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[galaxyproject/galaxy] dda11d: [17.01] Fix container resolver log statements expo...
by GitHub 01 Mar '17

01 Mar '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: dda11d21c2e88f6b935f9f90f270a7aeccd929da https://github.com/galaxyproject/galaxy/commit/dda11d21c2e88f6b935f9f90f270… Author: John Chilton <jmchilton(a)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/ca5bb99ee043587fe37cc9354885… Author: Björn Grüning <bjoern(a)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. Compare: https://github.com/galaxyproject/galaxy/compare/7824cd31fd7b...ca5bb99ee043

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[galaxyproject/galaxy] fd0826: Parse name to label on module initialization
by GitHub 01 Mar '17

01 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fd082663866c06afb35a179327b1df6efd9c77c7 https://github.com/galaxyproject/galaxy/commit/fd082663866c06afb35a179327b1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Parse name to label on module initialization Commit: 8a4c0eb7e3ea096ed56471a010003e6717f31957 https://github.com/galaxyproject/galaxy/commit/8a4c0eb7e3ea096ed56471a01000… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Use shared initialization procedure for subworkflows Commit: fc1e0702542af846c28e2910d77cbd07f0913769 https://github.com/galaxyproject/galaxy/commit/fc1e0702542af846c28e2910d77c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Hide name input fields for data input modules Commit: b91680a5b2dfc83b8ee974fdc9ed6f2ab405829c https://github.com/galaxyproject/galaxy/commit/b91680a5b2dfc83b8ee974fdc9ed… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Use shared label/annotation input parameter building process Commit: e13958ffcd14f2eb62b29f446a535487dd344904 https://github.com/galaxyproject/galaxy/commit/e13958ffcd14f2eb62b29f446a53… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Remove tool module related annotation input parameter Commit: 92bd559c11e62ef1ab704b967621966a31f71e39 https://github.com/galaxyproject/galaxy/commit/92bd559c11e62ef1ab704b967621… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Move label/annotation input parameters at top for all modules Commit: 0f742a6d8380af15ac87a9e654e1119a177bd426 https://github.com/galaxyproject/galaxy/commit/0f742a6d8380af15ac87a9e654e1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: R client/galaxy/scripts/mvc/tool/tool-form-workflow.js A client/galaxy/scripts/mvc/workflow/workflow-view-form.js M client/galaxy/scripts/mvc/workflow/workflow-view.js R static/maps/mvc/tool/tool-form-workflow.js.map A static/maps/mvc/workflow/workflow-view-form.js.map M static/maps/mvc/workflow/workflow-view.js.map R static/scripts/mvc/tool/tool-form-workflow.js A static/scripts/mvc/workflow/workflow-view-form.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Move workflow related tool form to workflow directory Commit: 3a7e6b0b744b9331ec175d8104a17519687fa464 https://github.com/galaxyproject/galaxy/commit/3a7e6b0b744b9331ec175d8104a1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: A client/galaxy/scripts/mvc/workflow/workflow-forms.js R client/galaxy/scripts/mvc/workflow/workflow-view-form.js M client/galaxy/scripts/mvc/workflow/workflow-view.js R static/maps/mvc/workflow/workflow-view-form.js.map M static/maps/mvc/workflow/workflow-view.js.map R static/scripts/mvc/workflow/workflow-view-form.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Enable labels for all modules, used shared building process Commit: ff7ab0853d6ea901253ba6175aa343fd9ef3a108 https://github.com/galaxyproject/galaxy/commit/ff7ab0853d6ea901253ba6175aa3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Fix comments, show default wrapper first in code file Commit: b03904b52c6064e77a378347d9213ec0b270ebb9 https://github.com/galaxyproject/galaxy/commit/b03904b52c6064e77a378347d921… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/workflow/workflow-view.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/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Allow input specific error handling, fix input parameter configuration Commit: c9b765794bb14adbaee13a44290e9df242778ffe https://github.com/galaxyproject/galaxy/commit/c9b765794bb14adbaee13a44290e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix form handler Commit: a967c088f78e39819d4cc0bd349166501e00d74e https://github.com/galaxyproject/galaxy/commit/a967c088f78e39819d4cc0bd3491… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Avoid parsing default names of inputs to labels Commit: f652e9c778af3835de929cfa7823cf1f0a0aed8a https://github.com/galaxyproject/galaxy/commit/f652e9c778af3835de929cfa7823… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Remove hidden input parameters, attempt to identify label directly from previous state Commit: a3de5b042e8edae2f7beee6554ae78e18f5f115b https://github.com/galaxyproject/galaxy/commit/a3de5b042e8edae2f7beee6554ae… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Move backward compatibility handling of former names out of modules to the workflow manager Commit: 81f799c01f38bab0c584e9b39872d2a1dd7f0348 