- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 3163dc: add python-ldap module if used in auth-conf.xml
by GitHub 27 Jul '16

27 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3163dc77f504a1923046e184c3d86822e34f940a https://github.com/galaxyproject/galaxy/commit/3163dc77f504a1923046e184c3d8… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-06-29 (Wed, 29 Jun 2016) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- add python-ldap module if used in auth-conf.xml Commit: 8b9d77ee3b8832c767dd2a34f23eb8bcc60d6423 https://github.com/galaxyproject/galaxy/commit/8b9d77ee3b8832c767dd2a34f23e… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-06-29 (Wed, 29 Jun 2016) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- detect actviedirectory too Commit: b08dfa2e72ec7d49a6b9e50241dba082825f8061 https://github.com/galaxyproject/galaxy/commit/b08dfa2e72ec7d49a6b9e50241db… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M .ci/py3_sources.txt M Makefile 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/form/form-data.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.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/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 client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/style/less/ui.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/jupyter/config/jupyter.xml M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/charts/forms/default.js M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js M config/plugins/visualizations/charts/static/library/datasets.js M config/plugins/visualizations/charts/static/library/jobs.js M config/plugins/visualizations/charts/static/library/storage.js R config/plugins/visualizations/charts/static/library/ui-table-form.js M 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tools/stats/aggregate_scores_in_intervals.py M tools/stats/gsummary.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into ldap Commit: 28e7f866cbab76e93f63179d4a7e6c2fd962b5b1 https://github.com/galaxyproject/galaxy/commit/28e7f866cbab76e93f63179d4a7e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Merge pull request #2576 from abretaud/ldap Add python-ldap module to conditional requirements Compare: https://github.com/galaxyproject/galaxy/compare/b74fd63feff0...28e7f866cbab

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[galaxyproject/galaxy] b79474: Merge pull request #2206 from dannon/master
by GitHub 27 Jul '16

