- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] eacbc7: Test tool_conf.xml changes for usegalaxy.* integra...
by Nate Coraor 04 Feb '19

04 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: eacbc7190e92f0055b11c856eda6a0b6c9c402b9 https://github.com/galaxyproject/usegalaxy-playbook/commit/eacbc7190e92f005… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M env/test/files/galaxy/config/tool_conf.xml Log Message: ----------- Test tool_conf.xml changes for usegalaxy.* integration Commit: e233c920e97a6b756db9951bf058d6ac4ee39bcd https://github.com/galaxyproject/usegalaxy-playbook/commit/e233c920e97a6b75… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/migrated_tools_conf.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Partial Test mutable config fixes for usegalaxy.* integration Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/4aeeb45287d2...…

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[galaxyproject/galaxy] 428c66: Remove errant space in intermine_simple_display.lo...
by Martin Cech 04 Feb '19

04 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 428c6632f0196ebd45a42d1c61776ac3402e985f https://github.com/galaxyproject/galaxy/commit/428c6632f0196ebd45a42d1c6177… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M tool-data/intermine_simple_display.loc.sample Log Message: ----------- Remove errant space in intermine_simple_display.loc.sample Commit: 526bebbb2817376b4c4e131890d75d1ea76b0e85 https://github.com/galaxyproject/galaxy/commit/526bebbb2817376b4c4e131890d7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M tool-data/intermine_simple_display.loc.sample Log Message: ----------- Merge pull request #7298 from blankenberg/intermine-loc-fix-19.01 [19.01] Remove errant space in intermine_simple_display.loc.sample Compare: https://github.com/galaxyproject/galaxy/compare/49cbad5debb6...526bebbb2817

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[galaxyproject/galaxy] 7dd921: Add longer pauses for some selenium tests, mark as...
by Aysam Guerler 04 Feb '19

04 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7dd9213fd874a4bf12d0eee86f03c48dd467a6f2 https://github.com/galaxyproject/galaxy/commit/7dd9213fd874a4bf12d0eee86f03… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_custom_builds.py Log Message: ----------- Add longer pauses for some selenium tests, mark as slow renders for easier tracking down and fixing. Commit: d59352224c8f41ba8a1a9219b2bafa24e1a1f142 https://github.com/galaxyproject/galaxy/commit/d59352224c8f41ba8a1a9219b2ba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M test/galaxy_selenium/driver_factory.py Log Message: ----------- Set chrome to run headlessly -- todo configure via env var or switch Commit: 78c66f260c4bad5b2d632919fe14307602c8fb4e https://github.com/galaxyproject/galaxy/commit/78c66f260c4bad5b2d632919fe14… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Wait for logout redirect. Commit: 9e879b731f27d7b17161c83a60ef559aa529ec63 https://github.com/galaxyproject/galaxy/commit/9e879b731f27d7b17161c83a60ef… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_custom_builds.py Log Message: ----------- Drop now unused slowrender Commit: 817a8469b69e37c48e72a081a75d5c734e636624 https://github.com/galaxyproject/galaxy/commit/817a8469b69e37c48e72a081a75d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M test/galaxy_selenium/cli.py M test/galaxy_selenium/driver_factory.py M test/selenium_tests/framework.py Log Message: ----------- Tie chrome native headless mode into existing HEADLESS logic, functioning with or without pyvirtualdisplay. Commit: 71b01b1be3f70f239fe9114b43eeef87fd9801d9 https://github.com/galaxyproject/galaxy/commit/71b01b1be3f70f239fe9114b43ee… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M test/galaxy_selenium/cli.py M test/galaxy_selenium/driver_factory.py M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/framework.py Log Message: ----------- Merge pull request #7287 from dannon/slow_selenium_tests Fix remaining selenium tests and add headless testing option. Compare: https://github.com/galaxyproject/galaxy/compare/645031578d31...71b01b1be3f7

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[galaxyproject/usegalaxy-playbook] 4aeeb4: update TTS
by Martin Cech 04 Feb '19

04 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4aeeb45287d27fc2e4cf19ccfae7e2d31ecc8e77 https://github.com/galaxyproject/usegalaxy-playbook/commit/4aeeb45287d27fc2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- update TTS

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[galaxyproject/usegalaxy-playbook] 6f0e88: update MTS
by Martin Cech 04 Feb '19

04 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6f0e88a96ebb95fceecc50ba7e93fd4ad02bc0fe https://github.com/galaxyproject/usegalaxy-playbook/commit/6f0e88a96ebb95fc… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M env/toolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- update MTS

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[galaxyproject/galaxy] 8293b5: fix ObjectNotFound exception when exporting an his...
by John Chilton 04 Feb '19

04 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8293b5bb0a3f93a37907beb47489646d22aaad07 https://github.com/galaxyproject/galaxy/commit/8293b5bb0a3f93a37907beb47489… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2019-01-31 (Thu, 31 Jan 2019) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- fix ObjectNotFound exception when exporting an history Commit: 645031578d31801eee84ac79013d2da358212078 https://github.com/galaxyproject/galaxy/commit/645031578d31801eee84ac79013d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Merge pull request #7286 from abretaud/export_bug Fix ObjectNotFound exception when exporting an history Compare: https://github.com/galaxyproject/galaxy/compare/e8e3b0ca15b4...645031578d31

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[galaxyproject/galaxy] 6589bf: Drop support for Python 3.4. Officially support Py...
by Marius van den Beek 03 Feb '19

