May 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 9d7c8a: Update Main nginx config for 18.05 changes to plug...
by GitHub 01 May '18

01 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9d7c8ab043ad5c6468b2bcbc168ecb4ed24c039d https://github.com/galaxyproject/usegalaxy-playbook/commit/9d7c8ab043ad5c64… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M env/main/templates/nginx/usegalaxy.j2 Log Message: ----------- Update Main nginx config for 18.05 changes to plugin static content layout **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] d07902: Add hostname metric
by GitHub 01 May '18

01 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d0790234bb8cd01875704dd53877ccb16fcc7bd2 https://github.com/galaxyproject/galaxy/commit/d0790234bb8cd01875704dd53877… Author: E Rasche <hxr(a)hx42.org> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M config/job_metrics_conf.xml.sample A lib/galaxy/jobs/metrics/instrumenters/hostname.py Log Message: ----------- Add hostname metric Commit: bd7cd04518a08c695b75cd922b7af006338a8730 https://github.com/galaxyproject/galaxy/commit/bd7cd04518a08c695b75cd922b7a… Author: E Rasche <hxr(a)hx42.org> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M config/job_metrics_conf.xml.sample M lib/galaxy/jobs/metrics/instrumenters/hostname.py Log Message: ----------- address review comments Commit: 543d5b2138473fe6936420b6d85dd8ce9c2a6629 https://github.com/galaxyproject/galaxy/commit/543d5b2138473fe6936420b6d85d… Author: E Rasche <hxr(a)hx42.org> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/cgroup.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/metrics/instrumenters/uname.py Log Message: ----------- also change import lines here Commit: 370590f9ed7f7177e10f0762b9c84398c6eb4cad https://github.com/galaxyproject/galaxy/commit/370590f9ed7f7177e10f0762b9c8… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/collectl.py Log Message: ----------- Fix import order Commit: 4c22203c8097b1b5bcb40864fdccf4df27ba7c45 https://github.com/galaxyproject/galaxy/commit/4c22203c8097b1b5bcb40864fdcc… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M config/job_metrics_conf.xml.sample M lib/galaxy/jobs/metrics/instrumenters/cgroup.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py A lib/galaxy/jobs/metrics/instrumenters/hostname.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/metrics/instrumenters/uname.py Log Message: ----------- Merge pull request #6021 from erasche/hostname Add hostname metric Compare: https://github.com/galaxyproject/galaxy/compare/0fac69bd5925...4c22203c8097 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] b56f28: update Test
by GitHub 01 May '18

01 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b56f28c6bbf2b5127e547286004dc804000e98c8 https://github.com/galaxyproject/usegalaxy-playbook/commit/b56f28c6bbf2b512… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- update Test **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 20c3d0: Fix run_tests.sh to respect args after --.
by GitHub 01 May '18

01 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 20c3d09d85bb29d7a1ff299abc7c93dbc6c6b772 https://github.com/galaxyproject/galaxy/commit/20c3d09d85bb29d7a1ff299abc7c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M run_tests.sh Log Message: ----------- Fix run_tests.sh to respect args after --. Bug fix because we are clearly parsing it above and then ignoring the arguments afterward anyway. This will allow me to divide up the Selenium tests without any changes using Jenkins' configuration matrix plugin I think. Commit: 8842e8d4512782db9c941098d091d1d8827eb868 https://github.com/galaxyproject/galaxy/commit/8842e8d4512782db9c941098d091… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #6025 from jmchilton/release_18.05_broken_tests [18.05] Fix run_tests.sh to respect args after --. Compare: https://github.com/galaxyproject/galaxy/compare/4043e1020c76...8842e8d45127 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] fad039: Disable broken tests.
by GitHub 01 May '18

01 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: fad0392166b6ff24cae0767e9fa6f9c25e28c10f https://github.com/galaxyproject/galaxy/commit/fad0392166b6ff24cae0767e9fa6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Disable broken tests. Commit: 4043e1020c765759ade1a762ec98751b1d263e95 https://github.com/galaxyproject/galaxy/commit/4043e1020c765759ade1a762ec98… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Merge pull request #6024 from jmchilton/release_18.05_broken_tests [18.05] Disable broken tests workflow annotation tests. Compare: https://github.com/galaxyproject/galaxy/compare/7f0df84ff70a...4043e1020c76

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[galaxyproject/galaxy] 54e89a: Fix broken imports
by GitHub 01 May '18

01 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 54e89ae4983490da43ab3a1035e2df7f73e11d09 https://github.com/galaxyproject/galaxy/commit/54e89ae4983490da43ab3a1035e2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/job/slurm.py M lib/galaxy/jobs/runners/util/cli/job/torque.py Log Message: ----------- Fix broken imports `from galaxy.util import enum` probably never worked. Commit: 65cb42d8d8b45d2d4bc879864bc929fa123a3c16 https://github.com/galaxyproject/galaxy/commit/65cb42d8d8b45d2d4bc879864bc9… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/job/torque.py Log Message: ----------- Fix PBS status reporting Without this commit only very short jobs completed successfully, because the status was always set to complete. This was because the status returned by qstat contains leading spaces before the `job_state = Q` part, so I'm adding a `.strip()`. Imported from https://github.com/galaxyproject/pulsar/commit/9acc5637780e553c3a9d0efb9cf7… Commit: d659058385c3ed52ed4cef43dd277f9917440753 https://github.com/galaxyproject/galaxy/commit/d659058385c3ed52ed4cef43dd27… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Simplify imports Commit: 0fac69bd59256391d2e99200e4c2915d1e14ff3f https://github.com/galaxyproject/galaxy/commit/0fac69bd59256391d2e99200e4c2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/job/slurm.py M lib/galaxy/jobs/runners/util/cli/job/torque.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #6014 from nsoranzo/fix_imports Fix some imports Compare: https://github.com/galaxyproject/galaxy/compare/740e1fc05c78...0fac69bd5925

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[galaxyproject/galaxy] aad435: rename the style for the renamed class
by GitHub 01 May '18

01 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: aad435e2655c252934b9f98a8c6962f9038c56ac https://github.com/galaxyproject/galaxy/commit/aad435e2655c252934b9f98a8c69… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- rename the style for the renamed class Commit: 7f0df84ff70a8062a8f12c23e60d21ab80ff77ac https://github.com/galaxyproject/galaxy/commit/7f0df84ff70a8062a8f12c23e60d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6019 from martenson/fix-paginationstyle [18.05] Fix grid pagination style Compare: https://github.com/galaxyproject/galaxy/compare/3ee40bfe5308...7f0df84ff70a

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