https://github.com/galaxyproject/galaxy/commit/81f799c01f38bab0c584e9b39872… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Revise comment Commit: afe2a6116a450fa69ae87705c14a4e43a7ef5830 https://github.com/galaxyproject/galaxy/commit/afe2a6116a450fa69ae87705c14a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Use label to connect workflow steps Commit: ae751adac8ae46d7f0eb2831666258143724bc0f https://github.com/galaxyproject/galaxy/commit/ae751adac8ae46d7f0eb28316662… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py M test/unit/workflows/test_modules.py Log Message: ----------- Adjust unit test to use labels instead of name through state Commit: 488c42aa4c3e3e903e0234804d3cd90277d9a930 https://github.com/galaxyproject/galaxy/commit/488c42aa4c3e3e903e0234804d3c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Use constants to filter default naming of input modules Commit: dde9ba83acfbedd50a59ccb211cf9d352c86de97 https://github.com/galaxyproject/galaxy/commit/dde9ba83acfbedd50a59ccb211cf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/datatypes/data.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-composite.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/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-composite.js A test/functional/tools/mulled_example_multi_incomplete.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'dev' into unify_label_name_000 Commit: 528b00667d4a053b3b8db4790323b0f655b18f9b https://github.com/galaxyproject/galaxy/commit/528b00667d4a053b3b8db4790323… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix comment Commit: 619bfeffd503681ab7d6072426f621fde7485fd5 https://github.com/galaxyproject/galaxy/commit/619bfeffd503681ab7d6072426f6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Attempt to use fixed default name for unlabeled subworkflow inputs Commit: 007b6599c21a4927d58629210f103829e947011f https://github.com/galaxyproject/galaxy/commit/007b6599c21a4927d58629210f10… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix name handling in build module Commit: 198d36f77bb444572f03a34aec7c695d0adc52e1 https://github.com/galaxyproject/galaxy/commit/198d36f77bb444572f03a34aec7c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.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-composite.js Log Message: ----------- Fix step title in composite tool form Commit: 05687b8a19785c89772db499d6ede5a097ba47ce https://github.com/galaxyproject/galaxy/commit/05687b8a19785c89772db499d6ed… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M test/unit/workflows/test_modules.py Log Message: ----------- Strip debug output Commit: 820c46cf63602b788ed282f4277a19129d4b3dd8 https://github.com/galaxyproject/galaxy/commit/820c46cf63602b788ed282f4277a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Repack scripts Commit: 2f53b1d6d12457e0eaba5ca5da8b95321c69ff54 https://github.com/galaxyproject/galaxy/commit/2f53b1d6d12457e0eaba5ca5da8b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/proteomics.py M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/linters/general.py M lib/galaxy/tools/linters/outputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/toolbox/base.py M scripts/bootstrap_history.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge branch 'dev' into unify_label_name_000 Commit: b9ba754ce6eb2d4b23c54aa557cb6c0a512c4082 https://github.com/galaxyproject/galaxy/commit/b9ba754ce6eb2d4b23c54aa557cb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/workflow/workflow-forms.js.map R static/maps/mvc/workflow/workflow.js.map M static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Fix repacked files Commit: c80380dc57305be36e615ec13d1d17aecd285114 https://github.com/galaxyproject/galaxy/commit/c80380dc57305be36e615ec13d1d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M .ci/flake8_blacklist.txt M client/galaxy/scripts/mvc/grid/grid-view.js M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/webapps/galaxy/controllers/history.py M scripts/bootstrap_history.py M static/maps/mvc/grid/grid-view.js.map M static/scripts/mvc/grid/grid-view.js M templates/grid_base.mako M tools/data_source/upload.py Log Message: ----------- Merge branch 'dev' into unify_label_name_000 Commit: d3840c5c4140807297b22ad1e9b7da97eb1a6570 https://github.com/galaxyproject/galaxy/commit/d3840c5c4140807297b22ad1e9b7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js R client/galaxy/scripts/mvc/tool/tool-form-workflow.js A client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.js.map R static/maps/mvc/tool/tool-form-workflow.js.map A static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-view.js.map R static/maps/mvc/workflow/workflow.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/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tool/tool-form-composite.js R static/scripts/mvc/tool/tool-form-workflow.js A static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js M test/unit/workflows/test_modules.py Log Message: ----------- Merge pull request #3644 from guerler/unify_label_name_000 Introduce labels for all modules, remove name handling field for data inputs Compare: https://github.com/galaxyproject/galaxy/compare/0b4e52c8e93a...d3840c5c4140

