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

[galaxyproject/usegalaxy-playbook] 1dd2f3: include one column of cards and one of twitter
by GitHub 12 Oct '18

12 Oct '18

Branch: refs/heads/new-welcome Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1dd2f3d65e621a15c111be0166f2ca559f2fa488 https://github.com/galaxyproject/usegalaxy-playbook/commit/1dd2f3d65e621a15… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M env/common/templates/galaxy/static/welcome.html.j2 Log Message: ----------- include one column of cards and one of twitter **NOTE:** This service has 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] 7246d5: Update Test
by GitHub 12 Oct '18

12 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7246d5f669b9cf58d6f71a5d4ebd11993daf05b3 https://github.com/galaxyproject/usegalaxy-playbook/commit/7246d5f669b9cf58… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test Commit: 3223a978e35a2140713d147c10d95d8f65d61021 https://github.com/galaxyproject/usegalaxy-playbook/commit/3223a978e35a2140… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main Commit: 0257084d6910b8d01759ea7f91a09c1a00093d1e https://github.com/galaxyproject/usegalaxy-playbook/commit/0257084d6910b8d0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M env/main/group_vars/galaxyservers/vault.yml Log Message: ----------- Update admin users Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/1f66079a08f4...… **NOTE:** This service has 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] d791a2: Revert selective metadata flushing - seems to brea...
by GitHub 12 Oct '18

12 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d791a2c80f3290d66c2252f29981a16a4459661b https://github.com/galaxyproject/galaxy/commit/d791a2c80f3290d66c2252f29981… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/model/metadata.py Log Message: ----------- Revert selective metadata flushing - seems to break upload changes. Commit: f3da0864b45a3aa307c7fe9eeb8c5d26dd9c8527 https://github.com/galaxyproject/galaxy/commit/f3da0864b45a3aa307c7fe9eeb8c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M test/api/test_tools.py A test/functional/tools/for_workflows/mapper_two.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test case for regression #6856. Commit: 01f1f1b95fba671a2d92d7111676229a7ed5d58a https://github.com/galaxyproject/galaxy/commit/01f1f1b95fba671a2d92d7111676… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/model/metadata.py M test/api/test_tools.py A test/functional/tools/for_workflows/mapper_two.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6858 from jmchilton/fix_metadata_revert [18.09] Revert selective metadata flushing - breaks multiple uploads/outputs. Commit: ca95d7a26e70ca02159febd971fa8b63c2667ab5 https://github.com/galaxyproject/galaxy/commit/ca95d7a26e70ca02159febd971fa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/model/metadata.py M test/api/test_tools.py A test/functional/tools/for_workflows/mapper_two.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/ff32e5434145...ca95d7a26e70 **NOTE:** This service has 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] 1f6607: Test mutable configs
by GitHub 12 Oct '18

12 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1f66079a08f4dbd7b62aa74cfd10800312ef4912 https://github.com/galaxyproject/usegalaxy-playbook/commit/1f66079a08f4dbd7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Test mutable configs **NOTE:** This service has 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] d791a2: Revert selective metadata flushing - seems to brea...
by GitHub 12 Oct '18

12 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: d791a2c80f3290d66c2252f29981a16a4459661b https://github.com/galaxyproject/galaxy/commit/d791a2c80f3290d66c2252f29981… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/model/metadata.py Log Message: ----------- Revert selective metadata flushing - seems to break upload changes. Commit: f3da0864b45a3aa307c7fe9eeb8c5d26dd9c8527 https://github.com/galaxyproject/galaxy/commit/f3da0864b45a3aa307c7fe9eeb8c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M test/api/test_tools.py A test/functional/tools/for_workflows/mapper_two.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test case for regression #6856. Commit: 01f1f1b95fba671a2d92d7111676229a7ed5d58a https://github.com/galaxyproject/galaxy/commit/01f1f1b95fba671a2d92d7111676… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/model/metadata.py M test/api/test_tools.py A test/functional/tools/for_workflows/mapper_two.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6858 from jmchilton/fix_metadata_revert [18.09] Revert selective metadata flushing - breaks multiple uploads/outputs. Compare: https://github.com/galaxyproject/galaxy/compare/4805304e0bf3...01f1f1b95fba **NOTE:** This service has 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] 19f716: Fix ``LocalShell`` doctest
by GitHub 12 Oct '18