27 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b79474083b08860923f7f28fc1e7442b53f925db https://github.com/galaxyproject/galaxy/commit/b79474083b08860923f7f28fc1e7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M config/tool_shed.ini.sample M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/workflow/modules.py M lib/tool_shed/util/shed_util_common.py M static/maps/layout/page.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-library-view.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/layout/page.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-library-view.js M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/workflow/run.mako M test/tool_shed/base/twilltestcase.py A test/tool_shed/functional/test_0310_hg_api_features.py R test/tool_shed/functional/test_0310_hg_push_from_api.py Log Message: ----------- Merge pull request #2206 from dannon/master Sanity check of master update. Commit: e77d3f009a8e2fb51e97f41b4c47e397c90cbcea https://github.com/galaxyproject/galaxy/commit/e77d3f009a8e2fb51e97f41b4c47… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/run.py M templates/webapps/galaxy/library/common/browse_library.mako M templates/webapps/galaxy/library/common/ldda_info.mako M test/tool_shed/base/twilltestcase.py Log Message: ----------- Merge branch 'release_16.01' Commit: e08dae34628d31f6685f9f7e031e2085c024f63b https://github.com/galaxyproject/galaxy/commit/e08dae34628d31f6685f9f7e031e… Author: balto <balto_59(a)hotmail.fr> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: A lib/galaxy/webapps/reports/controllers/history.py A templates/webapps/reports/history_and_dataset_per_user.mako A templates/webapps/reports/history_and_dataset_type.mako M templates/webapps/reports/index.mako Log Message: ----------- Creation of the history category that contains two pages: history and dataset per type/user. Commit: cd2b61a3a1426cdd62f9af3fe506affa3c097688 https://github.com/galaxyproject/galaxy/commit/cd2b61a3a1426cdd62f9af3fe506… Author: balto <balto_59(a)hotmail.fr> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: A lib/galaxy/webapps/reports/controllers/tools.py Log Message: ----------- Creation of the tools controller and each methods for each template. Commit: e4d8c7d88556a201a91ac21b67d08feecd57f819 https://github.com/galaxyproject/galaxy/commit/e4d8c7d88556a201a91ac21b67d0… Author: balto <balto_59(a)hotmail.fr> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: 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_peer_month.mako A templates/webapps/reports/tools_and_job_state.mako A templates/webapps/reports/tools_and_job_state_peer_month.mako Log Message: ----------- Implementation of tools-related pages. Commit: fdd778f244b6f647aa8c56e133c3226bbed8ed72 https://github.com/galaxyproject/galaxy/commit/fdd778f244b6f647aa8c56e133c3… Author: balto <balto_59(a)hotmail.fr> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/webapps/reports/controllers/users.py A templates/webapps/reports/history_per_user.mako M templates/webapps/reports/index.mako Log Message: ----------- Implementation of a new page listing histories per users. Commit: 71fc940c8f048d3c3b4e929320bd895c2361e342 https://github.com/galaxyproject/galaxy/commit/71fc940c8f048d3c3b4e929320bd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/webapps/reports/controllers/history.py Log Message: ----------- Gets reports/controllers/history.py up to passing style. Commit: a66800465614042b75c0f30217b0c1d9075aaed1 https://github.com/galaxyproject/galaxy/commit/a66800465614042b75c0f30217b0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/webapps/reports/controllers/history.py Log Message: ----------- Slight bit of extra import cleanup in reports/controllers/history Commit: 5c47820e01576854a111b54f220993415258ffc8 https://github.com/galaxyproject/galaxy/commit/5c47820e01576854a111b54f2209… Author: BalthazarPavot <balthazar.pavot(a)hotmail.fr> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M lib/galaxy/webapps/reports/controllers/history.py Log Message: ----------- Merge pull request #1 from dannon/dev_reports This brings the history file up to style guidelines and will fix the build. Commit: 3107cfed9d502ea9baf0cab14a19cbf3c8bdec61 https://github.com/galaxyproject/galaxy/commit/3107cfed9d502ea9baf0cab14a19… Author: BalthazarPavot <balthazar.pavot(a)hotmail.fr> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M lib/galaxy/webapps/reports/controllers/tools.py Log Message: ----------- Update tools.py Commit: 12c65d4a6365e34660c78dab7bb43b2cf292eb61 https://github.com/galaxyproject/galaxy/commit/12c65d4a6365e34660c78dab7bb4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/webapps/reports/controllers/tools.py Log Message: ----------- fix import of and_ operator Commit: 28a990470738ac821a6a2851306dac9723767c12 https://github.com/galaxyproject/galaxy/commit/28a990470738ac821a6a2851306d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/webapps/reports/controllers/history.py M lib/galaxy/webapps/reports/controllers/tools.py M lib/galaxy/webapps/reports/controllers/users.py M templates/webapps/reports/history_and_dataset_per_user.mako M templates/webapps/reports/history_and_dataset_type.mako M templates/webapps/reports/history_per_user.mako M templates/webapps/reports/index.mako M templates/webapps/reports/tool_execution_time.mako R templates/webapps/reports/tool_execution_time_peer_month.mako A templates/webapps/reports/tool_execution_time_per_month.mako M templates/webapps/reports/tools_and_job_state.mako R templates/webapps/reports/tools_and_job_state_peer_month.mako A templates/webapps/reports/tools_and_job_state_per_month.mako Log Message: ----------- fix menu items to actually display new templates reword certain texts reorder imports and fix style remove unnecessary imports Commit: 295f3f93e1db89b13040b42c8945cd5491ccda02 https://github.com/galaxyproject/galaxy/commit/295f3f93e1db89b13040b42c8945… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M templates/webapps/reports/history_and_dataset_per_user.mako M templates/webapps/reports/history_and_dataset_type.mako M templates/webapps/reports/history_per_user.mako M templates/webapps/reports/tool_execution_time.mako M templates/webapps/reports/tool_execution_time_per_month.mako M templates/webapps/reports/tools_and_job_state.mako M templates/webapps/reports/tools_and_job_state_per_month.mako Log Message: ----------- change css classes and html markup for new report pages Commit: 8483f2ce8bffbdee0ee9ffd65b7212ed8c54e8a4 https://github.com/galaxyproject/galaxy/commit/8483f2ce8bffbdee0ee9ffd65b72… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/webapps/reports/controllers/tools.py Log Message: ----------- Fix E731 Commit: b74fd63feff0c2c324009b9a48757ff146d69cdc https://github.com/galaxyproject/galaxy/commit/b74fd63feff0c2c324009b9a4875… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: A lib/galaxy/webapps/reports/controllers/history.py A lib/galaxy/webapps/reports/controllers/tools.py M lib/galaxy/webapps/reports/controllers/users.py 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 Log Message: ----------- Merge pull request #2664 from dannon/dev_reports Reports: new pages and improvements Compare: https://github.com/galaxyproject/galaxy/compare/fa4085be548a...b74fd63feff0

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[galaxyproject/galaxy] 1cdc53: Reduce server sided refresh requests to changes in...
by GitHub 27 Jul '16

