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[galaxyproject/galaxy] 809c08: - add Webhooks tests
by GitHub 29 Jan '17

29 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 809c087a8a50e30c7606b7b09e8c989d2b3ed6c8 https://github.com/galaxyproject/galaxy/commit/809c087a8a50e30c7606b7b09e8c… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M lib/galaxy/webhooks/__init__.py A test/api/test_webhooks.py Log Message: ----------- - add Webhooks tests - small code improvements Commit: 867e8dc4ca9aa3055a0149de594bae8fab4f8d13 https://github.com/galaxyproject/galaxy/commit/867e8dc4ca9aa3055a0149de594b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M config/galaxy.ini.sample R config/plugins/webhooks/demo/history_test1/config/history_test1.yml R config/plugins/webhooks/demo/history_test2/config/history_test2.yml R config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml R config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml R config/plugins/webhooks/demo/phdcomics/helper/__init__.py R config/plugins/webhooks/demo/phdcomics/static/script.js R config/plugins/webhooks/demo/phdcomics/static/styles.css R config/plugins/webhooks/demo/trans_object/config/trans_object.yaml R config/plugins/webhooks/demo/trans_object/helper/__init__.py R config/plugins/webhooks/demo/xkcd/config/xkcd.yml R config/plugins/webhooks/demo/xkcd/static/script.js R config/plugins/webhooks/demo/xkcd/static/styles.css M lib/galaxy/webhooks/__init__.py M run.sh M test/base/driver_util.py A test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/config/phdcomics.yaml A test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/static/script.js A test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/trans_object/config/trans_object.yaml A test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/static/script.js A test/functional/webhooks/xkcd/static/styles.css Log Message: ----------- Treat demo/test webhooks like demo/test tools. - Populate test server with demo webhooks by default. - Eliminate special logic needed to treat the demo directory differently. - Document how to enable the demo webhooks in galaxy.ini.sample. - Populate the demo webhooks when starting Galaxy with GALAXY_RUN_WITH_TEST_TOOLS=1 set. Commit: 8b30d874b539aa9665387bc298e1fbb528c242d0 https://github.com/galaxyproject/galaxy/commit/8b30d874b539aa9665387bc298e1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M test/api/test_webhooks.py Log Message: ----------- Update webhooks API test to set expectations independent of implementation. It may seem like this is testing less since fewer API calls are being made - but when you use the backend to generate the data you trust in the test case - the correlation lands up meaning relatively less is tested. For instance, if there is some problem arises in the to_dict method of a webhook - it is going to arise in both the implementation and in the test case and so the test case will just be asserting that the response is broken ... and it will be. Testing more concrete things is also good for ensuring backward compatibility. Commit: a9ba71c07be195f0e0b1774a802ed919d3a4f2b1 https://github.com/galaxyproject/galaxy/commit/a9ba71c07be195f0e0b1774a802e… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M config/galaxy.ini.sample R config/plugins/webhooks/demo/history_test1/config/history_test1.yml R config/plugins/webhooks/demo/history_test2/config/history_test2.yml R config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml R config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml R config/plugins/webhooks/demo/phdcomics/helper/__init__.py R config/plugins/webhooks/demo/phdcomics/static/script.js R config/plugins/webhooks/demo/phdcomics/static/styles.css R config/plugins/webhooks/demo/trans_object/config/trans_object.yaml R config/plugins/webhooks/demo/trans_object/helper/__init__.py R config/plugins/webhooks/demo/xkcd/config/xkcd.yml R config/plugins/webhooks/demo/xkcd/static/script.js R config/plugins/webhooks/demo/xkcd/static/styles.css M lib/galaxy/webhooks/__init__.py M run.sh M test/api/test_webhooks.py M test/base/driver_util.py A test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/config/phdcomics.yaml A test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/static/script.js A test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/trans_object/config/trans_object.yaml A test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/static/script.js A test/functional/webhooks/xkcd/static/styles.css Log Message: ----------- Merge pull request #3 from jmchilton/webhooks_reorg Improve abstraction in webhook API tests. Commit: 41d4eac28ff14b334bf413e75e81401a458334e0 https://github.com/galaxyproject/galaxy/commit/41d4eac28ff14b334bf413e75e81… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-29 (Sun, 29 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/run_galaxy.bash M .ci/py3_sources.txt M README.rst M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js A client/galaxy/scripts/mvc/workflow/workflow-icons.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 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test/functional/workflow.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml M test/galaxy_selenium/sizzle.py A test/integration/resubmission_default_job_conf.xml M test/integration/resubmission_runners.py M test/integration/test_job_resubmission.py M test/integration/test_resolvers.py M test/manual/workflows_scaling.py M test/qunit/tests/workflow_editor_tests.js 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_history_sharing.py M test/selenium_tests/test_stock_tours.py A 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/test_conda_resolution.py M test/unit/tools/test_tool_deps.py M test/unit/tools_support.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py M tools/evolution/add_scores.xml M tools/extract/extract_genomic_dna.xml M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py R tools/filters/gff/sort_gtf.py 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/plotting/bar_chart.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into feature/webhooks_tests Commit: 4cb7617bb815b455edb5307759318822944f5a3c https://github.com/galaxyproject/galaxy/commit/4cb7617bb815b455edb530775931… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-29 (Sun, 29 Jan 2017) Changed paths: M config/galaxy.ini.sample R config/plugins/webhooks/demo/history_test1/config/history_test1.yml R config/plugins/webhooks/demo/history_test2/config/history_test2.yml R config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml R config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml R config/plugins/webhooks/demo/phdcomics/helper/__init__.py R config/plugins/webhooks/demo/phdcomics/static/script.js R config/plugins/webhooks/demo/phdcomics/static/styles.css R config/plugins/webhooks/demo/trans_object/config/trans_object.yaml R config/plugins/webhooks/demo/trans_object/helper/__init__.py R config/plugins/webhooks/demo/xkcd/config/xkcd.yml R config/plugins/webhooks/demo/xkcd/static/script.js R config/plugins/webhooks/demo/xkcd/static/styles.css M lib/galaxy/webhooks/__init__.py M run.sh A test/api/test_webhooks.py M test/base/driver_util.py A test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/config/phdcomics.yaml A test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/static/script.js A test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/trans_object/config/trans_object.yaml A test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/static/script.js A test/functional/webhooks/xkcd/static/styles.css Log Message: ----------- Merge pull request #3469 from anatskiy/feature/webhooks_tests Webhooks: add tests Compare: https://github.com/galaxyproject/galaxy/compare/30b462190ac7...4cb7617bb815

