- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 128a31: Use OSX-compatible sed syntax
by GitHub 08 Dec '16

08 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 128a3174ebc425dfe750767eef40374d0b282448 https://github.com/galaxyproject/galaxy/commit/128a3174ebc425dfe750767eef40… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M doc/Makefile Log Message: ----------- Use OSX-compatible sed syntax Commit: 13ae374f84926e71b3dde7080d8d74ad443916e3 https://github.com/galaxyproject/galaxy/commit/13ae374f84926e71b3dde7080d8d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M doc/Makefile A doc/fix_schema_rst.sh Log Message: ----------- Move sed commands to a script to resolve interferences with Make which happen only under OSX Commit: ca99753590abf62df2c34e80a87b1ae2ec3424e2 https://github.com/galaxyproject/galaxy/commit/ca99753590abf62df2c34e80a87b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M doc/Makefile A doc/fix_schema_rst.sh Log Message: ----------- Merge pull request #3281 from nsoranzo/release_16.10_fix_doc_Makefile [16.10] Use OSX-compatible sed syntax Compare: https://github.com/galaxyproject/galaxy/compare/2cbf9a9138b6...ca99753590ab

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[galaxyproject/galaxy] dabc54: Clearly state which are the 'Procedure Documents'
by GitHub 08 Dec '16

08 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dabc54e40e17e7bcee323c583c77612603670da8 https://github.com/galaxyproject/galaxy/commit/dabc54e40e17e7bcee323c583c77… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Clearly state which are the 'Procedure Documents' Commit: 16167bd01cf8fd0128dd7e7abf25a4fbfd9468ed https://github.com/galaxyproject/galaxy/commit/16167bd01cf8fd0128dd7e7abf25… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Move 'Direct Commit Access' subsection to 'Committers' section Commit: 8de85e4b470c65ddcfe7a39911a92b1fa01e1449 https://github.com/galaxyproject/galaxy/commit/8de85e4b470c65ddcfe7a39911a9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Clarify that only PRs modifying tagged release branches require 2 +1 votes Commit: d478cc41a6734a537bb12a44eeebe7907f71c19b https://github.com/galaxyproject/galaxy/commit/d478cc41a6734a537bb12a44eeeb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Merge pull request #3240 from nsoranzo/procedures_clarifications [PROCEDURES] Procedures clarifications Compare: https://github.com/galaxyproject/galaxy/compare/6f5d8fb6ac2b...d478cc41a673

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[galaxyproject/galaxy] 7da5b1: Add a useful logging statement in run_tests.sh.
by GitHub 08 Dec '16

08 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7da5b17cac75ad7d60454e4ef5bac6d36550bf86 https://github.com/galaxyproject/galaxy/commit/7da5b17cac75ad7d60454e4ef5ba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M run_tests.sh Log Message: ----------- Add a useful logging statement in run_tests.sh. Commit: 0ee095024005862aa2aed585569af1086bbb557e https://github.com/galaxyproject/galaxy/commit/0ee095024005862aa2aed585569a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M run_tests.sh Log Message: ----------- Fix for new run_tests.sh option to clean PYC files. Commit: 6f5d8fb6ac2bbe68bc178346c102f5d6df756770 https://github.com/galaxyproject/galaxy/commit/6f5d8fb6ac2bbe68bc178346c102… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #3285 from jmchilton/run_tests_touchups Small touchups to run_tests.sh. Compare: https://github.com/galaxyproject/galaxy/compare/e3d1bd6e0d82...6f5d8fb6ac2b

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[galaxyproject/galaxy] d79d6b: Improved logging for selenium docker-compose probl...
by GitHub 08 Dec '16

08 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d79d6b96816759bde4234523bbd7a2384474f420 https://github.com/galaxyproject/galaxy/commit/d79d6b96816759bde4234523bbd7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-04 (Sun, 04 Dec 2016) Changed paths: M .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Improved logging for selenium docker-compose problems. If containers fail to start, (as the Galaxy container for the selenium test appears to fail currently) print docker logs for that container. Commit: 5fb334aaee5bff40b51bdca955bb06e21e2a07d8 https://github.com/galaxyproject/galaxy/commit/5fb334aaee5bff40b51bdca955bb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-04 (Sun, 04 Dec 2016) Changed paths: M .ci/jenkins/selenium/run_galaxy.bash Log Message: ----------- Increase timeout based on logging on docker.galaxyproject.org. Commit: 851f66f3e8996c34ed306c09de7f1e8b661e25ea https://github.com/galaxyproject/galaxy/commit/851f66f3e8996c34ed306c09de7f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Actually dump all logs on failure... Commit: e3d1bd6e0d82eaaea4efa638fa32bd8648f9cddb https://github.com/galaxyproject/galaxy/commit/e3d1bd6e0d82eaaea4efa638fa32… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Merge pull request #3264 from jmchilton/improved_selenium_logging Improved logging for selenium docker-compose problems. Compare: https://github.com/galaxyproject/galaxy/compare/cbd527b9a467...e3d1bd6e0d82

