August 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 85c971: Remove existing wrong tool version associations in...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 85c971287ba6b316a970053a2d76f8c49d82f16b https://github.com/galaxyproject/galaxy/commit/85c971287ba6b316a970053a2d76… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Remove existing wrong tool version associations in ToolVersionManager.handle_tool_versions() . Fix #552. To fix a tool with a wrong lineage, click on "Set tool versions" on the "Repository Actions" menu. Commit: 360a6ad76d4325a634bbd13314351028f2965bff https://github.com/galaxyproject/galaxy/commit/360a6ad76d4325a634bbd1331435… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge pull request #634 from nsoranzo/release_14.10 [14.10] Backport tool lineage fix. Commit: 46e67b5bfa041050f6fa5e99aee945953e1c5cc2 https://github.com/galaxyproject/galaxy/commit/46e67b5bfa041050f6fa5e99aee9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_14.10' into release_15.01 Commit: b23acda7d8657bb9ab66c4c3dbc37706ae6bc4bd https://github.com/galaxyproject/galaxy/commit/b23acda7d8657bb9ab66c4c3dbc3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: 5b604253364eb29fecf94ed4cd4adca5e69bc060 https://github.com/galaxyproject/galaxy/commit/5b604253364eb29fecf94ed4cd4a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Commit: 60d3e71f0e10c3997a57a78268361ac9cbcd4560 https://github.com/galaxyproject/galaxy/commit/60d3e71f0e10c3997a57a7826836… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: e51c6bba46c83cdb8ecd1b42b34da8280ece180c https://github.com/galaxyproject/galaxy/commit/e51c6bba46c83cdb8ecd1b42b34d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_15.07' Compare: https://github.com/galaxyproject/galaxy/compare/d055102596d8...e51c6bba46c8

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[galaxyproject/galaxy] 85c971: Remove existing wrong tool version associations in...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: 85c971287ba6b316a970053a2d76f8c49d82f16b https://github.com/galaxyproject/galaxy/commit/85c971287ba6b316a970053a2d76… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Remove existing wrong tool version associations in ToolVersionManager.handle_tool_versions() . Fix #552. To fix a tool with a wrong lineage, click on "Set tool versions" on the "Repository Actions" menu. Commit: 360a6ad76d4325a634bbd13314351028f2965bff https://github.com/galaxyproject/galaxy/commit/360a6ad76d4325a634bbd1331435… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge pull request #634 from nsoranzo/release_14.10 [14.10] Backport tool lineage fix. Commit: 46e67b5bfa041050f6fa5e99aee945953e1c5cc2 https://github.com/galaxyproject/galaxy/commit/46e67b5bfa041050f6fa5e99aee9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_14.10' into release_15.01 Commit: b23acda7d8657bb9ab66c4c3dbc37706ae6bc4bd https://github.com/galaxyproject/galaxy/commit/b23acda7d8657bb9ab66c4c3dbc3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: 5b604253364eb29fecf94ed4cd4adca5e69bc060 https://github.com/galaxyproject/galaxy/commit/5b604253364eb29fecf94ed4cd4a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Commit: 60d3e71f0e10c3997a57a78268361ac9cbcd4560 https://github.com/galaxyproject/galaxy/commit/60d3e71f0e10c3997a57a7826836… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Compare: https://github.com/galaxyproject/galaxy/compare/e8f90429e2ca...60d3e71f0e10

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[galaxyproject/galaxy] 85c971: Remove existing wrong tool version associations in...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/release_15.05 Home: https://github.com/galaxyproject/galaxy Commit: 85c971287ba6b316a970053a2d76f8c49d82f16b https://github.com/galaxyproject/galaxy/commit/85c971287ba6b316a970053a2d76… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Remove existing wrong tool version associations in ToolVersionManager.handle_tool_versions() . Fix #552. To fix a tool with a wrong lineage, click on "Set tool versions" on the "Repository Actions" menu. Commit: 360a6ad76d4325a634bbd13314351028f2965bff https://github.com/galaxyproject/galaxy/commit/360a6ad76d4325a634bbd1331435… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge pull request #634 from nsoranzo/release_14.10 [14.10] Backport tool lineage fix. Commit: 46e67b5bfa041050f6fa5e99aee945953e1c5cc2 https://github.com/galaxyproject/galaxy/commit/46e67b5bfa041050f6fa5e99aee9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_14.10' into release_15.01 Commit: b23acda7d8657bb9ab66c4c3dbc37706ae6bc4bd https://github.com/galaxyproject/galaxy/commit/b23acda7d8657bb9ab66c4c3dbc3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: 5b604253364eb29fecf94ed4cd4adca5e69bc060 https://github.com/galaxyproject/galaxy/commit/5b604253364eb29fecf94ed4cd4a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Compare: https://github.com/galaxyproject/galaxy/compare/c569f7856d41...5b604253364e