27 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1cdc532ff1817f59b5693cb9ef6e787be5374e9d https://github.com/galaxyproject/galaxy/commit/1cdc532ff1817f59b5693cb9ef6e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: 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-workflow.js M lib/galaxy/tools/parameters/basic.py 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-workflow.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-workflow.js Log Message: ----------- Reduce server sided refresh requests to changes in data associated input fields Commit: fa4085be548a6b893745f467deb71cd0ec0dfcec https://github.com/galaxyproject/galaxy/commit/fa4085be548a6b893745f467deb7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: 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-workflow.js M lib/galaxy/tools/parameters/basic.py 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-workflow.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-workflow.js Log Message: ----------- Merge pull request #2652 from guerler/reduce_refreshs Reduce server sided refresh requests to changes in data associated input fields Compare: https://github.com/galaxyproject/galaxy/compare/8b597ed01a6f...fa4085be548a

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[galaxyproject/galaxy] 4a8310: Generate metadata in separate conda environment
by GitHub 26 Jul '16

26 Jul '16

Branch: refs/heads/release_16.04 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 Compare: https://github.com/galaxyproject/galaxy/compare/1de7beca98d0...8f978b8957f0

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[galaxyproject/galaxy] c07bbe: Add import order linting using tox and flake8-impo...
by GitHub 26 Jul '16

26 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c07bbe010ee350d6bb63006ff8829a16d0d9d4a9 https://github.com/galaxyproject/galaxy/commit/c07bbe010ee350d6bb63006ff882… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: A .ci/flake8_lint_include_list.txt A .ci/flake8_wrapper_imports.sh M .travis.yml M setup.cfg M tox.ini Log Message: ----------- Add import order linting using tox and flake8-import-order. Adds two tasks: - Add a task that just lints everything the way Galaxy's default linting is (py27-lint-imports) and don't enforce it passes on Travis. - Add a task that just lints a subset we expect to past, hopefully we can grow this subset over time. Once the inverse of the subset we are testing is just the blacklist, we can eliminate bothtasks and just wrap this into Galaxy's default linting. These tasks require an older flake8 until https://github.com/PyCQA/flake8-import-order/issues/79#issuecomment-2350522… is part of a released version of flake8. Commit: 8b597ed01a6fd4335b78ba66875a40f430423c34 https://github.com/galaxyproject/galaxy/commit/8b597ed01a6fd4335b78ba66875a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: A .ci/flake8_lint_include_list.txt A .ci/flake8_wrapper_imports.sh M .travis.yml M setup.cfg M tox.ini Log Message: ----------- Merge pull request #2661 from jmchilton/lint_imports Add import order linting using tox and flake8-import-order. Compare: https://github.com/galaxyproject/galaxy/compare/71151c6b2dd3...8b597ed01a6f

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[galaxyproject/galaxy] 26b141: made changes to tool-form-base.js, this should all...
by GitHub 26 Jul '16

26 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 26b141c83f906dbc7d11c14da968f323eaa632e8 https://github.com/galaxyproject/galaxy/commit/26b141c83f906dbc7d11c14da968… Author: nturaga <nitesh.turaga(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/mvc/tool/tool-form-base.js.map 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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form.js Log Message: ----------- made changes to tool-form-base.js, this should allow the tool-form to listen to history. Thanks @guerler for walking me through backbone Commit: c172641c9deda5d9c193e212a2d74d150eb64f79 https://github.com/galaxyproject/galaxy/commit/c172641c9deda5d9c193e212a2d7… Author: nturaga <nitesh.turaga(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.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-base.js Log Message: ----------- added refresh in _buildform as per @guerler 's suggestion Commit: fd34553cb142e9ccff6b7b295247dd09801d3fb0 https://github.com/galaxyproject/galaxy/commit/fd34553cb142e9ccff6b7b295247… Author: nturaga <nitesh.turaga(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.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-base.js Log Message: ----------- removing options.needs_update as it is not used anymore, per @guerlers suggestion Commit: 6414478ad1ab669c8725d0fb784e1b438ddb40dd https://github.com/galaxyproject/galaxy/commit/6414478ad1ab669c8725d0fb784e… Author: nturaga <nitesh.turaga(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.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-base.js Log Message: ----------- added self.deferred() in refresh Commit: a6e288fe301c00e88893e0ffe3cbe9f9572aba5e https://github.com/galaxyproject/galaxy/commit/a6e288fe301c00e88893e0ffe3cb… Author: nturaga <nitesh.turaga(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- changes' Commit: 71151c6b2dd3038ac04a77bbb8543e77875b9cc1 https://github.com/galaxyproject/galaxy/commit/71151c6b2dd3038ac04a77bbb854… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/mvc/tool/tool-form-base.js.map 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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form.js Log Message: ----------- Merge pull request #2476 from nturaga/tool_form_listen_history Allow tool form to listen to history Compare: https://github.com/galaxyproject/galaxy/compare/3d0f5577b105...71151c6b2dd3

