galaxy-commits January 2019

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[galaxyproject/galaxy] 3fa43d: Swap to normal event bindings for multipanel drop....
by GitHub 15 Jan '19

15 Jan '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 3fa43dfecea37a5f56e3675afad0bd65d3196f56 https://github.com/galaxyproject/galaxy/commit/3fa43dfecea37a5f56e3675afad0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js Log Message: ----------- Swap to normal event bindings for multipanel drop. get(0) isn't great, but we'll overhaul this more in the future. Commit: 7c13cdf006733182b4bfb07ced24df729600e670 https://github.com/galaxyproject/galaxy/commit/7c13cdf006733182b4bfb07ced24… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js Log Message: ----------- Merge pull request #7218 from dannon/fix_multipanel_drop [19.01] Swap to normal event bindings for multipanel drag/drop. Compare: https://github.com/galaxyproject/galaxy/compare/af21a8fa58fc...7c13cdf00673 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 1befc3: Update ``use_interactive`` default in docs
by GitHub 15 Jan '19

15 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1befc3881067b9b2178dce2a77a6fee7e50a8d79 https://github.com/galaxyproject/galaxy/commit/1befc3881067b9b2178dce2a77a6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- Update ``use_interactive`` default in docs This was never enabled by default in the code, but it was explicitly set to True in `config/galaxy.ini.sample` . Since we moved to `galaxy.yml.sample`, this has defaulted to False in practice. Commit: 1887e9f54a1c1fde6962ae7a47f956337854c71d https://github.com/galaxyproject/galaxy/commit/1887e9f54a1c1fde6962ae7a47f9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- Merge pull request #7221 from nsoranzo/use_interactive_docs Update ``use_interactive`` default in docs Compare: https://github.com/galaxyproject/galaxy/compare/9ada3b4d6e4c...1887e9f54a1c **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] ac74d1: Lock pygments back to same version as -dev depenen...
by GitHub 15 Jan '19

15 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ac74d1b589b1ad62f93393a8f98f1850e92c63f1 https://github.com/galaxyproject/galaxy/commit/ac74d1b589b1ad62f93393a8f98f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Lock pygments back to same version as -dev depenency, avoiding conflicting uninstall/reinstall on startup. Commit: dc4d4fbacf8f82a70e96ddfcc73669438b855690 https://github.com/galaxyproject/galaxy/commit/dc4d4fbacf8f82a70e96ddfcc736… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- lower conditional req's; pypi is case insensitive and this matches the other requirements files for easier grepping Commit: 8ff1a6a1b7a3f59bd7ffcba45a3813742af64199 https://github.com/galaxyproject/galaxy/commit/8ff1a6a1b7a3f59bd7ffcba45a38… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- drop pygments conditional requirements and rely on it being a weberror dep, since we never use it directly Commit: 9ada3b4d6e4c4da26a05c23bd3a70c5fe42049c5 https://github.com/galaxyproject/galaxy/commit/9ada3b4d6e4c4da26a05c23bd3a7… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Merge pull request #7219 from dannon/update-and-lock-pygments Drop conditional pygmentz requirement (autoinstalled as necessary), minor formatting in conditional-reqs Compare: https://github.com/galaxyproject/galaxy/compare/72459797a610...9ada3b4d6e4c **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] c96092: Allow passing test_history in verify_tool func
by GitHub 15 Jan '19

