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

[galaxyproject/galaxy] d144f1: Fix typo in GIE nginx proxy docs
by GitHub 11 Nov '16

11 Nov '16

Branch: refs/heads/gie-doc-fix Home: https://github.com/galaxyproject/galaxy Commit: d144f18e7a6eaa5276b2d63f51457eda1befd679 https://github.com/galaxyproject/galaxy/commit/d144f18e7a6eaa5276b2d63f5145… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Fix typo in GIE nginx proxy docs

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[galaxyproject/galaxy] 9c37c6: Fixes for flake8-import-order 0.11
by GitHub 11 Nov '16

11 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9c37c6df896312de5d07f93d2c6e1bdcaeff3e53 https://github.com/galaxyproject/galaxy/commit/9c37c6df896312de5d07f93d2c6e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/tool_shed/tools/tool_validator.py M scripts/api/filter_failed_datasets_from_collection.py Log Message: ----------- Fixes for flake8-import-order 0.11 Also fix Python3 compatibility. Commit: 2d8cf6b3376b41a6dd9a9ff3f4a82aaae1baa209 https://github.com/galaxyproject/galaxy/commit/2d8cf6b3376b41a6dd9a9ff3f4a8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/tool_shed/tools/tool_validator.py M scripts/api/filter_failed_datasets_from_collection.py Log Message: ----------- Merge pull request #3154 from nsoranzo/fixes_for_new_flake8_import_order Fixes for flake8-import-order 0.11 Compare: https://github.com/galaxyproject/galaxy/compare/4b2e875802dc...2d8cf6b3376b

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[galaxyproject/usegalaxy-playbook] 6731a5: Updated dynamic rules
by GitHub 10 Nov '16

10 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6731a5819bfbca076126e12cb48ccd5282333dd0 https://github.com/galaxyproject/usegalaxy-playbook/commit/6731a5819bfbca07… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-10 (Thu, 10 Nov 2016) Changed paths: A files/galaxy/common/dynamic_rules/bridges_select.py M files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py Log Message: ----------- Updated dynamic rules

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[galaxyproject/usegalaxy-playbook] c544f1: Upding slide rotation. Swapping events.
by GitHub 10 Nov '16

10 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c544f1a17001df1d42fe03983129867a10491159 https://github.com/galaxyproject/usegalaxy-playbook/commit/c544f1a17001df1d… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2016-11-10 (Thu, 10 Nov 2016) Changed paths: A files/galaxy/common/static/welcome_img/EDGW2017.jpg A files/galaxy/common/static/welcome_img/GAMe2017TalkAbstracts.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Upding slide rotation. Swapping events.

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[galaxyproject/galaxy] d3a5c4: Catch and display exceptions triggered by tool fil...
by GitHub 09 Nov '16

09 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d3a5c4c7205b269830547fcb647528e3e2a9663f https://github.com/galaxyproject/galaxy/commit/d3a5c4c7205b269830547fcb6475… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Catch and display exceptions triggered by tool filter functions Commit: 300c9616306f69579b1d492aa78a17985e21f738 https://github.com/galaxyproject/galaxy/commit/300c9616306f69579b1d492aa78a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Use as instead of comma Commit: 1c740833e0c1884d43a42dc4417eb3f02adfafab https://github.com/galaxyproject/galaxy/commit/1c740833e0c1884d43a42dc4417e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix import order Commit: 7456b1f9218dabd6eab0d2fa6c3acc285c6c20c3 https://github.com/galaxyproject/galaxy/commit/7456b1f9218dabd6eab0d2fa6c3a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Remove unnecessary slashes Commit: 4d623a4d5a391a6aed2faf4b45f03c87b8f11a90 https://github.com/galaxyproject/galaxy/commit/4d623a4d5a391a6aed2faf4b45f0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Ensure that label key exists before attempting removal Commit: 4b2e875802dcdc0015fb1c05d669e31eb60f01ab https://github.com/galaxyproject/galaxy/commit/4b2e875802dcdc0015fb1c05d669… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-09 (Wed, 09 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #3123 from guerler/fix_tool_filters Display an error message when toolbox filters fails Compare: https://github.com/galaxyproject/galaxy/compare/93a09d2eb033...4b2e875802dc

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[galaxyproject/galaxy] 7f630e: Fix flake8 linting broken in 7bee2651aa8f08ea0495d...
by GitHub 09 Nov '16

09 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7f630ea2ddb279ce963070d87573bac4c66d5027 https://github.com/galaxyproject/galaxy/commit/7f630ea2ddb279ce963070d87573… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-09 (Wed, 09 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/webapps/reports/config.py Log Message: ----------- Fix flake8 linting broken in 7bee2651aa8f08ea0495d167e33d317a22ae3ef9 Also fix import order and Python3 compatibility. Commit: 93a09d2eb033d8bc8b98a7ca94e80bbb1a80fe60 https://github.com/galaxyproject/galaxy/commit/93a09d2eb033d8bc8b98a7ca94e8… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-11-09 (Wed, 09 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/webapps/reports/config.py Log Message: ----------- Merge pull request #3141 from nsoranzo/followup_on_3139 Fix flake8 linting broken in 7bee2651aa8f08ea0495d167e33d317a22ae3ef9 Compare: https://github.com/galaxyproject/galaxy/compare/00edc474274a...93a09d2eb033

