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[galaxyproject/galaxy] f5dcf6: Fix and test anonymous error reports
by GitHub 20 Sep '18

20 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f5dcf60561703086a070a2b59ad3918df68cbd0e https://github.com/galaxyproject/galaxy/commit/f5dcf60561703086a070a2b59ad3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Fix and test anonymous error reports Fixes https://github.com/galaxyproject/galaxy/issues/6675 Commit: 56f5bf743a50afadc74e253bc95fcef4bb6d599d https://github.com/galaxyproject/galaxy/commit/56f5bf743a50afadc74e253bc95f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Make newer unit tests more robust with a looped wait... ... instead of raw sleep. Commit: d014469f070e62a0b3dc8bdbd93128e4c7a308f8 https://github.com/galaxyproject/galaxy/commit/d014469f070e62a0b3dc8bdbd931… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Merge pull request #6742 from mvdbeek/fix_error_reporting [18.05] Fix and test anonymous error reports Commit: 5eb7e5ce6f16e4e6978e44637b419ff3fb1b8e87 https://github.com/galaxyproject/galaxy/commit/5eb7e5ce6f16e4e6978e44637b41… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: d312c48ea76876bd4219f544b8c03e2e909ac6f5 https://github.com/galaxyproject/galaxy/commit/d312c48ea76876bd4219f544b8c0… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #6748 from jmchilton/1809_robust_sleep [18.09] Make newer unit tests more robust with a looped wait... Commit: bae08f3ca226711e14256258ed34b916ef73c83f https://github.com/galaxyproject/galaxy/commit/bae08f3ca226711e14256258ed34… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/101f2009f81d...bae08f3ca226 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 56f5bf: Make newer unit tests more robust with a looped wa...
by GitHub 20 Sep '18

20 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 56f5bf743a50afadc74e253bc95fcef4bb6d599d https://github.com/galaxyproject/galaxy/commit/56f5bf743a50afadc74e253bc95f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Make newer unit tests more robust with a looped wait... ... instead of raw sleep. Commit: d312c48ea76876bd4219f544b8c03e2e909ac6f5 https://github.com/galaxyproject/galaxy/commit/d312c48ea76876bd4219f544b8c0… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #6748 from jmchilton/1809_robust_sleep [18.09] Make newer unit tests more robust with a looped wait... Compare: https://github.com/galaxyproject/galaxy/compare/5eb7e5ce6f16...d312c48ea768 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] f5dcf6: Fix and test anonymous error reports
by GitHub 20 Sep '18

20 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: f5dcf60561703086a070a2b59ad3918df68cbd0e https://github.com/galaxyproject/galaxy/commit/f5dcf60561703086a070a2b59ad3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Fix and test anonymous error reports Fixes https://github.com/galaxyproject/galaxy/issues/6675 Commit: d014469f070e62a0b3dc8bdbd93128e4c7a308f8 https://github.com/galaxyproject/galaxy/commit/d014469f070e62a0b3dc8bdbd931… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Merge pull request #6742 from mvdbeek/fix_error_reporting [18.05] Fix and test anonymous error reports Commit: 5eb7e5ce6f16e4e6978e44637b419ff3fb1b8e87 https://github.com/galaxyproject/galaxy/commit/5eb7e5ce6f16e4e6978e44637b41… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Compare: https://github.com/galaxyproject/galaxy/compare/7a22f38a2e52...5eb7e5ce6f16 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] f5dcf6: Fix and test anonymous error reports
by GitHub 20 Sep '18

20 Sep '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: f5dcf60561703086a070a2b59ad3918df68cbd0e https://github.com/galaxyproject/galaxy/commit/f5dcf60561703086a070a2b59ad3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Fix and test anonymous error reports Fixes https://github.com/galaxyproject/galaxy/issues/6675 Commit: d014469f070e62a0b3dc8bdbd93128e4c7a308f8 https://github.com/galaxyproject/galaxy/commit/d014469f070e62a0b3dc8bdbd931… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Merge pull request #6742 from mvdbeek/fix_error_reporting [18.05] Fix and test anonymous error reports Compare: https://github.com/galaxyproject/galaxy/compare/840041744505...d014469f070e **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 420f43: map the favicon in uwsgi config
by GitHub 19 Sep '18

19 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 420f43645af9b37c32eb126f89c4266f36f6edb0 https://github.com/galaxyproject/galaxy/commit/420f43645af9b37c32eb126f89c4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/uwsgi_schema.yml M scripts/get_uwsgi_args.py Log Message: ----------- map the favicon in uwsgi config Commit: b45c3531dedc71b4ea8142fe5aa9f17f10bfb997 https://github.com/galaxyproject/galaxy/commit/b45c3531dedc71b4ea8142fe5aa9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- dispose of tooltip when the delete is being called Commit: 33eb06c9b872f75fd22e06297a2043f8685d1df2 https://github.com/galaxyproject/galaxy/commit/33eb06c9b872f75fd22e06297a20… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/uwsgi_schema.yml Log Message: ----------- remove something that should have never been where it was look at me, I do not know what I am doing Commit: b64754dee94c571112c79ccb15fe515545337e15 https://github.com/galaxyproject/galaxy/commit/b64754dee94c571112c79ccb15fe… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py M scripts/get_uwsgi_args.py Log Message: ----------- Merge pull request #6743 from martenson/fix-favicon-uwsgi [18.09] fix favicon.ico for uwsgi deployments Commit: 7a22f38a2e5229ebca109836396b17bf8785af37 https://github.com/galaxyproject/galaxy/commit/7a22f38a2e5229ebca109836396b… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Merge pull request #6744 from martenson/dispose-tooltip-on-delete [18.09] dispose of dataset tooltip when the delete is being called Commit: 101f2009f81d3c884ac1343a6d369be5fdfb03d4 https://github.com/galaxyproject/galaxy/commit/101f2009f81d3c884ac1343a6d36… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py M scripts/get_uwsgi_args.py Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/4723ad6672fe...101f2009f81d **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] b45c35: dispose of tooltip when the delete is being called
by GitHub 19 Sep '18

