- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] bb209c: Add a password strength evaluation bar
by GitHub 01 Aug '16

01 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bb209c6e59e240bb1dc73d88a1fddd34fcc0f9e9 https://github.com/galaxyproject/galaxy/commit/bb209c6e59e240bb1dc73d88a1fd… Author: Ben Fulton <befulton(a)iu.edu> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M client/bower.json A client/galaxy/scripts/libs/jquery.complexify.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M client/galaxy/style/less/base.less M client/grunt-tasks/install-libs.js M client/webpack.config.js A static/maps/libs/jquery.complexify.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/raven.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/libs/jquery.complexify.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/raven.js M static/style/blue/base.css M templates/user/change_password.mako M templates/user/register.mako Log Message: ----------- Add a password strength evaluation bar Modify the register and change_password pages to show a bar evaluating the strength of the password. Bar displays in red for passwords < 6 chars or below a certain minimum complexity; green otherwise. Adds a dependency on Complexify, a password evaluator written by Dan Palmer. Commit: d8c22b70e897afa2f988751c30294e90f1df8985 https://github.com/galaxyproject/galaxy/commit/d8c22b70e897afa2f988751c3029… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M client/bower.json A client/galaxy/scripts/libs/jquery.complexify.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M client/galaxy/style/less/base.less M client/grunt-tasks/install-libs.js M client/webpack.config.js A static/maps/libs/jquery.complexify.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/raven.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/libs/jquery.complexify.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/raven.js M static/style/blue/base.css M templates/user/change_password.mako M templates/user/register.mako Log Message: ----------- Merge branch 'PasswordStrengthBar' into dev Compare: https://github.com/galaxyproject/galaxy/compare/dd4eabb48426...d8c22b70e897

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[galaxyproject/galaxy] 2b4a85: History, UI: use id of displayed history in delete
by GitHub 01 Aug '16

01 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2b4a8557f1f0057447c729717f22452d14ac11ef https://github.com/galaxyproject/galaxy/commit/2b4a8557f1f0057447c729717f22… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-25 (Mon, 25 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- History, UI: use id of displayed history in delete - Refactor `delete current` to `delete` and require an id arg. - Update history options menu to pass the id of the displayed/ current history to the above delete controller endpoint. This means that the current history panel will delete the history that's displayed (instead of potentially a different history that's been set to the current history on the server side). Note: this isn't an ideal refactoring but should solve the below issue temporarily until we move more of the session state out of API. Closes #894 Commit: 877655c1f06e5076512e2f0e16cc7d1458471643 https://github.com/galaxyproject/galaxy/commit/877655c1f06e5076512e2f0e16cc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-25 (Mon, 25 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/ui/ui-buttons.js M static/style/blue/base.css M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into history.delete_current-id Commit: cdab64820c554120545d7207d3861612d2a99ea9 https://github.com/galaxyproject/galaxy/commit/cdab64820c554120545d7207d386… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M .ci/flake8_blacklist.txt A .ci/flake8_lint_include_list.txt A .ci/flake8_wrapper_imports.sh M .travis.yml M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/ui.less M config/galaxy.ini.sample M config/object_store_conf.xml.sample A config/plugins/interactive_environments/neo/config/allowed_images.yml.sample A config/plugins/interactive_environments/neo/config/neo.ini.sample A config/plugins/interactive_environments/neo/config/neo.xml A config/plugins/interactive_environments/neo/static/js/neo.js A config/plugins/interactive_environments/neo/templates/neo.mako M doc/source/lib/galaxy.objectstore.rst M lib/galaxy/config.py M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/model/mapping.py M lib/galaxy/objectstore/__init__.py A lib/galaxy/objectstore/azure_blob.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/parameters/basic.py A lib/galaxy/tools/toolbox/requirements.py M lib/galaxy/version.py M lib/galaxy/web/__init__.py M lib/galaxy/web/buildapp.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py A lib/galaxy/webapps/reports/controllers/history.py A lib/galaxy/webapps/reports/controllers/tools.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/tool_shed/config.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/util/shed_util_common.py M setup.cfg M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/style/blue/base.css M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/preview_repository.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/base/base_panels.mako A templates/webapps/reports/history_and_dataset_per_user.mako A templates/webapps/reports/history_and_dataset_type.mako A templates/webapps/reports/history_per_user.mako M templates/webapps/reports/index.mako A templates/webapps/reports/tool_error_messages.mako A templates/webapps/reports/tool_execution_time.mako A templates/webapps/reports/tool_execution_time_per_month.mako A templates/webapps/reports/tools_and_job_state.mako A templates/webapps/reports/tools_and_job_state_per_month.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/export_repository.mako M test/base/driver_util.py M test/base/twilltestcase.py A test/integration/test_resolvers.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into history.delete_current-id Commit: dd4eabb48426a24ca6c960469b3fbb39edff821f https://github.com/galaxyproject/galaxy/commit/dd4eabb48426a24ca6c960469b3f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Merge pull request #2654 from carlfeberhard/history.delete_current-id History, UI: use id of displayed history in delete Compare: https://github.com/galaxyproject/galaxy/compare/6db43585c16c...dd4eabb48426

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[galaxyproject/galaxy] 2c7555: Fix sed usage in Makefile to be compatible with bo...
by GitHub 01 Aug '16

01 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2c75551a026ee02efd8127084f6f21e2327886a9 https://github.com/galaxyproject/galaxy/commit/2c75551a026ee02efd8127084f6f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M Makefile Log Message: ----------- Fix sed usage in Makefile to be compatible with both gnu and bsd sed. -i's argument is not optional for bsd, but an empty string (no backup extension) works fine and has the same behavior as gnu sed. Commit: 00e41385d75f83bbb35abc5830e3859715a2039e https://github.com/galaxyproject/galaxy/commit/00e41385d75f83bbb35abc5830e3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M Makefile Log Message: ----------- The previous approach to sed worked great on bsd sed, but gnu sed doesn't understand an empty '' in-place extension the same way. So, fixed one, broke the other. This approach with the -e argument feels like a total hack since it explits the fact that bsd sed consumes the -e as the argument to -i, but it still has the command interpreted correctly. Commit: ef0d27d677b482d81b89d843cc06d46048a08d03 https://github.com/galaxyproject/galaxy/commit/ef0d27d677b482d81b89d843cc06… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M Makefile Log Message: ----------- Change extension of the file that gets immediately deleted to address nsoranzo's concern about bsd utilities. Commit: 6db43585c16c22bb28f5e19c4e1db49444c7971d https://github.com/galaxyproject/galaxy/commit/6db43585c16c22bb28f5e19c4e1d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M Makefile Log Message: ----------- Merge pull request #2695 from dannon/sed_compat sed bsd compatibility for release versioning in Makefile Compare: https://github.com/galaxyproject/galaxy/compare/3fd0e405fd6c...6db43585c16c

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[galaxyproject/galaxy] af3f8c: Redefine svg datatype as subclass of GenericXml
by GitHub 29 Jul '16

