- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 7429c6: Redirect a page from a faulty username that Chai w...
by GitHub 01 Jun '16

01 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7429c6db3e877ac4b03dec577dec30e60cc78d53 https://github.com/galaxyproject/usegalaxy-playbook/commit/7429c6db3e877ac4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-01 (Wed, 01 Jun 2016) Changed paths: M templates/nginx/usegalaxy_rewrites.conf.j2 Log Message: ----------- Redirect a page from a faulty username that Chai was using

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[galaxyproject/infrastructure-playbook] 33eb35: Scale back Jetstream usage with IU charging coming...
by GitHub 01 Jun '16

01 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 33eb35459be7e6a19aa46fc61a5bc6329d896656 https://github.com/galaxyproject/infrastructure-playbook/commit/33eb35459be… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-01 (Wed, 01 Jun 2016) Changed paths: M jetstreamiuenv/group_vars/slurmclients.yml M jetstreamiuenv/inventory Log Message: ----------- Scale back Jetstream usage with IU charging coming soon

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[galaxyproject/infrastructure-playbook] 5af09f: Set up PSU stratum 1
by GitHub 01 Jun '16

01 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 5af09f869141b06f6922141dc3dddeb9185126dc https://github.com/galaxyproject/infrastructure-playbook/commit/5af09f86914… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-01 (Wed, 01 Jun 2016) Changed paths: A galaxyenv/host_vars/cvmfs1-psu0.galaxyproject.org.yml M galaxyenv/inventory M roles/cvmfs/tasks/stratum0.yml M roles/cvmfs/tasks/stratum1.yml Log Message: ----------- Set up PSU stratum 1

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[galaxyproject/infrastructure-playbook] e4ecc4: Changes for managing CVMFS stratum 0s, add stratum...
by GitHub 01 Jun '16

01 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: e4ecc417bd191c115c7c1704789e89bcb11f8b44 https://github.com/galaxyproject/infrastructure-playbook/commit/e4ecc417bd1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-01 (Wed, 01 Jun 2016) Changed paths: A galaxyenv/host_vars/cvmfs0-tacc0.galaxyproject.org.yml M galaxyenv/inventory M galaxyenv/playbook.yml A galaxyenv/secret_host_vars/cvmfs0-tacc0.galaxyproject.org.yml M roles/cvmfs/defaults/main.yml M roles/cvmfs/tasks/client.yml M roles/cvmfs/tasks/main.yml A roles/cvmfs/tasks/stratum0.yml M roles/cvmfs/tasks/stratum1.yml Log Message: ----------- Changes for managing CVMFS stratum 0s, add stratum 0 @ TACC

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[galaxyproject/galaxy] 6da322: Update Galaxy testing to target latest galaxy-lib.
by GitHub 01 Jun '16

01 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6da322344951bf40d31fff0136bf152d18c6f1f6 https://github.com/galaxyproject/galaxy/commit/6da322344951bf40d31fff0136bf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-31 (Tue, 31 May 2016) Changed paths: M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/verify/__init__.py M test/base/twilltestcase.py A test/functional/tools/checksum.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Update Galaxy testing to target latest galaxy-lib. Incorporates https://github.com/galaxyproject/galaxy-lib/pull/10 which modifies the interface to the test output verification code to allow reuse from within Planemo in both non-tool and non-Galaxy contexts. I also think this represents a better separation of concerns. One upshot of this is that CWL-style checksum verification is now possible from within Galaxy tools - a test case of this is included. Commit: 25a26d8c9c4f21e84e39741c98755f10c4519d8b https://github.com/galaxyproject/galaxy/commit/25a26d8c9c4f21e84e39741c9875… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-06-01 (Wed, 01 Jun 2016) Changed paths: M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/verify/__init__.py M test/base/twilltestcase.py A test/functional/tools/checksum.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #2436 from jmchilton/galaxy_lib_testing_update Update Galaxy testing to target latest galaxy-lib. Compare: https://github.com/galaxyproject/galaxy/compare/835797c4bacf...25a26d8c9c4f