15 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c960924e892c44d91436a618bd8169a60ef74142 https://github.com/galaxyproject/galaxy/commit/c960924e892c44d91436a618bd81… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M lib/galaxy/tools/verify/interactor.py Log Message: ----------- Allow passing test_history in verify_tool func Commit: 4b920afba2e0b2ad24bbe00511a51297e60a2f06 https://github.com/galaxyproject/galaxy/commit/4b920afba2e0b2ad24bbe00511a5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M lib/galaxy/tools/verify/interactor.py A test/api/test_galaxy_interactor.py Log Message: ----------- Make interactor changes backwards compatible Commit: 338020f2a5203afad239e3a1b6e0becf7edad22b https://github.com/galaxyproject/galaxy/commit/338020f2a5203afad239e3a1b6e0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- Fix error in view_tool_metadata (https://sentry.galaxyproject.org/sentry/toolshed/issues/294272/) Commit: 141c2a1ef37ae29b4c6e481337c6efd3a41fcd1d https://github.com/galaxyproject/galaxy/commit/141c2a1ef37ae29b4c6e481337c6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/tools/tool_validator.py Log Message: ----------- Fix indentation Broken in commit cf2645f9a658c5e122fea0309bf73a1f64590c39 . Commit: 72bb23fc2df3e00d55e59259d4a995e5ad939eb8 https://github.com/galaxyproject/galaxy/commit/72bb23fc2df3e00d55e59259d4a9… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M lib/galaxy/tools/verify/interactor.py A test/api/test_galaxy_interactor.py Log Message: ----------- Merge pull request #7199 from mvdbeek/backport_interactor_improvements [19.01] Backport #7167 - interactor improvements Commit: 105a1d8a61ef6ec79992017d2cff3a18decab113 https://github.com/galaxyproject/galaxy/commit/105a1d8a61ef6ec79992017d2cff… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/tools/tool_validator.py Log Message: ----------- Merge pull request #7201 from mvdbeek/fix_view_metadata_error [18.09] Fix error in view_tool_metadata Commit: af21a8fa58fcd6945786cc307a5a258775854fe5 https://github.com/galaxyproject/galaxy/commit/af21a8fa58fcd6945786cc307a5a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/tools/tool_validator.py Log Message: ----------- Merge branch 'release_18.09' into release_19.01 Commit: 72459797a610774d45758e66fb579b19f9e4ffd8 https://github.com/galaxyproject/galaxy/commit/72459797a610774d45758e66fb57… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/tools/tool_validator.py Log Message: ----------- Merge branch 'release_19.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/107f67495713...72459797a610 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] ea6d26: Remove fixed color from ui styles
by GitHub 15 Jan '19