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[galaxyproject/galaxy] 1e142d: User activation emails are sent without a From: ad...
by GitHub 08 Nov '16

08 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1e142dd33d505436e081306bc08f044bb7b5886a https://github.com/galaxyproject/galaxy/commit/1e142dd33d505436e081306bc08f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- User activation emails are sent without a From: address if email_from is unset. Fix this by using `galaxy-no-reply@host` as with other emails we send. Commit: 00edc474274a671c1ba4d7e2a64335e0abb614c5 https://github.com/galaxyproject/galaxy/commit/00edc474274a671c1ba4d7e2a643… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #3140 from natefoo/activation-from Ensure a From: address is set for user activation emails Compare: https://github.com/galaxyproject/galaxy/compare/3d69a2d1a5f7...00edc474274a

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[galaxyproject/galaxy] 0ba54e: Treat the value of `message_box_visible` in galaxy...
by GitHub 08 Nov '16

08 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0ba54e922046733e582b7c5b4066525edc3957aa https://github.com/galaxyproject/galaxy/commit/0ba54e922046733e582b7c5b4066… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Treat the value of `message_box_visible` in galaxy.ini as a boolean Commit: 7bee2651aa8f08ea0495d167e33d317a22ae3ef9 https://github.com/galaxyproject/galaxy/commit/7bee2651aa8f08ea0495d167e33d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- string_as_bool for message_box_visible on webapps Commit: 3d69a2d1a5f7ee5606834c45e34e341fa4822721 https://github.com/galaxyproject/galaxy/commit/3d69a2d1a5f7ee5606834c45e34e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Merge pull request #3139 from natefoo/message-box-bool Treat the value of `message_box_visible` in galaxy.ini as a boolean Compare: https://github.com/galaxyproject/galaxy/compare/6a8ca92dd70b...3d69a2d1a5f7

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[galaxyproject/galaxy] 7c030e: Use sed instead of pandoc to insert TOC in schema ...
by GitHub 07 Nov '16

07 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7c030ebf2f51c6800966a2fc2d1b0048f0930f1d https://github.com/galaxyproject/galaxy/commit/7c030ebf2f51c6800966a2fc2d1b… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M doc/Makefile Log Message: ----------- Use sed instead of pandoc to insert TOC in schema doc pandoc < 1.14 adds the TOC depth as a float, which is not recognised by Sphinx. Also, move the TOC after the introduction, which looks nicer. Commit: 6a8ca92dd70bc88bee962cd079460118f998c351 https://github.com/galaxyproject/galaxy/commit/6a8ca92dd70bc88bee962cd07946… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M doc/Makefile Log Message: ----------- Merge pull request #3135 from nsoranzo/followup_on_3086 Use sed instead of pandoc to insert TOC in schema doc Compare: https://github.com/galaxyproject/galaxy/compare/3b8f543ebdd1...6a8ca92dd70b

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[galaxyproject/galaxy] 192f66: Update galaxy.xsd
by GitHub 07 Nov '16

07 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 192f66a714f3c7dd320550def43d7cd283dfa6af https://github.com/galaxyproject/galaxy/commit/192f66a714f3c7dd320550def43d… Author: Gildas Le Corguillé <lecorguille(a)users.noreply.github.com> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Update galaxy.xsd Add `hidden_data` in `ParamType` The context [cufflinks](https://github.com/galaxyproject/tools-devteam/blob/master/tool_… `planemo lint .` ``` Applying linter tool_xsd... FAIL .. ERROR: Invalid tmpw5U2MV found. Errors [/tmp/tmpw5U2MV:144:0:ERROR:SCHEMASV:SCHEMAV_CVC_ENUMERATION_VALID: Element 'param', attribute 'type': [facet 'enumeration'] The value 'hidden_data' is not an element of the set {'text', 'integer', 'float', 'color', 'boolean', 'genomebuild', 'library_data', 'select', 'data_column', 'hidden', 'baseurl', 'file', 'data', 'drill_down', 'data_collection'}. /tmp/tmpw5U2MV:144:0:ERROR:SCHEMASV:SCHEMAV_CVC_DATATYPE_VALID_1_2_1: Element 'param', attribute 'type': 'hidden_data' is not a valid value of the atomic type 'ParamType'. ``` I don’t know so much this tag `hidden_data`, but it seems that it’s still in the [Galaxy doc](https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-inputs-p… Commit: 3b8f543ebdd1307c91c3ae719bbb7072476d7b9a https://github.com/galaxyproject/galaxy/commit/3b8f543ebdd1307c91c3ae719bbb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #3132 from lecorguille/patch-2 Update galaxy.xsd Compare: https://github.com/galaxyproject/galaxy/compare/78dfb95f0264...3b8f543ebdd1

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