29 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: af3f8cf8464a1c3d055ad9adb7122a4adc541dda https://github.com/galaxyproject/galaxy/commit/af3f8cf8464a1c3d055ad9adb712… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Redefine svg datatype as subclass of GenericXml SVG is XML-based and Python Pillow does not support it. Commit: 5b52b73fbb3a92a842cc6f9e36091c62ed7727f0 https://github.com/galaxyproject/galaxy/commit/5b52b73fbb3a92a842cc6f9e3609… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Datatype classes fixes: wrong file_ext, import order, Python3 - Specify some classes are abstracts - Use super() to call superclass methods - Various simplifications Commit: 3fd0e405fd6cb3333397ec19e627a4cf6ae36fe6 https://github.com/galaxyproject/galaxy/commit/3fd0e405fd6cb3333397ec19e627… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #2690 from nsoranzo/datatypes_fixes Misc datatypes fixes and enhancements Compare: https://github.com/galaxyproject/galaxy/compare/9aac1569f4b0...3fd0e405fd6c

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[galaxyproject/galaxy] 62fdbd: Fix the sanitization of None values in utils. Thi...
by GitHub 29 Jul '16

29 Jul '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 62fdbd526ae34357d3fbb44cedc46635c4df7cbb https://github.com/galaxyproject/galaxy/commit/62fdbd526ae34357d3fbb44cedc4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Fix the sanitization of None values in utils. This had previously not happened because Params had only been sanitizing strings coming in as part of the request, but if you're passing off (potentially manipulated, as in adding None default params) to a secondary request for a response, this can happen. Commit: ed7c357668df5bbb3381fae94353465594c7e184 https://github.com/galaxyproject/galaxy/commit/ed7c357668df5bbb3381fae94353… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #2693 from dannon/utils_fix_sanitization_of_none [16.07] Fix the sanitization of None values in utils. This had previously no… Compare: https://github.com/galaxyproject/galaxy/compare/62815aff39c2...ed7c357668df

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[galaxyproject/galaxy] 5c3822: A different form of upstream check that works on o...
by GitHub 29 Jul '16

29 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5c3822197195a932c4056b582c49b6b209a9f3d5 https://github.com/galaxyproject/galaxy/commit/5c3822197195a932c4056b582c49… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M Makefile Log Message: ----------- A different form of upstream check that works on osx (and hopefully still other locations). Commit: 820d545d3adae3a47384b831926992126f165b36 https://github.com/galaxyproject/galaxy/commit/820d545d3adae3a47384b8319269… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M Makefile Log Message: ----------- Roll the check into the rule so it gets reevaluated Commit: 6be8d6356d7f6b15ab3ddabf0efe286d398f1216 https://github.com/galaxyproject/galaxy/commit/6be8d6356d7f6b15ab3ddabf0efe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M Makefile Log Message: ----------- Remove unused def Commit: dc668a0bf3792af7052df9bffa07ab42d1b8b894 https://github.com/galaxyproject/galaxy/commit/dc668a0bf3792af7052df9bffa07… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M Makefile Log Message: ----------- Checkout dev again prior to version branch deletion. This prevents error: Cannot delete the branch 'blah' which you are currently on Commit: 9aac1569f4b082ba6eb3317ee1d287abfd724027 https://github.com/galaxyproject/galaxy/commit/9aac1569f4b082ba6eb3317ee1d2… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M Makefile Log Message: ----------- Merge pull request #2688 from dannon/makefile_updates Makefile updates for compatibility with OSX Compare: https://github.com/galaxyproject/galaxy/compare/e291012afd64...9aac1569f4b0

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[galaxyproject/galaxy] 1a0052: Merge pull request #2685 from dannon/version-16.07
by GitHub 29 Jul '16

29 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1a0052aa71ea2b78d3c1a5b8594c7109928bb454 https://github.com/galaxyproject/galaxy/commit/1a0052aa71ea2b78d3c1a5b8594c… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #2685 from dannon/version-16.07 Update version to 16.07.rc1 Commit: f06c895d618164af36cc419f4b1a717d6c595e89 https://github.com/galaxyproject/galaxy/commit/f06c895d618164af36cc419f4b1a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- Update INDETERMINATE_DEPENDENCY to NullDependency Fix unit test broken in https://github.com/galaxyproject/galaxy/pull/2554 Commit: 5e7f0c4b18eb26f3e7781206ba5e8ff17c854306 https://github.com/galaxyproject/galaxy/commit/5e7f0c4b18eb26f3e7781206ba5e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M run_tests.sh M scripts/nosetests.py Log Message: ----------- Fix unit tests exit status Broken in https://github.com/galaxyproject/galaxy/pull/2564 Also update scripts/nosetests.py Commit: 62815aff39c29a589f8bf3073cd0b19aa882a58d https://github.com/galaxyproject/galaxy/commit/62815aff39c29a589f8bf3073cd0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M run_tests.sh M scripts/nosetests.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #2691 from nsoranzo/release_16.07_fix_tests [16.07] Fix unit tests Commit: e291012afd6474f493c4984a14044a7a4667617a https://github.com/galaxyproject/galaxy/commit/e291012afd6474f493c4984a1404… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M run_tests.sh M scripts/nosetests.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c9a5d2913485...e291012afd64

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[galaxyproject/galaxy] f06c89: Update INDETERMINATE_DEPENDENCY to NullDependency
by GitHub 29 Jul '16

29 Jul '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: f06c895d618164af36cc419f4b1a717d6c595e89 https://github.com/galaxyproject/galaxy/commit/f06c895d618164af36cc419f4b1a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- Update INDETERMINATE_DEPENDENCY to NullDependency Fix unit test broken in https://github.com/galaxyproject/galaxy/pull/2554 Commit: 5e7f0c4b18eb26f3e7781206ba5e8ff17c854306 https://github.com/galaxyproject/galaxy/commit/5e7f0c4b18eb26f3e7781206ba5e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M run_tests.sh M scripts/nosetests.py Log Message: ----------- Fix unit tests exit status Broken in https://github.com/galaxyproject/galaxy/pull/2564 Also update scripts/nosetests.py Commit: 62815aff39c29a589f8bf3073cd0b19aa882a58d https://github.com/galaxyproject/galaxy/commit/62815aff39c29a589f8bf3073cd0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M run_tests.sh M scripts/nosetests.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #2691 from nsoranzo/release_16.07_fix_tests [16.07] Fix unit tests Compare: https://github.com/galaxyproject/galaxy/compare/1a0052aa71ea...62815aff39c2

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[galaxyproject/galaxy] 09aef7: mention need to update P4's conf when freezing
by GitHub 29 Jul '16

29 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 09aef7eda5b4a57051d65346130d979bbd6c894c https://github.com/galaxyproject/galaxy/commit/09aef7eda5b4a57051d65346130d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- mention need to update P4's conf when freezing Commit: c9a5d2913485d22845a5df7d0ab99e11041dbc58 https://github.com/galaxyproject/galaxy/commit/c9a5d2913485d22845a5df7d0ab9… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #2689 from martenson/add_p4_bootstrap mention need to update P4's conf when freezing Compare: https://github.com/galaxyproject/galaxy/compare/b2fbfcd6aca3...c9a5d2913485

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[galaxyproject/usegalaxy-playbook] 9cc02c: Add mo to admin users.
by GitHub 29 Jul '16

29 Jul '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9cc02ce8f1d6796984b4bddcf2c4d4d8ec70e4a4 https://github.com/galaxyproject/usegalaxy-playbook/commit/9cc02ce8f1d67969… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M production/secret_vars/galaxyservers.yml M stage/secret_vars/galaxyservers.yml Log Message: ----------- Add mo to admin users.