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[galaxyproject/galaxy] 85c971: Remove existing wrong tool version associations in...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/release_15.03 Home: https://github.com/galaxyproject/galaxy Commit: 85c971287ba6b316a970053a2d76f8c49d82f16b https://github.com/galaxyproject/galaxy/commit/85c971287ba6b316a970053a2d76… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Remove existing wrong tool version associations in ToolVersionManager.handle_tool_versions() . Fix #552. To fix a tool with a wrong lineage, click on "Set tool versions" on the "Repository Actions" menu. Commit: 360a6ad76d4325a634bbd13314351028f2965bff https://github.com/galaxyproject/galaxy/commit/360a6ad76d4325a634bbd1331435… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge pull request #634 from nsoranzo/release_14.10 [14.10] Backport tool lineage fix. Commit: 46e67b5bfa041050f6fa5e99aee945953e1c5cc2 https://github.com/galaxyproject/galaxy/commit/46e67b5bfa041050f6fa5e99aee9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_14.10' into release_15.01 Commit: b23acda7d8657bb9ab66c4c3dbc37706ae6bc4bd https://github.com/galaxyproject/galaxy/commit/b23acda7d8657bb9ab66c4c3dbc3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Compare: https://github.com/galaxyproject/galaxy/compare/e06d6a1ccae7...b23acda7d865

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[galaxyproject/galaxy] 85c971: Remove existing wrong tool version associations in...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/release_15.01 Home: https://github.com/galaxyproject/galaxy Commit: 85c971287ba6b316a970053a2d76f8c49d82f16b https://github.com/galaxyproject/galaxy/commit/85c971287ba6b316a970053a2d76… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Remove existing wrong tool version associations in ToolVersionManager.handle_tool_versions() . Fix #552. To fix a tool with a wrong lineage, click on "Set tool versions" on the "Repository Actions" menu. Commit: 360a6ad76d4325a634bbd13314351028f2965bff https://github.com/galaxyproject/galaxy/commit/360a6ad76d4325a634bbd1331435… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge pull request #634 from nsoranzo/release_14.10 [14.10] Backport tool lineage fix. Commit: 46e67b5bfa041050f6fa5e99aee945953e1c5cc2 https://github.com/galaxyproject/galaxy/commit/46e67b5bfa041050f6fa5e99aee9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_14.10' into release_15.01 Compare: https://github.com/galaxyproject/galaxy/compare/4d2651a08540...46e67b5bfa04

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[galaxyproject/galaxy] 85c971: Remove existing wrong tool version associations in...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/release_14.10 Home: https://github.com/galaxyproject/galaxy Commit: 85c971287ba6b316a970053a2d76f8c49d82f16b https://github.com/galaxyproject/galaxy/commit/85c971287ba6b316a970053a2d76… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Remove existing wrong tool version associations in ToolVersionManager.handle_tool_versions() . Fix #552. To fix a tool with a wrong lineage, click on "Set tool versions" on the "Repository Actions" menu. Commit: 360a6ad76d4325a634bbd13314351028f2965bff https://github.com/galaxyproject/galaxy/commit/360a6ad76d4325a634bbd1331435… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge pull request #634 from nsoranzo/release_14.10 [14.10] Backport tool lineage fix. Compare: https://github.com/galaxyproject/galaxy/compare/cbae8fab672e...360a6ad76d43

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[galaxyproject/galaxy] 682406: * Fix get_latest_installable_revision to use paths...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 68240630668848b454aa51690ed1ac7bbfbc16e2 https://github.com/galaxyproject/galaxy/commit/68240630668848b454aa51690ed1… Author: chambm <matt.chambers42(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/tool_shed/util/common_util.py Log Message: ----------- * Fix get_latest_installable_revision to use pathspec and params to work with recent changes to common_util.url_join * Fix common_util.url_join to handle a string as pathspec, instead of treating it as an a/r/r/a/y/ /o/f/ /c/h/a/r/a/c/t/e/r/s Commit: d375a8cc034acaea43e221cb60fe58ece5f5d4d6 https://github.com/galaxyproject/galaxy/commit/d375a8cc034acaea43e221cb60fe… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/tool_shed/util/common_util.py Log Message: ----------- Merge pull request #632 from chambm/bug/url_join-latest_revision-2 Cleaner commit history for #629 and array syntax for pathspec Compare: https://github.com/galaxyproject/galaxy/compare/eb59844dd2fa...d375a8cc034a

