January 2019 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 42052d: Do not skip the client build in dockerized seleniu...
by Dannon 29 Jan '19

29 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 42052d6b8d62df625a099141364a2c5dad8ed0b2 https://github.com/galaxyproject/galaxy/commit/42052d6b8d62df625a099141364a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-29 (Tue, 29 Jan 2019) Changed paths: M .ci/jenkins/selenium-py3/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M run_tests.sh Log Message: ----------- Do not skip the client build in dockerized selenium tests This allows the removal of the `docker run` of `make client-production-maps`, which was run on a docker image for the wrong version of `node`. Commit: 884c7962ce48edaca18f7aab9f04d375b4a8d084 https://github.com/galaxyproject/galaxy/commit/884c7962ce48edaca18f7aab9f04… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-01-29 (Tue, 29 Jan 2019) Changed paths: M .ci/jenkins/selenium-py3/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M run_tests.sh Log Message: ----------- Merge pull request #7280 from nsoranzo/selenium_client_build Do not skip the client build in dockerized selenium tests Compare: https://github.com/galaxyproject/galaxy/compare/8cb4ee92a67c...884c7962ce48

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[galaxyproject/galaxy] d83db6: Stop with tool migrations by default, they are not...
by Marius van den Beek 29 Jan '19

29 Jan '19

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: d83db6a53796137c8ccc96efe3b40f3f3f88f694 https://github.com/galaxyproject/galaxy/commit/d83db6a53796137c8ccc96efe3b4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-27 (Sun, 27 Jan 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Stop with tool migrations by default, they are not needed in modern Galaxies... ... and even problematic in some ways. Commit: c8b3d5e4c415514ef626b2009791476d51f9cf9b https://github.com/galaxyproject/galaxy/commit/c8b3d5e4c415514ef626b2009791… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-01-29 (Tue, 29 Jan 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #7275 from jmchilton/1901_migrate_tools [18.09] Stop tool migrations checking by default... Compare: https://github.com/galaxyproject/galaxy/compare/6a660e9893b6...c8b3d5e4c415

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[galaxyproject/galaxy] d95ba2: Fix saving imported subworkflows
by GitHub 28 Jan '19

28 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d95ba26a24ce2960bc565f5a021338a9ec68d061 https://github.com/galaxyproject/galaxy/commit/d95ba26a24ce2960bc565f5a0213… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-23 (Wed, 23 Jan 2019) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Fix saving imported subworkflows whose child-workflow is included more than once. Fixes https://github.com/galaxyproject/galaxy/issues/7261 and probably https://github.com/galaxyproject/galaxy/issues/6032 Commit: 8cb4ee92a67c86a29a88acb350b984c4bda5e4ca https://github.com/galaxyproject/galaxy/commit/8cb4ee92a67c86a29a88acb350b9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-28 (Mon, 28 Jan 2019) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #7262 from mvdbeek/fix_saving_imported_subworkflows Fix saving imported subworkflows Compare: https://github.com/galaxyproject/galaxy/compare/0b95564789c3...8cb4ee92a67c **NOTE:** GitHub Services has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ We will provide an alternative path for the email notifications by January 31st, 2019.

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[galaxyproject/ansible-galaxy]
by GitHub 27 Jan '19

27 Jan '19

Branch: refs/tags/0.8.2 Home: https://github.com/galaxyproject/ansible-galaxy **NOTE:** GitHub Services has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ We will provide an alternative path for the email notifications by January 31st, 2019.

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[galaxyproject/ansible-galaxy] 971f7d: Also trigger restarts on changes to galaxy_config_...
by GitHub 27 Jan '19

27 Jan '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 971f7dd5b063d464b662b1f1816a70ab84a2a296 https://github.com/galaxyproject/ansible-galaxy/commit/971f7dd5b063d464b662… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-01-27 (Sun, 27 Jan 2019) Changed paths: M tasks/static_setup.yml Log Message: ----------- Also trigger restarts on changes to galaxy_config_files and galaxy_config_templates **NOTE:** GitHub Services has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ We will provide an alternative path for the email notifications by January 31st, 2019.