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[galaxyproject/galaxy] 214e75: Only scan the last 16 MB of a job's stderr for slu...
by GitHub 31 May '16

31 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 214e757d81623e9c12d171f3dcfc516c7dcc5e32 https://github.com/galaxyproject/galaxy/commit/214e757d81623e9c12d171f3dcfc… Author: Nate Coraor <nate(a)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/dcb28e095012fef3be769f677fa5… Author: Nate Coraor <nate(a)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/ceb825bea8b28c8908c8a719919b… Author: Dannon Baker <dannon.baker(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/6094990e43f6...ceb825bea8b2

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[galaxyproject/galaxy] 24451e: add and/or correct missing EDAM formats/data to da...
by GitHub 30 May '16

30 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 24451e75d422d5d063c674cee353b6b80a0503e6 https://github.com/galaxyproject/galaxy/commit/24451e75d422d5d063c674cee353… Author: Hervé Ménager <hmenager(a)pasteur.fr> Date: 2016-05-30 (Mon, 30 May 2016) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- add and/or correct missing EDAM formats/data to datatypes. Commit: c450763e137e528392afdf17ad51c92426c267cf https://github.com/galaxyproject/galaxy/commit/c450763e137e528392afdf17ad51… Author: Hervé Ménager <hmenager(a)pasteur.fr> Date: 2016-05-30 (Mon, 30 May 2016) Changed paths: M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/style/less/frame.less M doc/source/dev/faq.rst M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/text.py 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/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py M lib/galaxy/model/migrate/versions/0061_tasks.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/watcher.py A lib/galaxy/tools/verify/__init__.py A lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/asserts/tabular.py A lib/galaxy/tools/verify/asserts/text.py A lib/galaxy/tools/verify/asserts/xml.py A lib/galaxy/tools/verify/test_data.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/workflow/extract.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.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 lib/tool_shed/util/common_util.py M lib/tool_shed/util/tool_dependency_util.py M static/maps/layout/scratchbook.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/ui/ui-frames.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/scratchbook.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/ui/ui-frames.js M static/style/blue/base.css M templates/show_params.mako M templates/webapps/galaxy/workflow/run.mako M test/api/test_tools.py M test/api/test_workflows.py R test/base/asserts/__init__.py R test/base/asserts/tabular.py R test/base/asserts/text.py R test/base/asserts/xml.py R test/base/test_data.py M test/base/twilltestcase.py M test/functional/test_toolbox.py A test/functional/tools/composite_output_tests.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/simple_constructs.yml M test/shed_functional/base/twilltestcase.py M test/unit/managers/test_HistoryManager.py M tools/filters/axt_to_lav.py M tools/stats/gsummary.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: 835797c4bacfdc8b4a95c67a342181c78c17af25 https://github.com/galaxyproject/galaxy/commit/835797c4bacfdc8b4a95c67a3421… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-05-30 (Mon, 30 May 2016) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #2428 from hmenager/dev Correct various EDAM data/format annotations in datatypes Compare: https://github.com/galaxyproject/galaxy/compare/eefc73abae11...835797c4bacf

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[galaxyproject/galaxy] 8aa629: Updates and fixes of the run workflow ui elements ...
by GitHub 28 May '16

28 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8aa629a98290876c7beab374d703b8d9ab24c576 https://github.com/galaxyproject/galaxy/commit/8aa629a98290876c7beab374d703… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-26 (Thu, 26 May 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Updates and fixes of the run workflow ui elements and views Commit: eefc73abae119f4e190af064905072aee9c0edca https://github.com/galaxyproject/galaxy/commit/eefc73abae119f4e190af0649050… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-28 (Sat, 28 May 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #2416 from guerler/tool_composite_000 Updates and fixes for the run workflow ui elements Compare: https://github.com/galaxyproject/galaxy/compare/3b73bb30382a...eefc73abae11