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[galaxyproject/galaxy] 19b363: Update version to 16.07.rc1
by GitHub 29 Jul '16

29 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 19b363cdcd0b23e9409f8beea387444b460768be https://github.com/galaxyproject/galaxy/commit/19b363cdcd0b23e9409f8beea387… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.07.rc1 Commit: 9789c116e65d9af974fdc997ec10890646b9197e https://github.com/galaxyproject/galaxy/commit/9789c116e65d9af974fdc997ec10… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.10.dev Commit: 7893f1a5713548d70d806da8f479827f0ee91e78 https://github.com/galaxyproject/galaxy/commit/7893f1a5713548d70d806da8f479… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Log Message: ----------- Merge branch 'version-16.07' into version-16.10.dev Commit: b2fbfcd6aca3a29440e7355101e579f4e649265b https://github.com/galaxyproject/galaxy/commit/b2fbfcd6aca3a29440e7355101e5… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #2686 from dannon/version-16.10.dev Version 16.10.dev Compare: https://github.com/galaxyproject/galaxy/compare/05c537e38478...b2fbfcd6aca3

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[galaxyproject/galaxy] 19b363: Update version to 16.07.rc1
by GitHub 29 Jul '16

29 Jul '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 19b363cdcd0b23e9409f8beea387444b460768be https://github.com/galaxyproject/galaxy/commit/19b363cdcd0b23e9409f8beea387… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.07.rc1 Commit: 1a0052aa71ea2b78d3c1a5b8594c7109928bb454 https://github.com/galaxyproject/galaxy/commit/1a0052aa71ea2b78d3c1a5b8594c… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #2685 from dannon/version-16.07 Update version to 16.07.rc1 Compare: https://github.com/galaxyproject/galaxy/compare/05c537e38478...1a0052aa71ea

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[galaxyproject/galaxy]
by GitHub 29 Jul '16

29 Jul '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] fcbaf8: Fix an error with getting the size of an object fr...
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fcbaf8d17a20b1a910c07d154b690c28689fcb63 https://github.com/galaxyproject/galaxy/commit/fcbaf8d17a20b1a910c07d154b69… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Fix an error with getting the size of an object from Azure. Attempted to future-proof it if the library is fixed. Commit: 05c537e38478ab0c4a674120860b5601f59bbf4a https://github.com/galaxyproject/galaxy/commit/05c537e38478ab0c4a674120860b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Merge pull request #2678 from dannon/azure_followup Fix an error with getting the size of an object from Azure. Attempte… Compare: https://github.com/galaxyproject/galaxy/compare/0066847e0ac1...05c537e38478

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[galaxyproject/galaxy] 4f1228: Limit creation of multitudes of default, empty his...
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4f1228213886bc9ba2443133ed75936c81e855e9 https://github.com/galaxyproject/galaxy/commit/4f1228213886bc9ba2443133ed75… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Limit creation of multitudes of default, empty histories. This was happening for every new session using remote auth Commit: 0066847e0ac19632c3091ac3148069de3bb3855f https://github.com/galaxyproject/galaxy/commit/0066847e0ac19632c3091ac31480… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #2684 from dannon/remote_auth_many_histories Limit creation of multitudes of default, empty histories. Compare: https://github.com/galaxyproject/galaxy/compare/5c2402f83741...0066847e0ac1

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[galaxyproject/galaxy] 5c79e2: Unpin flake8 in py27-lint-imports* test environmen...
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5c79e27436446f064674f29bbcd08760a419506f https://github.com/galaxyproject/galaxy/commit/5c79e27436446f064674f29bbcd0… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M tox.ini Log Message: ----------- Unpin flake8 in py27-lint-imports* test environments flake8-import-order 0.9 has been released Commit: ec6e6255c109b5c6a9096fcd281a02e6559dd585 https://github.com/galaxyproject/galaxy/commit/ec6e6255c109b5c6a9096fcd281a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M .ci/flake8_lint_include_list.txt Log Message: ----------- Extend the list to all files already passing Generated with: find . -path ./.venv -prune -o -path ./.tox -prune -o -path ./eggs -prune -o -path ./database -prune -o -name '*.py' -print0 | sort -z | xargs -0 -L 1 -I '{}' sh -c 'flake8 -qq {} && echo {}' | sed 's|^\./||' > .ci/flake8_lint_include_list.txt followed by some manual editing. Commit: 5c2402f837411972bb534918c4b72891a58a3816 https://github.com/galaxyproject/galaxy/commit/5c2402f837411972bb534918c4b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M .ci/flake8_lint_include_list.txt M tox.ini Log Message: ----------- Merge pull request #2682 from nsoranzo/flake8-import-order Extend the list of files tested with flake8-import-order to all files already passing Compare: https://github.com/galaxyproject/galaxy/compare/e8f2a74f21e0...5c2402f83741

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[galaxyproject/galaxy] 497817: Break tool parameter help words if necessary
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4978173e4ed6b76ef4520f6d395788d2c14cf888 https://github.com/galaxyproject/galaxy/commit/4978173e4ed6b76ef4520f6d3957… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Break tool parameter help words if necessary Commit: addc15179744ee01c2f11b198ae4c5f60f25b27d https://github.com/galaxyproject/galaxy/commit/addc15179744ee01c2f11b198ae4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Use word-wrap instead of word-break to apply break-word due to better browser support Commit: e8f2a74f21e034831c562b965e6c0189b719df7e https://github.com/galaxyproject/galaxy/commit/e8f2a74f21e034831c562b965e6c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Merge pull request #2681 from guerler/help_word_break Break tool parameter help words if necessary Compare: https://github.com/galaxyproject/galaxy/compare/c096be04bd53...e8f2a74f21e0