12 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 19f716de9141080ecf3043fe3aeac391c55b8158 https://github.com/galaxyproject/galaxy/commit/19f716de9141080ecf3043fe3aea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py Log Message: ----------- Fix ``LocalShell`` doctest Broken in commit 57a1f19b069597bde97852b3e0d0a3e1c0068bc4 . Commit: 4805304e0bf3b1612c3cd425d94d33990f076d6a https://github.com/galaxyproject/galaxy/commit/4805304e0bf3b1612c3cd425d94d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py Log Message: ----------- Merge pull request #6863 from nsoranzo/release_18.09_fix_LocalShell_doctest [18.09] Fix ``LocalShell`` doctest Commit: ff32e5434145dbae5138d20972e510835eae8b06 https://github.com/galaxyproject/galaxy/commit/ff32e5434145dbae5138d20972e5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/cfbe2bf42b9f...ff32e5434145 **NOTE:** This service has 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] bc226e: Use more generic destination name
by GitHub 12 Oct '18

12 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bc226e6d41d64d4ace6887a54394b57dbf4ae45b https://github.com/galaxyproject/galaxy/commit/bc226e6d41d64d4ace6887a54394… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M test/integration/test_cli_runners.py Log Message: ----------- Use more generic destination name xref. https://github.com/galaxyproject/galaxy/pull/6845#pullrequestreview-1636172… Commit: 91a395430730f6871ba5daa31d6ead281c12270c https://github.com/galaxyproject/galaxy/commit/91a395430730f6871ba5daa31d6e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M doc/source/dev/index.rst Log Message: ----------- Index ``finding_and_improving_slow_code`` page in dev docs Commit: 4e0f814f618625d3cae8578a2fd027ee1c855f3f https://github.com/galaxyproject/galaxy/commit/4e0f814f618625d3cae8578a2fd0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Add documentation for ``conda_use_local`` config directive Commit: c54c3c99b1d52816260406260e5e7fc8dc595f45 https://github.com/galaxyproject/galaxy/commit/c54c3c99b1d52816260406260e5e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Standardise ``__init__()`` of ``ToolParameter`` subclasses Commit: cfbe2bf42b9f738f480059353c043438ef8d85b5 https://github.com/galaxyproject/galaxy/commit/cfbe2bf42b9f738f480059353c04… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/dev/index.rst M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/integration/test_cli_runners.py Log Message: ----------- Merge pull request #6861 from nsoranzo/misc Small fixes Compare: https://github.com/galaxyproject/galaxy/compare/5e71401a7eb5...cfbe2bf42b9f **NOTE:** This service has 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] 19f716: Fix ``LocalShell`` doctest
by GitHub 12 Oct '18

12 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 19f716de9141080ecf3043fe3aeac391c55b8158 https://github.com/galaxyproject/galaxy/commit/19f716de9141080ecf3043fe3aea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py Log Message: ----------- Fix ``LocalShell`` doctest Broken in commit 57a1f19b069597bde97852b3e0d0a3e1c0068bc4 . Commit: 4805304e0bf3b1612c3cd425d94d33990f076d6a https://github.com/galaxyproject/galaxy/commit/4805304e0bf3b1612c3cd425d94d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py Log Message: ----------- Merge pull request #6863 from nsoranzo/release_18.09_fix_LocalShell_doctest [18.09] Fix ``LocalShell`` doctest Compare: https://github.com/galaxyproject/galaxy/compare/d22f652f918f...4805304e0bf3 **NOTE:** This service has 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] 6233a4: Release notes templated; still needs manual curati...
by GitHub 12 Oct '18