15 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ea6d26923fd03b8d4aeea2beafe56519210faefc https://github.com/galaxyproject/galaxy/commit/ea6d26923fd03b8d4aeea2beafe5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M client/galaxy/style/scss/ui.scss Log Message: ----------- Remove fixed color from ui styles Commit: 2a3bd642f58c32ae6a763f6b4fa1fc1c2985e9db https://github.com/galaxyproject/galaxy/commit/2a3bd642f58c32ae6a763f6b4fa1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M client/galaxy/style/scss/upload.scss Log Message: ----------- Use panel background for upload button initial background Commit: 8cabc95a4a48b1bdfbd5618d96497c6d45ee4092 https://github.com/galaxyproject/galaxy/commit/8cabc95a4a48b1bdfbd5618d9649… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M client/galaxy/style/scss/upload.scss Log Message: ----------- Use default text color for upload paste field Commit: 55b22bee08fefaec45c7046e96679f830d3a0f03 https://github.com/galaxyproject/galaxy/commit/55b22bee08fefaec45c7046e9667… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M client/galaxy/style/scss/frame.scss Log Message: ----------- Use theme colors for scratchbook Commit: 535c2ae5fbdaec72957075f4a6d6a5890d7526de https://github.com/galaxyproject/galaxy/commit/535c2ae5fbdaec72957075f4a6d6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M client/galaxy/style/scss/charts.scss Log Message: ----------- Use panel button color in charts Commit: d5539a4472f5b82afb4f1ce2478a32bef9327c7b https://github.com/galaxyproject/galaxy/commit/d5539a4472f5b82afb4f1ce2478a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Replace a subset of fixed color in base styles Commit: 63fe99662870834baa00bedc6c7bc8f462fe343f https://github.com/galaxyproject/galaxy/commit/63fe99662870834baa00bedc6c7b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Replace footer text color Commit: 76a0bea2627774e93985df5a50cfd95575372f9b https://github.com/galaxyproject/galaxy/commit/76a0bea2627774e93985df5a50cf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Remove custom tool title style variation Commit: 58926ae2fe81fdc60237c1800e5662b696b472da https://github.com/galaxyproject/galaxy/commit/58926ae2fe81fdc60237c1800e56… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Remove unused styles, reuse existing colors in base styles Commit: 17aa51cb85a084e57d99ca70c208bca2dc8079af https://github.com/galaxyproject/galaxy/commit/17aa51cb85a084e57d99ca70c208… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- Introduce brand color parameters, leave actual ui colors unchanged Commit: f1ca1a92156531bf0b269de12f3c87cfc7e722b8 https://github.com/galaxyproject/galaxy/commit/f1ca1a92156531bf0b269de12f3c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- Replace with actual color values Commit: f806e7b4f1c60d826c8604a725d52a5c78cf2e78 https://github.com/galaxyproject/galaxy/commit/f806e7b4f1c60d826c8604a725d5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/frame.scss M client/galaxy/style/scss/theme/blue.scss M client/galaxy/style/scss/tour.scss Log Message: ----------- Consolidate base colors Commit: d8801ecd595142166fa41afbdfa18fa622fb4915 https://github.com/galaxyproject/galaxy/commit/d8801ecd595142166fa41afbdfa1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- Replace fixed masthead toggle color Commit: 3bce850b05599622eb876c51be8504f7d9c69134 https://github.com/galaxyproject/galaxy/commit/3bce850b05599622eb876c51be85… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss M client/galaxy/style/scss/ui.scss Log Message: ----------- Remove duplicate border color Commit: 8cce43838bda9b56a7448ccf1d37e18571ae442f https://github.com/galaxyproject/galaxy/commit/8cce43838bda9b56a7448ccf1d37… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- Consolidate panel related footer color, remove duplicates Commit: 85713f4d4dbc15f6e6a04b55929b64f2d368774c https://github.com/galaxyproject/galaxy/commit/85713f4d4dbc15f6e6a04b55929b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- Fix table accent color Commit: 2e4f5fb52fc48c6be921582805194d1ba9f9fc35 https://github.com/galaxyproject/galaxy/commit/2e4f5fb52fc48c6be92158280519… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- Fix unused colors Commit: daf601e8342e2fabe05f9b45ed4a3f71b7bd22ee https://github.com/galaxyproject/galaxy/commit/daf601e8342e2fabe05f9b45ed4a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Remove unused input style specs Commit: 9d0d1231efd16c95ae1da0e90338349002172444 https://github.com/galaxyproject/galaxy/commit/9d0d1231efd16c95ae1da0e90338… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/theme/blue.scss M client/galaxy/style/scss/ui.scss Log Message: ----------- Resolve background panel portlet contrast Commit: 5a36b9dd2cc2091bf278ace6ee78e551a3e87089 https://github.com/galaxyproject/galaxy/commit/5a36b9dd2cc2091bf278ace6ee78… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M static/welcome.html.sample Log Message: ----------- Remove rounded borders from welcome box Commit: 2d9ccf5e9fdae128938827447781a50b73795ffc https://github.com/galaxyproject/galaxy/commit/2d9ccf5e9fdae128938827447781… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/ui/search-input.scss Log Message: ----------- Fix tool search icon position Commit: e6cd79bd424e3f8126d1ef5fe7bc29b720b000e1 https://github.com/galaxyproject/galaxy/commit/e6cd79bd424e3f8126d1ef5fe7bc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/frame.scss M client/galaxy/style/scss/theme/blue.scss M client/galaxy/style/scss/tour.scss Log Message: ----------- Consolidate base color Commit: b998553b3afa9c5a88e70ffc908b0d3283336b45 https://github.com/galaxyproject/galaxy/commit/b998553b3afa9c5a88e70ffc908b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/frame.scss M client/galaxy/style/scss/theme/blue.scss M client/galaxy/style/scss/ui.scss Log Message: ----------- Consolidate text and border colors Fix Commit: b6271da34db8156ffd189ebd313f4dd2f5b45cda https://github.com/galaxyproject/galaxy/commit/b6271da34db8156ffd189ebd313f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/style/scss/base.scss Log Message: ----------- Fix grid search field style Commit: f30989343a5435cd59a68d3108e5ff1659022223 https://github.com/galaxyproject/galaxy/commit/f30989343a5435cd59a68d3108e5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- Fix alert text level, fix search field background Commit: 34de1db38acdd699c764a3ce5bb2fab03382bc13 https://github.com/galaxyproject/galaxy/commit/34de1db38acdd699c764a3ce5bb2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-12 (Sat, 12 Jan 2019) Changed paths: M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- Fix running status brightness Commit: 258975879b95f95afeb138350747d3e1d7a9e421 https://github.com/galaxyproject/galaxy/commit/258975879b95f95afeb138350747… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-14 (Mon, 14 Jan 2019) Changed paths: M client/galaxy/scripts/qunit/tests/form_tests.js Log Message: ----------- Fix color related test case Commit: 107f67495713ea71dd97e9f83656f4ded8dccc9f https://github.com/galaxyproject/galaxy/commit/107f67495713ea71dd97e9f83656… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/qunit/tests/form_tests.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/charts.scss M client/galaxy/style/scss/frame.scss M client/galaxy/style/scss/theme/blue.scss M client/galaxy/style/scss/tour.scss M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/ui/search-input.scss M client/galaxy/style/scss/upload.scss M static/welcome.html.sample M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #7203 from guerler/color_handling Replace custom UI colors with equivalent theme colors, consolidate color handling Compare: https://github.com/galaxyproject/galaxy/compare/e42dcfab2a93...107f67495713 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] d5dea3: Pin pysam to 0.15.2 . Update all dependencies
by GitHub 15 Jan '19