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[galaxyproject/galaxy] 4a8310: Generate metadata in separate conda environment
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4a831033ed820e3f1220d9d326f8bd8079c390f9 https://github.com/galaxyproject/galaxy/commit/4a831033ed820e3f1220d9d326f8… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Generate metadata in separate conda environment Galaxy supports generating metadata in a separate command (enable beta_tool_command_isolation). This command has its own dependency resolution, that may interfere with thedependency resolution of the actual tool, if the same environment is being used. With this PR we create a new environment when resolving metadata dependencies with conda, that will be active only for metadata generation. Commit: 28da4b6371b23c69d15e7fc59473d4bde5639fde https://github.com/galaxyproject/galaxy/commit/28da4b6371b23c69d15e7fc59473… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Fix whitespace and comma use Commit: f8cf81d73693e5f075b6c9e612244221bbd6e5bb https://github.com/galaxyproject/galaxy/commit/f8cf81d73693e5f075b6c9e61224… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M .ci/flake8_blacklist.txt Log Message: ----------- Ignore .tox directory. Used to be ignored by default w/ flake8 apparently, but not anymore. Commit: f0024d64e15815dcb6c2ac027ed5fb2977651e64 https://github.com/galaxyproject/galaxy/commit/f0024d64e15815dcb6c2ac027ed5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/web/framework/helpers/__init__.py M test/base/driver_util.py Log Message: ----------- Apply @nsoranzo's fix for noqa changes (must end the line, comment comes before it) Commit: 8f978b8957f0cbc7e5d78ca3f3bce9e87e6e8f76 https://github.com/galaxyproject/galaxy/commit/8f978b8957f0cbc7e5d78ca3f3bc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/web/framework/helpers/__init__.py M test/base/driver_util.py Log Message: ----------- Merge pull request #2662 from jmchilton/backport_2253 [16.04] Backport #2253 as requested by Eagle Eyes Commit: 5d8d932425c879177c40a008a5a2ef3e45020b73 https://github.com/galaxyproject/galaxy/commit/5d8d932425c879177c40a008a5a2… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- Add hg38 to main for ucsc_build_sites.txt.sample (cherry picked from commit 04b7d11f053e66b14232440e6ff534a62ff26666) Commit: e4ca3bf80fcab185e8ea3502926563707b047236 https://github.com/galaxyproject/galaxy/commit/e4ca3bf80fcab185e8ea35029265… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- Merge pull request #2673 from blankenberg/ucsc-hg38-display-16.04 [16.04] Add hg38 to main for ucsc_build_sites.txt.sample Commit: c096be04bd53c8184a4c5880c99abe02649e7570 https://github.com/galaxyproject/galaxy/commit/c096be04bd53c8184a4c5880c99a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/fdbaf437c9ba...c096be04bd53

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[galaxyproject/galaxy] 5d8d93: Add hg38 to main for ucsc_build_sites.txt.sample
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 5d8d932425c879177c40a008a5a2ef3e45020b73 https://github.com/galaxyproject/galaxy/commit/5d8d932425c879177c40a008a5a2… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- Add hg38 to main for ucsc_build_sites.txt.sample (cherry picked from commit 04b7d11f053e66b14232440e6ff534a62ff26666) Commit: e4ca3bf80fcab185e8ea3502926563707b047236 https://github.com/galaxyproject/galaxy/commit/e4ca3bf80fcab185e8ea35029265… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- Merge pull request #2673 from blankenberg/ucsc-hg38-display-16.04 [16.04] Add hg38 to main for ucsc_build_sites.txt.sample Compare: https://github.com/galaxyproject/galaxy/compare/8f978b8957f0...e4ca3bf80fca

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[galaxyproject/galaxy] 8dbc35: Collections should be populated regardless of the ...
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8dbc35784e209c640f0c010077452f5c32be463c https://github.com/galaxyproject/galaxy/commit/8dbc35784e209c640f0c01007745… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Collections should be populated regardless of the availability of other values Commit: 25fd142667a716775f7230e5e38aadeb3365b9e9 https://github.com/galaxyproject/galaxy/commit/25fd142667a716775f7230e5e38a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Initialize empty other_values dictionary when populating collections Commit: fdbaf437c9bac1c9179347b3bc54093bcdc52ceb https://github.com/galaxyproject/galaxy/commit/fdbaf437c9bac1c9179347b3bc54… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2672 from guerler/fix_populating_collections Properly populate collections regardless of context values Compare: https://github.com/galaxyproject/galaxy/compare/fed3665fcfa9...fdbaf437c9ba

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[galaxyproject/galaxy] 12a789: Adjust tests for 8cca7be
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 12a789f3e19c7ac02f9648461cb2cd3dbd2727eb https://github.com/galaxyproject/galaxy/commit/12a789f3e19c7ac02f9648461cb2… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py Log Message: ----------- Adjust tests for 8cca7be Commit: fed3665fcfa96809a00fb4d9b4dfe287123d84f3 https://github.com/galaxyproject/galaxy/commit/fed3665fcfa96809a00fb4d9b4df… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py Log Message: ----------- Merge pull request #2680 from mvdbeek/toolshed_test_fixes Fix broken toolshed tests with #2554 Compare: https://github.com/galaxyproject/galaxy/compare/c7caeb3c3959...fed3665fcfa9

