8... Author: Daniel Blankenberg dan.blankenberg@gmail.com Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths: M lib/galaxy/jobs/runners/__init__.py
Log Message: ----------- Merge pull request #3803 from jmchilton/1701_fixes_0
[17.01] Fix problem with cleaning up jobs in local runner.
Commit: d8af125af4d3798c32b31793c10f9b9426d7dfe2 https://github.com/galaxyproject/galaxy/commit/d8af125af4d3798c32b31793c10f9... Author: Hans-Rudolf Hotz hrhotz@users.noreply.github.com Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths: M lib/galaxy/tools/__init__.py
Log Message: ----------- Update __init__.py
Commit: 3068c9f053554c448a30388d46b91a6979e39cb7 https://github.com/galaxyproject/galaxy/commit/3068c9f053554c448a30388d46b91... Author: John Chilton jmchilton@gmail.com Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths: M lib/galaxy/tools/__init__.py
Log Message: ----------- Fix CONVERTER_gff_to_fli_0 for striping Galaxy from Python environment.
Taking another stab at fixing #3499 which was broken with #3364. Last attempt at fixing converters didn't cover this (#3690) but I missed this tool and bed to fli fixed in #3822.
Commit: 70b22dffc28830b4f9fc3c9a89845d6ccf32e559 https://github.com/galaxyproject/galaxy/commit/70b22dffc28830b4f9fc3c9a89845... Author: Martin Cech marten@bx.psu.edu Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths: M lib/galaxy/tools/__init__.py
Log Message: ----------- Merge pull request #3824 from jmchilton/more_tool_env_fixes
[17.01] More CONVERTER fixes for restricting tools' Python environment.
Commit: 1fbdb35d6edb84a3700ea1392dcf32f1a42f8225 https://github.com/galaxyproject/galaxy/commit/1fbdb35d6edb84a3700ea1392dcf3... Author: Daniel Blankenberg dan.blankenberg@gmail.com Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths: M display_applications/igv/bigwig.xml
Log Message: ----------- Have IGV bigWig display application make use of build_sites/ site_type config instead of direct filename.
Commit: a2b5c41de00505179c7ce5a5f28ac0d9f0f1dee7 https://github.com/galaxyproject/galaxy/commit/a2b5c41de00505179c7ce5a5f28ac... Author: John Chilton jmchilton@gmail.com Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths: M display_applications/igv/bigwig.xml
Log Message: ----------- Merge pull request #3828 from blankenberg/17.01_bigwig_igv
[17.01] Have IGV bigWig display application make use of build_sites/ site_typ…
Commit: 4beb98e973000e0bd51b06ad35301ddb8b905ec1 https://github.com/galaxyproject/galaxy/commit/4beb98e973000e0bd51b06ad35301... Author: John Chilton jmchilton@gmail.com Date: 2017-03-29 (Wed, 29 Mar 2017)
Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/run.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/data/test_workflow_pause.ga M test/base/populators.py A test/integration/test_maximum_worklfow_invocation_duration.py
Log Message: ----------- [17.01] By default, do not allow workflow invocations to schedule indefinitely.
Give up after a month but allow admins to reduce this amount as well.
Commit: 8f8526bf307d083c64330859793c112a9823b5d8 https://github.com/galaxyproject/galaxy/commit/8f8526bf307d083c64330859793c1... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-03-30 (Thu, 30 Mar 2017)
Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/run.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/data/test_workflow_pause.ga M test/base/populators.py A test/integration/test_maximum_worklfow_invocation_duration.py
Log Message: ----------- Merge pull request #3659 from jmchilton/1701_maximum_workflow_invocation_duration
[17.01] By default, do not allow workflow invocations to schedule indefinitely.
Commit: 52b5e62de498f08ccd55f792d555c884f8bd6e98 https://github.com/galaxyproject/galaxy/commit/52b5e62de498f08ccd55f792d555c... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-03-30 (Thu, 30 Mar 2017)
Changed paths: M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M display_applications/igv/bigwig.xml M doc/source/releases/17.01_announce.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/unzip_collection.xml M lib/galaxy/tools/zip_collection.xml M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/run.py M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako A templates/webapps/galaxy/user/manage_info.mako M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/data/test_workflow_pause.ga M test/base/populators.py A test/integration/test_maximum_worklfow_invocation_duration.py M test/shed_functional/functional/test_1150_datatype_converters.py
Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01'
Compare: https://github.com/galaxyproject/galaxy/compare/3a2ff46c2817...52b5e62de498