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[galaxyproject/galaxy] a6b169: Do not select first value as default if select val...
by GitHub 28 Jan '17

28 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a6b16954796a3e32ee405779647ea337d1cc86d9 https://github.com/galaxyproject/galaxy/commit/a6b16954796a3e32ee405779647e… Author: guerler <aysam.guerler(a)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/46fb84aa34fe2a3d49ffa13446be… Author: guerler <aysam.guerler(a)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/e1f87f17fc118d84646007ec3a55… Author: guerler <aysam.guerler(a)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/74bddbfee7be79b5f330722f216b… Author: guerler <aysam.guerler(a)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/251842e452adebe111418e85b308… Author: guerler <aysam.guerler(a)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/3aa6a3b94f7c14fb40f8fb4ca668… Author: guerler <aysam.guerler(a)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/6838593f2287f6a17aaaf3fc0b8e… Author: guerler <aysam.guerler(a)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/30b462190ac7b6795935a0de7fa4… Author: Björn Grüning <bjoern(a)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

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[galaxyproject/usegalaxy-playbook] 62539b: Dropped PAG slide from rotation.
by GitHub 27 Jan '17

27 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 62539b46cf0145f10efd3be24732df4dc3897208 https://github.com/galaxyproject/usegalaxy-playbook/commit/62539b46cf0145f1… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Dropped PAG slide from rotation.