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[galaxyproject/galaxy] e3fbbc: add small touches to release notes
by GitHub 08 Dec '16

08 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: e3fbbc52b999f9e25e7b02c4edf44ddd43a63622 https://github.com/galaxyproject/galaxy/commit/e3fbbc52b999f9e25e7b02c4edf4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M doc/source/releases/16.10_announce.rst Log Message: ----------- add small touches to release notes Commit: c01e25ddf8854e20a96040b3c8616136ec517574 https://github.com/galaxyproject/galaxy/commit/c01e25ddf8854e20a96040b3c861… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M doc/source/releases/16.10_announce.rst Log Message: ----------- missing articles Commit: 2cbf9a9138b6fb89d06f41398539908a5df4585e https://github.com/galaxyproject/galaxy/commit/2cbf9a9138b6fb89d06f41398539… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M doc/source/releases/16.10_announce.rst Log Message: ----------- Merge pull request #3284 from martenson/notes-tinies [16.10] add small touches to release notes Compare: https://github.com/galaxyproject/galaxy/compare/83de83e7edc2...2cbf9a9138b6

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[galaxyproject/galaxy] 3e0e96: add work on release notes 16.10, improve docs for ...
by GitHub 07 Dec '16

07 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 3e0e96657d765f4023bb6801ace2e96a1ffc4505 https://github.com/galaxyproject/galaxy/commit/3e0e96657d765f4023bb6801ace2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M doc/source/admin/index.rst M doc/source/admin/webhooks.rst M doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst Log Message: ----------- add work on release notes 16.10, improve docs for webhooks Conflicts: doc/source/releases/16.10.rst doc/source/releases/16.10_announce.rst Commit: 739fb59cba5b7747a32e685a3632f96effad4c11 https://github.com/galaxyproject/galaxy/commit/739fb59cba5b7747a32e685a3632… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- fix the fix Commit: 5784a838a554f8dcf9e132e26be01240a37a3e65 https://github.com/galaxyproject/galaxy/commit/5784a838a554f8dcf9e132e26be0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M doc/source/releases/16.10.rst Log Message: ----------- fix bad merge Commit: 83de83e7edc230d7f9841a6d9770d87d0c89d06f https://github.com/galaxyproject/galaxy/commit/83de83e7edc230d7f9841a6d9770… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M doc/source/admin/index.rst M doc/source/admin/webhooks.rst M doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst Log Message: ----------- Merge pull request #3282 from martenson/release_16.10 [16.10] work on release notes 16.10 Compare: https://github.com/galaxyproject/galaxy/compare/d0f39ceff518...83de83e7edc2

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[galaxyproject/galaxy] a84601: Add 16.10 release notes.
by GitHub 07 Dec '16