12 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6233a408cc93152a379651db3cc143d368f78dda https://github.com/galaxyproject/galaxy/commit/6233a408cc93152a379651db3cc1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: A doc/source/releases/18.09.rst A doc/source/releases/18.09_announce.rst A doc/source/releases/19.01_announce.rst Log Message: ----------- Release notes templated; still needs manual curation Commit: 25fc1617030d392f85abb65ccd95f913561919e2 https://github.com/galaxyproject/galaxy/commit/25fc1617030d392f85abb65ccd95… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Update RN with new merges. Commit: 8c05e2f5f1677950a3279ffa30ccbf8949aa35e4 https://github.com/galaxyproject/galaxy/commit/8c05e2f5f1677950a3279ffa30cc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add grapdot datatype. Commit: 6ac5966c5e1a95e93c5923a4eddf5fa971518bd6 https://github.com/galaxyproject/galaxy/commit/6ac5966c5e1a95e93c5923a4eddf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add removal of upgrade logic specific to datatypes from 17.05 Commit: 0698a71861afadb7f16be765223819178d294c30 https://github.com/galaxyproject/galaxy/commit/0698a71861afadb7f16be7652238… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Another few stragglers. Commit: d3db21fa82a834d0d9fa90106b3fa2b4911708dc https://github.com/galaxyproject/galaxy/commit/d3db21fa82a834d0d9fa90106b3f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6755 Commit: 6cb4c32eb4e613b4d90680450d11804779e5b4a5 https://github.com/galaxyproject/galaxy/commit/6cb4c32eb4e613b4d90680450d11… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6768 Commit: ee47fdb50cef70dd2b940c42594611863e51bde7 https://github.com/galaxyproject/galaxy/commit/ee47fdb50cef70dd2b940c425946… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6753, 6771 Commit: c51178578dcf67c8dbe16d3d8320f660e0c80027 https://github.com/galaxyproject/galaxy/commit/c51178578dcf67c8dbe16d3d8320… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Four more PRs Commit: ff65263ab2ee1351bbed11709d8536de694a5776 https://github.com/galaxyproject/galaxy/commit/ff65263ab2ee1351bbed11709d85… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6789 Commit: 96d77b0791592b35fb6e4201d011f5c223060cfe https://github.com/galaxyproject/galaxy/commit/96d77b0791592b35fb6e4201d011… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-30 (Sun, 30 Sep 2018) Changed paths: M doc/source/releases/18.09.rst M doc/source/releases/18.09_announce.rst Log Message: ----------- More PRs, stub out proposed features. Commit: 3d772dc03bf0ffa1c6d010596488c5cd3a26901d https://github.com/galaxyproject/galaxy/commit/3d772dc03bf0ffa1c6d010596488… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6791 Commit: ce3d43221a8d4e843a25c49c679a4ab75fd3756c https://github.com/galaxyproject/galaxy/commit/ce3d43221a8d4e843a25c49c679a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- More Prs for the release notes. Commit: b5f7955c5addba2664b6375aa87c9873b2949fad https://github.com/galaxyproject/galaxy/commit/b5f7955c5addba2664b6375aa87c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Announce Python 3 Beta Support Commit: 90718843096f115324be8a086d7a6089e0086703 https://github.com/galaxyproject/galaxy/commit/90718843096f115324be8a086d7a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Add deprecation notice for username being null Commit: afffd9bdaa66b4fcadbd790a25387654c23e4aa6 https://github.com/galaxyproject/galaxy/commit/afffd9bdaa66b4fcadbd790a2538… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add final PR. Commit: eacec03d10c00503fdbb4da107254c06082507bb https://github.com/galaxyproject/galaxy/commit/eacec03d10c00503fdbb4da10725… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09.rst M doc/source/releases/18.09_announce.rst Log Message: ----------- Update.... Commit: 4d165a567139abc3b4ad3baac422c9c0ebbaf554 https://github.com/galaxyproject/galaxy/commit/4d165a567139abc3b4ad3baac422… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09.rst M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge branch '18.09_release_notes' of github.com:jmchilton/galaxy into 18.09_release_notes Commit: 386229d1ce58522be4bece11b8f9473f5dce56b9 https://github.com/galaxyproject/galaxy/commit/386229d1ce58522be4bece11b8f9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Re-add