Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a6b16954796a3e32ee405779647ea337d1cc86d9 https://github.com/galaxyproject/galaxy/commit/a6b16954796a3e32ee405779647ea... Author: guerler <aysam.guerler@gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Do not select first value as default if select value is optional in repeats Commit: 46fb84aa34fe2a3d49ffa13446bee75c21519d54 https://github.com/galaxyproject/galaxy/commit/46fb84aa34fe2a3d49ffa13446bee... Author: guerler <aysam.guerler@gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove space Commit: e1f87f17fc118d84646007ec3a55960fd18657d1 https://github.com/galaxyproject/galaxy/commit/e1f87f17fc118d84646007ec3a559... Author: guerler <aysam.guerler@gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove secondary initial value handling from basic parameters Commit: 74bddbfee7be79b5f330722f216b9507c288961b https://github.com/galaxyproject/galaxy/commit/74bddbfee7be79b5f330722f216b9... Author: guerler <aysam.guerler@gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Determine initial values in tool.pys to_json/build_module caller Commit: 251842e452adebe111418e85b308d5f1b510a5c9 https://github.com/galaxyproject/galaxy/commit/251842e452adebe111418e85b308d... Author: guerler <aysam.guerler@gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix inherited to_dict caller Commit: 3aa6a3b94f7c14fb40f8fb4ca668f0c38cd943c2 https://github.com/galaxyproject/galaxy/commit/3aa6a3b94f7c14fb40f8fb4ca668f... Author: guerler <aysam.guerler@gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix tests, remove redundant initial value callers Commit: 6838593f2287f6a17aaaf3fc0b8ec9fc608db968 https://github.com/galaxyproject/galaxy/commit/6838593f2287f6a17aaaf3fc0b8ec... Author: guerler <aysam.guerler@gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M README.rst M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/base.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/local_conda_mapping.yml.sample M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst M lib/galaxy/config.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/json.py M lib/galaxy/util/properties.py M lib/galaxy/version.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/steps.py M lib/tool_shed/util/workflow_util.py M run.sh A scripts/manage_tool_dependencies.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/workflow/workflow-canvas.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/viz/trackster/tracks.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/form/form-parameters.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/viz/trackster/tracks.js M static/style/blue/base.css R templates/webapps/galaxy/workflow/editor_generic_form.mako R templates/webapps/galaxy/workflow/editor_tool_form.mako M test/api/test_workflows.py A test/functional/tools/legacy_r.xml A test/functional/tools/param_text_option.xml M test/functional/tools/samples_tool_conf.xml M test/integration/test_resolvers.py M test/qunit/tests/workflow_editor_tests.js M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_tool_deps.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_workflow_progress.py M tools/evolution/add_scores.xml M tools/extract/extract_genomic_dna.xml M tools/filters/pasteWrapper.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/macros.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_gen_conv.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tox.ini Log Message: ----------- Merge branch 'dev' into fix_repeat_defaults Commit: 30b462190ac7b6795935a0de7fa41118ff23af3d https://github.com/galaxyproject/galaxy/commit/30b462190ac7b6795935a0de7fa41... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-01-28 (Sat, 28 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #3472 from guerler/fix_repeat_defaults Do not select first value as default if select value is optional Compare: https://github.com/galaxyproject/galaxy/compare/1b179e2b57b2...30b462190ac7