galaxy-commits September 2018

galaxy-commits@lists.galaxyproject.org

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[galaxyproject/galaxy] d645d8: Update bx-python to 0.8.2
by GitHub 05 Sep '18

05 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d645d80443c23d89fc65f3bb33caf4be9c9c7f21 https://github.com/galaxyproject/galaxy/commit/d645d80443c23d89fc65f3bb33ca… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Update bx-python to 0.8.2 to include https://github.com/bxlab/bx-python/pull/35 . Fix https://github.com/galaxyproject/galaxy/issues/6379 and https://github.com/galaxyproject/galaxy/issues/6598 . Commit: 309c13b5ba42dc3ee27982202b3ed320d9ecb214 https://github.com/galaxyproject/galaxy/commit/309c13b5ba42dc3ee27982202b3e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-05 (Wed, 05 Sep 2018) Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/8e7088b1a074...309c13b5ba42 **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] d645d8: Update bx-python to 0.8.2
by GitHub 05 Sep '18

05 Sep '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: d645d80443c23d89fc65f3bb33caf4be9c9c7f21 https://github.com/galaxyproject/galaxy/commit/d645d80443c23d89fc65f3bb33ca… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Update bx-python to 0.8.2 to include https://github.com/bxlab/bx-python/pull/35 . Fix https://github.com/galaxyproject/galaxy/issues/6379 and https://github.com/galaxyproject/galaxy/issues/6598 . **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] 85cab9: Update bx-python to 0.8.2
by GitHub 05 Sep '18

05 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 85cab90689f07fd17b15f7d52efc5e0cae720056 https://github.com/galaxyproject/galaxy/commit/85cab90689f07fd17b15f7d52efc… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Update bx-python to 0.8.2 to include https://github.com/bxlab/bx-python/pull/35 . Fix https://github.com/galaxyproject/galaxy/issues/6379 and https://github.com/galaxyproject/galaxy/issues/6598 . Commit: 8e7088b1a0744df3c35871d24b91dfd76fe310c3 https://github.com/galaxyproject/galaxy/commit/8e7088b1a0744df3c35871d24b91… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #6670 from nsoranzo/release_18.05_bx-python_0.8.2 [18.05] Update bx-python to 0.8.2 Compare: https://github.com/galaxyproject/galaxy/compare/09f6e1f9ee08...8e7088b1a074 **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] 296105: row ids that are all numeric become ints...
by GitHub 05 Sep '18