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[galaxyproject/galaxy] d10f74: The user controller functions for changing informa...
by GitHub 01 Mar '17

01 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d10f740cff8e3520383c004a16830700b2789c9f https://github.com/galaxyproject/galaxy/commit/d10f740cff8e3520383c004a1683… Author: Dannon Baker <dannon.baker(a)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/6f3c8c7447e9a71c580ef9307395… Author: Dannon Baker <dannon.baker(a)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/4be00d3058396ed30da4f6f0958a… Author: Dannon Baker <dannon.baker(a)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/456acf0b84004c85c94d3129f0a8… Author: Dannon Baker <dannon.baker(a)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/b46ac475a93fbf0da71272861677… Author: Dannon Baker <dannon.baker(a)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/64036a441284151e1b1a3e930553… Author: Martin Cech <cech.marten(a)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/0636053901545a26662ed8f42a15… Author: Dannon Baker <dannon.baker(a)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/895351cdf8e8867452d28dffb89a… Author: Dannon Baker <dannon.baker(a)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/45d75e3da55e43a4444c1a7982e1… Author: Dannon Baker <dannon.baker(a)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/c373bf27e79e48bc2e8ba983e9f0… Author: Dannon Baker <dannon.baker(a)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/00b1591f05af4743d8b16b7d1bbb… Author: Dannon Baker <dannon.baker(a)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/5a5dbb97f1e04dfe15fbf71c441e… Author: Martin Cech <cech.marten(a)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/53c00df805e7ae7e509c08374bc9… Author: Dannon Baker <dannon.baker(a)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/d4b677bc38b221678bc991e0fddc… Author: Nicola Soranzo <nsoranzo(a)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/28875de584ac1967a8f2c0cdc8f5… Author: Daniel Blankenberg <dan.blankenberg(a)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/0997348a1c0a450986d376a96af0… Author: Martin Cech <cech.marten(a)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/c11cb3dd4572e7a4f1f814a31a45… Author: Martin Cech <cech.marten(a)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/169b45b138685164010043be95ce… Author: guerler <aysam.guerler(a)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/e23facb966c9962bb5bd1fdd07bf… Author: John Chilton <jmchilton(a)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/7824cd31fd7b9351efa1cf8274b8… Author: Björn Grüning <bjoern(a)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: 0b4e52c8e93aa5693f97ff1fc5d0a4c272f58b18 https://github.com/galaxyproject/galaxy/commit/0b4e52c8e93aa5693f97ff1fc5d0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M doc/source/releases/17.01_announce.rst M lib/galaxy/queue_worker.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/webapps/galaxy/controllers/user.py A templates/webapps/galaxy/user/manage_info.mako Log Message: ----------- Merge branch 'release_17.01' into dev Conflicts: lib/galaxy/managers/workflows.py Discarded all changes made to lib/galaxy/managers/workflows.py in https://github.com/galaxyproject/galaxy/pull/3681 Compare: https://github.com/galaxyproject/galaxy/compare/f0a26f309dd3...0b4e52c8e93a

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[galaxyproject/galaxy] 169b45: Fix step name display for 17.01
by GitHub 01 Mar '17

