galaxy-commits February 2019

galaxy-commits@lists.galaxyproject.org

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152 discussions

[galaxyproject/usegalaxy-playbook] be2c2c: Update Test
by Nate Coraor 27 Feb '19

27 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: be2c2cebf7414eab5dde8a0d556092fc1e5a69aa https://github.com/galaxyproject/usegalaxy-playbook/commit/be2c2cebf7414eab… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-27 (Wed, 27 Feb 2019) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test

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[galaxyproject/usegalaxy-playbook] 229869: Update main.
by Dave B. 27 Feb '19

27 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 229869c2381722eba8fa3c338c48ffdb3cd1d969 https://github.com/galaxyproject/usegalaxy-playbook/commit/229869c2381722eb… Author: Dave B <dave(a)bx.psu.edu> Date: 2019-02-27 (Wed, 27 Feb 2019) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update main. Commit: 1e95e6fa2aa6ba42445a18179b2cafb77ee355c6 https://github.com/galaxyproject/usegalaxy-playbook/commit/1e95e6fa2aa6ba42… Author: Dave B <dave(a)bx.psu.edu> Date: 2019-02-27 (Wed, 27 Feb 2019) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Update TRANSIT tools on test, add GFF3 to prot_table converter. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/95d0cf780e06...…

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[galaxyproject/infrastructure-playbook] 0f9484: More Mailman 3 production stuff
by Nate Coraor 27 Feb '19

27 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 0f9484e5ecd7241c99c35b7a7c3d80ccc7b436e2 https://github.com/galaxyproject/infrastructure-playbook/commit/0f9484e5ecd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-27 (Wed, 27 Feb 2019) Changed paths: M common_roles M env/galaxy/group_vars/sshclients/vault.yml M env/galaxy/group_vars/sshservers/vault.yml M env/mailman/TODO.txt M env/mailman/group_vars/all.yml R env/mailman/group_vars/listservers.yml A env/mailman/group_vars/listservers/vars.yml A env/mailman/group_vars/listservers/vault.yml R env/mailman/group_vars/mailservers-mx.yml A env/mailman/group_vars/mailservers-mx/vars.yml A env/mailman/group_vars/mailservers-mx/vault.yml A env/mailman/group_vars/sshclients A env/mailman/group_vars/sshservers M env/mailman/inventory M env/mailman/listservers.yml M env/mailman/templates/nginx/mailman.j2 Log Message: ----------- More Mailman 3 production stuff

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[galaxyproject/infrastructure-playbook] d783c8: Fix naming of postgresql role in TACC playbook
by Nate Coraor 27 Feb '19

27 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d783c8ad0289947f1c850189eeac8044e3ccaa62 https://github.com/galaxyproject/infrastructure-playbook/commit/d783c8ad028… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-27 (Wed, 27 Feb 2019) Changed paths: M env/tacc/playbook.yml Log Message: ----------- Fix naming of postgresql role in TACC playbook

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[galaxyproject/infrastructure-playbook] 549300: Add additional roles installed from Ansible Galaxy...
by Nate Coraor 27 Feb '19

27 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 549300580e494f517a5026657ff43478d24b9e59 https://github.com/galaxyproject/infrastructure-playbook/commit/549300580e4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-27 (Wed, 27 Feb 2019) Changed paths: M .gitignore Log Message: ----------- Add additional roles installed from Ansible Galaxy to .gitignore

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[galaxyproject/infrastructure-playbook] 23d66e: Move nginx and postgresql roles to requirements in...
by Nate Coraor 27 Feb '19