05 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 296105ee395194c48d962671a8c367469ea74907 https://github.com/galaxyproject/galaxy/commit/296105ee395194c48d962671a8c3… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- row ids that are all numeric become ints... Since the "F" prefix is checked with substring, row_id must always be a string Commit: 55d350d015f20afc1c350130caaa0aa9858b7aa0 https://github.com/galaxyproject/galaxy/commit/55d350d015f20afc1c350130caaa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M static/scripts/admin.toolshed.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/chart.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/galaxy.interactive_environments.js M static/scripts/galaxy.js M static/scripts/galaxy.library.js M static/scripts/galaxy.pages.js M static/scripts/i18n.js M static/scripts/layout/communication-server-view.js M static/scripts/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/modal.js M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/layout/router.js M static/scripts/layout/scratchbook.js M static/scripts/legacy/grid/grid-model.js M static/scripts/legacy/grid/grid-template.js M static/scripts/legacy/grid/grid-view.js M static/scripts/mocha/test.js M static/scripts/mocha/tests/rules_tests.js M static/scripts/mvc/annotation.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-choice.js M 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static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-model.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/upload/upload-utils.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/visualization/chart/chart-client.js M static/scripts/mvc/visualization/chart/components/model.js M static/scripts/mvc/visualization/chart/components/screenshot.js M static/scripts/mvc/visualization/chart/utilities/datasets.js M static/scripts/mvc/visualization/chart/utilities/jobs.js M static/scripts/mvc/visualization/chart/utilities/series.js M static/scripts/mvc/visualization/chart/views/description.js M static/scripts/mvc/visualization/chart/views/editor.js M static/scripts/mvc/visualization/chart/views/groups.js M static/scripts/mvc/visualization/chart/views/menu.js M static/scripts/mvc/visualization/chart/views/settings.js M static/scripts/mvc/visualization/chart/views/viewer.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/webhooks.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/de/locale.js M static/scripts/nls/es/locale.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/scripts/onload.js M static/scripts/polyfills.js M static/scripts/reports/run_stats.js M static/scripts/toolshed/groups/group-detail-view.js M static/scripts/toolshed/groups/group-list-view.js M static/scripts/toolshed/groups/group-listrow-view.js M static/scripts/toolshed/groups/group-model.js M static/scripts/toolshed/toolshed.groups.js M static/scripts/ui/autocom_tagging.js M static/scripts/ui/editable-text.js M static/scripts/ui/fa-icon-button.js M static/scripts/ui/filter-control.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/ui/popupmenu.js M static/scripts/ui/scroll-panel.js M static/scripts/ui/search-input.js M static/scripts/utils/add-logging.js M static/scripts/utils/ajax-queue.js M static/scripts/utils/async-save-text.js M static/scripts/utils/config.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/levenshtein.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/natural-sort.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/bbi-data-manager.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/scripts/viz/viz_views.js Log Message: ----------- Add static for 2a148ff1ec37c68e280c431fceee88ee0510e017 Commit: 03c485ee45e96784b269896a23223d233c566b89 https://github.com/galaxyproject/galaxy/commit/03c485ee45e96784b269896a2322… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/admin.toolshed.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/chart.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/galaxy.interactive_environments.js M static/scripts/galaxy.js M static/scripts/galaxy.library.js M static/scripts/galaxy.pages.js M static/scripts/i18n.js M static/scripts/layout/communication-server-view.js M static/scripts/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/modal.js M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/layout/router.js M static/scripts/layout/scratchbook.js M static/scripts/legacy/grid/grid-model.js M static/scripts/legacy/grid/grid-template.js M static/scripts/legacy/grid/grid-view.js M static/scripts/mocha/test.js M static/scripts/mocha/tests/rules_tests.js M static/scripts/mvc/annotation.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-choice.js M 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static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-model.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/upload/upload-utils.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/visualization/chart/chart-client.js M static/scripts/mvc/visualization/chart/components/model.js M static/scripts/mvc/visualization/chart/components/screenshot.js M static/scripts/mvc/visualization/chart/utilities/datasets.js M static/scripts/mvc/visualization/chart/utilities/jobs.js M static/scripts/mvc/visualization/chart/utilities/series.js M static/scripts/mvc/visualization/chart/views/description.js M static/scripts/mvc/visualization/chart/views/editor.js M static/scripts/mvc/visualization/chart/views/groups.js M static/scripts/mvc/visualization/chart/views/menu.js M static/scripts/mvc/visualization/chart/views/settings.js M static/scripts/mvc/visualization/chart/views/viewer.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/webhooks.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/de/locale.js M static/scripts/nls/es/locale.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/scripts/onload.js M static/scripts/polyfills.js M static/scripts/reports/run_stats.js M static/scripts/toolshed/groups/group-detail-view.js M static/scripts/toolshed/groups/group-list-view.js M static/scripts/toolshed/groups/group-listrow-view.js M static/scripts/toolshed/groups/group-model.js M static/scripts/toolshed/toolshed.groups.js M static/scripts/ui/autocom_tagging.js M static/scripts/ui/editable-text.js M static/scripts/ui/fa-icon-button.js M static/scripts/ui/filter-control.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/ui/popupmenu.js M static/scripts/ui/scroll-panel.js M static/scripts/ui/search-input.js M static/scripts/utils/add-logging.js M static/scripts/utils/ajax-queue.js M static/scripts/utils/async-save-text.js M static/scripts/utils/config.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/levenshtein.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/natural-sort.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/bbi-data-manager.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/scripts/viz/viz_views.js Log Message: ----------- Merge pull request #6639 from bwlang/patch-2 [18.05] row ids that are all numeric become ints... Commit: 09f6e1f9ee08f4da770d18e2fb33e6434c64ba90 https://github.com/galaxyproject/galaxy/commit/09f6e1f9ee08f4da770d18e2fb33… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/8148bd91deb4...09f6e1f9ee08 **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] 0b6444: Skip tool tests in test/functional/known_broken_to...
by GitHub 05 Sep '18