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[galaxyproject/galaxy] 3afe31: minor docs touch
by GitHub 27 May '16

27 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3afe31649fd64a9f5641584ec5f3a75e12b72e09 https://github.com/galaxyproject/galaxy/commit/3afe31649fd64a9f5641584ec5f3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-27 (Fri, 27 May 2016) Changed paths: M doc/source/dev/faq.rst Log Message: ----------- minor docs touch Commit: 3b73bb30382a19ee69632efe76815b575fb1cb40 https://github.com/galaxyproject/galaxy/commit/3b73bb30382a19ee69632efe7681… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-27 (Fri, 27 May 2016) Changed paths: M doc/source/dev/faq.rst Log Message: ----------- Merge pull request #2427 from martenson/minor-docs minor docs touch Compare: https://github.com/galaxyproject/galaxy/compare/26ea3404cec5...3b73bb30382a

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[galaxyproject/galaxy] a27e86: wrap bare str raises with generic Exception()
by GitHub 26 May '16

26 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: a27e86786ad031eafcbfeb39ffdadf71d80dcfad https://github.com/galaxyproject/galaxy/commit/a27e86786ad031eafcbfeb39ffda… Author: Martin Cech <cech.marten(a)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/fe64a8198bca75f2e535efc7c381… Author: Martin Cech <cech.marten(a)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/6094990e43f6510833395885d234… Author: John Chilton <jmchilton(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/c63bf911bc9c...6094990e43f6

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[galaxyproject/galaxy] 939a10: Fix to 4a61a4c: add hids for dataset inputs
by GitHub 26 May '16

26 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 939a107f37aabe18bf42265c1469da846bfcaee8 https://github.com/galaxyproject/galaxy/commit/939a107f37aabe18bf42265c1469… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Fix to 4a61a4c: add hids for dataset inputs Commit: 26ea3404cec55c882a7064774ced31ed5a5514ad https://github.com/galaxyproject/galaxy/commit/26ea3404cec55c882a7064774ced… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-26 (Thu, 26 May 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Merge pull request #2415 from carlfeberhard/fix.show-params-hid Fix to 4a61a4c: add hids for dataset inputs Compare: https://github.com/galaxyproject/galaxy/compare/ef417464c7cf...26ea3404cec5

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[galaxyproject/galaxy] d72eee: wrap bare str raises with generic Exception()
by GitHub 26 May '16

26 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d72eee3d4a136e99ff3bb1927bb3a4ad1a3e4b0e https://github.com/galaxyproject/galaxy/commit/d72eee3d4a136e99ff3bb1927bb3… Author: Martin Cech <cech.marten(a)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: 125453707588cab9157aba497803f89f700971e5 https://github.com/galaxyproject/galaxy/commit/125453707588cab9157aba497803… Author: Martin Cech <cech.marten(a)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: ef417464c7cf25b5c9a4526ed31817d80553420a https://github.com/galaxyproject/galaxy/commit/ef417464c7cf25b5c9a4526ed318… Author: Dannon Baker <dannon.baker(a)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 #2421 from martenson/wrap-str-raises wrap bare str raises with generic Exception() Compare: https://github.com/galaxyproject/galaxy/compare/35da049d4299...ef417464c7cf

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[galaxyproject/galaxy] 03a92a: Python3: use log.warning() instead of deprecated l...
by GitHub 26 May '16

