March 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] a8c22e: Remove twill functional tests we don't actively ru...
by GitHub 26 Mar '16

26 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a8c22ee9dbc8eb0f59ea55748db7a9c5cae50bc0 https://github.com/galaxyproject/galaxy/commit/a8c22ee9dbc8eb0f59ea55748db7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: R test/functional/test_admin_features.py R test/functional/test_data_security.py R test/functional/test_dataset_features.py R test/functional/test_get_data.py R test/functional/test_library_features.py R test/functional/test_library_security.py R test/functional/test_metadata_editing.py R test/functional/test_sample_tracking.py R test/functional/test_tags.py R test/functional/test_ucsc_table_browser.py R test/functional/test_user_info.py Log Message: ----------- Remove twill functional tests we don't actively run. Commit: 5b16589f290139cba11b693452bae5570a60e47d https://github.com/galaxyproject/galaxy/commit/5b16589f290139cba11b693452ba… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-26 (Sat, 26 Mar 2016) Changed paths: R test/functional/test_admin_features.py R test/functional/test_data_security.py R test/functional/test_dataset_features.py R test/functional/test_get_data.py R test/functional/test_library_features.py R test/functional/test_library_security.py R test/functional/test_metadata_editing.py R test/functional/test_sample_tracking.py R test/functional/test_tags.py R test/functional/test_ucsc_table_browser.py R test/functional/test_user_info.py Log Message: ----------- Merge pull request #2019 from jmchilton/remove_twill_tests Remove twill functional tests we don't actively run. Compare: https://github.com/galaxyproject/galaxy/compare/c093c793b7ba...5b16589f2901

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[galaxyproject/galaxy] 85ef86: Improvements to workflow scaling performance testi...
by GitHub 25 Mar '16

25 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 85ef86ab2ee904c62d00f84e7220c661bd31e58c https://github.com/galaxyproject/galaxy/commit/85ef86ab2ee904c62d00f84e7220… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/workflow/scheduling_manager.py M scripts/summarize_timings.py A test/functional/tools/for_workflows/create_input_collection.xml A test/functional/tools/for_workflows/split.xml M test/functional/tools/samples_tool_conf.xml A test/manual/launch_and_run.sh A test/manual/workflow_job_conf.xml M test/manual/workflows_scaling.py Log Message: ----------- Improvements to workflow scaling performance testing scripts. - Implement a wrapper script for launching a docker-galaxy-stable setup a many ways for this task including: - Configure container's Galaxy with outer Galaxy's lib and test directory. - Collect log files. - Log a statement for interacting with the container easily while the test is running. - Disable unneeded services. - Implement a fan-in-fan-out style workflow for performance testing. - Add an option to test performance of scheduling workflows without actually running jobs. - Sample tool for creating large collections easily at beginning of tests (much faster than uploads). - Sample tool for splitting a file into a collection for fan in and out workflow test. - Assume Python 2.7 in scripts to simplify things. - Add documentation. Commit: da1f1bd8b2ae1ce7910b14c3dab0791dc0a67050 https://github.com/galaxyproject/galaxy/commit/da1f1bd8b2ae1ce7910b14c3dab0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M test/functional/tools/for_workflows/create_input_collection.xml Log Message: ----------- Fixes to create_input_collection.xml based on comments from @nsoranzo. Commit: c093c793b7ba589c41e7df3041585922ddc840d8 https://github.com/galaxyproject/galaxy/commit/c093c793b7ba589c41e7df304158… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/workflow/scheduling_manager.py M scripts/summarize_timings.py A test/functional/tools/for_workflows/create_input_collection.xml A test/functional/tools/for_workflows/split.xml M test/functional/tools/samples_tool_conf.xml A test/manual/launch_and_run.sh A test/manual/workflow_job_conf.xml M test/manual/workflows_scaling.py Log Message: ----------- Merge pull request #1958 from jmchilton/workflow_scheduling_testing Improvements to workflow scaling performance testing scripts. Compare: https://github.com/galaxyproject/galaxy/compare/d9177a81e548...c093c793b7ba

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[galaxyproject/galaxy] 142383: Fix collection handling
by GitHub 25 Mar '16

25 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1423836f1e3ef1032ce38128a5fd1191fb7d217a https://github.com/galaxyproject/galaxy/commit/1423836f1e3ef1032ce38128a5fd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix collection handling Commit: d9177a81e5488f0248fba7a6e22e55885779f4a5 https://github.com/galaxyproject/galaxy/commit/d9177a81e5488f0248fba7a6e22e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2015 from guerler/fix_collection_001 Fix collection handling Compare: https://github.com/galaxyproject/galaxy/compare/494b2f3e2726...d9177a81e548