05 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0b64442ed3d06bd7fdf9f0fbb53520d28e9332b9 https://github.com/galaxyproject/galaxy/commit/0b64442ed3d06bd7fdf9f0fbb535… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: A test/functional/known_broken_tools.txt M test/functional/test_toolbox_pytest.py Log Message: ----------- Skip tool tests in test/functional/known_broken_tools.txt Commit: 300ab73c10332968a98eb5f77a85abc66a3f4686 https://github.com/galaxyproject/galaxy/commit/300ab73c10332968a98eb5f77a85… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M pytest.ini M test/functional/test_toolbox_pytest.py Log Message: ----------- Mark skipped tests instead of not collecting them Also marks tests as tool or data_manager, so `pytest -m <tool|data_manager>` can be used to select a subset of tests. Commit: 6f299202313c3b40d357468e9ba0e9b32f858038 https://github.com/galaxyproject/galaxy/commit/6f299202313c3b40d357468e9ba0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Use pytest for -framework, -installed, -data_manager, -migrated tests Commit: 546b90a6985cc6a8e4d87482778c8ac275c9903f https://github.com/galaxyproject/galaxy/commit/546b90a6985cc6a8e4d87482778c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Add additional test target for tools in tool_conf.xml.main Commit: e73257f8ed2556a94a6e58efff62ed1873709f42 https://github.com/galaxyproject/galaxy/commit/e73257f8ed2556a94a6e58efff62… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M test/functional/test_toolbox_pytest.py Log Message: ----------- Set conda_auto_init and conda_auto_install to true for pytest driver Commit: 7f807ce971e8d743dca0f0438e5ce078f742ec65 https://github.com/galaxyproject/galaxy/commit/7f807ce971e8d743dca0f0438e5c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Fix shell syntax Commit: 9099e73a3e00658082891fae7ea3de0774cce2ad https://github.com/galaxyproject/galaxy/commit/9099e73a3e00658082891fae7ea3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M .coveragerc Log Message: ----------- Add include-ignored, otherwise spams stderr out Commit: d476fcc072dbcb8e3b19f511dc43ae731e7c97e0 https://github.com/galaxyproject/galaxy/commit/d476fcc072dbcb8e3b19f511dc43… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M lib/galaxy/jobs/runners/util/kill.py Log Message: ----------- Fix LocalShell on python3 Commit: 1c64cdd674fcbfc0f077f5d31947dd9b6c6e9149 https://github.com/galaxyproject/galaxy/commit/1c64cdd674fcbfc0f077f5d31947… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M pytest.ini M run_tests.sh M tox.ini Log Message: ----------- Use pytest to run unit and doctests Commit: 1152a19fd2cd5d6589becde3c7ebdd6435a33cff https://github.com/galaxyproject/galaxy/commit/1152a19fd2cd5d6589becde3c7eb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Use pytest-cov for testing coverage Commit: 66c64ccfe46cfd91bcffabaf2b4bddd7b86cef91 https://github.com/galaxyproject/galaxy/commit/66c64ccfe46cfd91bcffabaf2b4b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py Log Message: ----------- Adapt dynamic_tool_destination unit tests to pytest as driver The log capturing seems to be a bit different Commit: d9a2c5a970aafabe101842991a34074701f8854c https://github.com/galaxyproject/galaxy/commit/d9a2c5a970aafabe101842991a34… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Don't test tools in tool_conf.xml.sample as part of -framework This replicates what the FrameworkToolsGalaxyTestDriver does. Commit: aa0becad0be33ee7fe1d430c64f1d89f475ca6e2 https://github.com/galaxyproject/galaxy/commit/aa0becad0be33ee7fe1d430c64f1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Simplify tool_conf selection in run_tests.sh Drops -with_framework_test_tools altogether. Thanks @nsoranzo. Commit: 8148bd91deb4d4f9b621b6e3097ae0f01ba81abd https://github.com/galaxyproject/galaxy/commit/8148bd91deb4d4f9b621b6e3097a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M .coveragerc M lib/galaxy/jobs/runners/util/kill.py M pytest.ini M run_tests.sh A test/functional/known_broken_tools.txt M test/functional/test_toolbox_pytest.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M tox.ini Log Message: ----------- Merge pull request #6638 from mvdbeek/move_tests_to_pytest_setup Move tests to pytest setup Compare: https://github.com/galaxyproject/galaxy/compare/bc1526ab2dd5...8148bd91deb4 **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] 73b6e8: Eliminate more queries in history.add_dataset(s) b...
by GitHub 04 Sep '18