19 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: b45c3531dedc71b4ea8142fe5aa9f17f10bfb997 https://github.com/galaxyproject/galaxy/commit/b45c3531dedc71b4ea8142fe5aa9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- dispose of tooltip when the delete is being called Commit: 7a22f38a2e5229ebca109836396b17bf8785af37 https://github.com/galaxyproject/galaxy/commit/7a22f38a2e5229ebca109836396b… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Merge pull request #6744 from martenson/dispose-tooltip-on-delete [18.09] dispose of dataset tooltip when the delete is being called Compare: https://github.com/galaxyproject/galaxy/compare/b64754dee94c...7a22f38a2e52 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 420f43: map the favicon in uwsgi config
by GitHub 19 Sep '18

19 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 420f43645af9b37c32eb126f89c4266f36f6edb0 https://github.com/galaxyproject/galaxy/commit/420f43645af9b37c32eb126f89c4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/uwsgi_schema.yml M scripts/get_uwsgi_args.py Log Message: ----------- map the favicon in uwsgi config Commit: 33eb06c9b872f75fd22e06297a2043f8685d1df2 https://github.com/galaxyproject/galaxy/commit/33eb06c9b872f75fd22e06297a20… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/uwsgi_schema.yml Log Message: ----------- remove something that should have never been where it was look at me, I do not know what I am doing Commit: b64754dee94c571112c79ccb15fe515545337e15 https://github.com/galaxyproject/galaxy/commit/b64754dee94c571112c79ccb15fe… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py M scripts/get_uwsgi_args.py Log Message: ----------- Merge pull request #6743 from martenson/fix-favicon-uwsgi [18.09] fix favicon.ico for uwsgi deployments Compare: https://github.com/galaxyproject/galaxy/compare/4ce8086c2052...b64754dee94c **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 4fc9fe: Fix target update for rule collection builder afte...
by GitHub 19 Sep '18