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[galaxyproject/galaxy] ea36a6: first commit
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ea36a627e48d71a5ef3482be36d64b3a57c10235 https://github.com/galaxyproject/galaxy/commit/ea36a627e48d71a5ef3482be36d6… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: A lib/galaxy/objectstore/azureObjectStore.py Log Message: ----------- first commit modeled off S3 adapter Commit: 596248ae0f2af5cb1a01dbb8de8f05c572c4bbcb https://github.com/galaxyproject/galaxy/commit/596248ae0f2af5cb1a01dbb8de8f… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-contents.js M config/plugins/visualizations/graphviz/config/graphviz.xml M config/plugins/visualizations/graphviz/static/js/graphVis.js M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js M config/plugins/visualizations/graphviz/templates/graphviz.mako M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/managers/base.py M lib/galaxy/managers/users.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/util/__init__.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/tag.py M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/data.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map 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/dataset/data.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-contents.js M templates/admin/impersonate.mako M templates/ind_share_base.mako M test/api/test_users.py M test/unit/managers/test_UserManager.py M tools/stats/gsummary.xml Log Message: ----------- Merge branch 'dev' into azure-blob-objectstore Commit: c3a074faf044fa21e73ae060e4d5a1872d8b9475 https://github.com/galaxyproject/galaxy/commit/c3a074faf044fa21e73ae060e4d5… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M config/object_store_conf.xml.sample Log Message: ----------- added object_store_conf.xml.sample Commit: b217ecde14d80f211bc550cb56fa4524872e23f9 https://github.com/galaxyproject/galaxy/commit/b217ecde14d80f211bc550cb56fa… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/datatypes/data.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js A test/unit/datatypes/test_data.py Log Message: ----------- Merge remote-tracking branch 'galaxyproject/dev' into azure-blob-objectstore Commit: 0a49f17411dec1235226a8dc0fc7237bc4f6a40a https://github.com/galaxyproject/galaxy/commit/0a49f17411dec1235226a8dc0fc7… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M doc/source/lib/galaxy.objectstore.rst Log Message: ----------- Modified galaxy.objectstore.rst Not sure how RST works — would appreciate some guidance here. Commit: 3a3074134fd0bbdf81c269e127934d1c87b0d8bd https://github.com/galaxyproject/galaxy/commit/3a3074134fd0bbdf81c269e12793… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/azureObjectStore.py Log Message: ----------- fixed most lint errors Commit: cb44eb372ef71d856804c3747e0e282e14176702 https://github.com/galaxyproject/galaxy/commit/cb44eb372ef71d856804c3747e0e… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M config/job_conf.xml.sample_advanced A config/tool_destinations.yml.sample M lib/galaxy/config.py M lib/galaxy/datatypes/data.py M lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M templates/webapps/galaxy/history/grid.mako M test/api/test_workflows.py A test/functional/tools/output_filter_exception_1.xml M test/functional/tools/samples_tool_conf.xml A test/unit/jobs/dynamic_tool_destination/__init__.py A test/unit/jobs/dynamic_tool_destination/data/dest_fail.yml A test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml A test/unit/jobs/dynamic_tool_destination/data/test.empty A test/unit/jobs/dynamic_tool_destination/data/test.fasta A test/unit/jobs/dynamic_tool_destination/data/test1.full A test/unit/jobs/dynamic_tool_destination/data/test3.full A test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml A test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml A test/unit/jobs/dynamic_tool_destination/data/test_users.yml A test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml A test/unit/jobs/dynamic_tool_destination/mockGalaxy.py A test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py A test/unit/jobs/dynamic_tool_destination/ymltests.py M tools/stats/gsummary.xml Log Message: ----------- Merge remote-tracking branch 'galaxyproject/dev' into azure-blob-objectstore Commit: c668baeea5d4106e439ebbb39d406ccc1f4848f2 https://github.com/galaxyproject/galaxy/commit/c668baeea5d4106e439ebbb39d40… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: R lib/galaxy/objectstore/azureObjectStore.py A lib/galaxy/objectstore/azure_blob.py Log Message: ----------- better naming Commit: 8bc8e38b369115d9970586a24626d04b101c6952 https://github.com/galaxyproject/galaxy/commit/8bc8e38b369115d9970586a24626… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- typo Commit: 4fa0c27bf1594a3f46209e3718d55fd7063bbbd9 https://github.com/galaxyproject/galaxy/commit/4fa0c27bf1594a3f46209e3718d5… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Another lint pass. Commit: 2405f558c8d3abc0cbbe1738208e682d9bc02502 https://github.com/galaxyproject/galaxy/commit/2405f558c8d3abc0cbbe1738208e… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Oops.. Commit: a2c5e33d021f61b0e2efa95b12fc6a9d3e7ae82e https://github.com/galaxyproject/galaxy/commit/a2c5e33d021f61b0e2efa95b12fc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Address minor azure objblob lint issues, and one UndefinedObject issue. Commit: ebe83e21bd25c5fc9d4c4f8018401e5967d5cd66 https://github.com/galaxyproject/galaxy/commit/ebe83e21bd25c5fc9d4c4f801840… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Merge pull request #1 from dannon/minor_azure_tweaks Address minor azure objblob lint issues, and one UndefinedObject issue. Commit: d9d549299171364576e141710637283176fd6dd4 https://github.com/galaxyproject/galaxy/commit/d9d549299171364576e141710637… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M config/object_store_conf.xml.sample Log Message: ----------- more consistent naming. Commit: 4a8a14d8cf593b84cc338062d7361140f8410851 https://github.com/galaxyproject/galaxy/commit/4a8a14d8cf593b84cc338062d736… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Merge remote-tracking branch 'galaxyproject/dev' into azure-blob-objectstore Commit: ca79c905f83aa20be3a598da94ec09919457511a https://github.com/galaxyproject/galaxy/commit/ca79c905f83aa20be3a598da94ec… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- oops again... Commit: 91081bf2802195f501595bca9a51b38b69c18669 https://github.com/galaxyproject/galaxy/commit/91081bf2802195f501595bca9a51… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- added dependency to azure Commit: 7dcc6374ccf9ce9903cc82f11f146a1f5aefdc87 https://github.com/galaxyproject/galaxy/commit/7dcc6374ccf9ce9903cc82f11f14… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- oops =) Commit: d36162a389586ffa0d692a446be26c53b1e7741d https://github.com/galaxyproject/galaxy/commit/d36162a389586ffa0d692a446be2… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- fixes the lint error I think. Commit: e59602fed14e0f7bea81309407e47e600a24a529 https://github.com/galaxyproject/galaxy/commit/e59602fed14e0f7bea81309407e4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Update check_azure_storage check, read the object store config to detect stores. Commit: 3199217448f7646c660c954c66e989f4a2e224fb https://github.com/galaxyproject/galaxy/commit/3199217448f7646c660c954c66e9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Remove debug print Commit: 0da66864e491e7b8b1a5454ee12a3db1ba52e9e1 https://github.com/galaxyproject/galaxy/commit/0da66864e491e7b8b1a5454ee12a… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Merge pull request #2 from dannon/azure-blob-objectstore Fixes azure_blob detection for conditional dependency resolution Commit: 0b1730fe7f94875edf378dec629f692da66c8ad3 https://github.com/galaxyproject/galaxy/commit/0b1730fe7f94875edf378dec629f… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- trying this... Commit: e349aafe047ce0e419634b96c34acef8b60549af https://github.com/galaxyproject/galaxy/commit/e349aafe047ce0e419634b96c34a… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- fix bug. Commit: 4dc8b7d8037defe9b29038ee05ab22b889cd2740 https://github.com/galaxyproject/galaxy/commit/4dc8b7d8037defe9b29038ee05ab… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- clean things up a little... Commit: b4896bc341ab9d40a255c74a7a5fdeb0db37f72a https://github.com/galaxyproject/galaxy/commit/b4896bc341ab9d40a255c74a7a5f… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- fix lint Commit: c7caeb3c3959e87e55e791aa4f87de63e71a9032 https://github.com/galaxyproject/galaxy/commit/c7caeb3c3959e87e55e791aa4f87… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M config/object_store_conf.xml.sample M doc/source/lib/galaxy.objectstore.rst M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/objectstore/__init__.py A lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Merge branch 'azure-blob-objectstore' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c4841b352140...c7caeb3c3959

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[galaxyproject/galaxy] 43f800: Modify persistent entry handling for select fields
by GitHub 27 Jul '16

27 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 43f800b56d3002248e42b4145df272a2ad572a7f https://github.com/galaxyproject/galaxy/commit/43f800b56d3002248e42b4145df2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Modify persistent entry handling for select fields Commit: 3dcc9adaaffa032e1adb57a42e9054ef8ddfe958 https://github.com/galaxyproject/galaxy/commit/3dcc9adaaffa032e1adb57a42e90… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form.js Log Message: ----------- Improve robustness of error message display on tool execution Commit: b9a02150fef9007391e79521b0712f898ed657b9 https://github.com/galaxyproject/galaxy/commit/b9a02150fef9007391e79521b071… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Filter on the basis of select field values instead of all attributes Commit: c4841b35214083a9cabb51fd816fe7fac3d53684 https://github.com/galaxyproject/galaxy/commit/c4841b35214083a9cabb51fd816f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Merge pull request #2677 from guerler/update_select Fix dataset selector update when deleting history items Compare: https://github.com/galaxyproject/galaxy/compare/d7a1776a9105...c4841b352140