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[galaxyproject/usegalaxy-playbook] 4cb0cb: Additional playbook updates
by GitHub 27 Jan '17

27 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4cb0cb7c5418f1fdcd6547be789db1f212f98c46 https://github.com/galaxyproject/usegalaxy-playbook/commit/4cb0cb7c5418f1fd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M galaxy.yml M stage/galaxy_version.yml M stage/group_vars/all.yml M templates/galaxy/usegalaxy.org/config/datatypes_conf.xml.j2 Log Message: ----------- Additional playbook updates

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[galaxyproject/galaxy] 3dcdad: Add sam_to_bam to list of tools requiring Galaxy's...
by GitHub 27 Jan '17

27 Jan '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 3dcdad9eba31bf1b689f9bfb2e95908f8c4c2c55 https://github.com/galaxyproject/galaxy/commit/3dcdad9eba31bf1b689f9bfb2e95… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Add sam_to_bam to list of tools requiring Galaxy's environment. Only a very old version of sam_to_bam required this - but I guess it is actively used on usegalaxy.org since there was a bug report from @jennaj. Commit: f51355a183852565a857f825776bd38321cf2ff8 https://github.com/galaxyproject/galaxy/commit/f51355a183852565a857f825776b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3506 from martenson/release_17.01 [17.01] Add sam_to_bam to list of tools requiring Galaxy's environment. Compare: https://github.com/galaxyproject/galaxy/compare/a396b280dc6a...f51355a18385

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[galaxyproject/galaxy] 3dcdad: Add sam_to_bam to list of tools requiring Galaxy's...
by GitHub 27 Jan '17

27 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3dcdad9eba31bf1b689f9bfb2e95908f8c4c2c55 https://github.com/galaxyproject/galaxy/commit/3dcdad9eba31bf1b689f9bfb2e95… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Add sam_to_bam to list of tools requiring Galaxy's environment. Only a very old version of sam_to_bam required this - but I guess it is actively used on usegalaxy.org since there was a bug report from @jennaj. Commit: 1b179e2b57b257ed6d60433e04d9d5766468e3ec https://github.com/galaxyproject/galaxy/commit/1b179e2b57b257ed6d60433e04d9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Log Message: ----------- Merge pull request #3505 from martenson/release_17.01 [17.01] Add sam_to_bam to list of tools requiring Galaxy's environment. Compare: https://github.com/galaxyproject/galaxy/compare/457083a7b767...1b179e2b57b2

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[galaxyproject/galaxy] d8196a: Add sam_to_bam to list of tools requiring Galaxy's...
by GitHub 27 Jan '17

27 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d8196a5808f13c499afba791ea0677f949a943cd https://github.com/galaxyproject/galaxy/commit/d8196a5808f13c499afba791ea06… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Add sam_to_bam to list of tools requiring Galaxy's environment. Only a very old version of sam_to_bam required this - but I guess it is actively used on usegalaxy.org since there was a bug report from @jennaj. Commit: 457083a7b7678948a48fbf6b8fed562ab988cf17 https://github.com/galaxyproject/galaxy/commit/457083a7b7678948a48fbf6b8fed… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3502 from jmchilton/galaxy_lib_tool_fixes [17.01] Add sam_to_bam to list of tools requiring Galaxy's environment. Compare: https://github.com/galaxyproject/galaxy/compare/3a44c793e3fb...457083a7b767

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[galaxyproject/galaxy] ebfd74: Fix selenium workflow tests broken with #3181.
by GitHub 27 Jan '17

