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

[galaxyproject/usegalaxy-playbook] 686959: merge upstream disposable domains list
by GitHub 28 Nov '16

28 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6869590f32208080f61dc800ffcdeb56530b8d8d https://github.com/galaxyproject/usegalaxy-playbook/commit/6869590f32208080… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M files/galaxy/common/config/disposable_email_blacklist.conf Log Message: ----------- merge upstream disposable domains list Commit: bd4f3a0eca9b4a88397d22ee1ebcb340a59cbd08 https://github.com/galaxyproject/usegalaxy-playbook/commit/bd4f3a0eca9b4a88… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M files/galaxy/common/config/disposable_email_blacklist.conf Log Message: ----------- Merge pull request #21 from galaxyproject/upstream-merge merge upstream disposable domains list Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/56bf24a6db25...…

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[galaxyproject/usegalaxy-playbook]
by GitHub 28 Nov '16

28 Nov '16

Branch: refs/heads/martenson-patch-1 Home: https://github.com/galaxyproject/usegalaxy-playbook

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[galaxyproject/usegalaxy-playbook]
by GitHub 28 Nov '16

28 Nov '16

Branch: refs/heads/update-welcome Home: https://github.com/galaxyproject/usegalaxy-playbook

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[galaxyproject/usegalaxy-playbook]
by GitHub 28 Nov '16

28 Nov '16

Branch: refs/heads/fix-welcome-tinies Home: https://github.com/galaxyproject/usegalaxy-playbook

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[galaxyproject/galaxy] 4499d8: Update committers list
by GitHub 28 Nov '16

28 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4499d870d3b31c009d2e61c4c976d9016d1df36e https://github.com/galaxyproject/galaxy/commit/4499d870d3b31c009d2e61c4c976… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Update committers list Commit: 5b4a0689d56eea376df0aa7488e5d913d314dbf3 https://github.com/galaxyproject/galaxy/commit/5b4a0689d56eea376df0aa7488e5… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Merge pull request #3189 from carlfeberhard/committers [PROCEDURES] Update committers list Compare: https://github.com/galaxyproject/galaxy/compare/7c4fac6f1c3b...5b4a0689d56e

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[galaxyproject/galaxy] 70bd8c: Small fixes to bootstrap_history.py
by GitHub 28 Nov '16

28 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 70bd8c9c45b263894ba96879bedce1af66adc283 https://github.com/galaxyproject/galaxy/commit/70bd8c9c45b263894ba96879bedc… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Small fixes to bootstrap_history.py Commit: 7c4fac6f1c3b1ef25809d7b343dd2fa1eff4973b https://github.com/galaxyproject/galaxy/commit/7c4fac6f1c3b1ef25809d7b343dd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #3223 from nsoranzo/bootstrap_history_fixes Small fixes to bootstrap_history.py Compare: https://github.com/galaxyproject/galaxy/compare/1ad89511540e...7c4fac6f1c3b

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[galaxyproject/galaxy] 7d945f: Fix https://github.com/galaxyproject/galaxy/issues...
by GitHub 23 Nov '16

23 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7d945f762e2ed61ebd88f613337b04c7e4c53e8a https://github.com/galaxyproject/galaxy/commit/7d945f762e2ed61ebd88f613337b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Fix https://github.com/galaxyproject/galaxy/issues/3213 discovered by @nsoranzo. Commit: 1ad89511540e6800cd2d0da5d878c1c77d8ccfe9 https://github.com/galaxyproject/galaxy/commit/1ad89511540e6800cd2d0da5d878… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #3216 from jmchilton/when_datatype_isinstance Fix conditional when datatype in XML schema. Compare: https://github.com/galaxyproject/galaxy/compare/ad0e6a437ed8...1ad89511540e

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[galaxyproject/galaxy] 3d57c2: Fix I201 errors from flake8-import-order
by GitHub 23 Nov '16