01 Mar '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 169b45b138685164010043be95cefe8148c6f713 https://github.com/galaxyproject/galaxy/commit/169b45b138685164010043be95ce… Author: guerler <aysam.guerler(a)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: 7824cd31fd7b9351efa1cf8274b89b2b9a0d811d https://github.com/galaxyproject/galaxy/commit/7824cd31fd7b9351efa1cf8274b8… Author: Björn Grüning <bjoern(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/e23facb966c9...7824cd31fd7b

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[galaxyproject/galaxy] 102fff: When using the new slow query logger, include para...
by GitHub 28 Feb '17

28 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 102fffd172963c0e97a7b469c394c3d239935e9c https://github.com/galaxyproject/galaxy/commit/102fffd172963c0e97a7b469c394… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- When using the new slow query logger, include parameters. Originally left these out, but 1) logs are assumed to be secure, and 2) it's super useful Commit: f0a26f309dd330e49e8e7ad227db5e40507f60cc https://github.com/galaxyproject/galaxy/commit/f0a26f309dd330e49e8e7ad227db… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Merge pull request #3649 from dannon/slowquery_tweak When using the new slow query logger, include parameters. Compare: https://github.com/galaxyproject/galaxy/compare/5efbab864cab...f0a26f309dd3

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[galaxyproject/galaxy] 33c528: Generate primary composite file after extra files ...
by GitHub 28 Feb '17

28 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 33c528ee13e6c4317ac4acc9b48ba157c5976b6c https://github.com/galaxyproject/galaxy/commit/33c528ee13e6c4317ac4acc9b48b… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Generate primary composite file after extra files collection. Commit: 5efbab864cab6693d4bde2159661a6ff6c7caafd https://github.com/galaxyproject/galaxy/commit/5efbab864cab6693d4bde2159661… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #3678 from blankenberg/composite-auto-after Generate primary composite file after extra files collection. Compare: https://github.com/galaxyproject/galaxy/compare/a505fa79ac26...5efbab864cab

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[galaxyproject/galaxy] 099734: fix tool search idnex building for tools with / in...
by GitHub 28 Feb '17

28 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 0997348a1c0a450986d376a96af024c73d4c7f37 https://github.com/galaxyproject/galaxy/commit/0997348a1c0a450986d376a96af0… Author: Martin Cech <cech.marten(a)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/c11cb3dd4572e7a4f1f814a31a45… Author: Martin Cech <cech.marten(a)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: e23facb966c9962bb5bd1fdd07bf6ee28d7d5930 https://github.com/galaxyproject/galaxy/commit/e23facb966c9962bb5bd1fdd07bf… Author: John Chilton <jmchilton(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/28875de584ac...e23facb966c9

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[galaxyproject/galaxy] cbc1fa: Set LDAP options only once.
by GitHub 28 Feb '17

28 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cbc1faf3a45d58353a9d352047fbbedb970e3215 https://github.com/galaxyproject/galaxy/commit/cbc1faf3a45d58353a9d352047fb… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Set LDAP options only once. Always check option value is not empty in _get_subs() Better log message for malformed <ldap_options> Commit: a505fa79ac26e2f30a4404f9a11f3b029abb5436 https://github.com/galaxyproject/galaxy/commit/a505fa79ac26e2f30a4404f9a11f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Merge pull request #3663 from nsoranzo/ldap_auth Set LDAP options only once. Compare: https://github.com/galaxyproject/galaxy/compare/1bac3b3be818...a505fa79ac26

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[galaxyproject/galaxy] f64525: Only keep the last path element when naming files ...
by GitHub 28 Feb '17

28 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f645259dd0633cfdac2768c7de2d1de918bc1bbe https://github.com/galaxyproject/galaxy/commit/f645259dd0633cfdac2768c7de2d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-27 (Mon, 27 Feb 2017) Changed paths: M tools/data_source/upload.py Log Message: ----------- Only keep the last path element when naming files uploaded via the URL paste method Commit: 1bac3b3be81821a4cbe687165985cfafd7989b46 https://github.com/galaxyproject/galaxy/commit/1bac3b3be81821a4cbe687165985… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M tools/data_source/upload.py Log Message: ----------- Merge pull request #3674 from natefoo/upload-drop-url-name Only keep the last path element when naming files uploaded via the URL paste method Compare: https://github.com/galaxyproject/galaxy/compare/194fb1eb07b6...1bac3b3be818