19 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4fc9fe2150690c04d4d6071994126a05b250379b https://github.com/galaxyproject/galaxy/commit/4fc9fe2150690c04d4d607199412… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-09-11 (Tue, 11 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Fix target update for rule collection builder after input selection Commit: a937bc5539414624fe42c49607416f14dadd425b https://github.com/galaxyproject/galaxy/commit/a937bc5539414624fe42c4960741… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-11 (Tue, 11 Sep 2018) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Client build. Commit: 2a79ae0ce1bbefe8a0340edb4882a00f07fc6de2 https://github.com/galaxyproject/galaxy/commit/2a79ae0ce1bbefe8a0340edb4882… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Merge pull request #6691 from jmchilton/backport_6326 [18.05] Backport #6326 Commit: bddabe3029335a7db51a0ef1c6a7508937db33fa https://github.com/galaxyproject/galaxy/commit/bddabe3029335a7db51a0ef1c6a7… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add missing route for API endpoint. Commit: 1dacc35332cf956ed5631fe8c6fa8e231dab663e https://github.com/galaxyproject/galaxy/commit/1dacc35332cf956ed5631fe8c6fa… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #6703 from davebx/updates_api [18.05] Add missing route for API endpoint. Commit: 7e2a77e8af152a501f124a6d0f702a66502e0dd3 https://github.com/galaxyproject/galaxy/commit/7e2a77e8af152a501f124a6d0f70… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Catch additional permutations of Slurm cgroup creation warnings Commit: f7c1d31dbc6f23eb4fba37b82aeb2808fd69224f https://github.com/galaxyproject/galaxy/commit/f7c1d31dbc6f23eb4fba37b82aeb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- unquote the tool_version in the tools API if the tool version includes '+', which is a recommended way of versioning per https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_x… this would fail the comparison down the line in the toolbox.get_tool() method this commit also downgrades the unquote_plus to unquote for tool_id for similar reasons since it also contains the version Commit: 1b6d422afdd0c1f7291a0999bfc54284b90972d2 https://github.com/galaxyproject/galaxy/commit/1b6d422afdd0c1f7291a0999bfc5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- unquote similarly to previous commit but in the workflow controller Commit: f513594c31a3738420889b3f5e36d39796946587 https://github.com/galaxyproject/galaxy/commit/f513594c31a3738420889b3f5e36… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #6707 from martenson/unqoute_tool_version [18.05] unquote the tool_version in the tools API Commit: 3d508a01d3d58908b667e428f125df91d8c599c1 https://github.com/galaxyproject/galaxy/commit/3d508a01d3d58908b667e428f125… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Improvements from @nsoranzo Commit: 6993dbb6fcd112e077fbad66deae716a53247d07 https://github.com/galaxyproject/galaxy/commit/6993dbb6fcd112e077fbad66deae… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #6705 from natefoo/slurm-cgroup-enospc [18.05] Catch additional permutations of Slurm cgroup creation warnings Commit: 18d99deb951a8d429be5695fac539c93e4c90e3e https://github.com/galaxyproject/galaxy/commit/18d99deb951a8d429be5695fac53… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/package.json M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/chart.bundled.js M static/scripts/bundled/extended.bundled.js Log Message: ----------- Decode tool id and version in the client, not in the API using `decodeUriComponent` from `decode-uri-component` JS package. Revert https://github.com/galaxyproject/galaxy/pull/6707 Remove unused `_get_tool()` method in `lib/galaxy/webapps/galaxy/api/workflows.py` . Rebuild client with: ``` make client-production-maps ``` Commit: 7f38e61caebe8e56ab1f6cf6d5b577c6b020c9d3 https://github.com/galaxyproject/galaxy/commit/7f38e61caebe8e56ab1f6cf6d5b5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: R lib/galaxy/dependencies/requirements.txt Log Message: ----------- Remove again lib/galaxy/dependencies/requirements.txt It was reintroduced (empty) by mistake in https://github.com/galaxyproject/galaxy/pull/4474 . Commit: 35754dc49a7d29a12fe10c444ce69c1af47b0a2b https://github.com/galaxyproject/galaxy/commit/35754dc49a7d29a12fe10c444ce6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M scripts/plugin_staging.py Log Message: ----------- Fix symlinking during plugin staging Remove also broken symlinks before creating the new ones. Commit: 5121275c1d5e7c724edbc3cef531f3401aea5225 https://github.com/galaxyproject/galaxy/commit/5121275c1d5e7c724edbc3cef531… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Remove stray debug statement. Commit: 1cdcb80fe88cd076f5c966b0b6a4acab37841877 https://github.com/galaxyproject/galaxy/commit/1cdcb80fe88cd076f5c966b0b6a4… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Merge pull request #6739 from jmchilton/remove_debug [18.09] Remove stray debug statement. Commit: 5635a05a2a70c3e8887c32b1a8675f124808fd49 https://github.com/galaxyproject/galaxy/commit/5635a05a2a70c3e8887c32b1a867… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/unit/workflows/test_modules.py Log Message: ----------- Look up collection_type if collection_type_source is set We do this in the wf-editor and in the backend, so this works for subworkflows. This should make quite some tools more usable in a workflow scenario. Should fix - https://github.com/galaxyproject/galaxy/issues/6514 - https://github.com/galaxyproject/galaxy/issues/6012 - https://github.com/galaxyproject/galaxy/issues/6569 - https://github.com/galaxyproject/galaxy/issues/1889 and perhaps more issues related to this. Commit: f7fe3418d63683a998425b99f4688872fef07b09 https://github.com/galaxyproject/galaxy/commit/f7fe3418d63683a998425b99f468… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Reset collection_type if collection_type_source has been removed Commit: a52ee84aede53ff2cb5a3e667e4ef03df1fd3acb https://github.com/galaxyproject/galaxy/commit/a52ee84aede53ff2cb5a3e667e4e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Drop invalid connections if type_source is unavailable Commit: 29f07f0b0ad49b86b50c34e9890eb2117e067a2b https://github.com/galaxyproject/galaxy/commit/29f07f0b0ad49b86b50c34e9890e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/unit/workflows/test_modules.py Log Message: ----------- Merge pull request #6741 from jmchilton/backport_type_source [18.09] Backport #6732 Commit: 840041744505402ab5af4f39b84ba76599cb8588 https://github.com/galaxyproject/galaxy/commit/840041744505402ab5af4f39b84b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/package.json R lib/galaxy/dependencies/requirements.txt M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M scripts/plugin_staging.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/chart.bundled.js M static/scripts/bundled/extended.bundled.js Log Message: ----------- Merge pull request #6737 from nsoranzo/release_18.05_revert_6707 [18.05] Decode tool id and version in the client, not in the API Commit: 4ce8086c2052a1abee4824456ddfd48ee5cb7c6a https://github.com/galaxyproject/galaxy/commit/4ce8086c2052a1abee4824456ddf… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/package.json R lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M scripts/plugin_staging.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: 4723ad6672fef064a75934604ab03150ec14e872 https://github.com/galaxyproject/galaxy/commit/4723ad6672fef064a75934604ab0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/package.json R lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/managers/users.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M scripts/plugin_staging.py Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c9f2361e8e1f...4723ad6672fe **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 4fc9fe: Fix target update for rule collection builder afte...
by GitHub 19 Sep '18