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[galaxyproject/ansible-galaxy]
by GitHub 27 Jan '19

27 Jan '19

Branch: refs/tags/0.8.1 Home: https://github.com/galaxyproject/ansible-galaxy **NOTE:** GitHub Services has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ We will provide an alternative path for the email notifications by January 31st, 2019.

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[galaxyproject/ansible-galaxy] 2cbee7: You can't override a handler, but you can template...
by GitHub 27 Jan '19

27 Jan '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 2cbee7edd4d9fa5bab6a5fd53487d239b529dc15 https://github.com/galaxyproject/ansible-galaxy/commit/2cbee7edd4d9fa5bab6a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-01-27 (Sun, 27 Jan 2019) Changed paths: M README.md M handlers/main.yml M tasks/clone.yml M tasks/static_setup.yml Log Message: ----------- You can't override a handler, but you can template a notification name. So finally you can at least write your own handler for restarting Galaxy Commit: f2ac9e9a60abf554d63a87db603b56753dcd3d55 https://github.com/galaxyproject/ansible-galaxy/commit/f2ac9e9a60abf554d63a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-01-27 (Sun, 27 Jan 2019) Changed paths: M tasks/dependencies.yml Log Message: ----------- Stop reporting changed when getting conditional deps Compare: https://github.com/galaxyproject/ansible-galaxy/compare/26eabd0bb3ce...f2ac… **NOTE:** GitHub Services has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ We will provide an alternative path for the email notifications by January 31st, 2019.

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[galaxyproject/ansible-pulsar] a4717d: Add dependency_resolvers_conf.xml
by GitHub 27 Jan '19

27 Jan '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-pulsar Commit: a4717da7b73ca2b2b6d53e2e930a87aa30a1bcb9 https://github.com/galaxyproject/ansible-pulsar/commit/a4717da7b73ca2b2b6d5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-01-27 (Sun, 27 Jan 2019) Changed paths: M tasks/main.yml A templates/dependency_resolvers_conf.xml.j2 Log Message: ----------- Add dependency_resolvers_conf.xml **NOTE:** GitHub Services has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ We will provide an alternative path for the email notifications by January 31st, 2019.

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[galaxyproject/ansible-pulsar] 3f1d16: Didn't notice that was completely disabling option...
by GitHub 27 Jan '19

27 Jan '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-pulsar Commit: 3f1d1643a182ece01f37f63a62d056dc3afd3e4d https://github.com/galaxyproject/ansible-pulsar/commit/3f1d1643a182ece01f37… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-01-27 (Sun, 27 Jan 2019) Changed paths: M tasks/main.yml Log Message: ----------- Didn't notice that was completely disabling optional dependencies. Disabling the environment stuff for now since it's broken anyway. **NOTE:** GitHub Services has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ We will provide an alternative path for the email notifications by January 31st, 2019.

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[galaxyproject/ansible-pulsar] f4917e: Work around an inscrutible error:
by GitHub 27 Jan '19

27 Jan '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-pulsar Commit: f4917e3e63e117f2d168569c9d0a87c665fca2ee https://github.com/galaxyproject/ansible-pulsar/commit/f4917e3e63e117f2d168… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-01-27 (Sun, 27 Jan 2019) Changed paths: M defaults/main.yml M tasks/main.yml Log Message: ----------- Work around an inscrutible error: fatal: [1.1.1.1]: FAILED! => {"msg": "The field 'environment' has an invalid value, which includes an undefined variable. The error was: 'list object' has no attribute 'split'\n\nThe error appears to have been in '/roles/galaxyproject.pulsar/tasks/main.yml': line 49, column 3, but may\nbe elsewhere in the file depending on the exact syntax problem.\n\nThe offending line appears to be:\n\n\n- name: Install Pulsar dependencies (optional)\n ^ here\n"} **NOTE:** GitHub Services has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ We will provide an alternative path for the email notifications by January 31st, 2019.

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