27 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ebfd740025893269940e67d4df8b446632bd9e76 https://github.com/galaxyproject/galaxy/commit/ebfd740025893269940e67d4df8b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Fix selenium workflow tests broken with #3181. Commit: 3a44c793e3fb9a27b47820b5c956b15b63043548 https://github.com/galaxyproject/galaxy/commit/3a44c793e3fb9a27b47820b5c956… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Merge pull request #3504 from jmchilton/selenium_fixes_4 Fix selenium workflow tests broken with #3181. Compare: https://github.com/galaxyproject/galaxy/compare/9de375fd01ca...3a44c793e3fb

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[galaxyproject/galaxy] 9a8a0a: include example of deps pinning
by GitHub 27 Jan '17

27 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9a8a0a9efec63cefbc17dcede4b8046116ed9aaa https://github.com/galaxyproject/galaxy/commit/9a8a0a9efec63cefbc17dcede4b8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-26 (Thu, 26 Jan 2017) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- include example of deps pinning Commit: 9de375fd01caef39454dd18c0b5962e266291479 https://github.com/galaxyproject/galaxy/commit/9de375fd01caef39454dd18c0b59… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #3496 from martenson/enhance-release-doc improve release issue docs Compare: https://github.com/galaxyproject/galaxy/compare/f8ef6e33a802...9de375fd01ca

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[galaxyproject/usegalaxy-playbook] 8d4d5c: Add public galaxy servers redirect to 'new' for an...
by GitHub 26 Jan '17

26 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8d4d5c3d2b633eebd774d054aa7db5106c81aaa6 https://github.com/galaxyproject/usegalaxy-playbook/commit/8d4d5c3d2b633eeb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-26 (Thu, 26 Jan 2017) Changed paths: M templates/nginx/galaxyproject.j2 Log Message: ----------- Add public galaxy servers redirect to 'new' for an interim URL.

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[galaxyproject/infrastructure-playbook] 05d240: Update getgalaxy redirect.
by GitHub 26 Jan '17

26 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 05d2406ed67f480e856670039653a7d229fecf3d https://github.com/galaxyproject/infrastructure-playbook/commit/05d2406ed67… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-26 (Thu, 26 Jan 2017) Changed paths: M galaxyenv/templates/nginx/galaxydomains.j2 Log Message: ----------- Update getgalaxy redirect.

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[galaxyproject/galaxy] 780119: Python3: use @six.add_metaclass() decorator
by GitHub 26 Jan '17

26 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 78011993a1c57485e0711e7ae7ec93aadb8452fc https://github.com/galaxyproject/galaxy/commit/78011993a1c57485e0711e7ae7ec… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/auth/providers/__init__.py M lib/galaxy/dataset_collections/types/__init__.py M lib/galaxy/jobs/datasets.py M lib/galaxy/jobs/metrics/instrumenters/__init__.py M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/job/__init__.py M lib/galaxy/jobs/runners/util/cli/job/slurm.py M lib/galaxy/jobs/runners/util/cli/shell/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/jobs/runners/util/condor/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/runners/util/retry.py M lib/galaxy/jobs/runners/util/sudo.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/installable.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/toolbox/tags.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/workflow/schedulers/__init__.py M lib/galaxy_utils/sequence/sequence.py Log Message: ----------- Python3: use @six.add_metaclass() decorator Also fix import order. Commit: f8ef6e33a802aeb9eab06f7ca6ff039ed40e8df5 https://github.com/galaxyproject/galaxy/commit/f8ef6e33a802aeb9eab06f7ca6ff… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/auth/providers/__init__.py M lib/galaxy/dataset_collections/types/__init__.py M lib/galaxy/jobs/datasets.py M lib/galaxy/jobs/metrics/instrumenters/__init__.py M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/job/__init__.py M lib/galaxy/jobs/runners/util/cli/job/slurm.py M lib/galaxy/jobs/runners/util/cli/shell/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/jobs/runners/util/condor/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/runners/util/retry.py M lib/galaxy/jobs/runners/util/sudo.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/installable.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/toolbox/tags.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/workflow/schedulers/__init__.py M lib/galaxy_utils/sequence/sequence.py Log Message: ----------- Merge pull request #3491 from nsoranzo/python3 Python3: use @six.add_metaclass() decorator Compare: https://github.com/galaxyproject/galaxy/compare/c163b70af23e...f8ef6e33a802