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[galaxyproject/galaxy] 497afd: Fix config.dynamic_proxy.
by GitHub 27 Jul '16

27 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 497afd86a6e4110d74b0caefe5e40f86baf257cd https://github.com/galaxyproject/galaxy/commit/497afd86a6e4110d74b0caefe5e4… Author: thoba <lose.thoba(a)gmail.com> Date: 2016-07-13 (Wed, 13 Jul 2016) Changed paths: M .gitignore A config/plugins/interactive_environments/neo/config/allowed_images.yml.sample A config/plugins/interactive_environments/neo/config/neo.ini.sample A config/plugins/interactive_environments/neo/config/neo.xml A config/plugins/interactive_environments/neo/static/js/neo.js A config/plugins/interactive_environments/neo/templates/neo.mako M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Fix config.dynamic_proxy. Commit: a188c1019749200da93b77401e098e978bdf7572 https://github.com/galaxyproject/galaxy/commit/a188c1019749200da93b77401e09… Author: thoba <lose.thoba(a)gmail.com> Date: 2016-07-13 (Wed, 13 Jul 2016) Changed paths: M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/neo/config/neo.xml M config/plugins/interactive_environments/neo/templates/neo.mako Log Message: ----------- Minor IE updates. Commit: 6732bea22dbd67b8f3ad02c81310bcb69549ec2d https://github.com/galaxyproject/galaxy/commit/6732bea22dbd67b8f3ad02c81310… Author: thoba <lose.thoba(a)gmail.com> Date: 2016-07-13 (Wed, 13 Jul 2016) Changed paths: M .ci/py3_sources.txt M Makefile M README.rst M client/bower.json M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/libs/backbone.js M client/galaxy/scripts/libs/bootstrap-tour.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/jquery/jquery.migrate.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js R client/galaxy/scripts/libs/tracekit.js M client/galaxy/scripts/libs/underscore.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-model.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 client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js R client/galaxy/scripts/mvc/tool/tool-template.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/ui/ui-frames.js M 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test/unit/web/framework/test_webapp.py M test/unit/workflows/test_run_parameters.py M tool_list.py M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_concat_fasta.xml M tools/filters/axt_to_fasta.xml M tools/filters/axt_to_lav.py M tools/filters/axt_to_lav.xml M tools/filters/bed2gff.xml M tools/filters/bed_to_bigbed.xml M tools/filters/bed_to_gff_converter.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff2bed.xml M tools/filters/gff_to_bed_converter.py M tools/filters/gtf2bedgraph.xml M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M 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tools/sr_mapping/bfast_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/filtering.xml M tools/stats/grouping.py M tools/stats/gsummary.py M tools/stats/gsummary.xml M tox.ini Log Message: ----------- Merge branch 'dev' of github.com:galaxyproject/galaxy into dev Commit: 4ae93fc0f2f3963a138947511db48febf71d37fc https://github.com/galaxyproject/galaxy/commit/4ae93fc0f2f3963a138947511db4… Author: thoba <lose.thoba(a)gmail.com> Date: 2016-07-13 (Wed, 13 Jul 2016) Changed paths: M .gitignore M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/neo/templates/neo.mako M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Removed extra proxy_command arg Added Newline Commit: 23f8aab6c6f462b4a343101bd95ed46a63005d16 https://github.com/galaxyproject/galaxy/commit/23f8aab6c6f462b4a343101bd95e… Author: thoba <lose.thoba(a)gmail.com> Date: 2016-07-14 (Thu, 14 Jul 2016) Changed paths: M config/plugins/interactive_environments/neo/config/neo.ini.sample Log Message: ----------- Default to internals. Commit: 79b325403094942dfde7d62afeab5a426d6259aa https://github.com/galaxyproject/galaxy/commit/79b325403094942dfde7d62afeab… Author: Thoba Lose <thobalose(a)users.noreply.github.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample Log Message: ----------- Added Docker image tag Commit: d7a1776a91051b70d2be08b04681083053419cb4 https://github.com/galaxyproject/galaxy/commit/d7a1776a91051b70d2be08b04681… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: A config/plugins/interactive_environments/neo/config/allowed_images.yml.sample A config/plugins/interactive_environments/neo/config/neo.ini.sample A config/plugins/interactive_environments/neo/config/neo.xml A config/plugins/interactive_environments/neo/static/js/neo.js A config/plugins/interactive_environments/neo/templates/neo.mako Log Message: ----------- Merge pull request #2610 from thobalose/dev Added Neo4j IE Compare: https://github.com/galaxyproject/galaxy/compare/a731ce2e2225...d7a1776a9105

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[galaxyproject/galaxy] fd9eb8: WIP re #39 - run dependency management during repo...
by GitHub 27 Jul '16