26 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 03a92abdb65a040b0feaf4ef8979ff24b9537bd6 https://github.com/galaxyproject/galaxy/commit/03a92abdb65a040b0feaf4ef8979… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-26 (Thu, 26 May 2016) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/tags.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py M lib/galaxy/model/migrate/versions/0061_tasks.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/util/__init__.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/workflow/extract.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/tool_dependency_util.py Log Message: ----------- Python3: use log.warning() instead of deprecated log.warn() $ python3 -Wd -c 'import logging; logging.warn("foo")' -c:1: DeprecationWarning: The 'warn' function is deprecated, use 'warning' instead WARNING:root:foo Commit: 35da049d4299e84db09dc46f9d23524acb15e35c https://github.com/galaxyproject/galaxy/commit/35da049d4299e84db09dc46f9d23… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-26 (Thu, 26 May 2016) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/tags.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py M lib/galaxy/model/migrate/versions/0061_tasks.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/util/__init__.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/workflow/extract.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/tool_dependency_util.py Log Message: ----------- Merge pull request #2420 from nsoranzo/log_warn Python3: use log.warning() instead of deprecated log.warn() Compare: https://github.com/galaxyproject/galaxy/compare/1453dbdb13fd...35da049d4299

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[galaxyproject/galaxy] ee314e: Update galaxy-lib related modules to latest in tha...
by GitHub 26 May '16

26 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ee314ee89b9a657a0845246b3dc1a5df785b4b50 https://github.com/galaxyproject/galaxy/commit/ee314ee89b9a657a0845246b3dc1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/verify/__init__.py Log Message: ----------- Update galaxy-lib related modules to latest in that project. Commit: 1453dbdb13fd2be177bcee58dfc47f7a4e8224f1 https://github.com/galaxyproject/galaxy/commit/1453dbdb13fd2be177bcee58dfc4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-26 (Thu, 26 May 2016) Changed paths: M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/verify/__init__.py Log Message: ----------- Merge pull request #2414 from jmchilton/lib-fix Update galaxy-lib related modules to latest in that project. Compare: https://github.com/galaxyproject/galaxy/compare/4eeb73ec8c84...1453dbdb13fd

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[galaxyproject/infrastructure-playbook] 5ea96f: Update access list
by GitHub 26 May '16

26 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 5ea96f95929f2c6c4408b34fba2cafc1c035e126 https://github.com/galaxyproject/infrastructure-playbook/commit/5ea96f95929… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-26 (Thu, 26 May 2016) Changed paths: M galaxyenv/secret_host_vars/delirium.galaxyproject.org.yml Log Message: ----------- Update access list

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[galaxyproject/usegalaxy-playbook] ff7695: Pulsar for Jetstream @ IU, also install Paste to f...
by GitHub 26 May '16

26 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ff769585ecdf0f79b23cdf47829f003c4a1980d4 https://github.com/galaxyproject/usegalaxy-playbook/commit/ff769585ecdf0f79… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-26 (Thu, 26 May 2016) Changed paths: A production/host_vars/jetstream-iu0.galaxyproject.org.yml M production/host_vars/jetstream-tacc0.galaxyproject.org.yml M production/inventory A stage/host_vars/jetstream-iu0.galaxyproject.org.yml M stage/host_vars/jetstream-tacc0.galaxyproject.org.yml M stage/inventory Log Message: ----------- Pulsar for Jetstream @ IU, also install Paste to fix Pulsar logging

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[galaxyproject/galaxy] 4bfcce: Raise Exception if watch_tools has an unrecognized...
by GitHub 26 May '16

26 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4bfcce0d563f25d88d88baa49be6fbdb324889ff https://github.com/galaxyproject/galaxy/commit/4bfcce0d563f25d88d88baa49be6… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-26 (Thu, 26 May 2016) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Raise Exception if watch_tools has an unrecognized value Also do not log message "Watchdog library unavailable" if watch_tools is False Commit: 4eeb73ec8c84fa8143a1232a9c88aa48b151afd9 https://github.com/galaxyproject/galaxy/commit/4eeb73ec8c84fa8143a1232a9c88… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-26 (Thu, 26 May 2016) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge pull request #2418 from nsoranzo/toolbox_watcher Raise Exception if watch_tools has an unrecognized value Compare: https://github.com/galaxyproject/galaxy/compare/27b70ca9849b...4eeb73ec8c84

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[galaxyproject/galaxy] be97d7: Replace frame dictionary with regular view
by GitHub 26 May '16