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[galaxyproject/usegalaxy-playbook] 372e04: update MTS to 17.01
by GitHub 25 Jan '17

25 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 372e044baebdbc6b604138004ffc270ebd06d541 https://github.com/galaxyproject/usegalaxy-playbook/commit/372e044baebdbc6b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M production/group_vars/toolshedservers.yml Log Message: ----------- update MTS to 17.01

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[galaxyproject/usegalaxy-playbook] cc08c4: Run update docker commands as the galaxy user
by GitHub 25 Jan '17

25 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: cc08c4faf5b51e05158368b87dfb4c68830d7f37 https://github.com/galaxyproject/usegalaxy-playbook/commit/cc08c4faf5b51e05… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M galaxy.yml Log Message: ----------- Run update docker commands as the galaxy user

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[galaxyproject/usegalaxy-playbook] cfd8d1: switch Main to release_17.01
by GitHub 25 Jan '17

25 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: cfd8d165cc8011898461131de74255f801491fab https://github.com/galaxyproject/usegalaxy-playbook/commit/cfd8d165cc801189… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M production/galaxy_version.yml Log Message: ----------- switch Main to release_17.01

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[galaxyproject/galaxy] a43d70: Dependency resolver documentation fixes
by GitHub 25 Jan '17

25 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a43d70e9bc694d50ebd091a8e2fed372c5a17e77 https://github.com/galaxyproject/galaxy/commit/a43d70e9bc694d50ebd091a8e2fe… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst Log Message: ----------- Dependency resolver documentation fixes Commit: c163b70af23effdd3a370c16b13120af586d6eb6 https://github.com/galaxyproject/galaxy/commit/c163b70af23effdd3a370c16b131… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst Log Message: ----------- Merge pull request #3490 from nsoranzo/followup_on_3483 Dependency resolver documentation fixes Compare: https://github.com/galaxyproject/galaxy/compare/27ec016cdf06...c163b70af23e

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[galaxyproject/galaxy] bf84ac: Attempt work around for race-y sort of condition i...
by GitHub 25 Jan '17

25 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf84aca059ea71c0755ee5c60a1a4214c4b0a5e5 https://github.com/galaxyproject/galaxy/commit/bf84aca059ea71c0755ee5c60a1a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M test/galaxy_selenium/sizzle.py Log Message: ----------- Attempt work around for race-y sort of condition in Selenium sizzle checkers. I believe this rare condition explains this failing test here - https://jenkins.galaxyproject.org/view/All/job/selenium/54/testReport/junit…. This test has never failed for me locally and this is the only time I've seen it fail on Jenkins as well. Commit: 27ec016cdf06ea57de73871396842affda3aeb2d https://github.com/galaxyproject/galaxy/commit/27ec016cdf06ea57de7387139684… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M test/galaxy_selenium/sizzle.py Log Message: ----------- Merge pull request #3451 from jmchilton/selenium_fixes_3 Attempt work around for race-y sort of condition in Selenium sizzle checkers. Compare: https://github.com/galaxyproject/galaxy/compare/e75242b95cb8...27ec016cdf06

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[galaxyproject/galaxy] c7df03: Add an example group filter for displaying tool pa...
by GitHub 25 Jan '17

25 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c7df034bbc749904568cfdeb897675ec501116bd https://github.com/galaxyproject/galaxy/commit/c7df034bbc749904568cfdeb8976… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M lib/galaxy/tools/toolbox/filters/examples.py.sample Log Message: ----------- Add an example group filter for displaying tool panel sections Commit: e75242b95cb88f54ad9c21d945d3da34f970d169 https://github.com/galaxyproject/galaxy/commit/e75242b95cb88f54ad9c21d945d3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M lib/galaxy/tools/toolbox/filters/examples.py.sample Log Message: ----------- Merge pull request #3484 from gregvonkuster/group_tool_filter Add an example group filter for displaying tool panel sections Compare: https://github.com/galaxyproject/galaxy/compare/3eaad9a84ec6...e75242b95cb8