03 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6589bf3314faf7425bdd8b680a6e47a21fba0163 https://github.com/galaxyproject/galaxy/commit/6589bf3314faf7425bdd8b680a6e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-31 (Thu, 31 Jan 2019) Changed paths: M .travis.yml M scripts/check_python.py M tox.ini Log Message: ----------- Drop support for Python 3.4. Officially support Python >=3.5 xref. https://github.com/galaxyproject/galaxy/issues/7260 Commit: 82adf46a8a8c50458f7cf3dde35c6b24ab1ed2bc https://github.com/galaxyproject/galaxy/commit/82adf46a8a8c50458f7cf3dde35c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Speficy sniff order for BAM datatypes Fix flakey ``test_upload_datatype_auto`` integration test: https://jenkins.galaxyproject.org/job/docker-integration-py3/125/testReport… Commit: e8e3b0ca15b41fa4c573323e5c17ac51ad411eda https://github.com/galaxyproject/galaxy/commit/e8e3b0ca15b41fa4c573323e5c17… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-02-03 (Sun, 03 Feb 2019) Changed paths: M .travis.yml M config/datatypes_conf.xml.sample M scripts/check_python.py M tox.ini Log Message: ----------- Merge pull request #7291 from nsoranzo/drop_python3.4 Drop support for Python 3.4. Officially support Python >=3.5 Compare: https://github.com/galaxyproject/galaxy/compare/8c2066f07ac7...e8e3b0ca15b4

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[galaxyproject/galaxy] 37a9f2: Update logging config docs:
by Daniel Blankenberg 02 Feb '19

02 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 37a9f2bcea99ea55f7b36b94aa481558702ca897 https://github.com/galaxyproject/galaxy/commit/37a9f2bcea99ea55f7b36b94aa48… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-01-07 (Mon, 07 Jan 2019) Changed paths: M doc/Makefile M doc/source/admin/config_logging.rst Log Message: ----------- Update logging config docs: - The example for split file logging was invalid (referenced the nonexistent "generic" formatter) - Switch YAML dicts from 4- to 2-space indent to match the indentation style in galaxy.yml.sample - Document setting the message format with the YAML config - Reword a few things to hopefully be a bit clearer Commit: 79672df45221e4417d2c363bb262c19a2eb48b1f https://github.com/galaxyproject/galaxy/commit/79672df45221e4417d2c363bb262… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-01-09 (Wed, 09 Jan 2019) Changed paths: M config/job_conf.xml.sample_advanced M doc/source/admin/scaling.md Log Message: ----------- Update documentation for handler assignment method configurability and remove some legacy stuff. Commit: e9773f17335bea2d9106aa364d29f1f53454c883 https://github.com/galaxyproject/galaxy/commit/e9773f17335bea2d9106aa364d29… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-09 (Wed, 09 Jan 2019) Changed paths: M doc/source/admin/config_logging.rst Log Message: ----------- Minor spello Commit: 35c60489e8d52a47e82ae4462dfd7af5ced26f2b https://github.com/galaxyproject/galaxy/commit/35c60489e8d52a47e82ae4462dfd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-01-09 (Wed, 09 Jan 2019) Changed paths: M doc/source/admin/apache.md M doc/source/admin/nginx.md Log Message: ----------- Fixed link to proxy_package_layout in proxy docs Commit: 9a133e91f84d31e0c4e39c36301a368d66c48508 https://github.com/galaxyproject/galaxy/commit/9a133e91f84d31e0c4e39c36301a… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Remove spurious characters Co-Authored-By: natefoo <nate(a)bx.psu.edu> Commit: 74fcf12fa0968ef448fecb3f0ff9bd4736f91cd2 https://github.com/galaxyproject/galaxy/commit/74fcf12fa0968ef448fecb3f0ff9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Incorporate suggestions from @nsoranzo Commit: 49cbad5debb649013e142134b3b4ad8361125914 https://github.com/galaxyproject/galaxy/commit/49cbad5debb649013e142134b3b4… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2019-02-02 (Sat, 02 Feb 2019) Changed paths: M config/job_conf.xml.sample_advanced M doc/Makefile M doc/source/admin/apache.md M doc/source/admin/config_logging.rst M doc/source/admin/nginx.md M doc/source/admin/scaling.md Log Message: ----------- Merge pull request #7191 from natefoo/admin-docs-19.01 [19.01] Properly document handler assignment method configuration and fix logging configuration docs Compare: https://github.com/galaxyproject/galaxy/compare/038d1a1d83fa...49cbad5debb6

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[galaxyproject/galaxy] 038d1a: Revert "Darker tool form in workflow editor"
by Helena Rasche 01 Feb '19

01 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 038d1a1d83fac689e0d00f85cb59057bfe79bfcc https://github.com/galaxyproject/galaxy/commit/038d1a1d83fac689e0d00f85cb59… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Revert "Darker tool form in workflow editor" This reverts commit bdc6243a78b0fcf1e0d0a89670ec19dcb3aa9479.

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[galaxyproject/galaxy] bdc624: Darker tool form in workflow editor
by Helena Rasche 01 Feb '19

01 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: bdc6243a78b0fcf1e0d0a89670ec19dcb3aa9479 https://github.com/galaxyproject/galaxy/commit/bdc6243a78b0fcf1e0d0a89670ec… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Darker tool form in workflow editor

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