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[galaxyproject/galaxy] 7a8d86: Ensure Galaxy's python binary is used for metadata...
by GitHub 26 Jul '16

26 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7a8d86aa9bd2b8adfbe8e6826e506dfedf997e22 https://github.com/galaxyproject/galaxy/commit/7a8d86aa9bd2b8adfbe8e6826e50… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Ensure Galaxy's python binary is used for metadata generation. Commit: 3d0f5577b10507cd774f3e4f92f6c8364a8a4407 https://github.com/galaxyproject/galaxy/commit/3d0f5577b10507cd774f3e4f92f6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Merge pull request #2660 from jmchilton/ensure_galaxy_python_for_metadata Ensure Galaxy's python binary is used for metadata generation. Compare: https://github.com/galaxyproject/galaxy/compare/9607e528be01...3d0f5577b105

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[galaxyproject/galaxy] 93ba35: Import pyparsing in testing so twill's older versi...
by GitHub 26 Jul '16

26 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 93ba35fdd16a96b46ccac6884b7efcb4a5d3e8a3 https://github.com/galaxyproject/galaxy/commit/93ba35fdd16a96b46ccac6884b7e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M test/base/twilltestcase.py Log Message: ----------- Import pyparsing in testing so twill's older version doesn't get loaded. There are unintended consequences if not, such as svgwrite not loading properly. Commit: 9607e528be01234b1107db29e0a910043d12507e https://github.com/galaxyproject/galaxy/commit/9607e528be01234b1107db29e0a9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M test/base/twilltestcase.py Log Message: ----------- Merge pull request #2656 from jmchilton/pyparsing_testing Import pyparsing in testing so twill's older version doesn't get loaded. Compare: https://github.com/galaxyproject/galaxy/compare/134f98854931...9607e528be01

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[galaxyproject/galaxy] 8559dc: Ignore .tox directory. Used to be ignored by defa...
by GitHub 25 Jul '16

25 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8559dc00b606551de5947d6bc5d74bb9feb9f184 https://github.com/galaxyproject/galaxy/commit/8559dc00b606551de5947d6bc5d7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-25 (Mon, 25 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: 10745f252f6e0cf59a47f097620d5d05034b1c1a https://github.com/galaxyproject/galaxy/commit/10745f252f6e0cf59a47f097620d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-25 (Mon, 25 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: cf800dce03949e928333a13b675fba76e612226f https://github.com/galaxyproject/galaxy/commit/cf800dce03949e928333a13b675f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-25 (Mon, 25 Jul 2016) Changed paths: M .ci/flake8_blacklist.txt Log Message: ----------- Add eggs to blacklist as well, to ignore it in local testing for folks with it still around. (nsoranzo's suggestion) Commit: 9f2237905b81205d0d6fec918fc15ddbea1e34ce https://github.com/galaxyproject/galaxy/commit/9f2237905b81205d0d6fec918fc1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-25 (Mon, 25 Jul 2016) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/web/__init__.py M lib/galaxy/web/buildapp.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 test/base/driver_util.py Log Message: ----------- Remove two #noqas and specify __all__ for those modules. Specify many more #noqas to skip the precise relevant exception. Commit: 0deae302852102c66e6386e16607c1db99cdeb07 https://github.com/galaxyproject/galaxy/commit/0deae302852102c66e6386e16607… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-25 (Mon, 25 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/forms.py Log Message: ----------- Remove two unused imports in forms controller. Commit: 134f988549314a4a384144c2eedc3d8b4ff7e2f3 https://github.com/galaxyproject/galaxy/commit/134f988549314a4a384144c2eedc… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-07-25 (Mon, 25 Jul 2016) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy/model/mapping.py M lib/galaxy/web/__init__.py M lib/galaxy/web/buildapp.py M lib/galaxy/web/framework/helpers/__init__.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 test/base/driver_util.py Log Message: ----------- Merge pull request #2650 from dannon/flake8_update_tox_default Ignore .tox directory. Used to be ignored by default w/ flake8 appar… Compare: https://github.com/galaxyproject/galaxy/compare/1e291e1ecdd1...134f98854931

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[galaxyproject/usegalaxy-playbook] 796678: update Main, update submodule
by GitHub 25 Jul '16

25 Jul '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 796678f38f5545c1efc9eb1b2ba1ffa8d1244019 https://github.com/galaxyproject/usegalaxy-playbook/commit/796678f38f5545c1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-25 (Mon, 25 Jul 2016) Changed paths: M common_roles M production/galaxy_version.yml Log Message: ----------- update Main, update submodule

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