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[galaxyproject/galaxy] fb17e5: Use former version of autocomplete module for grid...
by GitHub 28 Feb '17

28 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fb17e55a1daf90220e19980fd8fd56dd70b2cde2 https://github.com/galaxyproject/galaxy/commit/fb17e55a1daf90220e19980fd8fd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-27 (Mon, 27 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-view.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Use former version of autocomplete module for grids Commit: 3efe748279711e89852bf7bf173612ff9cbe45de https://github.com/galaxyproject/galaxy/commit/3efe748279711e89852bf7bf1736… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-27 (Mon, 27 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/grid/grid-view.js.map M static/scripts/mvc/grid/grid-view.js M templates/grid_base.mako Log Message: ----------- Strip partially removed autocomplete feature for history names, removed in #1303 Commit: 194fb1eb07b627682b258d5c302aeb75b266cf89 https://github.com/galaxyproject/galaxy/commit/194fb1eb07b627682b258d5c302a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/grid/grid-view.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/grid/grid-view.js M templates/grid_base.mako Log Message: ----------- Merge pull request #3676 from guerler/fix_jquery_autocomplete Strip broken autocomplete feature, webbrowsers console error is an artifact Compare: https://github.com/galaxyproject/galaxy/compare/c8dd5f9b25ac...194fb1eb07b6

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[galaxyproject/galaxy] 5a5dbb: improve 17.01 get galaxy release notes
by GitHub 28 Feb '17

28 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 5a5dbb97f1e04dfe15fbf71c441eb50ae4b70b11 https://github.com/galaxyproject/galaxy/commit/5a5dbb97f1e04dfe15fbf71c441e… Author: Martin Cech <cech.marten(a)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: 28875de584ac1967a8f2c0cdc8f5fa7b37e70f21 https://github.com/galaxyproject/galaxy/commit/28875de584ac1967a8f2c0cdc8f5… Author: Daniel Blankenberg <dan.blankenberg(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/d4b677bc38b2...28875de584ac

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[galaxyproject/galaxy] 063605: Use pgcalc when possible
by GitHub 27 Feb '17

27 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 0636053901545a26662ed8f42a15bb67407f2231 https://github.com/galaxyproject/galaxy/commit/0636053901545a26662ed8f42a15… Author: Dannon Baker <dannon.baker(a)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/895351cdf8e8867452d28dffb89a… Author: Dannon Baker <dannon.baker(a)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/45d75e3da55e43a4444c1a7982e1… Author: Dannon Baker <dannon.baker(a)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/c373bf27e79e48bc2e8ba983e9f0… Author: Dannon Baker <dannon.baker(a)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/00b1591f05af4743d8b16b7d1bbb… Author: Dannon Baker <dannon.baker(a)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: 53c00df805e7ae7e509c08374bc941d31d20000d https://github.com/galaxyproject/galaxy/commit/53c00df805e7ae7e509c08374bc9… Author: Dannon Baker <dannon.baker(a)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/d4b677bc38b221678bc991e0fddc… Author: Nicola Soranzo <nsoranzo(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/64036a441284...d4b677bc38b2

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[galaxyproject/galaxy] d3f2df: improve wording of getgalaxy in bootstrapping scri...
by GitHub 26 Feb '17

26 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d3f2df57699bf6b85fdb16f85d023d562342f778 https://github.com/galaxyproject/galaxy/commit/d3f2df57699bf6b85fdb16f85d02… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-25 (Sat, 25 Feb 2017) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- improve wording of getgalaxy in bootstrapping script for RN Commit: c8dd5f9b25ac222ff37fe06bed5d1834f292e485 https://github.com/galaxyproject/galaxy/commit/c8dd5f9b25ac222ff37fe06bed5d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-26 (Sun, 26 Feb 2017) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #3671 from martenson/improve-bootstrapping improve wording of getgalaxy in bootstrapping script for RN Compare: https://github.com/galaxyproject/galaxy/compare/a5ea10622bf2...c8dd5f9b25ac

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[galaxyproject/galaxy] 585c10: Display an error message when IE loading raises an...
by GitHub 24 Feb '17

