galaxy-commits July 2017

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[galaxyproject/galaxy] 0ff61d: Fix Registry.get_datatype_by_extension() to return...
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 0ff61d9ffc93063f8c2e6261a1ea6c36c1176d77 https://github.com/galaxyproject/galaxy/commit/0ff61d9ffc93063f8c2e6261a1ea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Fix Registry.get_datatype_by_extension() to return None if ext is unknown Without this fix, the Cheetah expression: $dataset.is_of_type('unknown_ext') in a tool command would be equivalent to: $dataset.is_of_type('txt') meaning that if the dataset datatype is a subclass of Text, the expression would evaluate to True without any warning. xref. https://github.com/galaxyproject/tools-iuc/issues/1373 Also add missing `xml` datatype to `test/functional/tools/sample_datatypes_conf.xml` which is needed by 3 test tools. Commit: 5a39d47b0adde675fc195c5d8b9c82c13917a233 https://github.com/galaxyproject/galaxy/commit/5a39d47b0adde675fc195c5d8b9c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge pull request #4230 from nsoranzo/release_16.07_backport_4224 [16.07] Backport #4224 Commit: fada8d2a60e625cf16fce7e20715422f86d6f40c https://github.com/galaxyproject/galaxy/commit/fada8d2a60e625cf16fce7e20715… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: bfb3ce6e79074c42803444701e814c65631ac0cd https://github.com/galaxyproject/galaxy/commit/bfb3ce6e79074c42803444701e81… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Conflicts: test/functional/tools/sample_datatypes_conf.xml Compare: https://github.com/galaxyproject/galaxy/compare/96e1cf58f480...bfb3ce6e7907

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[galaxyproject/galaxy] 0ff61d: Fix Registry.get_datatype_by_extension() to return...
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 0ff61d9ffc93063f8c2e6261a1ea6c36c1176d77 https://github.com/galaxyproject/galaxy/commit/0ff61d9ffc93063f8c2e6261a1ea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Fix Registry.get_datatype_by_extension() to return None if ext is unknown Without this fix, the Cheetah expression: $dataset.is_of_type('unknown_ext') in a tool command would be equivalent to: $dataset.is_of_type('txt') meaning that if the dataset datatype is a subclass of Text, the expression would evaluate to True without any warning. xref. https://github.com/galaxyproject/tools-iuc/issues/1373 Also add missing `xml` datatype to `test/functional/tools/sample_datatypes_conf.xml` which is needed by 3 test tools. Commit: 5a39d47b0adde675fc195c5d8b9c82c13917a233 https://github.com/galaxyproject/galaxy/commit/5a39d47b0adde675fc195c5d8b9c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge pull request #4230 from nsoranzo/release_16.07_backport_4224 [16.07] Backport #4224 Commit: fada8d2a60e625cf16fce7e20715422f86d6f40c https://github.com/galaxyproject/galaxy/commit/fada8d2a60e625cf16fce7e20715… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Compare: https://github.com/galaxyproject/galaxy/compare/490e565611b5...fada8d2a60e6

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[galaxyproject/galaxy] f88ee3: avoids broken mercurial conda version
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f88ee34792d86766fb68109fc518d9defcc469bd https://github.com/galaxyproject/galaxy/commit/f88ee34792d86766fb68109fc518… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M lib/galaxy/dependencies/conda-environment.txt Log Message: ----------- avoids broken mercurial conda version Commit: 7baf86f7c1373572db5d5b18a4686a7b90056b89 https://github.com/galaxyproject/galaxy/commit/7baf86f7c1373572db5d5b18a468… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/dependencies/conda-environment.txt Log Message: ----------- Merge pull request #4227 from bwlang/galaxy_with_conda_python avoids broken version of mercurial in conda Compare: https://github.com/galaxyproject/galaxy/compare/20ef3eebcf2c...7baf86f7c137