19 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 4fc9fe2150690c04d4d6071994126a05b250379b https://github.com/galaxyproject/galaxy/commit/4fc9fe2150690c04d4d607199412… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-09-11 (Tue, 11 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Fix target update for rule collection builder after input selection Commit: a937bc5539414624fe42c49607416f14dadd425b https://github.com/galaxyproject/galaxy/commit/a937bc5539414624fe42c4960741… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-11 (Tue, 11 Sep 2018) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Client build. Commit: 2a79ae0ce1bbefe8a0340edb4882a00f07fc6de2 https://github.com/galaxyproject/galaxy/commit/2a79ae0ce1bbefe8a0340edb4882… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Merge pull request #6691 from jmchilton/backport_6326 [18.05] Backport #6326 Commit: bddabe3029335a7db51a0ef1c6a7508937db33fa https://github.com/galaxyproject/galaxy/commit/bddabe3029335a7db51a0ef1c6a7… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add missing route for API endpoint. Commit: 1dacc35332cf956ed5631fe8c6fa8e231dab663e https://github.com/galaxyproject/galaxy/commit/1dacc35332cf956ed5631fe8c6fa… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #6703 from davebx/updates_api [18.05] Add missing route for API endpoint. Commit: 7e2a77e8af152a501f124a6d0f702a66502e0dd3 https://github.com/galaxyproject/galaxy/commit/7e2a77e8af152a501f124a6d0f70… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Catch additional permutations of Slurm cgroup creation warnings Commit: f7c1d31dbc6f23eb4fba37b82aeb2808fd69224f https://github.com/galaxyproject/galaxy/commit/f7c1d31dbc6f23eb4fba37b82aeb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- unquote the tool_version in the tools API if the tool version includes '+', which is a recommended way of versioning per https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_x… this would fail the comparison down the line in the toolbox.get_tool() method this commit also downgrades the unquote_plus to unquote for tool_id for similar reasons since it also contains the version Commit: 1b6d422afdd0c1f7291a0999bfc54284b90972d2 https://github.com/galaxyproject/galaxy/commit/1b6d422afdd0c1f7291a0999bfc5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- unquote similarly to previous commit but in the workflow controller Commit: f513594c31a3738420889b3f5e36d39796946587 https://github.com/galaxyproject/galaxy/commit/f513594c31a3738420889b3f5e36… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #6707 from martenson/unqoute_tool_version [18.05] unquote the tool_version in the tools API Commit: 3d508a01d3d58908b667e428f125df91d8c599c1 https://github.com/galaxyproject/galaxy/commit/3d508a01d3d58908b667e428f125… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Improvements from @nsoranzo Commit: 6993dbb6fcd112e077fbad66deae716a53247d07 https://github.com/galaxyproject/galaxy/commit/6993dbb6fcd112e077fbad66deae… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #6705 from natefoo/slurm-cgroup-enospc [18.05] Catch additional permutations of Slurm cgroup creation warnings Commit: 18d99deb951a8d429be5695fac539c93e4c90e3e https://github.com/galaxyproject/galaxy/commit/18d99deb951a8d429be5695fac53… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/package.json M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/chart.bundled.js M static/scripts/bundled/extended.bundled.js Log Message: ----------- Decode tool id and version in the client, not in the API using `decodeUriComponent` from `decode-uri-component` JS package. Revert https://github.com/galaxyproject/galaxy/pull/6707 Remove unused `_get_tool()` method in `lib/galaxy/webapps/galaxy/api/workflows.py` . Rebuild client with: ``` make client-production-maps ``` Commit: 7f38e61caebe8e56ab1f6cf6d5b577c6b020c9d3 https://github.com/galaxyproject/galaxy/commit/7f38e61caebe8e56ab1f6cf6d5b5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: R lib/galaxy/dependencies/requirements.txt Log Message: ----------- Remove again lib/galaxy/dependencies/requirements.txt It was reintroduced (empty) by mistake in https://github.com/galaxyproject/galaxy/pull/4474 . Commit: 35754dc49a7d29a12fe10c444ce69c1af47b0a2b https://github.com/galaxyproject/galaxy/commit/35754dc49a7d29a12fe10c444ce6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M scripts/plugin_staging.py Log Message: ----------- Fix symlinking during plugin staging Remove also broken symlinks before creating the new ones. Commit: 840041744505402ab5af4f39b84ba76599cb8588 https://github.com/galaxyproject/galaxy/commit/840041744505402ab5af4f39b84b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/package.json R lib/galaxy/dependencies/requirements.txt M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M scripts/plugin_staging.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/chart.bundled.js M static/scripts/bundled/extended.bundled.js Log Message: ----------- Merge pull request #6737 from nsoranzo/release_18.05_revert_6707 [18.05] Decode tool id and version in the client, not in the API Commit: 4ce8086c2052a1abee4824456ddfd48ee5cb7c6a https://github.com/galaxyproject/galaxy/commit/4ce8086c2052a1abee4824456ddf… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/package.json R lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M scripts/plugin_staging.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Compare: https://github.com/galaxyproject/galaxy/compare/29f07f0b0ad4...4ce8086c2052 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 18d99d: Decode tool id and version in the client, not in t...
by GitHub 19 Sep '18

19 Sep '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 18d99deb951a8d429be5695fac539c93e4c90e3e https://github.com/galaxyproject/galaxy/commit/18d99deb951a8d429be5695fac53… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/package.json M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/chart.bundled.js M static/scripts/bundled/extended.bundled.js Log Message: ----------- Decode tool id and version in the client, not in the API using `decodeUriComponent` from `decode-uri-component` JS package. Revert https://github.com/galaxyproject/galaxy/pull/6707 Remove unused `_get_tool()` method in `lib/galaxy/webapps/galaxy/api/workflows.py` . Rebuild client with: ``` make client-production-maps ``` Commit: 7f38e61caebe8e56ab1f6cf6d5b577c6b020c9d3 https://github.com/galaxyproject/galaxy/commit/7f38e61caebe8e56ab1f6cf6d5b5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: R lib/galaxy/dependencies/requirements.txt Log Message: ----------- Remove again lib/galaxy/dependencies/requirements.txt It was reintroduced (empty) by mistake in https://github.com/galaxyproject/galaxy/pull/4474 . Commit: 35754dc49a7d29a12fe10c444ce69c1af47b0a2b https://github.com/galaxyproject/galaxy/commit/35754dc49a7d29a12fe10c444ce6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M scripts/plugin_staging.py Log Message: ----------- Fix symlinking during plugin staging Remove also broken symlinks before creating the new ones. Commit: 840041744505402ab5af4f39b84ba76599cb8588 https://github.com/galaxyproject/galaxy/commit/840041744505402ab5af4f39b84b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/package.json R lib/galaxy/dependencies/requirements.txt M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M scripts/plugin_staging.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/chart.bundled.js M static/scripts/bundled/extended.bundled.js Log Message: ----------- Merge pull request #6737 from nsoranzo/release_18.05_revert_6707 [18.05] Decode tool id and version in the client, not in the API Compare: https://github.com/galaxyproject/galaxy/compare/6993dbb6fcd1...840041744505 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 5635a0: Look up collection_type if collection_type_source ...
by GitHub 19 Sep '18