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[galaxyproject/galaxy] 3cca45: Dependency resolver documentation revisions.
by GitHub 25 Jan '17

25 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3cca45b2bb570bb213d9a77764d606633aea7cfc https://github.com/galaxyproject/galaxy/commit/3cca45b2bb570bb213d9a77764d6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst Log Message: ----------- Dependency resolver documentation revisions. - Add documentation for cached dependency management as solution to LOCKERRORS. - Add documentation for overcoming problems with hard links. (Different approaches) - Add documentation on upgrading Conda as needed. - Correct and fill out documentation of defaults. - Fix some bugs in the Galaxy packages documentation. - Expand Galaxy package documentation to include a simpler example. - Update Conda configuration option documentation to reflect new defaults. - Update Conda configuration option documentation to discuss copy_dependencies. - Cross link Conda and dependency resolver documentation as it makes sense. - Add a link to the Bioconda channel order documentation for future reference. - Make things a bit more concise in places - start with the implicit tl;dr. Commit: 088e246006ff750e9a78849c4dbca6bfcccbf84f https://github.com/galaxyproject/galaxy/commit/088e246006ff750e9a78849c4dbc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- fix two typos Commit: f3810f842fa1bb4d960262d1d91ccd5207738f30 https://github.com/galaxyproject/galaxy/commit/f3810f842fa1bb4d960262d1d91c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M doc/source/admin/dependency_resolvers.rst Log Message: ----------- minor adjustments Commit: f40489e66ea479f56e96f9ba62b1040294a04ba5 https://github.com/galaxyproject/galaxy/commit/f40489e66ea479f56e96f9ba62b1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- 2 more typos spotted by @mvdbeek Commit: 133dc79d3eef9ebab5558d28b840acb80395a034 https://github.com/galaxyproject/galaxy/commit/133dc79d3eef9ebab5558d28b840… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M doc/source/admin/dependency_resolvers.rst Log Message: ----------- typo spotted by @mvdbeek Commit: 3eaad9a84ec6bda5f4dce190864b966b9d6287a5 https://github.com/galaxyproject/galaxy/commit/3eaad9a84ec6bda5f4dce190864b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst Log Message: ----------- Merge pull request #3483 from jmchilton/doc_revision_0 [17.01] Dependency resolver documentation revisions. Compare: https://github.com/galaxyproject/galaxy/compare/71876f6de7d9...3eaad9a84ec6

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[galaxyproject/galaxy] 04eee6: Fix logs and unit tests for Conda placeholder bug ...
by GitHub 25 Jan '17

25 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 04eee6459a8e9f4566da61f819a937f4b04d1c40 https://github.com/galaxyproject/galaxy/commit/04eee6459a8e9f4566da61f819a9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M test/unit/tools/test_conda_resolution.py Log Message: ----------- Fix logs and unit tests for Conda placeholder bug resolution. Commit: 71876f6de7d9a92fc482b0ae0c2ed0ad4588b906 https://github.com/galaxyproject/galaxy/commit/71876f6de7d9a92fc482b0ae0c2e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M test/unit/tools/test_conda_resolution.py Log Message: ----------- Merge pull request #3482 from jmchilton/placeholder_fixes [17.01] Fix logs and unit tests for Conda placeholder bug resolution. Compare: https://github.com/galaxyproject/galaxy/compare/29c0c41666e4...71876f6de7d9

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[galaxyproject/galaxy] 7f232a: Fix path to Smat datatype
by GitHub 25 Jan '17