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[galaxyproject/galaxy] 3240c2: Swap analyse to analyze to be consistent.
by GitHub 25 Mar '16

25 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3240c20a4b5cd29a1f2e3764a8aa6cf84ca1e48d https://github.com/galaxyproject/galaxy/commit/3240c20a4b5cd29a1f2e3764a8aa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js 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/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Swap analyse to analyze to be consistent. Commit: 494b2f3e272662d2f497ab9dd1a870f3f661554c https://github.com/galaxyproject/galaxy/commit/494b2f3e272662d2f497ab9dd1a8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js 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/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #2020 from dannon/analyse Swap analyse to analyze to be consistent across the app. Compare: https://github.com/galaxyproject/galaxy/compare/b9ccf17376f6...494b2f3e2726

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[galaxyproject/galaxy] 87ea37: add 'create history &import to it' feature
by GitHub 25 Mar '16

25 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 87ea37ca28f791624eeabdbaa26d5fd01d7a9297 https://github.com/galaxyproject/galaxy/commit/87ea37ca28f791624eeabdbaa26d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/style/less/library.less M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- add 'create history &import to it' feature various refactorings and fixes to UX glitches Commit: ce1b9aeb38d68893004c0d9de6d0637983145de7 https://github.com/galaxyproject/galaxy/commit/ce1b9aeb38d68893004c0d9de6d0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- minor adjustments to markup; improve logging; repack Commit: b9ccf17376f631cf1d004ee3af0571d2925cd7aa https://github.com/galaxyproject/galaxy/commit/b9ccf17376f631cf1d004ee3af05… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/style/less/library.less M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Merge pull request #2017 from martenson/import-to-new-history libraries: add 'create history &import to it' feature Compare: https://github.com/galaxyproject/galaxy/compare/0d5001eea78e...b9ccf17376f6

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[galaxyproject/galaxy] 4f2661: Fix PJA creation in tool bursting threads.
by GitHub 25 Mar '16

25 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 4f2661a1e9b3179b8df7ff773b71d15aa756dd8d https://github.com/galaxyproject/galaxy/commit/4f2661a1e9b3179b8df7ff773b71… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Fix PJA creation in tool bursting threads. Potentially fixes #1657. Commit: 948a4aa55bf9409a69b7af75b9987d60f09890f3 https://github.com/galaxyproject/galaxy/commit/948a4aa55bf9409a69b7af75b998… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #2013 from jmchilton/fix_1657_stable [16.01] Fix PJA creation in tool bursting threads. Compare: https://github.com/galaxyproject/galaxy/compare/425f0daa2d90...948a4aa55bf9

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[galaxyproject/galaxy] 7d1b52: The response from dataproviders here can return da...
by GitHub 25 Mar '16

25 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 7d1b525682c9dd0786b7ccca23c3b0695b3c0751 https://github.com/galaxyproject/galaxy/commit/7d1b525682c9dd0786b7ccca23c3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M lib/galaxy/webapps/galaxy/api/datasets.py M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/viz/trackster/tracks.js Log Message: ----------- The response from dataproviders here can return data===null in addition to being simply undefined. This corrects the logic shortcutting and prevents errors like 'Cannot read property 'min' of null' Commit: 425f0daa2d9030a36c2af5b144a4d563542153a2 https://github.com/galaxyproject/galaxy/commit/425f0daa2d9030a36c2af5b144a4… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M lib/galaxy/webapps/galaxy/api/datasets.py M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/viz/trackster/tracks.js Log Message: ----------- Merge pull request #2014 from dannon/trackster_dataprovider_fix [16.01] Fix trackster erroring when fetching data from regions or datasets with no content. Compare: https://github.com/galaxyproject/galaxy/compare/8accc56132ff...425f0daa2d90

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[galaxyproject/galaxy] dc49a9: Fix unbound error that is possible if using tool b...
by GitHub 25 Mar '16

25 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dc49a9cbc1b24fb4abd1c5b98eba433218a3042d https://github.com/galaxyproject/galaxy/commit/dc49a9cbc1b24fb4abd1c5b98eba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-24 (Thu, 24 Mar 2016) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- Fix unbound error that is possible if using tool bursting. Commit: 8accc56132ff5863ff4d0e3127d9aa5c8fc419d4 https://github.com/galaxyproject/galaxy/commit/8accc56132ff5863ff4d0e3127d9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- Merge pull request #2009 from jmchilton/execute_params_fix [16.01] Fix unbound error that is possible if using tool bursting. Commit: 0d5001eea78e21f126299a1f8295e01f84c2d8ee https://github.com/galaxyproject/galaxy/commit/0d5001eea78e21f126299a1f8295… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- Merge branch 'release_16.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/ec3fe67ddd2a...0d5001eea78e