19 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 5635a05a2a70c3e8887c32b1a8675f124808fd49 https://github.com/galaxyproject/galaxy/commit/5635a05a2a70c3e8887c32b1a867… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/unit/workflows/test_modules.py Log Message: ----------- Look up collection_type if collection_type_source is set We do this in the wf-editor and in the backend, so this works for subworkflows. This should make quite some tools more usable in a workflow scenario. Should fix - https://github.com/galaxyproject/galaxy/issues/6514 - https://github.com/galaxyproject/galaxy/issues/6012 - https://github.com/galaxyproject/galaxy/issues/6569 - https://github.com/galaxyproject/galaxy/issues/1889 and perhaps more issues related to this. Commit: f7fe3418d63683a998425b99f4688872fef07b09 https://github.com/galaxyproject/galaxy/commit/f7fe3418d63683a998425b99f468… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Reset collection_type if collection_type_source has been removed Commit: a52ee84aede53ff2cb5a3e667e4ef03df1fd3acb https://github.com/galaxyproject/galaxy/commit/a52ee84aede53ff2cb5a3e667e4e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Drop invalid connections if type_source is unavailable Commit: 29f07f0b0ad49b86b50c34e9890eb2117e067a2b https://github.com/galaxyproject/galaxy/commit/29f07f0b0ad49b86b50c34e9890e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/unit/workflows/test_modules.py Log Message: ----------- Merge pull request #6741 from jmchilton/backport_type_source [18.09] Backport #6732 Compare: https://github.com/galaxyproject/galaxy/compare/1cdcb80fe88c...29f07f0b0ad4 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 90e4bc: Ignore run_selenium_tests.html
by GitHub 19 Sep '18

19 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 90e4bc5aa3ec6fc6471d42603205ae8af3c0490c https://github.com/galaxyproject/galaxy/commit/90e4bc5aa3ec6fc6471d42603205… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M .gitignore Log Message: ----------- Ignore run_selenium_tests.html Commit: ff19438039360bf46bc0642655b6a6d5daac4b42 https://github.com/galaxyproject/galaxy/commit/ff19438039360bf46bc0642655b6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M .ci/jenkins/api-py3/run_tests.sh M .ci/jenkins/api/run_tests.sh M .ci/jenkins/framework-py3/run_tests.sh M .ci/jenkins/framework/run_tests.sh M .ci/jenkins/main-tools-py3/run_tests.sh M .ci/jenkins/main-tools/run_tests.sh M .ci/jenkins/selenium-py3/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .ci/jenkins/toolshed/run_tests.sh Log Message: ----------- Make run_tests.sh scripts in .ci/jenkins/ executable Commit: c9f2361e8e1f6244893f43bb361a0e3b5242518d https://github.com/galaxyproject/galaxy/commit/c9f2361e8e1f6244893f43bb361a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M .ci/jenkins/api-py3/run_tests.sh M .ci/jenkins/api/run_tests.sh M .ci/jenkins/framework-py3/run_tests.sh M .ci/jenkins/framework/run_tests.sh M .ci/jenkins/main-tools-py3/run_tests.sh M .ci/jenkins/main-tools/run_tests.sh M .ci/jenkins/selenium-py3/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .ci/jenkins/toolshed/run_tests.sh M .gitignore Log Message: ----------- Merge pull request #6738 from nsoranzo/local_testing_improvs Small local testing improvements Compare: https://github.com/galaxyproject/galaxy/compare/da421294f80d...c9f2361e8e1f **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 512127: Remove stray debug statement.
by GitHub 19 Sep '18

19 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 5121275c1d5e7c724edbc3cef531f3401aea5225 https://github.com/galaxyproject/galaxy/commit/5121275c1d5e7c724edbc3cef531… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Remove stray debug statement. Commit: 1cdcb80fe88cd076f5c966b0b6a4acab37841877 https://github.com/galaxyproject/galaxy/commit/1cdcb80fe88cd076f5c966b0b6a4… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Merge pull request #6739 from jmchilton/remove_debug [18.09] Remove stray debug statement. Compare: https://github.com/galaxyproject/galaxy/compare/8462df83c9b3...1cdcb80fe88c **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] a44baa: Look up collection_type if collection_type_source ...
by GitHub 19 Sep '18

19 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a44baa56427ba2a2ea4e084570f47aa1537fea06 https://github.com/galaxyproject/galaxy/commit/a44baa56427ba2a2ea4e084570f4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/unit/workflows/test_modules.py Log Message: ----------- Look up collection_type if collection_type_source is set We do this in the wf-editor and in the backend, so this works for subworkflows. This should make quite some tools more usable in a workflow scenario. Should fix - https://github.com/galaxyproject/galaxy/issues/6514 - https://github.com/galaxyproject/galaxy/issues/6012 - https://github.com/galaxyproject/galaxy/issues/6569 - https://github.com/galaxyproject/galaxy/issues/1889 and perhaps more issues related to this. Commit: 696ed3093586fea8c7e019507b05f685ae74676d https://github.com/galaxyproject/galaxy/commit/696ed3093586fea8c7e019507b05… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Reset collection_type if collection_type_source has been removed Commit: 42931c21a1a307739b755df38c6bca97df7fe15a https://github.com/galaxyproject/galaxy/commit/42931c21a1a307739b755df38c6b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Drop invalid connections if type_source is unavailable Commit: da421294f80df9036141c97b05f66b79fc218296 https://github.com/galaxyproject/galaxy/commit/da421294f80df9036141c97b05f6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/unit/workflows/test_modules.py Log Message: ----------- Merge pull request #6732 from mvdbeek/propagate_collection_type Look up collection_type if collection_type_source is set Compare: https://github.com/galaxyproject/galaxy/compare/5ace7d4015d5...da421294f80d **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] e78109: Set PYTHONPATH for impersonate to include dynamic ...
by GitHub 18 Sep '18