04 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 73b6e81a0ab2f646de7d3709bcbf9e4284a1c439 https://github.com/galaxyproject/galaxy/commit/73b6e81a0ab2f646de7d3709bcbf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py Log Message: ----------- Eliminate more queries in history.add_dataset(s) by using cached IDs. Commit: 74bb5434a0e9020673f1d4acaab98a6bd9865268 https://github.com/galaxyproject/galaxy/commit/74bb5434a0e9020673f1d4acaab9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Eliminate old and invalid tool optimization comment. Commit: b2fe48a6be69bd5c05357ae0a8a7fe07f8d314db https://github.com/galaxyproject/galaxy/commit/b2fe48a6be69bd5c05357ae0a8a7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Allow history_id to be specified instead of history in check_elements. Commit: bc1526ab2dd5044f3ea274c176fcb43b490b0c63 https://github.com/galaxyproject/galaxy/commit/bc1526ab2dd5044f3ea274c176fc… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-04 (Tue, 04 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #6644 from jmchilton/add_datasets Small Optimizations to Adding Datasets to History Compare: https://github.com/galaxyproject/galaxy/compare/3ca449fa73fc...bc1526ab2dd5 **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] 3c5991: Allow group tag selection also for multiple="true"...
by GitHub 04 Sep '18

04 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3c5991632246d5fd404b269507642f819abf7d68 https://github.com/galaxyproject/galaxy/commit/3c5991632246d5fd404b26950764… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Allow group tag selection also for multiple="true" inputs Commit: 3ca449fa73fcc18389876756814fdaa5bb6e2aed https://github.com/galaxyproject/galaxy/commit/3ca449fa73fcc18389876756814f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-04 (Tue, 04 Sep 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Merge pull request #6661 from mvdbeek/group_tags_for_multiple_true_inputs Allow group tag selection also for multiple="true" inputs Compare: https://github.com/galaxyproject/galaxy/compare/b9d07aed22c5...3ca449fa73fc **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] 77706a: Update application documentation
by GitHub 03 Sep '18