24 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 585c1070f29260895497c01bc7723317e3751934 https://github.com/galaxyproject/galaxy/commit/585c1070f29260895497c01bc772… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Display an error message when IE loading raises an exception Commit: a5ea10622bf2616278827221d43a4ab635932edd https://github.com/galaxyproject/galaxy/commit/a5ea10622bf2616278827221d43a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Merge pull request #3662 from natefoo/ie-error-message Display an error message when IE loading raises an exception Compare: https://github.com/galaxyproject/galaxy/compare/0baae35c56cf...a5ea10622bf2

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[galaxyproject/galaxy] b4ba27: Ignore Node modules installed for the IE proxy whe...
by GitHub 24 Feb '17

24 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b4ba2768a246c3788bc9f4adc5f2741dd7ab4956 https://github.com/galaxyproject/galaxy/commit/b4ba2768a246c3788bc9f4adc5f2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M .ci/flake8_blacklist.txt Log Message: ----------- Ignore Node modules installed for the IE proxy when linting Commit: 0baae35c56cfa26908ebff9a3124640489459c31 https://github.com/galaxyproject/galaxy/commit/0baae35c56cfa26908ebff9a3124… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M .ci/flake8_blacklist.txt Log Message: ----------- Merge pull request #3664 from natefoo/lint-ignore-js-proxy Ignore Node modules installed for the IE proxy when linting Compare: https://github.com/galaxyproject/galaxy/compare/77a47d2f6f94...0baae35c56cf

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[galaxyproject/galaxy] 10d0f6: Bump Jupyter container version to 16.01.1
by GitHub 24 Feb '17

24 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 10d0f627dcdfac2bd24085a599a7087809cec1bf https://github.com/galaxyproject/galaxy/commit/10d0f627dcdfac2bd24085a599a7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample Log Message: ----------- Bump Jupyter container version to 16.01.1 Commit: 77a47d2f6f947a1ec7d24d068538bbabdf5e88dd https://github.com/galaxyproject/galaxy/commit/77a47d2f6f947a1ec7d24d068538… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample Log Message: ----------- Merge pull request #3665 from natefoo/jupyter-16.01.1 Bump Jupyter container version to 16.01.1 Compare: https://github.com/galaxyproject/galaxy/compare/d5e4dc4753b8...77a47d2f6f94

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[galaxyproject/galaxy] 99397f: add the mzData datatype
by GitHub 24 Feb '17

24 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 99397fad74d3e47c27073f44e36300d43f48a181 https://github.com/galaxyproject/galaxy/commit/99397fad74d3e47c27073f44e363… Author: lecorguille <lecorguille(a)users.noreply.github.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/proteomics.py Log Message: ----------- add the mzData datatype Commit: 036df2ac2003ab378f6a0227e4642d980639a5ab https://github.com/galaxyproject/galaxy/commit/036df2ac2003ab378f6a0227e464… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Fix linting Commit: d5e4dc4753b8e6ab4a079b5fedb0ad1834bda157 https://github.com/galaxyproject/galaxy/commit/d5e4dc4753b8e6ab4a079b5fedb0… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Merge pull request #3661 from lecorguille/datatype_mzdata add the mzData datatype Compare: https://github.com/galaxyproject/galaxy/compare/73c444eaf407...d5e4dc4753b8

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[galaxyproject/usegalaxy-playbook] 02dfd5: Wait up to 65 seconds for uWSGI to stop (it brutal...
by GitHub 23 Feb '17

23 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 02dfd5bb9fecf1a99eb84e94158482afdfbe6d50 https://github.com/galaxyproject/usegalaxy-playbook/commit/02dfd5bb9fecf1a9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M templates/supervisor/galaxy.j2 Log Message: ----------- Wait up to 65 seconds for uWSGI to stop (it brutally kills workers after 60) Commit: 358979ed7b084c9f63b7b7e82d59ae50a67dcd6f https://github.com/galaxyproject/usegalaxy-playbook/commit/358979ed7b084c9f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Mutable configs Commit: b13a169e3f6ac22eb0722423a93374a8dd6a90d1 https://github.com/galaxyproject/usegalaxy-playbook/commit/b13a169e3f6ac22e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M galaxy.yml Log Message: ----------- Fix the no-restart tag so it actually updates Galaxy Commit: e018710445c6c3935df2985d39adf69cc51b2186 https://github.com/galaxyproject/usegalaxy-playbook/commit/e018710445c6c393… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M templates/galaxy/usegalaxy.org/config/uwsgi.ini.j2 Log Message: ----------- Update Main, switch to new zerg mode setup Commit: 3f3d614c52f0fbea7c9de5600799ee33ca724b7d https://github.com/galaxyproject/usegalaxy-playbook/commit/3f3d614c52f0fbea… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M production/galaxy_version.yml M production/group_vars/all.yml M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Update Main, use NVC dynamic rule Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/a83ebd9b4ee4...…

