October 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] fa1781: Include check for updates to dependencies in tox a...
by GitHub 26 Oct '17

26 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fa178108d6bbd1defd2bfcc177f23d98f9d8c9ab https://github.com/galaxyproject/galaxy/commit/fa178108d6bbd1defd2bfcc177f2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M .travis.yml M Makefile M tox.ini Log Message: ----------- Include check for updates to dependencies in tox and Makefile. Commit: 862212ad40f408978a29dcc2c2e386ba087cb39c https://github.com/galaxyproject/galaxy/commit/862212ad40f408978a29dcc2c2e3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M .travis.yml M Makefile M tox.ini Log Message: ----------- Merge pull request #4788 from jmchilton/check_dependencies Include check for updates to dependencies in tox, Makefile, Travis. Compare: https://github.com/galaxyproject/galaxy/compare/82df013b66f9...862212ad40f4

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[galaxyproject/galaxy] ada0be: Updated QUnit testing.
by GitHub 26 Oct '17

26 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ada0be18f2e975ecdee8b24a4ba1c3ec06327a5d https://github.com/galaxyproject/galaxy/commit/ada0be18f2e975ecdee8b24a4ba1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M test/qunit/Gruntfile.js M test/qunit/package.json M test/qunit/test-app.js M test/qunit/test-common.js R test/qunit/test-libs/qunit-1.23.1.css R test/qunit/test-libs/qunit-1.23.1.js R test/qunit/test-libs/sinon-1.17.7.js R test/qunit/test-libs/sinon-qunit-1.0.0.js M test/qunit/tests/form_tests.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/graph.js M test/qunit/tests/hda-base.js M test/qunit/tests/history_contents_model_tests.js M test/qunit/tests/job-dag.js M test/qunit/tests/list-of-pairs-collection-creator.js M test/qunit/tests/masthead_tests.js M test/qunit/tests/metrics-logger.js M test/qunit/tests/modal_tests.js M test/qunit/tests/page_tests.js M test/qunit/tests/popover_tests.js M test/qunit/tests/ui_tests.js M test/qunit/tests/upload_dialog_tests.js M test/qunit/tests/utils_test.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Updated QUnit testing. - Update to QUnit from 1.23 to 2.0. - Update Sinon from 1.17 to 4.0.1. - Replace sinon-qunit with just basic calls to sinon itself (sinon-qunit not compatible with QUnit 2.0). - Replace all QUnit globals with dependency injected values (a lot of this had to be done for QUnit 2.0 anyway). - Improved error reporting in test-common.js if things don't go well loading modules. - Improved verbose logging in test Gruntfile. - Replace in-repo sinon and QUnit asserts (JS/CSS) with npm packges. Commit: 82df013b66f94c3acbf5e77202d9d9dec54c7767 https://github.com/galaxyproject/galaxy/commit/82df013b66f94c3acbf5e77202d9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M test/qunit/Gruntfile.js M test/qunit/package.json M test/qunit/test-app.js M test/qunit/test-common.js R test/qunit/test-libs/qunit-1.23.1.css R test/qunit/test-libs/qunit-1.23.1.js R test/qunit/test-libs/sinon-1.17.7.js R test/qunit/test-libs/sinon-qunit-1.0.0.js M test/qunit/tests/form_tests.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/graph.js M test/qunit/tests/hda-base.js M test/qunit/tests/history_contents_model_tests.js M test/qunit/tests/job-dag.js M test/qunit/tests/list-of-pairs-collection-creator.js M test/qunit/tests/masthead_tests.js M test/qunit/tests/metrics-logger.js M test/qunit/tests/modal_tests.js M test/qunit/tests/page_tests.js M test/qunit/tests/popover_tests.js M test/qunit/tests/ui_tests.js M test/qunit/tests/upload_dialog_tests.js M test/qunit/tests/utils_test.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge pull request #4855 from jmchilton/qunit_2.0 Updated QUnit testing. Compare: https://github.com/galaxyproject/galaxy/compare/efc9dbfb6cee...82df013b66f9

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[galaxyproject/infrastructure-playbook] fd646f: Set the pypiserver fallback URL to https://pypi in...
by GitHub 26 Oct '17

26 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: fd646f57d366dc1df48b86cf557c89105c07df91 https://github.com/galaxyproject/infrastructure-playbook/commit/fd646f57d36… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M galaxyenv/templates/supervisor/pypiserver.j2 Log Message: ----------- Set the pypiserver fallback URL to https://pypi instead of http:// due to PyPI discontinuing redirection of API endpoints. The default should be fixed with the release of a fix for pypiserver/pypiserver#179.

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[galaxyproject/galaxy] 08cb27: Add various elements to the Tool XML doc page
by GitHub 26 Oct '17

26 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 08cb278cc9612a70dcb9dd77ff3bfbdfd333ce2b https://github.com/galaxyproject/galaxy/commit/08cb278cc9612a70dcb9dd77ff3b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M doc/schema_template.md M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Add various elements to the Tool XML doc page In particular: - macros - edam_topics - edam_operations - environment_variables and subelement - request_param_translation and subelements Also: - reorder elements to follow IUC coding style - in examples: - use lowercase ``true`` and ``false`` for boolean attributes - add/use single quotes - minor doc fixes Commit: efc9dbfb6ceeaa3b9e2441a14417ba4f3913b8ef https://github.com/galaxyproject/galaxy/commit/efc9dbfb6ceeaa3b9e2441a14417… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M doc/schema_template.md M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #4871 from nsoranzo/tool_schema_improv Add various elements to the Tool XML doc page Compare: https://github.com/galaxyproject/galaxy/compare/7cfbb56a550c...efc9dbfb6cee