26 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: be97d7e6db1d963c64dceeb06c68440500177ba5 https://github.com/galaxyproject/galaxy/commit/be97d7e6db1d963c64dceeb06c68… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/style/less/frame.less M static/maps/layout/scratchbook.js.map M static/maps/mvc/ui/ui-frames.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/scratchbook.js M static/scripts/mvc/ui/ui-frames.js M static/style/blue/base.css Log Message: ----------- Replace frame dictionary with regular view Commit: b9e2983e909cc74509214e864820467a256ea336 https://github.com/galaxyproject/galaxy/commit/b9e2983e909cc74509214e864820… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/style/less/frame.less M static/maps/mvc/ui/ui-frames.js.map M static/scripts/mvc/ui/ui-frames.js Log Message: ----------- Remove grid lock feature Commit: 53fa566a54eb8d6be69e769ebd9799a9d392db3f https://github.com/galaxyproject/galaxy/commit/53fa566a54eb8d6be69e769ebd97… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-frames.js M static/maps/mvc/ui/ui-frames.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-frames.js M static/style/blue/base.css Log Message: ----------- Use regular initialization from frame shadow view Commit: 44bd042624602648d87a24805e94e110102286ed https://github.com/galaxyproject/galaxy/commit/44bd042624602648d87a24805e94… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/style/less/frame.less M static/maps/layout/scratchbook.js.map M static/maps/mvc/ui/ui-frames.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/scratchbook.js M static/scripts/mvc/ui/ui-frames.js M static/style/blue/base.css Log Message: ----------- Add support for optional header items/icons Commit: e16c3f34f39d0705a26081eafc5c321d6aca56c9 https://github.com/galaxyproject/galaxy/commit/e16c3f34f39d0705a26081eafc5c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-frames.js M static/maps/mvc/ui/ui-frames.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-frames.js Log Message: ----------- Remove unused class variables, reduce indention Commit: 64cb97cfc90fc93e550c1b74e1c62a9a0d4e656c https://github.com/galaxyproject/galaxy/commit/64cb97cfc90fc93e550c1b74e1c6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/ui/ui-frames.js M static/maps/layout/scratchbook.js.map M static/maps/mvc/ui/ui-frames.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/scratchbook.js M static/scripts/mvc/ui/ui-frames.js Log Message: ----------- Parse view instead of content dom on click Commit: 617cd2de82caca3f174479d3602bb45236da5175 https://github.com/galaxyproject/galaxy/commit/617cd2de82caca3f174479d3602b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/style/less/frame.less M static/maps/layout/scratchbook.js.map M static/maps/mvc/ui/ui-frames.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/scratchbook.js M static/scripts/mvc/ui/ui-frames.js M static/style/blue/base.css Log Message: ----------- Add event handlers to navigate through history Commit: a12c1cb45ba3026c2ff6d8cc9d70c622e26718f6 https://github.com/galaxyproject/galaxy/commit/a12c1cb45ba3026c2ff6d8cc9d70… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M client/galaxy/scripts/layout/scratchbook.js M static/maps/layout/scratchbook.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/scratchbook.js Log Message: ----------- Cache histories individually Commit: 197f2283f92ed851c8a8254eb6c020b90023188d https://github.com/galaxyproject/galaxy/commit/197f2283f92ed851c8a8254eb6c0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/managers/histories.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py A lib/galaxy/tools/verify/__init__.py A lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/asserts/tabular.py A lib/galaxy/tools/verify/asserts/text.py A lib/galaxy/tools/verify/asserts/xml.py A lib/galaxy/tools/verify/test_data.py M static/maps/mvc/history/history-model.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/history/history-model.js M templates/show_params.mako M test/api/test_tools.py M test/api/test_workflows.py R test/base/asserts/__init__.py R test/base/asserts/tabular.py R test/base/asserts/text.py R test/base/asserts/xml.py R test/base/test_data.py M test/base/twilltestcase.py M test/functional/test_toolbox.py A test/functional/tools/composite_output_tests.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/simple_constructs.yml M test/shed_functional/base/twilltestcase.py M test/unit/managers/test_HistoryManager.py M tools/stats/gsummary.xml Log Message: ----------- Merge branch 'dev' into scratchbook_slider_000 Commit: 27b70ca9849b241c93958c4b18af38ec576cbd3e https://github.com/galaxyproject/galaxy/commit/27b70ca9849b241c93958c4b18af… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-05-26 (Thu, 26 May 2016) Changed paths: M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/style/less/frame.less M static/maps/layout/scratchbook.js.map M static/maps/mvc/ui/ui-frames.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/scratchbook.js M static/scripts/mvc/ui/ui-frames.js M static/style/blue/base.css Log Message: ----------- Merge pull request #2396 from guerler/scratchbook_slider_000 Add history navigation options for dataset frames to scratch book Compare: https://github.com/galaxyproject/galaxy/compare/50359e1633b5...27b70ca9849b

