Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a27e86786ad031eafcbfeb39ffdadf71d80dcfad https://github.com/galaxyproject/galaxy/commit/a27e86786ad031eafcbfeb39ffdad... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-05-26 (Thu, 26 May 2016) Changed paths: M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/repository_types/metadata.py M tools/filters/axt_to_lav.py Log Message: ----------- wrap bare str raises with generic Exception() as Pyton 2.7 does not support bare str Commit: fe64a8198bca75f2e535efc7c3813d24810904ab https://github.com/galaxyproject/galaxy/commit/fe64a8198bca75f2e535efc7c3813... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-05-26 (Thu, 26 May 2016) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- fix the mess made with mass edit Commit: 6094990e43f6510833395885d234a2264e7d44f1 https://github.com/galaxyproject/galaxy/commit/6094990e43f6510833395885d234a... Author: John Chilton <jmchilton@gmail.com> Date: 2016-05-26 (Thu, 26 May 2016) Changed paths: M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/repository_types/metadata.py M tools/filters/axt_to_lav.py Log Message: ----------- Merge pull request #2424 from martenson/port-exceptionwrap-16.04 [16.04] wrap bare str exceptions Commit: 214e757d81623e9c12d171f3dcfc516c7dcc5e32 https://github.com/galaxyproject/galaxy/commit/214e757d81623e9c12d171f3dcfc5... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-05-31 (Tue, 31 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Only scan the last 16 MB of a job's stderr for slurm memory warning messages. Commit: dcb28e095012fef3be769f677fa572f13d4ed88a https://github.com/galaxyproject/galaxy/commit/dcb28e095012fef3be769f677fa57... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-05-31 (Tue, 31 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Fix linting error Commit: ceb825bea8b28c8908c8a719919b9167bedabe55 https://github.com/galaxyproject/galaxy/commit/ceb825bea8b28c8908c8a719919b9... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-05-31 (Tue, 31 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2432 from natefoo/job-output-memory-fix [16.04] Only scan the last 16 MB of a job's stderr for slurm memory warning messages Commit: 7cb527ac595591c99401436757168b366f86a526 https://github.com/galaxyproject/galaxy/commit/7cb527ac595591c99401436757168... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-06-02 (Thu, 02 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Overwrite the correct part of stderr - Skip partial line - Seek back to the correct position after readlines() - Use the same approach in __check_memory_limit() Commit: 58f3f5c7dd4c622adce0f18d24a0ee950d1d4dfd https://github.com/galaxyproject/galaxy/commit/58f3f5c7dd4c622adce0f18d24a0e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-06-02 (Thu, 02 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2447 from nsoranzo/release_16.04_fix_for_2432 [16.04] Overwrite the correct part of stderr Commit: 84ece6da372ea0e0537bf68c6981962437e0d330 https://github.com/galaxyproject/galaxy/commit/84ece6da372ea0e0537bf68c69819... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-06-02 (Thu, 02 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/ec476c7cb46a...84ece6da372e