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[galaxyproject/galaxy] 0ff61d: Fix Registry.get_datatype_by_extension() to return...
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 0ff61d9ffc93063f8c2e6261a1ea6c36c1176d77 https://github.com/galaxyproject/galaxy/commit/0ff61d9ffc93063f8c2e6261a1ea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Fix Registry.get_datatype_by_extension() to return None if ext is unknown Without this fix, the Cheetah expression: $dataset.is_of_type('unknown_ext') in a tool command would be equivalent to: $dataset.is_of_type('txt') meaning that if the dataset datatype is a subclass of Text, the expression would evaluate to True without any warning. xref. https://github.com/galaxyproject/tools-iuc/issues/1373 Also add missing `xml` datatype to `test/functional/tools/sample_datatypes_conf.xml` which is needed by 3 test tools. Commit: 5a39d47b0adde675fc195c5d8b9c82c13917a233 https://github.com/galaxyproject/galaxy/commit/5a39d47b0adde675fc195c5d8b9c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge pull request #4230 from nsoranzo/release_16.07_backport_4224 [16.07] Backport #4224 Compare: https://github.com/galaxyproject/galaxy/compare/80ecc79a4cb8...5a39d47b0add

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[galaxyproject/galaxy] c8eff8: Remove float style from color picker label
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: c8eff858d68cdbea85524c4e366cc479ba556dcd https://github.com/galaxyproject/galaxy/commit/c8eff858d68cdbea85524c4e366c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Remove float style from color picker label Commit: bd2d52800e7776ead1c8c7af53995d13cd288397 https://github.com/galaxyproject/galaxy/commit/bd2d52800e7776ead1c8c7af5399… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Merge pull request #4233 from guerler/fix_color_picker_release [17.05] Remove float style from color picker label Compare: https://github.com/galaxyproject/galaxy/compare/9dca211e2fe5...bd2d52800e77

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[galaxyproject/galaxy] 6f9863: Fix import order and Python3 compatibility for 51 ...
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6f98634dd51ac40848a2e16662782378f8022bfd https://github.com/galaxyproject/galaxy/commit/6f98634dd51ac40848a2e1666278… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/registry.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/types/list.py M lib/galaxy/dataset_collections/types/paired.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/coverage.py M lib/galaxy/datatypes/dataproviders/chunk.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/decorators.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/datatypes/dataproviders/hierarchy.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/display_applications/parameters.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/sniff.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/model/base.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/search.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/model/tool_shed_install/mapping.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/webhooks/__init__.py M lib/galaxy/work/context.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/render.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/scheduling_manager.py M lib/log_tempfile.py Log Message: ----------- Fix import order and Python3 compatibility for 51 files xref. https://github.com/galaxyproject/galaxy/issues/1715 Also remove unused `get_track_window()` method of some datatypes. Commit: 20ef3eebcf2cf02fa79ca752f79e430b14802800 https://github.com/galaxyproject/galaxy/commit/20ef3eebcf2cf02fa79ca752f79e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/registry.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/types/list.py M lib/galaxy/dataset_collections/types/paired.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/coverage.py M lib/galaxy/datatypes/dataproviders/chunk.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/decorators.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/datatypes/dataproviders/hierarchy.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/display_applications/parameters.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/sniff.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/model/base.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/search.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/model/tool_shed_install/mapping.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/webhooks/__init__.py M lib/galaxy/work/context.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/render.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/scheduling_manager.py M lib/log_tempfile.py Log Message: ----------- Merge pull request #4236 from nsoranzo/python3 Fix import order and Python3 compatibility for 51 files Compare: https://github.com/galaxyproject/galaxy/compare/79f3dc00a61d...20ef3eebcf2c