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[galaxyproject/galaxy] 66947c: Provide backward-compatible galaxy.datatypes.check...
by GitHub 25 May '16

25 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 66947c20ef2c0db3532d7e4f3edc5897d7d75ab7 https://github.com/galaxyproject/galaxy/commit/66947c20ef2c0db3532d7e4f3edc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-23 (Mon, 23 May 2016) Changed paths: A lib/galaxy/datatypes/checkers.py M lib/galaxy/util/checkers.py Log Message: ----------- Provide backward-compatible galaxy.datatypes.checkers module. xref http://dev.list.galaxyproject.org/STACKS-error-td4669428.html Commit: 5fbb65e5033d23b9751251a4a935b4c76ffd65d5 https://github.com/galaxyproject/galaxy/commit/5fbb65e5033d23b9751251a4a935… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-24 (Tue, 24 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Catch all exceptions in slurm's _complete_terminal_job() to prevent looping job completion Commit: b6d65da83d77167482a3fe3a706c249abad6dbfa https://github.com/galaxyproject/galaxy/commit/b6d65da83d77167482a3fe3a706c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-24 (Tue, 24 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Fix linting error Commit: 2a29e92ef9d8e560988d6e64d06c5cbbf79098a1 https://github.com/galaxyproject/galaxy/commit/2a29e92ef9d8e560988d6e64d06c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-24 (Tue, 24 May 2016) Changed paths: M lib/galaxy/managers/histories.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- API, history: fix order in most_recently_used - Fix ascending order used in HistoryManager.most_recent to descending - Slightly update the docs to reflect actual value better - Add tests Commit: 47a65160960003244091d4fd441111c257e9e8d9 https://github.com/galaxyproject/galaxy/commit/47a65160960003244091d4fd4411… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/managers/histories.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge pull request #2407 from carlfeberhard/fix.most_recently_used [16.01] API, history: fix order in most_recently_used Commit: 7dcf850ed5203196371fa3d20800b0b864c01158 https://github.com/galaxyproject/galaxy/commit/7dcf850ed5203196371fa3d20800… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2402 from natefoo/slurm-fixes [16.04] Catch all exceptions in slurm's _complete_terminal_job() to prevent looping job completion Commit: 5db5e1395880876ac3066fc91397e7cb1618ea62 https://github.com/galaxyproject/galaxy/commit/5db5e1395880876ac3066fc91397… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/managers/histories.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: test/unit/managers/test_HistoryManager.py Commit: 71f9d9621640ca77880a879da3a149467f5ec934 https://github.com/galaxyproject/galaxy/commit/71f9d9621640ca77880a879da3a1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/datatypes/checkers.py M lib/galaxy/util/checkers.py Log Message: ----------- Remove HTML_CHECK_LINES from checkers export. As suggested by @nsoranzo and @dannon, we will restore if and only if someone finds a datatype that uses it. Commit: c63bf911bc9cae4d0400a3f3fad03402c3f7a18a https://github.com/galaxyproject/galaxy/commit/c63bf911bc9cae4d0400a3f3fad0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: A lib/galaxy/datatypes/checkers.py M lib/galaxy/util/checkers.py Log Message: ----------- Merge pull request #2389 from jmchilton/checkers_restore [16.04] Provide backward compatible galaxy.datatypes.checkers module... Commit: 5a97b8feac49df3f1e9fe0b2e0645b9240eb8291 https://github.com/galaxyproject/galaxy/commit/5a97b8feac49df3f1e9fe0b2e064… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: A lib/galaxy/datatypes/checkers.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/managers/histories.py M lib/galaxy/util/checkers.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge branch 'release_16.04' Compare: https://github.com/galaxyproject/galaxy/compare/ac5a328e5f56...5a97b8feac49