18 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e78109aeca27a50602c93a03ff128fa5de5c1aa3 https://github.com/galaxyproject/usegalaxy-playbook/commit/e78109aeca27a506… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M env/common/templates/supervisor/galaxy_impersonate.j2 Log Message: ----------- Set PYTHONPATH for impersonate to include dynamic rules **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] b422fd: Swap main to 18.09 branch, update.
by GitHub 18 Sep '18

18 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b422fd722203473ca7a5ae672f78ef23f3146c99 https://github.com/galaxyproject/usegalaxy-playbook/commit/b422fd722203473c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml M env/main/group_vars/all.yml Log Message: ----------- Swap main to 18.09 branch, update. **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] d573fa: Update test
by GitHub 18 Sep '18

18 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d573fab922e246008ebfc8348522f742403e47c3 https://github.com/galaxyproject/usegalaxy-playbook/commit/d573fab922e24600… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update test **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] dfff5c: Add Loom datatype and remove rdata.seurat.
by GitHub 18 Sep '18

18 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dfff5c966342b38603514d8bfd3ed8e5b6e0bed9 https://github.com/galaxyproject/galaxy/commit/dfff5c966342b38603514d8bfd3e… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.loom Log Message: ----------- Add Loom datatype and remove rdata.seurat. Commit: f06da87189ccabd209f60509dd438bc690fc5523 https://github.com/galaxyproject/galaxy/commit/f06da87189ccabd209f60509dd43… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- remove comment Commit: 8462df83c9b3d5bdba93025f25dd182b7f22ea34 https://github.com/galaxyproject/galaxy/commit/8462df83c9b3d5bdba93025f25dd… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.loom Log Message: ----------- Merge pull request #6723 from blankenberg/18.09-loom [18.09] Add Loom datatype and remove rdata.seurat Commit: 5ace7d4015d5b5a21095ad1dc80344a90d13914d https://github.com/galaxyproject/galaxy/commit/5ace7d4015d5b5a21095ad1dc803… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.loom Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/ed147ee052a1...5ace7d4015d5 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] dfff5c: Add Loom datatype and remove rdata.seurat.
by GitHub 18 Sep '18

18 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: dfff5c966342b38603514d8bfd3ed8e5b6e0bed9 https://github.com/galaxyproject/galaxy/commit/dfff5c966342b38603514d8bfd3e… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.loom Log Message: ----------- Add Loom datatype and remove rdata.seurat. Commit: f06da87189ccabd209f60509dd438bc690fc5523 https://github.com/galaxyproject/galaxy/commit/f06da87189ccabd209f60509dd43… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- remove comment Commit: 8462df83c9b3d5bdba93025f25dd182b7f22ea34 https://github.com/galaxyproject/galaxy/commit/8462df83c9b3d5bdba93025f25dd… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.loom Log Message: ----------- Merge pull request #6723 from blankenberg/18.09-loom [18.09] Add Loom datatype and remove rdata.seurat Compare: https://github.com/galaxyproject/galaxy/compare/aca30f0b158a...8462df83c9b3 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] c8cb16: Merge pull request #6687 from dannon/version-18.09
by GitHub 18 Sep '18