27 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fd9eb822b470dfedc508511ae27e79fd02f317b3 https://github.com/galaxyproject/galaxy/commit/fd9eb822b470dfedc508511ae27e… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- WIP re #39 - run dependency management during repository installation working: - fetching valid tool list - identifying unique requirements not working: File '/Users/langhorst/src/galaxy_hackathon/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1138 in prepare_for_install [view.manager_dependency(req) for req in uniq_reqs.values()] TypeError: manager_dependency() takes exactly 1 argument (2 given) Commit: dcb57a6f17f5f351d585bb2b0535c0f0c04c9f4f https://github.com/galaxyproject/galaxy/commit/dcb57a6f17f5f351d585bb2b0535… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Need to unnpack kwargs (ping @bwlang) Commit: de6bbf1f755ac6659ff733146a396013cebbf231 https://github.com/galaxyproject/galaxy/commit/de6bbf1f755ac6659ff733146a39… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Move get_unique_requirements to shed_util_common (ping @bwlang) Commit: 179d02c701ad92902ec7c718a4c453de1fff858b https://github.com/galaxyproject/galaxy/commit/179d02c701ad92902ec7c718a4c4… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Iterate over all tools in a repository Commit: f7d5f5d1912c46fa024bd61adedbee3e7f059a03 https://github.com/galaxyproject/galaxy/commit/f7d5f5d1912c46fa024bd61adedb… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Fix the parsing logic Commit: 07ed963d8b4cac3ebec3af1289908eb6566b8b11 https://github.com/galaxyproject/galaxy/commit/07ed963d8b4cac3ebec3af128990… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Be a bit more defensive about parsing requirements Commit: f0f6d88e34ece5e083e960e1cf1d2eb750226feb https://github.com/galaxyproject/galaxy/commit/f0f6d88e34ece5e083e960e1cf1d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Fix indentation Commit: e7aaf99392c95ded8f620adc2827700c1a3d3f2a https://github.com/galaxyproject/galaxy/commit/e7aaf99392c95ded8f620adc2827… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- passed a “manual install” argument to the dependency resolve so that we can both respect a users wishes (independent of auto_install config) and so that we can avoid attempting to create a conda_env in a nonexistent job directory Commit: 523baf380fe5798e3838480f802feda582361746 https://github.com/galaxyproject/galaxy/commit/523baf380fe5798e3838480f802f… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/views.py Log Message: ----------- Probably better not to have a fake directory here… other places check for job_directory=None Commit: 0252acce55f32c2751570547c4ddc4548e5d29c1 https://github.com/galaxyproject/galaxy/commit/0252acce55f32c2751570547c4dd… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako Log Message: ----------- ask for tool dependency installation always. I think a tool with no requirements is probably rare, and the new language should cover that situation. I think it’s not worth the API call to fetch the requirements just to ask this question. Commit: dade96c4af3a265010fd068e3d9562612996aff7 https://github.com/galaxyproject/galaxy/commit/dade96c4af3a265010fd068e3d95… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- this view is not necessary for the current implementation Commit: 609898b73c8a11412b110c0e6370617a95cf3a89 https://github.com/galaxyproject/galaxy/commit/609898b73c8a11412b110c0e6370… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M templates/admin/tool_shed_repository/common.mako Log Message: ----------- strangely… we need %if tool_dependencies_root_folder or missing_tool_dependencies_root_folder: to avoid breaking the export repository code Commit: c59fd5ec955c853f8306622d669a095562ed6350 https://github.com/galaxyproject/galaxy/commit/c59fd5ec955c853f8306622d669a… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- resolving style issue better comments Commit: 753587931ed3a460e57334de398d5048bc35f6b9 https://github.com/galaxyproject/galaxy/commit/753587931ed3a460e57334de398d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/toolbox/base.py A lib/galaxy/tools/toolbox/requirements.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add api route to fetch all requirements and method that determines requirement status This should be used in the UI to inform the admin of the dependency resolution status. Also make galaxy package resolution more robust to other files in the shed_tools directory (like condarc). Commit: 1a9e2e72663902287a2963464d38894aa6f8e4aa https://github.com/galaxyproject/galaxy/commit/1a9e2e72663902287a2963464d38… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Continue dependency resolver API routes and start work on displaying dependency status on a per repository view Commit: 672480fb1b6e1ff2b58f9f1e1fd11f4692884d74 https://github.com/galaxyproject/galaxy/commit/672480fb1b6e1ff2b58f9f1e1fd1… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Add first pass for displaying dependency status info Commit: a8068679dae232a2eb7f119f367b2c7c7ff76b71 https://github.com/galaxyproject/galaxy/commit/a8068679dae232a2eb7f119f367b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Add name and version to returned dependency Commit: 2a7f67b8b508536ca6828d78f1f3a1c7bfb0460b https://github.com/galaxyproject/galaxy/commit/2a7f67b8b508536ca6828d78f1f3… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Hack in name and version into dictified representation of Dependency instance (For NullDependency we do want to show the missing requirements) Commit: 4bd0013648c589deb1be6191ece977dd6e13075c https://github.com/galaxyproject/galaxy/commit/4bd0013648c589deb1be6191ece9… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- add status field with icons Commit: ee33ad8f6065ac9e8c674db61ac939a66eb7c063 https://github.com/galaxyproject/galaxy/commit/ee33ad8f6065ac9e8c674db61ac9… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- whitespace fix Commit: e7f8a13ecb9189c0b1a553bf3532b7849f5cc84e https://github.com/galaxyproject/galaxy/commit/e7f8a13ecb9189c0b1a553bf3532… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Address @nsoranzo's review. - Skip unncessary list() - Sort keys when dumping requirements to json - Rename tools_requirements to all_tools_requirements - Use list comprehension where appropriate Commit: cc085cb9a2f3afb2467e5bbe8192bf6b7a9021bf https://github.com/galaxyproject/galaxy/commit/cc085cb9a2f3afb2467e5bbe8192… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Work on conda install revision Commit: 69480a6c041973d6aa507ba6d2e568f848a7d397 https://github.com/galaxyproject/galaxy/commit/69480a6c041973d6aa507ba6d2e5… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py Log Message: ----------- Fix dependency typo Commit: 7a8265b0b0f2301516bde01e5b4f7e2bab75baa5 https://github.com/galaxyproject/galaxy/commit/7a8265b0b0f2301516bde01e5b4f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/manage_repository.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Make api return more detailed requirements status, move tool_requirements and tool_requirements_status to Tool class Commit: 983f4a09195be21dcb77fc355b16310ca5e976af https://github.com/galaxyproject/galaxy/commit/983f4a09195be21dcb77fc355b16… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Use list comprehension to generate list of all requirements Commit: 2e7099c772e25c0e0a40c4729716b66c6c132a51 https://github.com/galaxyproject/galaxy/commit/2e7099c772e25c0e0a40c4729716… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix logic error in message Commit: 93579a6373712b53678f585a1a4d074d75d18bdd https://github.com/galaxyproject/galaxy/commit/93579a6373712b53678f585a1a4d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/views.py M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Display whether dependency is exactly resolved (check), inexactly resolved (warning) or not resolved (error) Commit: 602ced89ce31e1d6e6a358f2cfacbe148890b57e https://github.com/galaxyproject/galaxy/commit/602ced89ce31e1d6e6a358f2cfac… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Close docstring example list Commit: f75a28e87c5453b8ed3cc3d2c56d74f5aae37a11 https://github.com/galaxyproject/galaxy/commit/f75a28e87c5453b8ed3cc3d2c56d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Trigger requirement install for new install method Commit: 414bc87d371b3ca593cffaf1b9c49ccb7ade58cd https://github.com/galaxyproject/galaxy/commit/414bc87d371b3ca593cffaf1b9c4… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/views.