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[galaxyproject/galaxy] 62ee8e: Fix Python environment hack to allow "fixing" tool...
by GitHub 23 Feb '17

23 Feb '17

Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: 62ee8e8404fb86155d9893a8eeab1cf58473d795 https://github.com/galaxyproject/galaxy/commit/62ee8e8404fb86155d9893a8eeab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix Python environment hack to allow "fixing" tool ids at some version. This is a less broken alternative to #3620 and something I intended to ultimately do anyway. sam-to-bam used to be broken but now it isn't, we need to express that. Ideally we would move most of the things from the unversioned list to the versioned list as they are fixed. xref https://github.com/galaxyproject/galaxy/pull/3620#issuecomment-280674067 xref https://github.com/galaxyproject/galaxy/commit/fe2a1d8ade4fbda158ae035c7813… xref #3351 xref galaxyproject/tools-iuc#1148 Commit: eb6c0e410e600171fa3ce4fffb78bc205aad5292 https://github.com/galaxyproject/galaxy/commit/eb6c0e410e600171fa3ce4fffb78… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Rework preserve python environment expression according to :eagle::eyes: suggestion. https://github.com/galaxyproject/galaxy/pull/3630#discussion_r101798306 Commit: 6733c36318bacce0bbf33a8d266f6a08de3ba019 https://github.com/galaxyproject/galaxy/commit/6733c36318bacce0bbf33a8d266f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- [17.01] Restore logging statement missing when resolve_all is used. Broken in #3391. Commit: 49ef352235f7c998e79ca5423fab9725ea28d8be https://github.com/galaxyproject/galaxy/commit/49ef352235f7c998e79ca5423fab… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #3646 from jmchilton/resolve_all_logging [17.01] Restore logging statement missing when resolve_all is used. Commit: 9ebe2d2dd6efde7a66c52681aa57c52342ad992d https://github.com/galaxyproject/galaxy/commit/9ebe2d2dd6efde7a66c52681aa57… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3630 from jmchilton/python_hack_scalpel [17.01] Fix Python environment hack to allow "fixing" tool ids at some version. Commit: 90de3f2588a61382e70b6209ea39293c6a3987f1 https://github.com/galaxyproject/galaxy/commit/90de3f2588a61382e70b6209ea39… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 17.01 Commit: d10f740cff8e3520383c004a16830700b2789c9f https://github.com/galaxyproject/galaxy/commit/d10f740cff8e3520383c004a1683… Author: Dannon Baker <dannon.baker(a)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/6f3c8c7447e9a71c580ef9307395… Author: Dannon Baker <dannon.baker(a)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/4be00d3058396ed30da4f6f0958a… Author: Dannon Baker <dannon.baker(a)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/456acf0b84004c85c94d3129f0a8… Author: Dannon Baker <dannon.baker(a)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/b46ac475a93fbf0da71272861677… Author: Dannon Baker <dannon.baker(a)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/64036a441284151e1b1a3e930553… Author: Martin Cech <cech.marten(a)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: a352b3c490c7f5d7fbcf4e28a129bc8a537d3b53 https://github.com/galaxyproject/galaxy/commit/a352b3c490c7f5d7fbcf4e28a129… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/version.py M lib/galaxy/webapps/galaxy/controllers/user.py A templates/webapps/galaxy/user/manage_info.mako Log Message: ----------- Merge branch 'release_17.01' into usegalaxy Compare: https://github.com/galaxyproject/galaxy/compare/277c4ed20bdf...a352b3c490c7

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[galaxyproject/usegalaxy-playbook] a83ebd: Don't leave unused zerglings around tying up memor...
by GitHub 23 Feb '17

23 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a83ebd9b4ee4f020e87ebd4178b39fc21c8f7c20 https://github.com/galaxyproject/usegalaxy-playbook/commit/a83ebd9b4ee4f020… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M templates/galaxy/test.galaxyproject.org/config/uwsgi.ini.j2 M templates/supervisor/galaxy.j2 Log Message: ----------- Don't leave unused zerglings around tying up memory/swap, fix the zergling startup race condition.