18 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c8cb164ab8ad4fe5d7ea9768e3f7e58051200525 https://github.com/galaxyproject/galaxy/commit/c8cb164ab8ad4fe5d7ea9768e3f7… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #6687 from dannon/version-18.09 Update version to 18.09.rc1 Commit: 471162eadb4408318db534c6d24f7685bedb29eb https://github.com/galaxyproject/galaxy/commit/471162eadb4408318db534c6d24f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-11 (Tue, 11 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/extract_dataset.xml Log Message: ----------- [18.09] Fix new extract dataset to perserve collection element identifier. Commit: ba4e7d199b4bc080dcd741710d2241147bdbe745 https://github.com/galaxyproject/galaxy/commit/ba4e7d199b4bc080dcd741710d22… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Make gro and top datatypes tabular subclasses I think that was the intention in https://github.com/galaxyproject/galaxy/commit/56d55399ebe2ecd614a7ba5a1467… Commit: 80266129fe3d3d4b9657da0a3c5e8232bfa2a46b https://github.com/galaxyproject/galaxy/commit/80266129fe3d3d4b9657da0a3c5e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/extract_dataset.xml Log Message: ----------- Merge pull request #6692 from jmchilton/1809_fix_extract_name [18.09] Fix new extract dataset tool to preserve collection element identifier. Commit: 1f8c234c2be8baac9db94e17f4727e6c3c6c55ef https://github.com/galaxyproject/galaxy/commit/1f8c234c2be8baac9db94e17f472… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Make top datatype inherit from Text. Commit: 17157dd0633b4deb91a39bbc76288dd2968423f5 https://github.com/galaxyproject/galaxy/commit/17157dd0633b4deb91a39bbc7628… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #9 from blankenberg/gro2 Make top datatype inherit from Text. Commit: 9657cd6b32ed0768d2c73dd9d63c38432afb4b71 https://github.com/galaxyproject/galaxy/commit/9657cd6b32ed0768d2c73dd9d63c… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #6695 from mvdbeek/fix_gro_top_datatypes [18.09] Make gro and top datatypes tabular subclasses Commit: b4b49dc2028da2064fd34d7345b23b47150a1039 https://github.com/galaxyproject/galaxy/commit/b4b49dc2028da2064fd34d7345b2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js Log Message: ----------- Add self help to error reporting interface. Commit: 88bf3435775e94217bccfc46a5215311dea321aa https://github.com/galaxyproject/galaxy/commit/88bf3435775e94217bccfc46a521… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js Log Message: ----------- Import Backbone consistently across the app Commit: 84d66bea6008dc534aa6a2331e824005b204da19 https://github.com/galaxyproject/galaxy/commit/84d66bea6008dc534aa6a2331e82… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js Log Message: ----------- h2!=h3 Commit: 32223161c7ca735647d53ebfe4b90f1cd4051051 https://github.com/galaxyproject/galaxy/commit/32223161c7ca735647d53ebfe4b9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js Log Message: ----------- Merge pull request #6711 from dannon/error_help [18.09] Add self help to error reporting interface Commit: df4fbe6b92457fa910f014bbd3a8dd84c25d3969 https://github.com/galaxyproject/galaxy/commit/df4fbe6b92457fa910f014bbd3a8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js Log Message: ----------- Swap badge-default to badge-primary Commit: b2193bddc2aea250a189171ae61ed992b0449c84 https://github.com/galaxyproject/galaxy/commit/b2193bddc2aea250a189171ae61e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/docs/bootstrap.md Log Message: ----------- Drop badge-default from docs, correctly refer to secondary. Commit: a9273218424c1687bedf112591f2bbf735d32aa8 https://github.com/galaxyproject/galaxy/commit/a9273218424c1687bedf112591f2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Client format. Commit: 0040c36d4561155af3f32262d186e186349d989d https://github.com/galaxyproject/galaxy/commit/0040c36d4561155af3f32262d186… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/docs/bootstrap.md M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #6726 from dannon/badge-default-fix [18.09] Badge default fix Commit: 072d40f3e9a9050f034f440b76c8b84536bc0ead https://github.com/galaxyproject/galaxy/commit/072d40f3e9a9050f034f440b76c8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- remove html tags and newlines from the help text this should improve the toolsearch for certain keywords and also make the search index smaller Commit: b7f16228575215c9be134d1bbc1cf9e37b700488 https://github.com/galaxyproject/galaxy/commit/b7f16228575215c9be134d1bbc1c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- replace the replacement for newline from empty string to space, that should avoid unwanted word merges Commit: 17d67e24c072c8953e482aff41e9b1faed78b4d3 https://github.com/galaxyproject/galaxy/commit/17d67e24c072c8953e482aff41e9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- use bleach isntead of custom regex thanks @nsoranzo Commit: 54d137edab3fb33beac87c23cd35fb19dd7f44fa https://github.com/galaxyproject/galaxy/commit/54d137edab3fb33beac87c23cd35… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Remove deprecated `decode_param_names` parameter It has been deprecated since WebOb 1.1 and ignored since WebOb 1.2 . Commit: 8ed19a3a09df9b66266f66bc53e504c781ae524d https://github.com/galaxyproject/galaxy/commit/8ed19a3a09df9b66266f66bc53e5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/verify/interactor.py Log Message: ----------- `async` is a reserved keyword in Python 3.7 - Remove unused `async` parameter of `stage_data_async()` method. - Rename `async` parameter of `quick_load()` method. Fix https://github.com/galaxyproject/galaxy/issues/6717 . xref. https://github.com/galaxyproject/galaxy/issues/1715 Commit: 8982212d396c1ab216c5c9ea0656e5231e05d745 https://github.com/galaxyproject/galaxy/commit/8982212d396c1ab216c5c9ea0656… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/util/xml_macros.py M scripts/loc_files/create_all_fasta_loc.py Log Message: ----------- Replace deprecated `xml.etree.ElementTree.Element.getiterator()` with `iter()` Commit: f0708488aa08393cfdf3ab3e0e45e37982d050d0 https://github.com/galaxyproject/galaxy/commit/f0708488aa08393cfdf3ab3e0e45… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M pytest.ini Log Message: ----------- pytest: disable test collection of classes starting with `Test` Fix warnings like: ``` /home/travis/build/galaxyproject/galaxy/lib/galaxy/tools/verify/test_data.py:29: PytestWarning: cannot collect test class 'TestDataResolver' because it has a __init__ constructor class TestDataResolver(object): ``` appearing e.g. in https://travis-ci.org/galaxyproject/galaxy/jobs/428114139 . See pytest documentation: https://docs.pytest.org/en/latest/reference.html#confval-python_classes Commit: 2874e87debcc1940e1f1143a7af4dacb38c95585 https://github.com/galaxyproject/galaxy/commit/2874e87debcc1940e1f1143a7af4… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- Merge pull request #6728 from martenson/fix-toolhelp-parsing [18.09] remove html tags and newlines from the help text Commit: 0974b130ef922e3177de27f6365ccd624bf194a7 https://github.com/galaxyproject/galaxy/commit/0974b130ef922e3177de27f6365c… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/util/xml_macros.py M lib/galaxy/web/framework/base.py M pytest.ini M scripts/loc_files/create_all_fasta_loc.py Log Message: ----------- Merge pull request #6730 from nsoranzo/release_18.09_backport_6722 [18.09] Partial backport of #6722 Commit: 376516610ef6ac28cef7a9558adab1a88d8c0c12 https://github.com/galaxyproject/galaxy/commit/376516610ef6ac28cef7a9558ada… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Bugfix - missing tests for data source sniffing. Ensure #6334 is fixed I think. Commit: aca30f0b158a9ab0647747b957f55ea6716a4d18 https://github.com/galaxyproject/galaxy/commit/aca30f0b158a9ab0647747b957f5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Merge pull request #6733 from jmchilton/1809_sniff_test [18.09] Fix missing tests for data source sniffing. Commit: ed147ee052a1628aa07e33b3849f1d4fb2778d2b https://github.com/galaxyproject/galaxy/commit/ed147ee052a1628aa07e33b3849f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M client/galaxy/docs/bootstrap.md M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/datatypes_conf.xml.sample M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/extract_dataset.xml M lib/galaxy/tools/search/__init__.py M test/api/test_tools.py Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/e049786c4c75...ed147ee052a1 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 376516: Bugfix - missing tests for data source sniffing.
by GitHub 18 Sep '18

