Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 20632b2757f789bc751faa280fa34eebe78e41db https://github.com/galaxyproject/galaxy/commit/20632b2757f789bc751faa280fa34... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/search/__init__.py M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Adding fuzzy search to tool search Commit: 659679005d0e0db7a9689cc738114742bf3140fc https://github.com/galaxyproject/galaxy/commit/659679005d0e0db7a9689cc738114... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-view.js 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/interactive_environments/rstudio/config/rstudio.xml M config/plugins/tours/core.history.yaml M lib/galaxy/config.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/images.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.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/container_resolvers/explicit.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/verify/asserts/text.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M run_tests.sh M scripts/functional_tests.py R scripts/run_selenium_tests.sh M static/maps/layout/menu.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/workflow/workflow-icons.js.map M 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test/api/test_workflow_map_reduce_pause.ga R test/api/test_workflow_matching_lists.ga R test/api/test_workflow_missing_tool.ga R test/api/test_workflow_pause.ga R test/api/test_workflow_topoambigouity.ga R test/api/test_workflow_topoambigouity_auto_laidout.ga R test/api/test_workflow_validation_1.ga R test/api/test_workflow_with_runtime_input.ga M test/api/test_workflows.py R test/api/workflows_format_2/README.txt R test/api/workflows_format_2/__init__.py R test/api/workflows_format_2/converter.py R test/api/workflows_format_2/interface.py R test/api/workflows_format_2/main.py A test/base/data/test_workflow_1.ga A test/base/data/test_workflow_2.ga A test/base/data/test_workflow_batch.ga A test/base/data/test_workflow_map_reduce_pause.ga A test/base/data/test_workflow_matching_lists.ga A test/base/data/test_workflow_missing_tool.ga A test/base/data/test_workflow_pause.ga A test/base/data/test_workflow_topoambigouity.ga A test/base/data/test_workflow_topoambigouity_auto_laidout.ga A test/base/data/test_workflow_validation_1.ga A test/base/data/test_workflow_with_runtime_input.ga M test/base/driver_util.py A test/base/populators.py A test/base/workflows_format_2/README.txt A test/base/workflows_format_2/__init__.py A test/base/workflows_format_2/converter.py A test/base/workflows_format_2/interface.py A test/base/workflows_format_2/main.py R test/casperjs/api-dataset-tests.js R test/casperjs/api-visualizations-tests.js M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh A test/functional/tools/for_workflows/mapper2.xml A test/functional/tools/python_environment_problem.py A test/functional/tools/python_environment_problem.xml M test/functional/tools/samples_tool_conf.xml R test/functional/workflow.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml A test/integration/resubmission_default_job_conf.xml M test/integration/resubmission_runners.py M test/integration/test_job_resubmission.py M test/manual/workflows_scaling.py A test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/framework.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_editor.py A test/selenium_tests/test_workflow_management.py A test/selenium_tests/test_workflow_run.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_configuration.py M test/unit/tools_support.py M test/unit/workflows/workflow_support.py R tools/filters/gff/sort_gtf.py M tox.ini Log Message: ----------- Merging with dev Commit: ea0d50648c2c64abb7093fba47acec020919163f https://github.com/galaxyproject/galaxy/commit/ea0d50648c2c64abb7093fba47ace... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M .ci/jenkins/selenium/run_galaxy.bash M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-misc.js M config/datatypes_conf.xml.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M config/plugins/webhooks/demo/phdcomics/static/script.js M doc/source/admin/webhooks.rst M doc/source/api/guidelines.rst M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml A lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml A lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml A lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/diamond_db.dmnd M lib/galaxy/jobs/actions/post.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__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/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/util/shed_util_common.py M run_tests.sh A static/maps/libs/showdown.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-misc.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 A static/scripts/libs/showdown.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-misc.js M templates/ind_share_base.mako M templates/webapps/galaxy/history/share.mako A test-data/1.fastqsanger.bz2 A test-data/1.fastqsanger.gz M test/api/test_workflows.py M test/docker/README.md A test/functional/tools/compressed_bz2_fastq_conversion.xml A test/functional/tools/compressed_bz2_fastq_no_conversion.xml A test/functional/tools/compressed_gz_fastq_conversion.xml A test/functional/tools/compressed_gz_fastq_no_conversion.xml A test/functional/tools/implicit_conversion.xml A test/functional/tools/mulled_example_conflict.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merging with dev Commit: a4dec71b7ac0fedcd5f14179b7ace172d1466308 https://github.com/galaxyproject/galaxy/commit/a4dec71b7ac0fedcd5f14179b7ace... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Adding Whoosh NgramFilter and making it configurable through config Commit: 28133bead15e955e70fcbec8e09d1de06598b345 https://github.com/galaxyproject/galaxy/commit/28133bead15e955e70fcbec8e09d1... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- Adding and removing blank lines Commit: 54b527b1fc35d6ea66215df04144491f42e558e4 https://github.com/galaxyproject/galaxy/commit/54b527b1fc35d6ea66215df041444... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merging with dev Commit: 2573699c0ac1a12f808acb4006bc9e5f05f822a9 https://github.com/galaxyproject/galaxy/commit/2573699c0ac1a12f808acb4006bc9... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- Adding line breaks for import section Commit: 5bd8a0fa0232f5fa56cc4ace557d3b8f0d5cbdf0 https://github.com/galaxyproject/galaxy/commit/5bd8a0fa0232f5fa56cc4ace557d3... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Merge pull request #3356 from bgruening/fuzzysearch Fuzzy search for tools search Compare: https://github.com/galaxyproject/galaxy/compare/4eade311dbeb...5bd8a0fa0232