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[galaxyproject/galaxy] 66947c: Provide backward-compatible galaxy.datatypes.check...
by GitHub 25 May '16

25 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 66947c20ef2c0db3532d7e4f3edc5897d7d75ab7 https://github.com/galaxyproject/galaxy/commit/66947c20ef2c0db3532d7e4f3edc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-23 (Mon, 23 May 2016) Changed paths: A lib/galaxy/datatypes/checkers.py M lib/galaxy/util/checkers.py Log Message: ----------- Provide backward-compatible galaxy.datatypes.checkers module. xref http://dev.list.galaxyproject.org/STACKS-error-td4669428.html Commit: 71f9d9621640ca77880a879da3a149467f5ec934 https://github.com/galaxyproject/galaxy/commit/71f9d9621640ca77880a879da3a1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/datatypes/checkers.py M lib/galaxy/util/checkers.py Log Message: ----------- Remove HTML_CHECK_LINES from checkers export. As suggested by @nsoranzo and @dannon, we will restore if and only if someone finds a datatype that uses it. Commit: c63bf911bc9cae4d0400a3f3fad03402c3f7a18a https://github.com/galaxyproject/galaxy/commit/c63bf911bc9cae4d0400a3f3fad0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: A lib/galaxy/datatypes/checkers.py M lib/galaxy/util/checkers.py Log Message: ----------- Merge pull request #2389 from jmchilton/checkers_restore [16.04] Provide backward compatible galaxy.datatypes.checkers module... Commit: 50359e1633b5ba3c19360cb4ed2d690ea69dd412 https://github.com/galaxyproject/galaxy/commit/50359e1633b5ba3c19360cb4ed2d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: A lib/galaxy/datatypes/checkers.py M lib/galaxy/util/checkers.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/f0a1bc8cbdfa...50359e1633b5

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[galaxyproject/galaxy] 66947c: Provide backward-compatible galaxy.datatypes.check...
by GitHub 25 May '16

25 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 66947c20ef2c0db3532d7e4f3edc5897d7d75ab7 https://github.com/galaxyproject/galaxy/commit/66947c20ef2c0db3532d7e4f3edc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-23 (Mon, 23 May 2016) Changed paths: A lib/galaxy/datatypes/checkers.py M lib/galaxy/util/checkers.py Log Message: ----------- Provide backward-compatible galaxy.datatypes.checkers module. xref http://dev.list.galaxyproject.org/STACKS-error-td4669428.html Commit: 71f9d9621640ca77880a879da3a149467f5ec934 https://github.com/galaxyproject/galaxy/commit/71f9d9621640ca77880a879da3a1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/datatypes/checkers.py M lib/galaxy/util/checkers.py Log Message: ----------- Remove HTML_CHECK_LINES from checkers export. As suggested by @nsoranzo and @dannon, we will restore if and only if someone finds a datatype that uses it. Commit: c63bf911bc9cae4d0400a3f3fad03402c3f7a18a https://github.com/galaxyproject/galaxy/commit/c63bf911bc9cae4d0400a3f3fad0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: A lib/galaxy/datatypes/checkers.py M lib/galaxy/util/checkers.py Log Message: ----------- Merge pull request #2389 from jmchilton/checkers_restore [16.04] Provide backward compatible galaxy.datatypes.checkers module... Compare: https://github.com/galaxyproject/galaxy/compare/5db5e1395880...c63bf911bc9c