removed PRs (bad merge I think) Commit: fdaf9ac8641cfa5fa0aad706310aec2b31692ac1 https://github.com/galaxyproject/galaxy/commit/fdaf9ac8641cfa5fa0aad706310a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Link up workflow PRs Commit: 381d6ad83183a822baebca44622e506d088f10b1 https://github.com/galaxyproject/galaxy/commit/381d6ad83183a822baebca44622e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add two recently merged PRs. Commit: 02410b270d025e5fb8cb4e2036fb627051c7850a https://github.com/galaxyproject/galaxy/commit/02410b270d025e5fb8cb4e2036fb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M lib/galaxy/util/monitors.py Log Message: ----------- Register job monitor as postfork function This should fix https://github.com/galaxyproject/galaxy/issues/6831, and might fix https://github.com/galaxyproject/galaxy/issues/6261. Commit: 6b62a57047f8877ba36e0767aaee04879bbc20c0 https://github.com/galaxyproject/galaxy/commit/6b62a57047f8877ba36e0767aaee… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Should fix bug Jen saw with history panel being masked at bottom Commit: 5844bdc7aa0a90d992c3b36e041abb8d103e3b95 https://github.com/galaxyproject/galaxy/commit/5844bdc7aa0a90d992c3b36e041a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/job_environment_explicit_shared_home.xml A test/integration/test_cli_runners.py M test/integration/test_job_environments.py Log Message: ----------- Add integration test for remote shell CLI runners This tests both the SecureShell and Paramiko shell plugins and the Slurm and Torque CLI runner. Commit: 57a1f19b069597bde97852b3e0d0a3e1c0068bc4 https://github.com/galaxyproject/galaxy/commit/57a1f19b069597bde97852b3e0d0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py Log Message: ----------- Fix slurm cli plugin by avoiding `shell=True` in subprocess Fixes the remaining issue in https://github.com/galaxyproject/galaxy/issues/6831#issuecomment-428097520 Commit: fc28e0bd83a2df59f11b80f0119e67da1326887f https://github.com/galaxyproject/galaxy/commit/fc28e0bd83a2df59f11b80f0119e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/rsh.py Log Message: ----------- Use long-form options Commit: 5e12e509bf20d7e4f4464a60f04c7479cb4e232d https://github.com/galaxyproject/galaxy/commit/5e12e509bf20d7e4f4464a60f04c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M test/integration/test_cli_runners.py Log Message: ----------- Fix selection of job plugin and image Thanks @nsoranzo. Commit: b08c6219c3fe771e00d0b6d8b9adb1c97e38e9a6 https://github.com/galaxyproject/galaxy/commit/b08c6219c3fe771e00d0b6d8b9ad… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M test/integration/test_cli_runners.py Log Message: ----------- Simplify ssh key handling in integration test Commit: ac3e1ca1d0d7bb85cc00e2e113f70e3576f0b048 https://github.com/galaxyproject/galaxy/commit/ac3e1ca1d0d7bb85cc00e2e113f7… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M test/integration/test_cli_runners.py Log Message: ----------- Use Crypto to generate SSH keys Also remove key files in `stop_ssh_docker()`. Commit: cd62461e8486bd4e44aee51907f7d515718ef3d8 https://github.com/galaxyproject/galaxy/commit/cd62461e8486bd4e44aee51907f7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6839 from dannon/unified-panel-style-tweaks [18.09] Unified panel style bottom padding fix Commit: a1f7634fd7dca45902a2d3f67d2279db3aa2270d https://github.com/galaxyproject/galaxy/commit/a1f7634fd7dca45902a2d3f67d22… Author: thobalose <lose.thoba(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M config/plugins/interactive_environments/neo/templates/neo.mako Log Message: ----------- Updated volume kwds. Commit: fe6c1738c0ea3ee35fa34fec8a2c2e8eb97ec044 https://github.com/galaxyproject/galaxy/commit/fe6c1738c0ea3ee35fa34fec8a2c… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M config/plugins/interactive_environments/neo/templates/neo.mako Log Message: ----------- Merge pull request #6851 from martenson/backport-gie-kwds [18.05] Updated volume kwds for GIEs Commit: fd0b24ecd2bff2f8baa636304e45eb2dbdcaf3a9 https://github.com/galaxyproject/galaxy/commit/fd0b24ecd2bff2f8baa636304e45… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/job_environment_explicit_shared_home.xml A test/integration/test_cli_runners.py