15 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d5dea33a86a79334b831776529956105c173673b https://github.com/galaxyproject/galaxy/commit/d5dea33a86a79334b83177652995… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2019-01-14 (Mon, 14 Jan 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Pin pysam to 0.15.2 . Update all dependencies with `make update-dependencies` using pipenv 2018.11.26 . Commit: ce5895f585878a8952e8cda7df952027b2c48c11 https://github.com/galaxyproject/galaxy/commit/ce5895f585878a8952e8cda7df95… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2019-01-14 (Mon, 14 Jan 2019) Changed paths: M doc/source/conf.py Log Message: ----------- Update recommonmark configuration in Sphinx See https://github.com/rtfd/recommonmark/pull/113 Commit: 4bb6f18b30d850019230cd4e347b574ac0593052 https://github.com/galaxyproject/galaxy/commit/4bb6f18b30d850019230cd4e347b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-14 (Mon, 14 Jan 2019) Changed paths: M doc/source/conf.py Log Message: ----------- Do not build rst files starting with '_' Commit: 46b3539a35c09fc3d8d2d9b2a7ec7fefbc53c95e https://github.com/galaxyproject/galaxy/commit/46b3539a35c09fc3d8d2d9b2a7ec… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-14 (Mon, 14 Jan 2019) Changed paths: M doc/source/admin/conda_faq.rst M doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/webhooks.rst M doc/source/dev/index.rst M doc/source/releases/16.07_announce.rst M doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst M doc/source/releases/17.01_announce.rst M doc/source/releases/18.01.rst Log Message: ----------- Fix doc bugs Use proper cross-referencing with `:doc:`. Commit: 891576627515febaa749981fbb7e0aa850df495a https://github.com/galaxyproject/galaxy/commit/891576627515febaa749981fbb7e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-14 (Mon, 14 Jan 2019) Changed paths: M doc/source/conf.py Log Message: ----------- Do not exclude releases docs when using ``GALAXY_DOCS_SKIP_SOURCE`` They are quite fast to build. Commit: 1f3eec2879e356a671a2280b3589e938c391c668 https://github.com/galaxyproject/galaxy/commit/1f3eec2879e356a671a2280b3589… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M test/api/test_galaxy_interactor.py Log Message: ----------- Fix ``GalaxyInteractorBackwardCompatTestCase.test_local_test_data_download`` API test Broken in commit bf851269c30996876c0614e7a5b57da495c44ac9 . Commit: b23a2a44d99c9d68def546bda3bbf0d7059c8f95 https://github.com/galaxyproject/galaxy/commit/b23a2a44d99c9d68def546bda3bb… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M lib/galaxy/web/framework/base.py M lib/galaxy/webhooks/__init__.py Log Message: ----------- Fix ``UnicodeDecodeError`` exception under Python3 Fix the following exception reported in the startup logs: ``` galaxy.webhooks ERROR 2019-01-15 11:31:18,095 'ascii' codec can't decode byte 0xef in position 8291: ordinal not in range(128) Traceback (most recent call last): File "/galaxy/lib/galaxy/webhooks/__init__.py", line 62, in load_webhooks self.load_webhook_from_config(directory, config_file_path) File "/galaxy/lib/galaxy/webhooks/__init__.py", line 96, in load_webhook_from_config webhook.script = file.read() File "/galaxy_venv3/lib/python3.5/encodings/ascii.py", line 26, in decode return codecs.ascii_decode(input, self.errors)[0] UnicodeDecodeError: 'ascii' codec can't decode byte 0xef in position 8291: ordinal not in range(128) ``` Also rename variables from `file` (Python2 standard library function and class) to `fh`. Commit: f70d24afb5ed151237d7c7e0491b5db9337fdefc https://github.com/galaxyproject/galaxy/commit/f70d24afb5ed151237d7c7e0491b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py M test/api/test_histories.py Log Message: ----------- Python3: open 2 files in binary mode Fix `HistoriesApiTestCase.test_import_metadata_regeneration()` API test introduced in commit 38f7aded0b11f4c75f2265ba95ed674e8d655e7d . See: https://jenkins.galaxyproject.org/job/docker-api-py3/193/testReport/junit/t… Commit: e42dcfab2a930e8d736b021ff69cb3428a77663e https://github.com/galaxyproject/galaxy/commit/e42dcfab2a930e8d736b021ff69c… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M doc/source/admin/conda_faq.rst M doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/webhooks.rst M doc/source/conf.py M doc/source/dev/index.rst M doc/source/releases/16.07_announce.rst M doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst M doc/source/releases/17.01_announce.rst M doc/source/releases/18.01.rst M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webhooks/__init__.py M test/api/test_galaxy_interactor.py M test/api/test_histories.py Log Message: ----------- Merge pull request #7215 from nsoranzo/recommonmark_0.5.0 Dependency update and doc fixes Compare: https://github.com/galaxyproject/galaxy/compare/c6a681fa8bb2...e42dcfab2a93 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] cbe875: Fix global non-sense in setup_external_metadata?
by GitHub 15 Jan '19