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[galaxyproject/galaxy] 093003: Fixed bug where max items per page was reset when ...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0930035a9f5629836702525822095daf598dce45 https://github.com/galaxyproject/galaxy/commit/0930035a9f562983670252582209… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M templates/spark_base.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako Log Message: ----------- Fixed bug where max items per page was reset when changing the amount of time sparklines spanned Commit: 673dd2b140791fade4c2943abc399d718b789950 https://github.com/galaxyproject/galaxy/commit/673dd2b140791fade4c2943abc39… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js M templates/base.mako Log Message: ----------- Refactored where d3 is coming from Commit: 78251936e8df0256828f22130c42922190800ecc https://github.com/galaxyproject/galaxy/commit/78251936e8df0256828f22130c42… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M templates/base.mako M templates/webapps/reports/run_stats.mako Log Message: ----------- Moved d3 import to run_stats Commit: 963d3fe6591a19c3940daeb20c13a5c4566653ad https://github.com/galaxyproject/galaxy/commit/963d3fe6591a19c3940daeb20c13… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/run_stats.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako Log Message: ----------- Fixed bug where column sorting reset paging info Commit: 245a3ccd9ef5c37f45529c69f3802b7269025333 https://github.com/galaxyproject/galaxy/commit/245a3ccd9ef5c37f45529c69f380… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M templates/webapps/reports/run_stats.mako Log Message: ----------- Fixed error on homepage Commit: eb59844dd2fa28734fb0ce3a051d582e2eac723f https://github.com/galaxyproject/galaxy/commit/eb59844dd2fa28734fb0ce3a051d… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js M templates/base.mako M templates/spark_base.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/run_stats.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako Log Message: ----------- Merge pull request #626 from Airistotal/dev Bug fix in Reports Compare: https://github.com/galaxyproject/galaxy/compare/950f471c2326...eb59844dd2fa

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[galaxyproject/usegalaxy-playbook] 84b736: hiding antons tools, they were adopted by devteam
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 84b736bf885b7df35aefd34625efb7a4c7ed6dd4 https://github.com/galaxyproject/usegalaxy-playbook/commit/84b736bf885b7df3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml Log Message: ----------- hiding antons tools, they were adopted by devteam