M test/integration/test_job_environments.py Log Message: ----------- Merge pull request #6845 from mvdbeek/fix_slurm_cli_on_secure_shell [18.05] Fix slurm cli on secure shell Commit: c1383bc2d55cb6565fbd63eb4088c734a805700e https://github.com/galaxyproject/galaxy/commit/c1383bc2d55cb6565fbd63eb4088… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Small fixes Commit: c6193ca4406450cdaa01b9c27bcfb871c916544c https://github.com/galaxyproject/galaxy/commit/c6193ca4406450cdaa01b9c27bcf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/source/releases/18.09.rst M scripts/bootstrap_history.py Log Message: ----------- Update DEVTEAM, rebuild, include a few new PRs. Commit: 7cb2eb57aca559c86b3d938912d8f7bde5da9f74 https://github.com/galaxyproject/galaxy/commit/7cb2eb57aca559c86b3d938912d8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge branch '18.09_release_notes' of github.com:galaxyproject/galaxy into 18.09_release_notes Commit: baa992d217032b809d321cb800cd2f41af401c63 https://github.com/galaxyproject/galaxy/commit/baa992d217032b809d321cb800cd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/util/monitors.py Log Message: ----------- Merge pull request #6836 from mvdbeek/fix_job_monitor_thread [18.01] Register job monitor thread as postfork function Commit: d33006cf33f71f4992eebefb7c3065606088aea1 https://github.com/galaxyproject/galaxy/commit/d33006cf33f71f4992eebefb7c30… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Final docs update Commit: d42b899b7805f722a77153c4e33fffcfad846ce0 https://github.com/galaxyproject/galaxy/commit/d42b899b7805f722a77153c4e33f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/source/releases/18.09.rst M scripts/bootstrap_history.py Log Message: ----------- Embellish 18.09 release notes Commit: 9251484e7236cd881cb4df64265a3cee2e654d83 https://github.com/galaxyproject/galaxy/commit/9251484e7236cd881cb4df64265a… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: A doc/source/releases/18.09.rst A doc/source/releases/18.09_announce.rst A doc/source/releases/19.01_announce.rst M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #6731 from galaxyproject/18.09_release_notes [18.09] 18.09 release notes Commit: 20f60a5a44842dda8ffe7b97d1b60b6c5ecfdd9d https://github.com/galaxyproject/galaxy/commit/20f60a5a44842dda8ffe7b97d1b6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- update paramiko dep Commit: 2c14c2afc4d39626096c3d15828b8c3001aab40f https://github.com/galaxyproject/galaxy/commit/2c14c2afc4d39626096c3d15828b… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #6859 from martenson/paramiko-update [18.09] update paramiko dep Commit: a8fa5a1d4a6c801fc230c037129671978955916c https://github.com/galaxyproject/galaxy/commit/a8fa5a1d4a6c801fc230c0371296… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/util/monitors.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: d22f652f918f7a49d80ede8652d335d41c478546 https://github.com/galaxyproject/galaxy/commit/d22f652f918f7a49d80ede8652d3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M config/plugins/interactive_environments/neo/templates/neo.mako M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/util/monitors.py M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/job_environment_explicit_shared_home.xml A test/integration/test_cli_runners.py M test/integration/test_job_environments.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: 5e71401a7eb502479c7a9b69e60a2351a82258d7 https://github.com/galaxyproject/galaxy/commit/5e71401a7eb502479c7a9b69e60a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M client/galaxy/style/scss/base.scss A doc/source/releases/18.09.rst A doc/source/releases/18.09_announce.rst A doc/source/releases/19.01_announce.rst M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/util/monitors.py M scripts/bootstrap_history.py M static/style/blue/base.css M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/job_environment_explicit_shared_home.xml A test/integration/test_cli_runners.py M test/integration/test_job_environments.py Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/b2477d1223df...5e71401a7eb5 **NOTE:** This service has 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] 02410b: Register job monitor as postfork function
by GitHub 12 Oct '18