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[galaxyproject/galaxy] edb51d: Rename tool_shed_get to url_get.
by GitHub 25 Mar '16

25 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: edb51d876b763d0fd321c85d429575d465b754d1 https://github.com/galaxyproject/galaxy/commit/edb51d876b763d0fd321c85d4295… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Rename tool_shed_get to url_get. Commit: 9e8890b25bb126a401b17eee616609ce7963f928 https://github.com/galaxyproject/galaxy/commit/9e8890b25bb126a401b17eee6166… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M Makefile M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/style/less/base.less M client/galaxy/style/less/library.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/tool_data_table_conf.xml.sample M contrib/galaxy.fedora-init A contrib/galaxy_reports.fedora-init A display_applications/iobio/bam.xml A display_applications/iobio/vcf.xml M doc/source/releases/index.rst A lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml A lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml A lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml A lib/galaxy/datatypes/converters/cml_to_smi_converter.xml A lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml A lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml A lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml A lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml A lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml A lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml A lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml A lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml A lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml A lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml A lib/galaxy/datatypes/converters/mol_to_cml_converter.xml A lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml A lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml A lib/galaxy/datatypes/converters/mol_to_smi_converter.xml A lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml A lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml A lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml A lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml A lib/galaxy/datatypes/converters/smi_to_cml_converter.xml A lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml A lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml A lib/galaxy/datatypes/converters/smi_to_mol_converter.xml A lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml A lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/datatypes/display_applications/application.py A lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/5e5z.pdb A lib/galaxy/datatypes/test/drugbank_drugs.cml A lib/galaxy/datatypes/test/drugbank_drugs.inchi A lib/galaxy/datatypes/test/drugbank_drugs.mol2 A lib/galaxy/datatypes/test/drugbank_drugs.sdf A lib/galaxy/datatypes/test/drugbank_drugs.smi A lib/galaxy/datatypes/test/q.fps M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py R lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/util/log/fluent_log.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/metrics.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/run.py M lib/tool_shed/tool_shed_registry.py M run.sh M run_reports.sh M run_tool_shed.sh M scripts/bootstrap_history.py M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map 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/layout/menu.js M static/scripts/layout/page.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js M static/style/blue/base.css M static/style/blue/library.css M templates/webapps/galaxy/workflow/display.mako M test/base/twilltestcase.py M test/functional/test_toolbox.py M test/functional/tools/collection_creates_list.xml M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py M test/unit/jobs/test_runner_local.py A tool-data/bam_iobio.loc.sample A tool-data/vcf_iobio.loc.sample Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into move_tsg Commit: 06b9737e0934823c807b02cbeaf590735437653d https://github.com/galaxyproject/galaxy/commit/06b9737e0934823c807b02cbeaf5… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Cleanup and fix tests. Commit: 7e14f5db6236a5ab1b9df988fe88cd34eaf8ba78 https://github.com/galaxyproject/galaxy/commit/7e14f5db6236a5ab1b9df988fe88… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/util/common_util.py Log Message: ----------- Address travis' complaints. Commit: ec3fe67ddd2a5fc2017b3d402bb2869c70bac368 https://github.com/galaxyproject/galaxy/commit/ec3fe67ddd2a5fc2017b3d402bb2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #1918 from davebx/move_tsg Rename tool_shed_get to url_get. Compare: https://github.com/galaxyproject/galaxy/compare/6e34858e0da7...ec3fe67ddd2a

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[galaxyproject/galaxy] 72b1ba: Fix parameter expansion for empty collections
by GitHub 25 Mar '16

25 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 72b1ba3714d223f14836a74a841fa811809d488b https://github.com/galaxyproject/galaxy/commit/72b1ba3714d223f14836a74a841f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-24 (Thu, 24 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix parameter expansion for empty collections Commit: 6e34858e0da7b08075bff946ae5cd2d9d09e6234 https://github.com/galaxyproject/galaxy/commit/6e34858e0da7b08075bff946ae5c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2010 from guerler/fix_collection_select Fix parameter expansion for empty collections Compare: https://github.com/galaxyproject/galaxy/compare/84044f9a5f3c...6e34858e0da7

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