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[galaxyproject/galaxy] a3e511: Merge branch 'release_15.05'
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a3e511292afe6dcdbb3bf533ef6b6e2520c2c652 https://github.com/galaxyproject/galaxy/commit/a3e511292afe6dcdbb3bf533ef6b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-select-content.js M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M static/maps/mvc/form/form-select-content.js.map M static/scripts/mvc/form/form-select-content.js Log Message: ----------- Merge branch 'release_15.05' Commit: a8a1a150c6ec1a474753052b96b25aec8a22813e https://github.com/galaxyproject/galaxy/commit/a8a1a150c6ec1a474753052b96b2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge branch 'release_15.05' Commit: 130004feb10f1fe3a26908401146b8e47c1202ff https://github.com/galaxyproject/galaxy/commit/130004feb10f1fe3a26908401146… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M .ci/flake8_wrapper.sh M .ci/pep8_sources.txt M .gitignore M CONTRIBUTING.md A CONTRIBUTORS.md M LICENSE.txt M README.rst M client/GruntFile.js M client/README.md M client/bower.json R client/galaxy/scripts/galaxy.workflow_editor.canvas.js R client/galaxy/scripts/galaxy.workflows.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M 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test/unit/tools/test_tool_loader.py M test/unit/unittest_utils/galaxy_mock.py A test/unit/visualizations/plugins/__init__.py A test/unit/visualizations/plugins/test_VisualizationPlugin.py A test/unit/visualizations/plugins/test_VisualizationsRegistry.py R test/unit/visualizations/test_VisualizationsRegistry.py M tools/data_source/bed_convert.xml M tools/data_source/genbank.xml M tools/data_source/import.xml M tools/data_source/microbial_import.xml M tools/data_source/ucsc_tablebrowser_archaea.xml M tools/data_source/ucsc_tablebrowser_test.xml M tools/data_source/upload.py M tools/data_source/upload.xml M tools/evolution/codingSnps.xml M tools/evolution/codingSnps_filter.py M tools/extract/liftOver_wrapper.xml M tools/filters/axt_to_lav.xml M tools/filters/axt_to_lav_code.py M tools/filters/catWrapper.xml M tools/filters/changeCase.xml M tools/filters/condense_characters.xml M tools/filters/cutWrapper.xml M tools/filters/gff/extract_GFF_Features.xml M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/gff/gtf_filter_by_attribute_values_list.xml M tools/filters/headWrapper.xml M tools/filters/joiner2.xml M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed.xml M tools/filters/lav_to_bed_code.py M tools/filters/pasteWrapper.xml M tools/filters/remove_beginning.xml M tools/filters/tailWrapper.xml M tools/filters/ucsc_gene_table_to_intervals.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.py M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_reverse_complement.py M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_to_fasta.xml M tools/plotting/bar_chart.xml M tools/plotting/boxplot.xml M tools/solid_tools/maq_cs_wrapper_code.py M tools/stats/filtering.xml M tools/stats/grouping.py M tools/stats/gsummary.py M tools/stats/gsummary.xml M tools/stats/gsummary.xml.groups M tools/visualization/LAJ.xml M tools/visualization/LAJ_code.py Log Message: ----------- Merge branch 'release_15.07' Commit: 737248d41d4e1d682361b85d48ea65574367e59d https://github.com/galaxyproject/galaxy/commit/737248d41d4e1d682361b85d48ea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix for valid height/width definitions in workflow rendering code. Commit: b8fd98979c775daf46a768572fb30f4467fd7458 https://github.com/galaxyproject/galaxy/commit/b8fd98979c775daf46a768572fb3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix the second (and final) issue preventing workflow rendering from generating valid SVGs -- incorrect usage of arrow_end; this is intended to be a unique identifier for the element and not a boolean. This wasn't preventing render (on firefox or chrome) like the previous issue, but it would cause warnings. Commit: 083789526105abda87a701835b8ff44e0ec89405 https://github.com/galaxyproject/galaxy/commit/083789526105abda87a701835b8f… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge pull request #625 from dannon/release_15.07 [release_15.07] Fix for valid height/width definitions in workflow rendering code, and fix identifiers. Commit: b29e81014979d2e72d704a22560a278cfec42927 https://github.com/galaxyproject/galaxy/commit/b29e81014979d2e72d704a22560a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix for valid height/width definitions in workflow rendering code. Commit: 4d2651a085405f2b4ba37f26fa917f9524584b1a https://github.com/galaxyproject/galaxy/commit/4d2651a085405f2b4ba37f26fa91… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix the second (and final) issue preventing workflow rendering from generating valid SVGs -- incorrect usage of arrow_end; this is intended to be a unique identifier for the element and not a boolean. This wasn't preventing render (on firefox or chrome) like the previous issue, but it would cause warnings. Commit: e06d6a1ccae792abb45ff96d63bf8ab51e685231 https://github.com/galaxyproject/galaxy/commit/e06d6a1ccae792abb45ff96d63bf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: c569f7856d41fe9b51808302569283c800a4eb93 https://github.com/galaxyproject/galaxy/commit/c569f7856d41fe9b518083025692… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Commit: e8f90429e2ca3efc6dbb9f02b1d5fbe8afc446a5 https://github.com/galaxyproject/galaxy/commit/e8f90429e2ca3efc6dbb9f02b1d5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: d055102596d85b5a3d6da90e8397016f6daf2271 https://github.com/galaxyproject/galaxy/commit/d055102596d85b5a3d6da90e8397… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/workflow/render.py M lib/tool_shed/metadata/repository_metadata_manager.py M scripts/cleanup_datasets/cleanup_datasets.py M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js M test/unit/test_galaxy_mapping.py Log Message: ----------- Merge branch 'release_15.07' Commit: 950f471c2326cc8d90c7efe372c063f47ed7f3e4 https://github.com/galaxyproject/galaxy/commit/950f471c2326cc8d90c7efe372c0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge branch 'master' into dev Compare: https://github.com/galaxyproject/galaxy/compare/795e30171149...950f471c2326

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