27 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 23d66eedbdcb3ad71626e30e9b2495c6dada916e https://github.com/galaxyproject/infrastructure-playbook/commit/23d66eedbdc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-27 (Wed, 27 Feb 2019) Changed paths: M .gitignore M README.md A requirements.yml R roles/galaxyproject.nginx/README.md R roles/galaxyproject.nginx/defaults/main.yml R roles/galaxyproject.nginx/handlers/main.yml R roles/galaxyproject.nginx/meta/.galaxy_install_info R roles/galaxyproject.nginx/meta/main.yml R roles/galaxyproject.nginx/tasks/apt.yml R roles/galaxyproject.nginx/tasks/main.yml R roles/galaxyproject.nginx/tasks/pkgin.yml R roles/galaxyproject.nginx/tasks/ssl.yml R roles/galaxyproject.nginx/tasks/yum.yml R roles/galaxyproject.nginx/templates/epel-nginx.conf.j2 R roles/galaxyproject.nginx/templates/http_options.conf.j2 R roles/galaxyproject.nginx/templates/pkgin-nginx.conf.j2 R roles/galaxyproject.nginx/templates/ssl.conf.j2 R roles/galaxyproject.nginx/templates/supervisord.conf.j2 R roles/galaxyproject.nginx/vars/pkgin.yml R roles/galaxyprojectdotorg.postgresql/.gitignore R roles/galaxyprojectdotorg.postgresql/README.md R roles/galaxyprojectdotorg.postgresql/defaults/main.yml R roles/galaxyprojectdotorg.postgresql/files/get_repo_rpm_release.py R roles/galaxyprojectdotorg.postgresql/handlers/main.yml R roles/galaxyprojectdotorg.postgresql/meta/.galaxy_install_info R roles/galaxyprojectdotorg.postgresql/meta/main.yml R roles/galaxyprojectdotorg.postgresql/tasks/backup.yml R roles/galaxyprojectdotorg.postgresql/tasks/debian.yml R roles/galaxyprojectdotorg.postgresql/tasks/main.yml R roles/galaxyprojectdotorg.postgresql/tasks/redhat.yml R roles/galaxyprojectdotorg.postgresql/templates/20ansible_backup.conf.j2 R roles/galaxyprojectdotorg.postgresql/templates/25ansible_postgresql.conf.j2 R roles/galaxyprojectdotorg.postgresql/templates/archive_wal.sh.j2 R roles/galaxyprojectdotorg.postgresql/templates/backup_working_wal.sh.j2 R roles/galaxyprojectdotorg.postgresql/templates/pg_hba.conf.debian.j2 R roles/galaxyprojectdotorg.postgresql/templates/pg_hba.conf.redhat.j2 R roles/galaxyprojectdotorg.postgresql/templates/scheduled_backup.sh.j2 R roles/galaxyprojectdotorg.postgresql/vars/debian.yml R roles/galaxyprojectdotorg.postgresql/vars/main.yml R roles/galaxyprojectdotorg.postgresql/vars/redhat.yml Log Message: ----------- Move nginx and postgresql roles to requirements instead of committed.

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[galaxyproject/galaxy] 51d167: Fix dependency installation in UI
by Martin Cech 27 Feb '19

27 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 51d167b85d218c3181ebd6f6f67c7333f981746a https://github.com/galaxyproject/galaxy/commit/51d167b85d218c3181ebd6f6f67c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-27 (Wed, 27 Feb 2019) Changed paths: M lib/galaxy/tools/deps/views.py Log Message: ----------- Fix dependency installation in UI We need to pass the install kwarg here. Broken in https://github.com/galaxyproject/galaxy/commit/2d3ab4ce1205aec24664225d74b2… Commit: 4dae35ea67be33cf4e9739433d3c4cec4f1ff46e https://github.com/galaxyproject/galaxy/commit/4dae35ea67be33cf4e9739433d3c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-27 (Wed, 27 Feb 2019) Changed paths: M lib/galaxy/tools/deps/views.py Log Message: ----------- Merge pull request #7418 from mvdbeek/fix_install_through_managment_ui [19.01] Fix dependency installation in UI Compare: https://github.com/galaxyproject/galaxy/compare/fdb18045b762...4dae35ea67be