25 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7f232a25b5a9c91131b64d8c72744a9f34d30045 https://github.com/galaxyproject/galaxy/commit/7f232a25b5a9c91131b64d8c7274… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Fix path to Smat datatype Commit: a396b280dc6a26581bb3e5059e6aebcc4790b6cb https://github.com/galaxyproject/galaxy/commit/a396b280dc6a26581bb3e5059e6a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #3475 from nsoranzo/release_17.01_fix_smat_datatype [17.01] Fix path to Smat datatype Commit: 29c0c41666e4f0a27ef18587f8b93a03bd413c5f https://github.com/galaxyproject/galaxy/commit/29c0c41666e4f0a27ef18587f8b9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge branch 'release_17.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/6077456135d4...29c0c41666e4

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[galaxyproject/galaxy] 7f232a: Fix path to Smat datatype
by GitHub 25 Jan '17

25 Jan '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 7f232a25b5a9c91131b64d8c72744a9f34d30045 https://github.com/galaxyproject/galaxy/commit/7f232a25b5a9c91131b64d8c7274… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Fix path to Smat datatype Commit: a396b280dc6a26581bb3e5059e6aebcc4790b6cb https://github.com/galaxyproject/galaxy/commit/a396b280dc6a26581bb3e5059e6a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #3475 from nsoranzo/release_17.01_fix_smat_datatype [17.01] Fix path to Smat datatype Compare: https://github.com/galaxyproject/galaxy/compare/191813ab80a2...a396b280dc6a

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[galaxyproject/galaxy] f882cb: Pin flake8 and plugins in tox.ini
by GitHub 25 Jan '17

25 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f882cb9b2ef45fd3b1dfb36d7bf1edb64b540e01 https://github.com/galaxyproject/galaxy/commit/f882cb9b2ef45fd3b1dfb36d7bf1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M tox.ini Log Message: ----------- Pin flake8 and plugins in tox.ini For all tox environments used in .travis.yml except the ones allowed to fail. Commit: 191813ab80a237476012333a1cb96834ce933124 https://github.com/galaxyproject/galaxy/commit/191813ab80a237476012333a1cb9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M tox.ini Log Message: ----------- Merge pull request #3476 from nsoranzo/release_17.01_pin_flake8 [17.01] Pin flake8 and plugins in tox.ini Commit: 111d2aa2c667f064961f7fd62122fe1d1fa43c0c https://github.com/galaxyproject/galaxy/commit/111d2aa2c667f064961f7fd62122… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M tox.ini Log Message: ----------- Merge branch 'release_17.01' into dev Commit: 79c3b23346f099601950935c957ca920f89f5770 https://github.com/galaxyproject/galaxy/commit/79c3b23346f099601950935c957c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M tox.ini Log Message: ----------- Un-pin flake8 and plugins in tox.ini Commit: 6077456135d42150d281767e4a99da8813986a9e https://github.com/galaxyproject/galaxy/commit/6077456135d42150d281767e4a99… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M tox.ini Log Message: ----------- Merge pull request #3478 from nsoranzo/merge_17.01 Merge 17.01 and un-pin flake8 and plugins Compare: https://github.com/galaxyproject/galaxy/compare/3c4413d31d99...6077456135d4

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[galaxyproject/usegalaxy-playbook] 61084c: update TTS
by GitHub 24 Jan '17

24 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 61084c54dfcb816fbc801ced5af700dba164fc92 https://github.com/galaxyproject/usegalaxy-playbook/commit/61084c54dfcb816f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M stage/group_vars/toolshedservers.yml Log Message: ----------- update TTS

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[galaxyproject/usegalaxy-playbook] 0b2699: update Test
by GitHub 24 Jan '17

24 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0b2699ed513300a2738ec55d7ff8a67347894f44 https://github.com/galaxyproject/usegalaxy-playbook/commit/0b2699ed513300a2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M stage/galaxy_version.yml Log Message: ----------- update Test

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