September 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 16a98b: Fixes to LDAP auth config sample.
by GitHub 04 Sep '15

04 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 16a98b50cce48150272289b409ae5a2a70fb9425 https://github.com/galaxyproject/galaxy/commit/16a98b50cce48150272289b409ae… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M config/auth_conf.xml.sample Log Message: ----------- Fixes to LDAP auth config sample. Commit: b962a8ded0661b1df940400cb544a0ddbcfb0686 https://github.com/galaxyproject/galaxy/commit/b962a8ded0661b1df940400cb544… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M lib/galaxy/auth/__init__.py Log Message: ----------- Style fixes. Commit: 474d58809ab1a001a64cb2f540e896d2de22cda5 https://github.com/galaxyproject/galaxy/commit/474d58809ab1a001a64cb2f540e8… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/mobile.py Log Message: ----------- Fix commented-out code. Commit: cafe2ece1e0a71870be6c368e569ff2b4ceab096 https://github.com/galaxyproject/galaxy/commit/cafe2ece1e0a71870be6c368e569… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M config/auth_conf.xml.sample M lib/galaxy/auth/__init__.py M lib/galaxy/webapps/galaxy/controllers/mobile.py Log Message: ----------- Merge pull request #696 from nsoranzo/dev Small fixes for LDAP auth. Compare: https://github.com/galaxyproject/galaxy/compare/2867f1149a01...cafe2ece1e0a

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[galaxyproject/galaxy] 197c7b: Fix for fix for fix for handling of unix permissio...
by GitHub 04 Sep '15

04 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 197c7b21b209a7b6fbdb9a8a11c232a2b88523fc https://github.com/galaxyproject/galaxy/commit/197c7b21b209a7b6fbdb9a8a11c2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Fix for fix for fix for handling of unix permissions in .zip files. Append common_prefix to extraction_path only when returning. Commit: 1203ccc49cbf8726bdf35441593eec0cf00df652 https://github.com/galaxyproject/galaxy/commit/1203ccc49cbf8726bdf35441593e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #689 from nsoranzo/release_15.07 [15.07] Fix for fix for fix for handling of unix permissions in .zip files. Commit: 2284b2242c72183b8218717ea728bdc0d2420ac8 https://github.com/galaxyproject/galaxy/commit/2284b2242c72183b8218717ea728… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge branch 'release_15.07' Commit: 2867f1149a019f840bc6f4d1da23b98aad702839 https://github.com/galaxyproject/galaxy/commit/2867f1149a019f840bc6f4d1da23… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge branch 'master' into dev Compare: https://github.com/galaxyproject/galaxy/compare/99e7ba43a0c4...2867f1149a01

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[galaxyproject/galaxy] 197c7b: Fix for fix for fix for handling of unix permissio...
by GitHub 04 Sep '15

04 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 197c7b21b209a7b6fbdb9a8a11c232a2b88523fc https://github.com/galaxyproject/galaxy/commit/197c7b21b209a7b6fbdb9a8a11c2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Fix for fix for fix for handling of unix permissions in .zip files. Append common_prefix to extraction_path only when returning. Commit: 1203ccc49cbf8726bdf35441593eec0cf00df652 https://github.com/galaxyproject/galaxy/commit/1203ccc49cbf8726bdf35441593e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #689 from nsoranzo/release_15.07 [15.07] Fix for fix for fix for handling of unix permissions in .zip files. Commit: 2284b2242c72183b8218717ea728bdc0d2420ac8 https://github.com/galaxyproject/galaxy/commit/2284b2242c72183b8218717ea728… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge branch 'release_15.07' Compare: https://github.com/galaxyproject/galaxy/compare/4557b27fea51...2284b2242c72

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[galaxyproject/galaxy] 197c7b: Fix for fix for fix for handling of unix permissio...
by GitHub 03 Sep '15

03 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: 197c7b21b209a7b6fbdb9a8a11c232a2b88523fc https://github.com/galaxyproject/galaxy/commit/197c7b21b209a7b6fbdb9a8a11c2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Fix for fix for fix for handling of unix permissions in .zip files. Append common_prefix to extraction_path only when returning. Commit: 1203ccc49cbf8726bdf35441593eec0cf00df652 https://github.com/galaxyproject/galaxy/commit/1203ccc49cbf8726bdf35441593e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #689 from nsoranzo/release_15.07 [15.07] Fix for fix for fix for handling of unix permissions in .zip files. Compare: https://github.com/galaxyproject/galaxy/compare/990501d2d947...1203ccc49cbf

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[galaxyproject/galaxy] 8430ca: UI, histories: correct allFetched setting in setCo...
by GitHub 03 Sep '15

03 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8430ca4e3fc506db41357312db0cced248ee43dd https://github.com/galaxyproject/galaxy/commit/8430ca4e3fc506db41357312db0c… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/multi-panel.js Log Message: ----------- UI, histories: correct allFetched setting in setCollection to allow fetching after changing collection order Commit: b325966e65398b6f7ff6bf493c44e2ab691cd042 https://github.com/galaxyproject/galaxy/commit/b325966e65398b6f7ff6bf493c44… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/style/less/history.less M static/style/blue/base.css Log Message: ----------- UI, histories: try to correct bootstrap popover dropdown width to keep caret inside button Commit: 99e7ba43a0c45a8777aafb0c5d0d9e773793d201 https://github.com/galaxyproject/galaxy/commit/99e7ba43a0c45a8777aafb0c5d0d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/style/less/history.less M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/multi-panel.js M static/style/blue/base.css Log Message: ----------- Merge pull request #695 from carlfeberhard/multi-history.all-fetched Fix multi-history fetch flag to allow re-fetching after collection sort Compare: https://github.com/galaxyproject/galaxy/compare/9df1dfafebe3...99e7ba43a0c4