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[galaxyproject/galaxy] 58a2cd: Refactor deactivate_or_uninstall_repository
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 58a2cde89fdc5e52c4b6b10842d47f1e1f24bfca https://github.com/galaxyproject/galaxy/commit/58a2cde89fdc5e52c4b6b10842d4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/installed_repository_manager.py Log Message: ----------- Refactor deactivate_or_uninstall_repository Move code that deals with repository uninstallation into InstalledRepositoryManager, so that this can be reused by the API. Commit: b29f23500d0b8ccb0ef94521cbb42aaae430c755 https://github.com/galaxyproject/galaxy/commit/b29f23500d0b8ccb0ef94521cbb4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Simplify uninstall message creation Commit: 67c66861c50f02475e497aa0c4feec7dfa16c2c2 https://github.com/galaxyproject/galaxy/commit/67c66861c50f02475e497aa0c4fe… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add `uninstall_repository` to ToolShedRepositoriesController And connect routes. It is now possible to POST to api/tool_shed_repositories to trigger a Repository installation and to DELETE to api/tool_shed_repositories to uninstall a repository. In addition one can also DELETE to api/tool_shed_repositories/<repository_id>, which will uninstall the repository with repository_id. Commit: 3492f0e18fe389496623d9a09b57c40fd113b7c8 https://github.com/galaxyproject/galaxy/commit/3492f0e18fe389496623d9a09b57… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-02 (Sun, 02 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Fix the uninstall/deactivate message that is send to the mako template Commit: 6a8f15bacb147e5189be983ad829a492d6dc0657 https://github.com/galaxyproject/galaxy/commit/6a8f15bacb147e5189be983ad829… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-04 (Tue, 04 Jul 2017) Changed paths: M lib/tool_shed/galaxy_install/installed_repository_manager.py A test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_toolbox.py Log Message: ----------- Add basic unittest for InstalledRepositoryManager that exercises the most basic functionality, which is the deactivate and to uninstall repositories. Also moves shared `_init_dynamic_tool_conf` method to BaseToolBoxTestCase Commit: 79f3dc00a61d2f6425f16cfa018d973b31fb4973 https://github.com/galaxyproject/galaxy/commit/79f3dc00a61d2f6425f16cfa018d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/installed_repository_manager.py A test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #4248 from mvdbeek/uninstall_repository_api_endpoint Add API repository uninstall endpoint Compare: https://github.com/galaxyproject/galaxy/compare/86caee96e91a...79f3dc00a61d

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[galaxyproject/galaxy] a4689b: Add test_errors to .gitignore.
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a4689b6bf36beb1ff9533addb5201b5e368e2e97 https://github.com/galaxyproject/galaxy/commit/a4689b6bf36beb1ff9533addb520… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M .gitignore Log Message: ----------- Add test_errors to .gitignore. Used to store information about selenium failures. Commit: 86caee96e91adbda035cbbbc6628f1d2378c6c4d https://github.com/galaxyproject/galaxy/commit/86caee96e91adbda035cbbbc6628… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M .gitignore Log Message: ----------- Merge pull request #4278 from jmchilton/gitignore Add test_errors to .gitignore. Compare: https://github.com/galaxyproject/galaxy/compare/932b8f59ec2e...86caee96e91a

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[galaxyproject/galaxy] bcdb8f: Spacing convention, -> util.asbool, atribute -> at...
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bcdb8fcbe731c78332f6b44710359c834d13fa0b https://github.com/galaxyproject/galaxy/commit/bcdb8fcbe731c78332f6b4471035… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Spacing convention, -> util.asbool, atribute -> attribute Commit: 932b8f59ec2e334ba0f3839a9b1d1d6c6bb2e2b8 https://github.com/galaxyproject/galaxy/commit/932b8f59ec2e334ba0f3839a9b1d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Merge pull request #4250 from bwlang/spelling_style_fixes Spacing convention, -> util.asbool, atribute -> attribute Compare: https://github.com/galaxyproject/galaxy/compare/7ce50a8ff724...932b8f59ec2e

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[galaxyproject/galaxy] 9af36b: change 'register or login' to just 'login' if 'all...
by GitHub 04 Jul '17

04 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9af36bd13b90eea2f2883ab623a4a60ccf58a8b8 https://github.com/galaxyproject/galaxy/commit/9af36bd13b90eea2f2883ab623a4… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-06-28 (Wed, 28 Jun 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/admin.bundled.js.map 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.map M static/scripts/layout/menu.js Log Message: ----------- change 'register or login' to just 'login' if 'allow_user_creation=False' Commit: 010beb8270bddbddcbf4712c6466cd9831cd2ae3 https://github.com/galaxyproject/galaxy/commit/010beb8270bddbddcbf4712c6466… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-07-04 (Tue, 04 Jul 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- code optimization - reuse userTab variable Commit: 7ce50a8ff72424ffb3403f6026ba4ada9bc32ba3 https://github.com/galaxyproject/galaxy/commit/7ce50a8ff72424ffb3403f6026ba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-04 (Tue, 04 Jul 2017) Changed paths: M CONTRIBUTING.md A SECURITY_POLICY.md M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M config/datatypes_conf.xml.sample M doc/source/project/organization.rst M lib/galaxy/app.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/plant_tribes.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.ptkscmp M lib/galaxy/managers/collections.py M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-base.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/history/history-list.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-base.js R templates/webapps/galaxy/history/shared_grid.mako M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into login_only Compare: https://github.com/galaxyproject/galaxy/compare/ac59d1d6e042...7ce50a8ff724

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galaxy-commits July 2017