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[galaxyproject/galaxy] 27dd83: WIP load shed tools w/o install DB
by John Chilton 27 Feb '19

27 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 27dd8362154b2f26850f05b0b8b558757b8ffa20 https://github.com/galaxyproject/galaxy/commit/27dd8362154b2f26850f05b0b8b5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- WIP load shed tools w/o install DB Commit: 1e7d8087d26829326edfde02b2a38119893aa8de https://github.com/galaxyproject/galaxy/commit/1e7d8087d26829326edfde02b2a3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix "show in toolshed" link Commit: d4e88636067733a4a5c9bf579692ba3968b5c9b0 https://github.com/galaxyproject/galaxy/commit/d4e88636067733a4a5c9bf579692… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/buildapp.py A lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- WIP broken support tool help w/out repository_id and start de-hackifying Commit: 90d61af69a7afd798a515164aec6aa760d39ed4b https://github.com/galaxyproject/galaxy/commit/90d61af69a7afd798a515164aec6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix generation of repo_path Commit: 9f27ae897ffc877db21b247e25ab2eafced1fb30 https://github.com/galaxyproject/galaxy/commit/9f27ae897ffc877db21b247e25ab… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py Log Message: ----------- Got tool help images working Commit: 8bc3f93b26963bf9d6043dfd90b339bea4850b4a https://github.com/galaxyproject/galaxy/commit/8bc3f93b26963bf9d6043dfd90b3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py Log Message: ----------- Better condition handling for populating a tool's shed info Commit: 4627546831224fcf0b85479a4c39893a4edaea8a https://github.com/galaxyproject/galaxy/commit/4627546831224fcf0b85479a4c39… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/tool_shed/tools/tool_validator.py Log Message: ----------- Fix silent failure when installing tools. Commit: 2e04301d6b4f1d18a2e1ad6b328001789c86a140 https://github.com/galaxyproject/galaxy/commit/2e04301d6b4f1d18a2e1ad6b3280… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/tools/__init__.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Fix installing TS tools Commit: 767c8497a5e0ca167a395ff56b3bd00c906068cd https://github.com/galaxyproject/galaxy/commit/767c8497a5e0ca167a395ff56b3b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py Log Message: ----------- Lint Commit: 1673d645ced97cb37fd4f5efb36b59de2ae7eba8 https://github.com/galaxyproject/galaxy/commit/1673d645ced97cb37fd4f5efb36b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Add unnecessary column Commit: 037202c3010aefb361b582127dc7d5b3b575a773 https://github.com/galaxyproject/galaxy/commit/037202c3010aefb361b582127dc7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-08 (Fri, 08 Feb 2019) Changed paths: M lib/tool_shed/tools/tool_validator.py Log Message: ----------- Log exceptions instead of raising. Commit: e1001d3754c7b469dd3d5e7a9989d13b89fa5d2f https://github.com/galaxyproject/galaxy/commit/e1001d3754c7b469dd3d5e7a9989… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cache.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Some small fixes and improvements Most notably only use tool_shed_repository while constructing a Tool, this avoids stale references to sqlalchemy objects. Commit: 6678a6baf0c61c7538425c7c82d0fadb6f27a3ea https://github.com/galaxyproject/galaxy/commit/6678a6baf0c61c7538425c7c82d0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py Log Message: ----------- Fix display of images in static/images Commit: 99447a9d299e8e8e52ff0367144bb9665627ccf3 https://github.com/galaxyproject/galaxy/commit/99447a9d299e8e8e52ff0367144b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/tools/repositories.py Log Message: ----------- Add dummy tool shed registry Commit: 0d6f4b13837e52371ddf12881375639cb198ef33 https://github.com/galaxyproject/galaxy/commit/0d6f4b13837e52371ddf12881375… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/tool_shed/util/readme_util.py Log Message: ----------- Remove useless lock Commit: 0b6e9cfd7c55f9eedde9a37719fa477ac8839fd8 https://github.com/galaxyproject/galaxy/commit/0b6e9cfd7c55f9eedde9a37719fa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Mock the mock shed registry Commit: 694dde1b07099fdf4a1b400eb5054fee59335ae7 https://github.com/galaxyproject/galaxy/commit/694dde1b07099fdf4a1b400eb505… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix set_image_path for tools in tool shed Commit: 8b9239172acc43969946b00c8f3fb94e403803d9 https://github.com/galaxyproject/galaxy/commit/8b9239172acc43969946b00c8f3f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Simplify getting changeset revision from path Commit: 2e57760086bba24df25b1c0e2650be3c90e90ecb https://github.com/galaxyproject/galaxy/commit/2e57760086bba24df25b1c0e2650… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Simplify some more Commit: 063a4a4e394dea128f4f2b9820ac08c97e6eaeef https://github.com/galaxyproject/galaxy/commit/063a4a4e394dea128f4f2b9820ac… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cache.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/repositories.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py M lib/tool_shed/util/readme_util.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #10 from mvdbeek/natefoo-installdbless-shed-tools Simplify loading repositories and fix tests Commit: 0a39badc798160ec4978e9f60a7f4b8275b5c299 https://github.com/galaxyproject/galaxy/commit/0a39badc798160ec4978e9f60a7f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-27 (Wed, 27 Feb 2019) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cache.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/repositories.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/buildapp.py A lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #7316 from natefoo/installdbless-shed-tools Support loading/using tools that are not in the install database Compare: https://github.com/galaxyproject/galaxy/compare/25aa54e28b18...0a39badc7981