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[galaxyproject/infrastructure-playbook] c5c03b: Run Pulsar with supervisor on Jetstream
by GitHub 25 May '16

25 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c5c03b561aa331a1029a5b4d7775370c4d4b941a https://github.com/galaxyproject/infrastructure-playbook/commit/c5c03b561aa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M jetstreamiuenv/group_vars/controllers.yml M jetstreamiuenv/playbook.yml A jetstreamiuenv/templates/supervisor/pulsar.j2 M jetstreamtaccenv/group_vars/controllers.yml A jetstreamtaccenv/templates/supervisor/pulsar.j2 Log Message: ----------- Run Pulsar with supervisor on Jetstream

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[galaxyproject/infrastructure-playbook] 6a9f81: Remote Pulsar stuff for Jetstream @ IU
by GitHub 25 May '16

25 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6a9f8174bf44a68b8c7a7010a984af4793d64835 https://github.com/galaxyproject/infrastructure-playbook/commit/6a9f8174bf4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M jetstreamiuenv/group_vars/controllers.yml M jetstreamiuenv/inventory M jetstreamiuenv/playbook.yml Log Message: ----------- Remote Pulsar stuff for Jetstream @ IU

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[galaxyproject/galaxy] 2e45e7: UI, history: correctly handle index API defaults
by GitHub 25 May '16

25 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2e45e77fa82b723ebb5dc6c398891c3a061c6961 https://github.com/galaxyproject/galaxy/commit/2e45e77fa82b723ebb5dc6c39889… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M static/maps/mvc/history/history-model.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/history/history-model.js Log Message: ----------- UI, history: correctly handle index API defaults Bypasses the histories.index default `deleted=False` flag when using HistoryCollection to fetch with `includeDeleted`. Commit: f0a1bc8cbdfa796e5293b66dbcc846ad6f624aa1 https://github.com/galaxyproject/galaxy/commit/f0a1bc8cbdfa796e5293b66dbcc8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M static/maps/mvc/history/history-model.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/history/history-model.js Log Message: ----------- Merge pull request #2413 from carlfeberhard/fix.history-collection UI, history: correctly handle index API defaults Compare: https://github.com/galaxyproject/galaxy/compare/81702e7fbaec...f0a1bc8cbdfa

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[galaxyproject/galaxy] 2eee6e: add is_target_available() to conda utils
by GitHub 25 May '16

25 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2eee6e2abc52a1ba37b4219d590bba023885ad02 https://github.com/galaxyproject/galaxy/commit/2eee6e2abc52a1ba37b4219d590b… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-05-23 (Mon, 23 May 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- add is_target_available() to conda utils Commit: 53604369f21f6adb75e58909158d49f9deed54bc https://github.com/galaxyproject/galaxy/commit/53604369f21f6adb75e58909158d… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-05-23 (Mon, 23 May 2016) Changed paths: M lib/galaxy/tools/deps/commands.py Log Message: ----------- stdin and stdout needs a PIPE to retrive the stdout Commit: 0b3832b952bb47fa03486cad2fcd5b6f7daf3e0e https://github.com/galaxyproject/galaxy/commit/0b3832b952bb47fa03486cad2fcd… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-05-24 (Tue, 24 May 2016) Changed paths: M lib/galaxy/tools/deps/commands.py Log Message: ----------- Fix bad merge. Commit: 81702e7fbaece36a5ddbeb7c8ca9456c8b9b64f7 https://github.com/galaxyproject/galaxy/commit/81702e7fbaece36a5ddbeb7c8ca9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-25 (Wed, 25 May 2016) Changed paths: M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #2395 from bgruening/conda_search Add conda search function Compare: https://github.com/galaxyproject/galaxy/compare/b16ad40bee21...81702e7fbaec

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