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- flake8 fixes Commit: 4eadf05ae9f9593694d71ecd91e1639c3d24b08a https://github.com/galaxyproject/galaxy/commit/4eadf05ae9f9593694d71ecd91e1… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add API endpoint to install (resolver) dependencies Commit: 503915fbdc9707a64fed8849ed77fefa3a0af434 https://github.com/galaxyproject/galaxy/commit/503915fbdc9707a64fed8849ed77… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_dependencies.py Log Message: ----------- Correct module description Commit: db0531315823e656662a6ca7d9bcaba7fc7be255 https://github.com/galaxyproject/galaxy/commit/db0531315823e656662a6ca7d9bc… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Trigger dependency installation in InstallRepositoryManager Commit: dcba01846d36de1a19df04203a6d074398cd0388 https://github.com/galaxyproject/galaxy/commit/dcba01846d36de1a19df04203a6d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/views.py Log Message: ----------- Add docstring to install_dependency Commit: a8670a2fb096beea324ba86ae5ebf184f4c8854b https://github.com/galaxyproject/galaxy/commit/a8670a2fb096beea324ba86ae5eb… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Revert manual_install mode (unncessary, better to use install_dependency) Commit: 6901cb1e9e6a4b3ab67709231251ddfce108809c https://github.com/galaxyproject/galaxy/commit/6901cb1e9e6a4b3ab67709231251… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/views.py Log Message: ----------- Introduce installable_resolver property Commit: 33b83e5c70d356168648b022d9c8d106d7182c1b https://github.com/galaxyproject/galaxy/commit/33b83e5c70d356168648b022d9c8… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/install_manager.py M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/preview_repository.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako Log Message: ----------- Add install resolver dependency button and add install_resolver_dependency to ToolShedRepositoriesController Commit: 4ed151a771e0f855571c837b604eea1f3baf01fc https://github.com/galaxyproject/galaxy/commit/4ed151a771e0f855571c837b604e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/export_repository.mako M test/shed_functional/base/twilltestcase.py Log Message: ----------- Revert mako hack to always display install_tool_dependency button - Add resolver checkbox - Add possibility to disable resolvers if initialization failed Commit: 886d074a9ed8c8916a4d29c8397e71df8ac2e0e7 https://github.com/galaxyproject/galaxy/commit/886d074a9ed8c8916a4d29c8397e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-23 (Sat, 23 Jul 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Make conda verbose install check configurable Move dependency installation from resolve() to install_dependency(). Commit: 201863200e824c98c8689b1c5fab145247f49d3c https://github.com/galaxyproject/galaxy/commit/201863200e824c98c8689b1c5fab… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-23 (Sat, 23 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Only return requirements of type package (for now) Commit: 0b242833959a5554d60488d6551da78c816020d4 https://github.com/galaxyproject/galaxy/commit/0b242833959a5554d60488d6551d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-23 (Sat, 23 Jul 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Use resolver.find_dep to determine dependency status Commit: b59b797f5036b492e6abee8757d487ad80e174af https://github.com/galaxyproject/galaxy/commit/b59b797f5036b492e6abee8757d4… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-25 (Mon, 25 Jul 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- Update INDETERMINATE_DEPENDENCY use to NullDependency instance Commit: c10d1cb172eb6458e8ad3ee6ca7f4f27665e619c https://github.com/galaxyproject/galaxy/commit/c10d1cb172eb6458e8ad3ee6ca7f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-25 (Mon, 25 Jul 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Remove unused DependencyResolver view from ToolBox Commit: 49dee6af10fdc81fec37fd593c4bd5537511ccd3 https://github.com/galaxyproject/galaxy/commit/49dee6af10fdc81fec37fd593c4b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-25 (Mon, 25 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py Log Message: ----------- Flake8 fix Commit: 6b135c6b1e04726c9cd8644a43601efe1e1cc96c https://github.com/galaxyproject/galaxy/commit/6b135c6b1e04726c9cd8644a4360… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-25 (Mon, 25 Jul 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- Drop INDETERMINATE_DEPENDENCY alias Commit: dd8f8f1de0adcfec7c85e70e8e60645f664ae697 https://github.com/galaxyproject/galaxy/commit/dd8f8f1de0adcfec7c85e70e8e60… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-25 (Mon, 25 Jul 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py Log Message: ----------- Fix NullDependency use and add default arguments to NullDependency Commit: b5fad4a04804e6cefec335fe888bf616c7eb7e0d https://github.com/galaxyproject/galaxy/commit/b5fad4a04804e6cefec335fe888b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-25 (Mon, 25 Jul 2016) Changed paths: A test/integration/test_resolvers.py Log Message: ----------- Add api test for conda dependency resolution Commit: deef480cadaf6161e1f59033925936d7eb7353c1 https://github.com/galaxyproject/galaxy/commit/deef480cadaf6161e1f590339259… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M test/integration/test_resolvers.py Log Message: ----------- Add more API tests for resolver dependencies Commit: e53a81c40d29686d00580349bae4482f21024a01 https://github.com/galaxyproject/galaxy/commit/e53a81c40d29686d00580349bae4… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M test/integration/test_resolvers.py Log Message: ----------- Fix syntax, return None if dependency not found Commit: 9917512f8f2e3193dba0fded5f9927ecb1158095 https://github.com/galaxyproject/galaxy/commit/9917512f8f2e3193dba0fded5f99… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M test/integration/test_resolvers.py Log Message: ----------- Revert svgwrite import, fixed in #2656 Commit: 645a89170604089c3a0b9e34bd4c50733b2bf3c6 https://github.com/galaxyproject/galaxy/commit/645a89170604089c3a0b9e34bd4c… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M test/integration/test_resolvers.py Log Message: ----------- Remove reference to /tmp Commit: 06e409ad401e4e0d099493e9443886d25a701935 https://github.com/galaxyproject/galaxy/commit/06e409ad401e4e0d099493e94438… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Use continue instead of unused NullDependency in Dependency_Manager.find_dep(), and requirement.version instead of None in Dependency_Manager.find_dep.dependency_shell_commands(). (thanks @nsoranzo) Commit: 2a5b043aaf8da9051ef959e4f9cf2dac99b9383a https://github.com/galaxyproject/galaxy/commit/2a5b043aaf8da9051ef959e4f9cf… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Simplify conda install logic Commit: 8cca7bef760691eedadac3e9f377efc22c63f92c https://github.com/galaxyproject/galaxy/commit/8cca7bef760691eedadac3e9f377… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako Log Message: ----------- Show conda install option even when no tool_dependencies.xml is available. Also reword different install options, I hope this is more clear - I do think it exposes les of the internal language to the end user. Commit: 483b66be270314859370f1ee84afbdae34460391 https://github.com/galaxyproject/galaxy/commit/483b66be270314859370f1ee84af… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py Log Message: ----------- Address @nsoranzo's review Commit: 924a913630f395e26b662171a5075090470b2388 https://github.com/galaxyproject/galaxy/commit/924a913630f395e26b662171a507… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M templates/admin/tool_shed_repository/common.mako Log Message: ----------- Mark conda install beta and move after TS options. Commit: 88fac719de191cad6896edb8ac6fcd3058a1accb https://github.com/galaxyproject/galaxy/commit/88fac719de191cad6896edb8ac6f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py Log Message: ----------- Merge remote-tracking branch 'bxlab/install_via_conda' into install_via_conda Commit: 12209ab634634eb8c8a566512dc43b0d9ba78255 https://github.com/galaxyproject/galaxy/commit/12209ab634634eb8c8a566512dc4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako Log Message: ----------- Merge pull request #56 from jmchilton/install_via_conda UI Tweaks Commit: a731ce2e22254d086452fc84eca15e65b444762d https://github.com/galaxyproject/galaxy/commit/a731ce2e22254d086452fc84eca1… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/deps/views.py A lib/galaxy/tools/toolbox/requirements.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/preview_repository.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/export_repository.mako A test/integration/test_resolvers.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge pull request #2554 from bxlab/install_via_conda Fix bugs in post. Compare: https://github.com/galaxyproject/galaxy/compare/64f4d2192745...a731ce2e2225

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