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[galaxyproject/galaxy] 85d4b7: Slight refactoring of parse_int, move to galaxy.ut...
by GitHub 03 Sep '15

03 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 85d4b747297f8bb2a2d7e39c8995d92e6e91911b https://github.com/galaxyproject/galaxy/commit/85d4b747297f8bb2a2d7e39c8995… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Slight refactoring of parse_int, move to galaxy.util and use default in invocation. Commit: 67322c5a440e2912be02c88d4d77e525fe8a7638 https://github.com/galaxyproject/galaxy/commit/67322c5a440e2912be02c88d4d77… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Don't overload language builtins min, max in parse_int Commit: 65182d3a623630a783aff3a1d4ebba14bb106e81 https://github.com/galaxyproject/galaxy/commit/65182d3a623630a783aff3a1d4eb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Include second file of commit fixing min/max overloading Commit: 2afcc658c7f4b7f945413050b5b7bdcdd0b3abaf https://github.com/galaxyproject/galaxy/commit/2afcc658c7f4b7f945413050b5b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Support 'None' and raise the ValueError when appropriate. Commit: 9df1dfafebe31c84d546aee4146be1239cc793dc https://github.com/galaxyproject/galaxy/commit/9df1dfafebe31c84d546aee4146b… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #684 from dannon/minor_parseint_tweaks Minor parseint refactoring, tweaks Compare: https://github.com/galaxyproject/galaxy/compare/39c2854f6525...9df1dfafebe3

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[galaxyproject/galaxy] 152c81: Set a default value for copy history dialog radio ...
by GitHub 03 Sep '15

03 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 152c81cf8acc45b1c686e26eba04ec87488c52a1 https://github.com/galaxyproject/galaxy/commit/152c81cf8acc45b1c686e26eba04… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M templates/webapps/galaxy/history/copy.mako Log Message: ----------- Set a default value for copy history dialog radio input (to copy *all*). Commit: 39c2854f652524f784a5179a7a2762fd375d67e5 https://github.com/galaxyproject/galaxy/commit/39c2854f652524f784a5179a7a27… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M templates/webapps/galaxy/history/copy.mako Log Message: ----------- Merge pull request #693 from dannon/copy_history_default Set a default value for copy history dialog radio input (to copy *all*). Compare: https://github.com/galaxyproject/galaxy/compare/0785dedd854c...39c2854f6525

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[galaxyproject/galaxy] 4dc5ed: add alt to images; include GitHub issues for repor...
by GitHub 03 Sep '15

03 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4dc5ed52f9a85770e1652557a021a3e531f471c8 https://github.com/galaxyproject/galaxy/commit/4dc5ed52f9a85770e1652557a021… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M README.rst Log Message: ----------- add alt to images; include GitHub issues for reporting Commit: 05f2c4bad0eaffa55782033a2c956f615ce955d8 https://github.com/galaxyproject/galaxy/commit/05f2c4bad0eaffa55782033a2c95… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M README.rst Log Message: ----------- switch links to https Commit: 0785dedd854c7f71c3360f1cbd8dfe3c1a9fb205 https://github.com/galaxyproject/galaxy/commit/0785dedd854c7f71c3360f1cbd8d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M README.rst Log Message: ----------- Merge pull request #690 from martenson/readme-changes Readme changes Compare: https://github.com/galaxyproject/galaxy/compare/6edaf458e89b...0785dedd854c

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[galaxyproject/galaxy] cac794: Add a code of conduct for the project.
by GitHub 03 Sep '15

03 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cac7940706f74c0104611c4bfc7860ac93802261 https://github.com/galaxyproject/galaxy/commit/cac7940706f74c0104611c4bfc78… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: A CODE_OF_CONDUCT.md Log Message: ----------- Add a code of conduct for the project. Commit: 7968f60d0374a15e0caf671867e711a66b8aabb4 https://github.com/galaxyproject/galaxy/commit/7968f60d0374a15e0caf671867e7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-25 (Tue, 25 Aug 2015) Changed paths: M CODE_OF_CONDUCT.md Log Message: ----------- Fix typo found by @nsoranzo. Commit: 6edaf458e89b3db7115c65f0242b781df7c77faa https://github.com/galaxyproject/galaxy/commit/6edaf458e89b3db7115c65f0242b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: A CODE_OF_CONDUCT.md Log Message: ----------- Merge pull request #646 from natefoo/code-of-conduct [PROCEDURES] Create a project code of conduct Compare: https://github.com/galaxyproject/galaxy/compare/88c57bf16b52...6edaf458e89b

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[galaxyproject/infrastructure-playbook] 365f48: Update users on n2
by GitHub 02 Sep '15

02 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 365f48597e1af187267850ae45e559daa4226a06 https://github.com/galaxyproject/infrastructure-playbook/commit/365f48597e1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M galaxyenv/secret_host_vars/n2.galaxyproject.org.yml Log Message: ----------- Update users on n2

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