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[galaxyproject/usegalaxy-playbook] 9d36d8: Increase memory for cummeRbund and run DEXseq in t...
by GitHub 26 Oct '17

26 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9d36d82b142abcca81d79010a78ffa07c6cbd846 https://github.com/galaxyproject/usegalaxy-playbook/commit/9d36d82b142abcca… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Increase memory for cummeRbund and run DEXseq in the multi partition. Commit: 51582db4caee56d1769b8a1908a7be962a7b64c0 https://github.com/galaxyproject/usegalaxy-playbook/commit/51582db4caee56d1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py M env/main/files/galaxy/galaxy_version.yml M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Merge branch 'master' of github.com:/galaxyproject/usegalaxy-playbook Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/6c09553c4706...…

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[galaxyproject/usegalaxy-playbook] 283532: Increase memory factory to 11x for RNASTAR jobs us...
by GitHub 26 Oct '17

26 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 28353244893278376ecf421b4058271af4778e73 https://github.com/galaxyproject/usegalaxy-playbook/commit/2835324489327837… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py Log Message: ----------- Increase memory factory to 11x for RNASTAR jobs using a custom genome. Commit: 45b3803be7ac629f9f23be2c2ffbf6ffa78fcd24 https://github.com/galaxyproject/usegalaxy-playbook/commit/45b3803be7ac629f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test Commit: 6c09553c4706db9e4d6fa946e95570973847ce8e https://github.com/galaxyproject/usegalaxy-playbook/commit/6c09553c4706db9e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/6e63eccbc5fa...…

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[galaxyproject/galaxy] dd6092: Only subqueryload latest_workflow instead of all w...
by GitHub 26 Oct '17

26 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dd609265a20a820da4313e21204075836ba51567 https://github.com/galaxyproject/galaxy/commit/dd609265a20a820da4313e212040… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Only subqueryload latest_workflow instead of all workflows Commit: b9adcc81e866a949601f815dd778b62bef631461 https://github.com/galaxyproject/galaxy/commit/b9adcc81e866a949601f815dd778… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #4844 from mvdbeek/workflow_performance_issues [17.09] Only subqueryload latest_workflow instead of all workflows Commit: 7cfbb56a550c6cbf814a09729303bb0eec22f509 https://github.com/galaxyproject/galaxy/commit/7cfbb56a550c6cbf814a09729303… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge remote-tracking branch 'origin/release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/800a7faf2703...7cfbb56a550c

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[galaxyproject/galaxy] 162bdd: Simple tests for data source responses.
by GitHub 26 Oct '17

26 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 162bddd96c160cbc7bf0e681fa097f14fee0d5e5 https://github.com/galaxyproject/galaxy/commit/162bddd96c160cbc7bf0e681fa09… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M test/api/test_tools.py A test/functional/tools/data_source.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/test_data_source.xml Log Message: ----------- Simple tests for data source responses. - Verify a simple data source works when responding via the API. - Verify a data source sending back a file:// parameter is blocked (GX-2017-0004/GX-2017-0003 - it is tracked different ways in the commit message and in the security issue tracker). Commit: acf39e8e025a42829a56bbc1adb5cf382daae6b2 https://github.com/galaxyproject/galaxy/commit/acf39e8e025a42829a56bbc1adb5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Fix tool XSD for data source tools. I guess it has never been applied to a data source? Commit: 800a7faf2703823651a450a02257fbbe9b85b077 https://github.com/galaxyproject/galaxy/commit/800a7faf2703823651a450a02257… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py A test/functional/tools/data_source.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/test_data_source.xml Log Message: ----------- Merge pull request #4863 from jmchilton/data_source_security_tests Simple tests for data source responses. Compare: https://github.com/galaxyproject/galaxy/compare/1ceb778b6381...800a7faf2703

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[galaxyproject/galaxy] dd6092: Only subqueryload latest_workflow instead of all w...
by GitHub 26 Oct '17

26 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: dd609265a20a820da4313e21204075836ba51567 https://github.com/galaxyproject/galaxy/commit/dd609265a20a820da4313e212040… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Only subqueryload latest_workflow instead of all workflows Commit: b9adcc81e866a949601f815dd778b62bef631461 https://github.com/galaxyproject/galaxy/commit/b9adcc81e866a949601f815dd778… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #4844 from mvdbeek/workflow_performance_issues [17.09] Only subqueryload latest_workflow instead of all workflows Compare: https://github.com/galaxyproject/galaxy/compare/1baed58e1e7c...b9adcc81e866

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[galaxyproject/galaxy] e780b0: Require flake8-import-order >=0.14
by GitHub 26 Oct '17

26 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e780b0fe91b4d7d8fe3e66847979f15d8467cdfb https://github.com/galaxyproject/galaxy/commit/e780b0fe91b4d7d8fe3e66847979… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M lib/galaxy/util/path/ntpath.py M tox.ini Log Message: ----------- Require flake8-import-order >=0.14 Commit: 1ceb778b63815433474519ac29d0ef46768ab335 https://github.com/galaxyproject/galaxy/commit/1ceb778b63815433474519ac29d0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M lib/galaxy/util/path/ntpath.py M tox.ini Log Message: ----------- Merge pull request #4869 from nsoranzo/flake8_0.14 Require flake8-import-order >=0.14 Compare: https://github.com/galaxyproject/galaxy/compare/561ccfe815e0...1ceb778b6381

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