18 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 376516610ef6ac28cef7a9558adab1a88d8c0c12 https://github.com/galaxyproject/galaxy/commit/376516610ef6ac28cef7a9558ada… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Bugfix - missing tests for data source sniffing. Ensure #6334 is fixed I think. Commit: aca30f0b158a9ab0647747b957f55ea6716a4d18 https://github.com/galaxyproject/galaxy/commit/aca30f0b158a9ab0647747b957f5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Merge pull request #6733 from jmchilton/1809_sniff_test [18.09] Fix missing tests for data source sniffing. Compare: https://github.com/galaxyproject/galaxy/compare/0974b130ef92...aca30f0b158a **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/usegalaxy-playbook] 1d4643: Update toolshed to 0974b130ef922e3177de27f6365ccd6...
by GitHub 18 Sep '18

18 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1d46435f76e456cee6ea1cd352a6e6cd01e12f92 https://github.com/galaxyproject/usegalaxy-playbook/commit/1d46435f76e456ce… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M env/toolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update toolshed to 0974b130ef922e3177de27f6365ccd624bf194a7 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 402506: Update testtoolshed to 0974b130ef922e3177de27f6365...
by GitHub 18 Sep '18

18 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 40250611b8876512c25c52a84aa01e006ec8fd87 https://github.com/galaxyproject/usegalaxy-playbook/commit/40250611b8876512… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update testtoolshed to 0974b130ef922e3177de27f6365ccd624bf194a7 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 6233a4: Release notes templated; still needs manual curati...
by GitHub 18 Sep '18

18 Sep '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: 6233a408cc93152a379651db3cc143d368f78dda https://github.com/galaxyproject/galaxy/commit/6233a408cc93152a379651db3cc1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: A doc/source/releases/18.09.rst A doc/source/releases/18.09_announce.rst A doc/source/releases/19.01_announce.rst Log Message: ----------- Release notes templated; still needs manual curation **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 54d137: Remove deprecated `decode_param_names` parameter
by GitHub 18 Sep '18

18 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 54d137edab3fb33beac87c23cd35fb19dd7f44fa https://github.com/galaxyproject/galaxy/commit/54d137edab3fb33beac87c23cd35… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Remove deprecated `decode_param_names` parameter It has been deprecated since WebOb 1.1 and ignored since WebOb 1.2 . Commit: 8ed19a3a09df9b66266f66bc53e504c781ae524d https://github.com/galaxyproject/galaxy/commit/8ed19a3a09df9b66266f66bc53e5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/verify/interactor.py Log Message: ----------- `async` is a reserved keyword in Python 3.7 - Remove unused `async` parameter of `stage_data_async()` method. - Rename `async` parameter of `quick_load()` method. Fix https://github.com/galaxyproject/galaxy/issues/6717 . xref. https://github.com/galaxyproject/galaxy/issues/1715 Commit: 8982212d396c1ab216c5c9ea0656e5231e05d745 https://github.com/galaxyproject/galaxy/commit/8982212d396c1ab216c5c9ea0656… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/util/xml_macros.py M scripts/loc_files/create_all_fasta_loc.py Log Message: ----------- Replace deprecated `xml.etree.ElementTree.Element.getiterator()` with `iter()` Commit: f0708488aa08393cfdf3ab3e0e45e37982d050d0 https://github.com/galaxyproject/galaxy/commit/f0708488aa08393cfdf3ab3e0e45… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M pytest.ini Log Message: ----------- pytest: disable test collection of classes starting with `Test` Fix warnings like: ``` /home/travis/build/galaxyproject/galaxy/lib/galaxy/tools/verify/test_data.py:29: PytestWarning: cannot collect test class 'TestDataResolver' because it has a __init__ constructor class TestDataResolver(object): ``` appearing e.g. in https://travis-ci.org/galaxyproject/galaxy/jobs/428114139 . See pytest documentation: https://docs.pytest.org/en/latest/reference.html#confval-python_classes Commit: 0974b130ef922e3177de27f6365ccd624bf194a7 https://github.com/galaxyproject/galaxy/commit/0974b130ef922e3177de27f6365c… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/util/xml_macros.py M lib/galaxy/web/framework/base.py M pytest.ini M scripts/loc_files/create_all_fasta_loc.py Log Message: ----------- Merge pull request #6730 from nsoranzo/release_18.09_backport_6722 [18.09] Partial backport of #6722 Compare: https://github.com/galaxyproject/galaxy/compare/2874e87debcc...0974b130ef92 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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