Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8833d1a8a49d7b6d4a9c849b0335d3260564b351 https://github.com/galaxyproject/galaxy/commit/8833d1a8a49d7b6d4a9c849b0335d... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- add security announcement to the rn Commit: e89290c33031d89365aa3ef3b6e4720d68390119 https://github.com/galaxyproject/galaxy/commit/e89290c33031d89365aa3ef3b6e47... Author: Mehmet Tekman <m.tekman@ucl.ac.uk> Date: 2018-03-18 (Sun, 18 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.rds A lib/galaxy/datatypes/test/test.sce A lib/galaxy/datatypes/test/test_error.rds Log Message: ----------- sniffers, test cases Commit: b0effc107af2bba7c0dfefbd7c5861a1597c9099 https://github.com/galaxyproject/galaxy/commit/b0effc107af2bba7c0dfefbd7c586... Author: Mehmet Tekman <m.tekman@ucl.ac.uk> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- fix to class test Commit: ea993a8912b870de7780c68c003c5433badb469d https://github.com/galaxyproject/galaxy/commit/ea993a8912b870de7780c68c003c5... Author: Mehmet Tekman <m.tekman@ucl.ac.uk> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- rpy2 library for loading/testing R objects Commit: 1d2a0117199bc902896ca97cf5e5aa5b9b20b132 https://github.com/galaxyproject/galaxy/commit/1d2a0117199bc902896ca97cf5e5a... Author: Mehmet Tekman <m.tekman@ucl.ac.uk> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- linting fix Commit: a280211ca65ca88b3a7cd92d0d3c1d15b874d462 https://github.com/galaxyproject/galaxy/commit/a280211ca65ca88b3a7cd92d0d3c1... Author: Mehmet Tekman <m.tekman@ucl.ac.uk> Date: 2018-04-13 (Fri, 13 Apr 2018) Log Message: ----------- Merge branch 'master' of github.com:galaxyproject/galaxy into singlecellobject Commit: d31c05a67d40daa12fc3a2dbcdea35d1971d0e3d https://github.com/galaxyproject/galaxy/commit/d31c05a67d40daa12fc3a2dbcdea3... Author: Mehmet Tekman <m.tekman@ucl.ac.uk> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- removed sniffers, removed pinned, removed classes Commit: 695ed3ac68d9f690f649b7e57c1bdf4625cc20fe https://github.com/galaxyproject/galaxy/commit/695ed3ac68d9f690f649b7e57c1bd... Author: Mehmet Tekman <m.tekman@ucl.ac.uk> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: R lib/galaxy/datatypes/test/test.rds R lib/galaxy/datatypes/test/test.sce R lib/galaxy/datatypes/test/test_error.rds Log Message: ----------- removed test data Commit: d5cb6f636b19128ce64934fbae91a82e21d4c668 https://github.com/galaxyproject/galaxy/commit/d5cb6f636b19128ce64934fbae91a... Author: Mehmet Tekman <m.tekman@ucl.ac.uk> Date: 2018-04-14 (Sat, 14 Apr 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- renamed type Commit: 8baea1f7c7551920bc2318b34247a29462a4e035 https://github.com/galaxyproject/galaxy/commit/8baea1f7c7551920bc2318b34247a... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M .ci/flake8_blacklist.txt M .gitignore M CONTRIBUTING.md M Makefile M README.rst M client/.babelrc M client/GruntFile.js M client/README.md M client/bower.json A client/galaxy/docs/bootstrap.md A client/galaxy/docs/galaxy-styles.md M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/HistoryView.vue A client/galaxy/scripts/components/PluginList.vue A client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue A client/galaxy/scripts/layout/communication-server-view.js R client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M 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lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/phylip.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.afg A lib/galaxy/datatypes/test/1.arff A lib/galaxy/datatypes/test/1.genbank A lib/galaxy/datatypes/test/1.genbank.gz A lib/galaxy/datatypes/test/1.hdt A lib/galaxy/datatypes/test/1.obo A lib/galaxy/datatypes/test/1.owl A lib/galaxy/datatypes/test/1.phyloxml A lib/galaxy/datatypes/test/1.stockholm A lib/galaxy/datatypes/test/1.ttl A lib/galaxy/datatypes/test/1.xmfa A lib/galaxy/datatypes/test/2.tabular A lib/galaxy/datatypes/test/2.txt A lib/galaxy/datatypes/test/3.txt A lib/galaxy/datatypes/test/Acanium.hmm M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/triples.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt R lib/galaxy/dependencies/pinned-hashed-requirements.txt A lib/galaxy/dependencies/pinned-requirements.txt R lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/dependencies/pipfiles/default/Pipfile A lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock R lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock R lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/managers/configuration.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/repositories.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/compression_utils.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/json.py M lib/galaxy/util/script.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/jobs.py A lib/galaxy/webapps/galaxy/api/plugins.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin.py A lib/galaxy/webapps/galaxy/controllers/authnz.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/modules.py A lib/galaxy/workflow/resources/__init__.py A lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py A scripts/apply_tags.py M scripts/bootstrap_history.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py R scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/common_startup.sh M scripts/communication/communication_server.py R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh M scripts/db_shell.py A scripts/docker_swarm_manager.py M scripts/galaxy-main M scripts/get_uwsgi_args.py M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py M scripts/helper.py M scripts/manage_db.py R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/transfer.py A static/images/fonts/FontAwesome.otf M static/images/fonts/fontawesome-webfont.eot A static/images/fonts/fontawesome-webfont.svg M static/images/fonts/fontawesome-webfont.ttf M static/images/fonts/fontawesome-webfont.woff A static/images/fonts/fontawesome-webfont.woff2 M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/circster.css M static/style/blue/embed_item.css M static/style/blue/library.css M static/style/blue/reports.css M static/style/blue/trackster.css M static/welcome.html.sample R templates/admin/view_data_tables_registry.mako M templates/admin/view_datatypes_registry.mako M templates/base/base_panels.mako M templates/sharing_base.mako M templates/user/login.mako M templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/reports/index.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako A test-data/rules/PRJDA60709.tsv A test-data/rules/PRJDB3920.tsv A test-data/rules/PRJNA355367.tsv A test-data/rules/uniprot.json A test-data/rules/uniprot.tsv M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_workflows.py A test/base/data/rules_dsl_spec.yml M test/base/populators.py A test/base/workflow_fixtures.py M test/base/workflows_format_2/main.py M test/docker/base/Dockerfile M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/components.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py A test/integration/test_scripts.py M test/integration/test_upload_configuration_options.py R test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/framework.py A test/selenium_tests/test_admin_app.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_library_landing.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/test_modules.py M tools/data_source/upload.py M tools/data_source/upload.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into singlecellobject Commit: 1c433d7d041d50d6e4c5bd886a606ff3af588d9f https://github.com/galaxyproject/galaxy/commit/1c433d7d041d50d6e4c5bd886a606... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #5716 from mtekman/singlecellobject Add datatype(s): RDS object and SingleCellExperiment class Compare: https://github.com/galaxyproject/galaxy/compare/fe4bff1fb9d8...1c433d7d041d