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[galaxyproject/galaxy] d10f74: The user controller functions for changing informa...
by GitHub 23 Feb '17

23 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: d10f740cff8e3520383c004a16830700b2789c9f https://github.com/galaxyproject/galaxy/commit/d10f740cff8e3520383c004a1683… Author: Dannon Baker <dannon.baker(a)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/6f3c8c7447e9a71c580ef9307395… Author: Dannon Baker <dannon.baker(a)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/4be00d3058396ed30da4f6f0958a… Author: Dannon Baker <dannon.baker(a)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/456acf0b84004c85c94d3129f0a8… Author: Dannon Baker <dannon.baker(a)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/b46ac475a93fbf0da71272861677… Author: Dannon Baker <dannon.baker(a)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/64036a441284151e1b1a3e930553… Author: Martin Cech <cech.marten(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/90de3f2588a6...64036a441284

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[galaxyproject/galaxy] d9d3b2: Update dynamic_tool_destination.py
by GitHub 23 Feb '17

23 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d9d3b22efdf5d7e0f4c9b371b0ea74a64ab53f46 https://github.com/galaxyproject/galaxy/commit/d9d3b22efdf5d7e0f4c9b371b0ea… Author: Gildas Le Corguillé <lecorguille(a)users.noreply.github.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Update dynamic_tool_destination.py Commit: 73c444eaf4074c98262b9de0011e686170b1b125 https://github.com/galaxyproject/galaxy/commit/73c444eaf4074c98262b9de0011e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Merge pull request #3655 from lecorguille/patch-3 Update dynamic_tool_destination.py Compare: https://github.com/galaxyproject/galaxy/compare/99fdc37b815a...73c444eaf407

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[galaxyproject/galaxy] 8130d8: Update against the latest changes in galaxy-dev.
by GitHub 23 Feb '17

23 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8130d8b4c88343cdd44243fe700eae3fb863cc1a https://github.com/galaxyproject/galaxy/commit/8130d8b4c88343cdd44243fe700e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/exceptions/error_codes.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/linters/general.py M lib/galaxy/tools/linters/outputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Update against the latest changes in galaxy-dev. Commit: 99fdc37b815ab9c26f15250d722f2d30ab9691b2 https://github.com/galaxyproject/galaxy/commit/99fdc37b815ab9c26f15250d722f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/exceptions/error_codes.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/linters/general.py M lib/galaxy/tools/linters/outputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #3654 from jmchilton/galaxy-lib-update Update against the latest changes in galaxy-lib Compare: https://github.com/galaxyproject/galaxy/compare/647fcad924a9...99fdc37b815a

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[galaxyproject/usegalaxy-playbook] 2805fe: Decrease limits for workshop
by GitHub 23 Feb '17

23 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2805fee3209d2e9452e4d0fb95fd39bd11b848da https://github.com/galaxyproject/usegalaxy-playbook/commit/2805fee3209d2e94… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Decrease limits for workshop

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[galaxyproject/galaxy] 2cfd83: Reduce indentation from 6 to 4 whitespaces
by GitHub 22 Feb '17

22 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2cfd833e457f513d5e83f9a7f8ca77f96741942e https://github.com/galaxyproject/galaxy/commit/2cfd833e457f513d5e83f9a7f8ca… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Reduce indentation from 6 to 4 whitespaces Fix a TODO Remove funny but unused sub-sub-items. Commit: 647fcad924a969ae35299b7ef6e60672ddb7a6a0 https://github.com/galaxyproject/galaxy/commit/647fcad924a969ae35299b7ef6e6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #3653 from nsoranzo/fix_bootstrap_history Fix RELEASE_ISSUE_TEMPLATE in bootstrap_history.py Compare: https://github.com/galaxyproject/galaxy/compare/18e514d9b72b...647fcad924a9

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