12 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 02410b270d025e5fb8cb4e2036fb627051c7850a https://github.com/galaxyproject/galaxy/commit/02410b270d025e5fb8cb4e2036fb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M lib/galaxy/util/monitors.py Log Message: ----------- Register job monitor as postfork function This should fix https://github.com/galaxyproject/galaxy/issues/6831, and might fix https://github.com/galaxyproject/galaxy/issues/6261. Commit: 5844bdc7aa0a90d992c3b36e041abb8d103e3b95 https://github.com/galaxyproject/galaxy/commit/5844bdc7aa0a90d992c3b36e041a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/job_environment_explicit_shared_home.xml A test/integration/test_cli_runners.py M test/integration/test_job_environments.py Log Message: ----------- Add integration test for remote shell CLI runners This tests both the SecureShell and Paramiko shell plugins and the Slurm and Torque CLI runner. Commit: 57a1f19b069597bde97852b3e0d0a3e1c0068bc4 https://github.com/galaxyproject/galaxy/commit/57a1f19b069597bde97852b3e0d0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py Log Message: ----------- Fix slurm cli plugin by avoiding `shell=True` in subprocess Fixes the remaining issue in https://github.com/galaxyproject/galaxy/issues/6831#issuecomment-428097520 Commit: fc28e0bd83a2df59f11b80f0119e67da1326887f https://github.com/galaxyproject/galaxy/commit/fc28e0bd83a2df59f11b80f0119e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/rsh.py Log Message: ----------- Use long-form options Commit: 5e12e509bf20d7e4f4464a60f04c7479cb4e232d https://github.com/galaxyproject/galaxy/commit/5e12e509bf20d7e4f4464a60f04c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M test/integration/test_cli_runners.py Log Message: ----------- Fix selection of job plugin and image Thanks @nsoranzo. Commit: b08c6219c3fe771e00d0b6d8b9adb1c97e38e9a6 https://github.com/galaxyproject/galaxy/commit/b08c6219c3fe771e00d0b6d8b9ad… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M test/integration/test_cli_runners.py Log Message: ----------- Simplify ssh key handling in integration test Commit: ac3e1ca1d0d7bb85cc00e2e113f70e3576f0b048 https://github.com/galaxyproject/galaxy/commit/ac3e1ca1d0d7bb85cc00e2e113f7… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M test/integration/test_cli_runners.py Log Message: ----------- Use Crypto to generate SSH keys Also remove key files in `stop_ssh_docker()`. Commit: a1f7634fd7dca45902a2d3f67d2279db3aa2270d https://github.com/galaxyproject/galaxy/commit/a1f7634fd7dca45902a2d3f67d22… Author: thobalose <lose.thoba(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M config/plugins/interactive_environments/neo/templates/neo.mako Log Message: ----------- Updated volume kwds. Commit: fe6c1738c0ea3ee35fa34fec8a2c2e8eb97ec044 https://github.com/galaxyproject/galaxy/commit/fe6c1738c0ea3ee35fa34fec8a2c… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M config/plugins/interactive_environments/neo/templates/neo.mako Log Message: ----------- Merge pull request #6851 from martenson/backport-gie-kwds [18.05] Updated volume kwds for GIEs Commit: fd0b24ecd2bff2f8baa636304e45eb2dbdcaf3a9 https://github.com/galaxyproject/galaxy/commit/fd0b24ecd2bff2f8baa636304e45… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/job_environment_explicit_shared_home.xml A test/integration/test_cli_runners.py M test/integration/test_job_environments.py Log Message: ----------- Merge pull request #6845 from mvdbeek/fix_slurm_cli_on_secure_shell [18.05] Fix slurm cli on secure shell Commit: baa992d217032b809d321cb800cd2f41af401c63 https://github.com/galaxyproject/galaxy/commit/baa992d217032b809d321cb800cd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/util/monitors.py Log Message: ----------- Merge pull request #6836 from mvdbeek/fix_job_monitor_thread [18.01] Register job monitor thread as postfork function Commit: a8fa5a1d4a6c801fc230c037129671978955916c https://github.com/galaxyproject/galaxy/commit/a8fa5a1d4a6c801fc230c0371296… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/util/monitors.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: d22f652f918f7a49d80ede8652d335d41c478546 https://github.com/galaxyproject/galaxy/commit/d22f652f918f7a49d80ede8652d3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M config/plugins/interactive_environments/neo/templates/neo.mako M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/util/monitors.py M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/job_environment_explicit_shared_home.xml A test/integration/test_cli_runners.py M test/integration/test_job_environments.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Compare: https://github.com/galaxyproject/galaxy/compare/2c14c2afc4d3...d22f652f918f **NOTE:** This service has 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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