03 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 77706a8e62f6c7ffafc923b9f94f3359089e8ee9 https://github.com/galaxyproject/galaxy/commit/77706a8e62f6c7ffafc923b9f94f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M doc/source/lib/galaxy.actions.rst M doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.authnz.rst M doc/source/lib/galaxy.containers.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.datatypes.rst R doc/source/lib/galaxy.external_services.result_handlers.rst R doc/source/lib/galaxy.external_services.rst R doc/source/lib/galaxy.jobs.deferred.rst M doc/source/lib/galaxy.jobs.metrics.instrumenters.rst M doc/source/lib/galaxy.jobs.rst R doc/source/lib/galaxy.jobs.runners.util.drmaa.rst M doc/source/lib/galaxy.jobs.runners.util.rst M doc/source/lib/galaxy.managers.rst M doc/source/lib/galaxy.objectstore.rst M doc/source/lib/galaxy.rst R doc/source/lib/galaxy.sample_tracking.rst M doc/source/lib/galaxy.tools.cwl.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.tools.deps.rst A doc/source/lib/galaxy.tools.error_reports.plugins.rst A doc/source/lib/galaxy.tools.error_reports.rst M doc/source/lib/galaxy.tools.parser.rst M doc/source/lib/galaxy.tools.rst M doc/source/lib/galaxy.tools.toolbox.lineages.rst M doc/source/lib/galaxy.tools.toolbox.rst M doc/source/lib/galaxy.tools.verify.rst R doc/source/lib/galaxy.util.backports.rst R doc/source/lib/galaxy.util.log.rst A doc/source/lib/galaxy.util.logging.rst A doc/source/lib/galaxy.util.path.rst M doc/source/lib/galaxy.util.rst M doc/source/lib/galaxy.visualization.plugins.rst R doc/source/lib/galaxy.web.base.controllers.rst M doc/source/lib/galaxy.web.base.rst M doc/source/lib/galaxy.web.framework.helpers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.web.framework.rst M doc/source/lib/galaxy.web.stack.rst M doc/source/lib/galaxy.webapps.galaxy.api.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst A doc/source/lib/galaxy.webapps.reports.framework.rst M doc/source/lib/galaxy.webapps.reports.rst M doc/source/lib/galaxy.webapps.rst A doc/source/lib/galaxy.workflow.resources.rst M doc/source/lib/galaxy.workflow.rst M doc/source/lib/tool_shed.util.rst Log Message: ----------- Update application documentation With ``` make -C doc/ updaterst ``` Commit: ad02c53154a3d3046a814b838cffdf0a79ac9a13 https://github.com/galaxyproject/galaxy/commit/ad02c53154a3d3046a814b838cff… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M config/error_report.yml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/tool_shed.yml.sample M doc/source/admin/cluster.md M doc/source/admin/conda_faq.rst M doc/source/admin/config.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M doc/source/admin/jobs.md M doc/source/admin/production.md M doc/source/admin/scaling.md M doc/source/admin/special_topics/performance_tracking.rst M doc/source/api_doc.rst M doc/source/conf.py M doc/source/releases/16.04_announce.rst M doc/source/releases/16.10.rst M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/model/search.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/uwsgi_schema.yml M run_tests.sh M scripts/api/README M scripts/slideshow/example.md M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/base/workflows_format_2/interface.py Log Message: ----------- Fix many links Commit: 59c1ed2266504a2bd03e80e9f4ec72664148524f https://github.com/galaxyproject/galaxy/commit/59c1ed2266504a2bd03e80e9f4ec… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M config/galaxy.yml.sample M doc/parse_gx_xsd.py M doc/schema_template.md M doc/source/admin/galaxy_options.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Various doc fixes Commit: b9d07aed22c59c2aeb92e30d18953bc6fecea0a6 https://github.com/galaxyproject/galaxy/commit/b9d07aed22c59c2aeb92e30d1895… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M config/error_report.yml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/tool_shed.yml.sample M doc/parse_gx_xsd.py M doc/schema_template.md M doc/source/admin/cluster.md M doc/source/admin/conda_faq.rst M doc/source/admin/config.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M doc/source/admin/jobs.md M doc/source/admin/production.md M doc/source/admin/scaling.md M doc/source/admin/special_topics/performance_tracking.rst M doc/source/api_doc.rst M doc/source/conf.py M doc/source/lib/galaxy.actions.rst M doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.authnz.rst M doc/source/lib/galaxy.containers.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.datatypes.rst R doc/source/lib/galaxy.external_services.result_handlers.rst R doc/source/lib/galaxy.external_services.rst R doc/source/lib/galaxy.jobs.deferred.rst M doc/source/lib/galaxy.jobs.metrics.instrumenters.rst M doc/source/lib/galaxy.jobs.rst R doc/source/lib/galaxy.jobs.runners.util.drmaa.rst M doc/source/lib/galaxy.jobs.runners.util.rst M doc/source/lib/galaxy.managers.rst M doc/source/lib/galaxy.objectstore.rst M doc/source/lib/galaxy.rst R doc/source/lib/galaxy.sample_tracking.rst M doc/source/lib/galaxy.tools.cwl.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.tools.deps.rst A doc/source/lib/galaxy.tools.error_reports.plugins.rst A doc/source/lib/galaxy.tools.error_reports.rst M doc/source/lib/galaxy.tools.parser.rst M doc/source/lib/galaxy.tools.rst M doc/source/lib/galaxy.tools.toolbox.lineages.rst M doc/source/lib/galaxy.tools.toolbox.rst M doc/source/lib/galaxy.tools.verify.rst R doc/source/lib/galaxy.util.backports.rst R doc/source/lib/galaxy.util.log.rst A doc/source/lib/galaxy.util.logging.rst A doc/source/lib/galaxy.util.path.rst M doc/source/lib/galaxy.util.rst M doc/source/lib/galaxy.visualization.plugins.rst R doc/source/lib/galaxy.web.base.controllers.rst M doc/source/lib/galaxy.web.base.rst M doc/source/lib/galaxy.web.framework.helpers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.web.framework.rst M doc/source/lib/galaxy.web.stack.rst M doc/source/lib/galaxy.webapps.galaxy.api.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst A doc/source/lib/galaxy.webapps.reports.framework.rst M doc/source/lib/galaxy.webapps.reports.rst M doc/source/lib/galaxy.webapps.rst A doc/source/lib/galaxy.workflow.resources.rst M doc/source/lib/galaxy.workflow.rst M doc/source/lib/tool_shed.util.rst M doc/source/releases/16.04_announce.rst M doc/source/releases/16.10.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/model/search.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/uwsgi_schema.yml M run_tests.sh M scripts/api/README M scripts/slideshow/example.md M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/base/workflows_format_2/interface.py Log Message: ----------- Merge pull request #6662 from nsoranzo/doc_fixes2 Various link and documentation fixes Compare: https://github.com/galaxyproject/galaxy/compare/76d89d020f56...b9d07aed22c5 **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] ea34aa: adding 4 new GROMACS datatypes: cpt, xtc, top, and...
by GitHub 03 Sep '18