15 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cbe87540dea874a8148e08e8d91d5a2e72c02529 https://github.com/galaxyproject/galaxy/commit/cbe87540dea874a8148e08e8d91d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-14 (Mon, 14 Jan 2019) Changed paths: M lib/galaxy/model/metadata.py Log Message: ----------- Fix global non-sense in setup_external_metadata? Commit: c6a681fa8bb212f4274ea436cf4b53fe0d3c9c1f https://github.com/galaxyproject/galaxy/commit/c6a681fa8bb212f4274ea436cf4b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M lib/galaxy/model/metadata.py Log Message: ----------- Merge pull request #7213 from jmchilton/metadata_globals_bad Fix global var badness in setup_external_metadata? Compare: https://github.com/galaxyproject/galaxy/compare/f954dc45fe94...c6a681fa8bb2 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 0a2049: Re-add a `py27-first-startup` Travis job on osx
by GitHub 14 Jan '19

14 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0a20498c67e5d9075a5566d2c8abf3073c611341 https://github.com/galaxyproject/galaxy/commit/0a20498c67e5d9075a5566d2c8ab… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M .travis.yml Log Message: ----------- Re-add a `py27-first-startup` Travis job on osx Commit: f954dc45fe94706f2ea04accc9fc92bcbcea892f https://github.com/galaxyproject/galaxy/commit/f954dc45fe94706f2ea04accc9fc… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-01-14 (Mon, 14 Jan 2019) Changed paths: M .travis.yml Log Message: ----------- Merge pull request #7207 from nsoranzo/readd_travis_osx Re-add a `py27-first-startup` Travis job on osx Compare: https://github.com/galaxyproject/galaxy/compare/b58bed1eefd4...f954dc45fe94 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] d91a66: Remove collect_outputs_from option.
by GitHub 07 Jan '19

07 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d91a666d5cc3cb84fac4051e8869e887728cccf8 https://github.com/galaxyproject/galaxy/commit/d91a666d5cc3cb84fac4051e8869… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-20 (Thu, 20 Dec 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/functional/tools/multi_output.xml M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- Remove collect_outputs_from option. And just disable dynamic discovery of outputs from new_file_path for legacy profile tools. This is part of an ongoing effort to kill new_file_path and simplify output discovery. This option was added by @natefoo 10 years ago and he switched main to disable new_file_path discovery and noone ever complained. So lets just do this for all Galaxies - if main hasn't run tools that require this functionality in a decade - I very much doubt any Galaxies require this. Commit: 681225bc9cb0f25c5e717658f37a4302c1c4166a https://github.com/galaxyproject/galaxy/commit/681225bc9cb0f25c5e717658f37a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-07 (Mon, 07 Jan 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/functional/tools/multi_output.xml M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- Merge pull request #7144 from jmchilton/remove_collect_outputs_from Remove collect_outputs_from option. Compare: https://github.com/galaxyproject/galaxy/compare/03b363a1ef92...681225bc9cb0 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy]
by GitHub 07 Jan '19

07 Jan '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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