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[galaxyproject/galaxy] 07806f: Simplify path tracking related to history exports.
by Marius van den Beek 27 Feb '19

27 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 07806f3a028542c2481a89bb12fe6ca1953985e7 https://github.com/galaxyproject/galaxy/commit/07806f3a028542c2481a89bb12fe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-24 (Sun, 24 Feb 2019) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Simplify path tracking related to history exports. This is a simpler model to think about and prevents us from needing to track new fields in the database for extensions such as collections. Commit: db78c26c74a29b02f0e5dad48409cd1ac4d73f0a https://github.com/galaxyproject/galaxy/commit/db78c26c74a29b02f0e5dad48409… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-24 (Sun, 24 Feb 2019) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py Log Message: ----------- Rework export history argument parsing. Other changes in #4532 would have caused export jobs that were created before an upgrade that added that PR to fail after the upgrade. This wouldn't have been a huge deal but the new format of the arguments is a bit cleaner and future proof anyway. Commit: 0fe769e2e4d9105460e6873d40e00507da9b0db4 https://github.com/galaxyproject/galaxy/commit/0fe769e2e4d9105460e6873d40e0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-24 (Sun, 24 Feb 2019) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py Log Message: ----------- Add --galaxy_version argument to export_history script. Commit: 25aa54e28b187ac7097809fa584386fb776926c3 https://github.com/galaxyproject/galaxy/commit/25aa54e28b187ac7097809fa5843… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-02-27 (Wed, 27 Feb 2019) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py Log Message: ----------- Merge pull request #7214 from jmchilton/history_export_clean_cli Cleanup History Export CLI Call Compare: https://github.com/galaxyproject/galaxy/compare/68c835e8ac2c...25aa54e28b18

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[galaxyproject/usegalaxy-playbook] 95d0cf: Updated slide rotation. Dropped admin training; a...
by Dave Clements 26 Feb '19

26 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 95d0cf780e066a58b1f955b65454febd62ffd6c4 https://github.com/galaxyproject/usegalaxy-playbook/commit/95d0cf780e066a58… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: A env/common/files/galaxy/static/welcome_img/gcc2019-plain.png M env/common/templates/galaxy/static/welcome.html.j2 Log Message: ----------- Updated slide rotation. Dropped admin training; added GCC2019 generic.

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galaxy-commits February 2019