07 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a84601ba80cb8620a396e740e9a69f3d6f1dfd37 https://github.com/galaxyproject/galaxy/commit/a84601ba80cb8620a396e740e9a6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: A doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst A doc/source/releases/17.01_announce.rst M scripts/bootstrap_history.py Log Message: ----------- Add 16.10 release notes. Commit: 8766e125091d0a5a83a0fd4daf274fe93551a443 https://github.com/galaxyproject/galaxy/commit/8766e125091d0a5a83a0fd4daf27… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js Log Message: ----------- Escape filename in upload dialog, default and composite. Pointed out by David Wyde. Commit: 13ab07030c8ffa5012a123671c2ab450bf14c40b https://github.com/galaxyproject/galaxy/commit/13ab07030c8ffa5012a123671c2a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/default/default-row.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Use consistent spacing. Commit: 75d327f165c730f95e181a2feff1db64074ab3e6 https://github.com/galaxyproject/galaxy/commit/75d327f165c730f95e181a2feff1… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js Log Message: ----------- Merge pull request #3278 from dannon/upload_escape_filename [16.10] Escape filename in upload dialog, default and composite. Commit: f6b94dc465a41e0ce25cd0d38b8cfa81ab4c5254 https://github.com/galaxyproject/galaxy/commit/f6b94dc465a41e0ce25cd0d38b8c… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M lib/tool_shed/util/tool_util.py Log Message: ----------- Fix for ToolShed install when copied sample data target exists, but is broken symlink. Commit: 70fc43b24090e537479a74b34a7ff9bc4e43de84 https://github.com/galaxyproject/galaxy/commit/70fc43b24090e537479a74b34a7f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M lib/tool_shed/util/tool_util.py Log Message: ----------- Merge pull request #3279 from blankenberg/16.10_ts_install_broken_symlink [16.10] Fix for ToolShed install when copied sample data target exists, but is broken symlink. Commit: d0f39ceff51843a95048dfdaf49035d07ce75c1d https://github.com/galaxyproject/galaxy/commit/d0f39ceff51843a95048dfdaf490… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: A doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst A doc/source/releases/17.01_announce.rst M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #3270 from jmchilton/16.10_release_notes_0 [16.10] Add 16.10 release notes. Commit: cbd527b9a4671c7abe9a22cf69e869b5d2de858a https://github.com/galaxyproject/galaxy/commit/cbd527b9a4671c7abe9a22cf69e8… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js A doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst A doc/source/releases/17.01_announce.rst M lib/tool_shed/util/tool_util.py M scripts/bootstrap_history.py M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js Log Message: ----------- Merge branch 'release_16.10' into dev Conflicts: static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map Compare: https://github.com/galaxyproject/galaxy/compare/33dec01ba218...cbd527b9a467

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[galaxyproject/galaxy] a84601: Add 16.10 release notes.
by GitHub 07 Dec '16

07 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: a84601ba80cb8620a396e740e9a69f3d6f1dfd37 https://github.com/galaxyproject/galaxy/commit/a84601ba80cb8620a396e740e9a6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: A doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst A doc/source/releases/17.01_announce.rst M scripts/bootstrap_history.py Log Message: ----------- Add 16.10 release notes. Commit: d0f39ceff51843a95048dfdaf49035d07ce75c1d https://github.com/galaxyproject/galaxy/commit/d0f39ceff51843a95048dfdaf490… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: A doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst A doc/source/releases/17.01_announce.rst M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #3270 from jmchilton/16.10_release_notes_0 [16.10] Add 16.10 release notes. Compare: https://github.com/galaxyproject/galaxy/compare/70fc43b24090...d0f39ceff518

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[galaxyproject/galaxy] f6b94d: Fix for ToolShed install when copied sample data t...
by GitHub 07 Dec '16

07 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: f6b94dc465a41e0ce25cd0d38b8cfa81ab4c5254 https://github.com/galaxyproject/galaxy/commit/f6b94dc465a41e0ce25cd0d38b8c… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M lib/tool_shed/util/tool_util.py Log Message: ----------- Fix for ToolShed install when copied sample data target exists, but is broken symlink. Commit: 70fc43b24090e537479a74b34a7ff9bc4e43de84 https://github.com/galaxyproject/galaxy/commit/70fc43b24090e537479a74b34a7f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M lib/tool_shed/util/tool_util.py Log Message: ----------- Merge pull request #3279 from blankenberg/16.10_ts_install_broken_symlink [16.10] Fix for ToolShed install when copied sample data target exists, but is broken symlink. Compare: https://github.com/galaxyproject/galaxy/compare/75d327f165c7...70fc43b24090

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[galaxyproject/galaxy] 8766e1: Escape filename in upload dialog, default and comp...
by GitHub 07 Dec '16

07 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 8766e125091d0a5a83a0fd4daf274fe93551a443 https://github.com/galaxyproject/galaxy/commit/8766e125091d0a5a83a0fd4daf27… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js Log Message: ----------- Escape filename in upload dialog, default and composite. Pointed out by David Wyde. Commit: 13ab07030c8ffa5012a123671c2ab450bf14c40b https://github.com/galaxyproject/galaxy/commit/13ab07030c8ffa5012a123671c2a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/default/default-row.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Use consistent spacing. Commit: 75d327f165c730f95e181a2feff1db64074ab3e6 https://github.com/galaxyproject/galaxy/commit/75d327f165c730f95e181a2feff1… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js Log Message: ----------- Merge pull request #3278 from dannon/upload_escape_filename [16.10] Escape filename in upload dialog, default and composite. Compare: https://github.com/galaxyproject/galaxy/compare/8a5ff5df21ef...75d327f165c7

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