03 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ea34aa84be9be03489e541b928ea57adfb087e80 https://github.com/galaxyproject/galaxy/commit/ea34aa84be9be03489e541b928ea… Author: simonbray <sbray1371(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/tabular.py R lib/galaxy/datatypes/test/em.trr A lib/galaxy/datatypes/test/md.cpt A lib/galaxy/datatypes/test/md.trr A lib/galaxy/datatypes/test/md.xtc M lib/galaxy/datatypes/text.py Log Message: ----------- adding 4 new GROMACS datatypes: cpt, xtc, top, and gro shrinking test files Commit: 6a730bc5821c94d25411cb51a7033ab56064617b https://github.com/galaxyproject/galaxy/commit/6a730bc5821c94d25411cb51a703… Author: simonbray <sbray1371(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py Log Message: ----------- linting Commit: 3c7d7d9d49d49781f822a36c3bdbd860ddc0e8f0 https://github.com/galaxyproject/galaxy/commit/3c7d7d9d49d49781f822a36c3bdb… Author: simonbray <sbray1371(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py Log Message: ----------- tightening up the sniffer functions Commit: 0d97c55cc7256ccff7285d57dd5ed3ec64616887 https://github.com/galaxyproject/galaxy/commit/0d97c55cc7256ccff7285d57dd5e… Author: sb635 <sb635(a)bmd6.physik.privat> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- add refs for trr/xtc/cpt binary magic numbers Commit: 56d55399ebe2ecd614a7ba5a146739f58e917541 https://github.com/galaxyproject/galaxy/commit/56d55399ebe2ecd614a7ba5a1467… Author: sb635 <sb635(a)bmd6.physik.privat> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py Log Message: ----------- removing top and gro sniffers, at least for now Commit: e59219deabe89cbf3a98f984bf54d314157d6599 https://github.com/galaxyproject/galaxy/commit/e59219deabe89cbf3a98f984bf54… Author: simonbray <sbray1371(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- created new GmxBinary class from which xtc, trr, cpt inherit Commit: 5d15063f7de0b7b07f7bad5d7dbbb31f5e872855 https://github.com/galaxyproject/galaxy/commit/5d15063f7de0b7b07f7bad5d7dbb… Author: simonbray <sbray1371(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- remove __init__() from GmxBinary subclasses Commit: 09d349cbfff5623a52f23ccd480b4975759f8d8b https://github.com/galaxyproject/galaxy/commit/09d349cbfff5623a52f23ccd480b… Author: Simon Bray <32272674+simonbray(a)users.noreply.github.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- default for magic_number None not 0 Commit: ed641aceb9d117aee7a83de9bbcd7a7876d20703 https://github.com/galaxyproject/galaxy/commit/ed641aceb9d117aee7a83de9bbcd… Author: simonbray <sbray1371(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- remove __init__ from GmxBinary Commit: 76d89d020f56e202939a26b06972e3bce489dd3b https://github.com/galaxyproject/galaxy/commit/76d89d020f56e202939a26b06972… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py R lib/galaxy/datatypes/test/em.trr A lib/galaxy/datatypes/test/md.cpt A lib/galaxy/datatypes/test/md.trr A lib/galaxy/datatypes/test/md.xtc Log Message: ----------- Merge pull request #6655 from simonbray/dev Adding 4 new GROMACS datatypes: cpt, xtc, top, and gro Compare: https://github.com/galaxyproject/galaxy/compare/410ec1927c34...76d89d020f56 **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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