23 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3d57c22b6324dda9e3ab6c92a2592dd20374abc6 https://github.com/galaxyproject/galaxy/commit/3d57c22b6324dda9e3ab6c92a259… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/actions/admin.py M lib/galaxy/datatypes/images.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py M lib/galaxy/jobs/splitters/basic.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/quota/__init__.py M lib/galaxy/tools/actions/data_manager.py M lib/galaxy/tools/actions/data_source.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/aliaspickler.py M lib/galaxy/util/dbkeys.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/galaxy/controllers/search.py M lib/galaxy/webapps/tool_shed/controllers/groups.py M lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py M lib/galaxy/webapps/tool_shed/util/ratings_util.py M lib/galaxy/workflow/steps.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py M lib/tool_shed/repository_types/unrestricted.py M lib/tool_shed/util/web_util.py M scripts/api/example_watch_folder.py M scripts/api/form_create_from_xml.py M scripts/api/history_create_history.py M scripts/api/history_delete_history.py M scripts/api/import_library_dataset_to_history.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/library_create_folder.py M scripts/api/library_create_library.py M scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/sequencer_configuration_create.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/build_toolbox.py M scripts/check_galaxy.py M scripts/check_python.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/drmaa_external_runner.py M test/api/test_datasets.py M test/api/test_history_contents_provenance.py M test/unit/test_sockets.py M tools/data_source/fetch.py Log Message: ----------- Fix I201 errors from flake8-import-order Also fix Python3 compatibility. Remove unused method galaxy.tools.parameters.sanitize.ToolParameterSanitizer.restore_param() . Commit: ad0e6a437ed8be4fdb5513574cac2c5f8570122a https://github.com/galaxyproject/galaxy/commit/ad0e6a437ed8be4fdb5513574cac… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/actions/admin.py M lib/galaxy/datatypes/images.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py M lib/galaxy/jobs/splitters/basic.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/quota/__init__.py M lib/galaxy/tools/actions/data_manager.py M lib/galaxy/tools/actions/data_source.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/aliaspickler.py M lib/galaxy/util/dbkeys.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/galaxy/controllers/search.py M lib/galaxy/webapps/tool_shed/controllers/groups.py M lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py M lib/galaxy/webapps/tool_shed/util/ratings_util.py M lib/galaxy/workflow/steps.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py M lib/tool_shed/repository_types/unrestricted.py M lib/tool_shed/util/web_util.py M scripts/api/example_watch_folder.py M scripts/api/form_create_from_xml.py M scripts/api/history_create_history.py M scripts/api/history_delete_history.py M scripts/api/import_library_dataset_to_history.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/library_create_folder.py M scripts/api/library_create_library.py M scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/sequencer_configuration_create.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/build_toolbox.py M scripts/check_galaxy.py M scripts/check_python.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/drmaa_external_runner.py M test/api/test_datasets.py M test/api/test_history_contents_provenance.py M test/unit/test_sockets.py M tools/data_source/fetch.py Log Message: ----------- Merge pull request #3215 from nsoranzo/flake8-import-order Fix I201 errors from flake8-import-order Compare: https://github.com/galaxyproject/galaxy/compare/fef5523ed443...ad0e6a437ed8

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[galaxyproject/galaxy] 6aab80: Tour routing tweaks, allows us to drop the model o...
by GitHub 23 Nov '16

23 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6aab802e5ad8e1f4e088e95f0e1483a60e6e4b7e https://github.com/galaxyproject/galaxy/commit/6aab802e5ad8e1f4e088e95f0e14… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M static/maps/layout/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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Tour routing tweaks, allows us to drop the model out of menu Commit: fef5523ed443c45b6d93dfd3ec72ae09f358019c https://github.com/galaxyproject/galaxy/commit/fef5523ed443c45b6d93dfd3ec72… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M static/maps/layout/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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Merge pull request #3214 from dannon/tour_routing Tour routing tweaks, allows us to drop the model out of menu Compare: https://github.com/galaxyproject/galaxy/compare/db93fd32859b...fef5523ed443

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[galaxyproject/galaxy] bbc403: Add cached dependency manager
by GitHub 23 Nov '16

23 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bbc403b2e1411f2a54fe3c28283dbd26dddbc780 https://github.com/galaxyproject/galaxy/commit/bbc403b2e1411f2a54fe3c28283d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Add cached dependency manager Similar to https://github.com/galaxyproject/galaxy/pull/2986, implement a mechanism that allows tool dependencies to be cached. If the `use_cached_dependency_manager` option is set to True in galaxy.ini, we build a hash of the combination of a tools' requirements, and store the resulting environment in a directory specified by the `tool_dependency_cache_dir` option in galaxy.ini. Commit: 185856f6afd36d627cd722402e687188b400333b https://github.com/galaxyproject/galaxy/commit/185856f6afd36d627cd722402e68… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Better phrasing of cache options in galaxy.ini.sample (Thanks @nsoranzo) Commit: 5606d84f22e2bb21966c65ff37fd8c47013961c9 https://github.com/galaxyproject/galaxy/commit/5606d84f22e2bb21966c65ff37fd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M config/galaxy.ini.sample 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/conda.py Log Message: ----------- Rework cached dependencies to be more robust to updates or changes in depedencies, folder structure and resolver configuration. Instead of hashing name, type and version of a dependency, hash the json representation of the dependencies returned by the dependency resolver, which include the path to the environment and the depedency type. This is only applied to resolvers whose cacheable attribute is set to True (conda-only, currently). Commit: 66af4295cbb669389a68dcc19403798b84d0f2bc https://github.com/galaxyproject/galaxy/commit/66af4295cbb669389a68dcc19403… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Build dependency cache at install time and only activate cached environments if they exist. Commit: df93db40b118777cad6887386d7fc03df3acbf92 https://github.com/galaxyproject/galaxy/commit/df93db40b118777cad6887386d7f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M lib/galaxy/tools/deps/requirements.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Only attempt to build cache once per install and override __eq__ for ToolRequirement, to simplify checking if ToolRequirements are already installed/cached. Commit: 21b859e555e6e199eece79cb1d718e7b17d827a1 https://github.com/galaxyproject/galaxy/commit/21b859e555e6e199eece79cb1d71… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix NameError Commit: db93fd32859b9b1f326877833cb843edffd48d66 https://github.com/galaxyproject/galaxy/commit/db93fd32859b9b1f326877833cb8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.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/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Merge pull request #3106 from mvdbeek/cached_dep_manager Add cached dependency manager Compare: https://github.com/galaxyproject/galaxy/compare/097300ea6219...db93fd32859b

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