Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cb09c35a07e3b9f8ca7e4eb5e8d37ffacdee6253 https://github.com/galaxyproject/galaxy/commit/cb09c35a07e3b9f8ca7e4eb5e8d37... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Fix line wrapping for peek of tabular files. Commit: 390c1fc275ba7128f22f533b0b512b0bc517e521 https://github.com/galaxyproject/galaxy/commit/390c1fc275ba7128f22f533b0b512... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Always install a specific version of Galaxy pip in common_startup.sh. Commit: 46471d61e4349bba2d0c702de18f91a5b201bb66 https://github.com/galaxyproject/galaxy/commit/46471d61e4349bba2d0c702de18f9... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- pip < 1.6 cannot parse requirement specifiers to the `install` command that contain a `+` in the version. For these older versions, directly install the wheel or install from the sdist. Technically 1.4 and later can install wheels, but in testing, only 1.5+ was able to install them properly with their scripts. The new heredoc execute and redirect syntax is Bourne-compatible. pip --pre is no longer necessary since the Galaxy pip version is no longer a development version of pip. Commit: 60062b020dc2b753e5b8f034272e0b982b8c2f6f https://github.com/galaxyproject/galaxy/commit/60062b020dc2b753e5b8f034272e0... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- pip 1.6 -> 6.0, thanks @nsoranzo Commit: 685fd1560e98e6d885d6cf627b691d2228807974 https://github.com/galaxyproject/galaxy/commit/685fd1560e98e6d885d6cf627b691... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #1595 from natefoo/fix-pip-wheel-version [16.01] Always install a specific version of Galaxy pip in common_startup.sh. Commit: 981f904c3f8a501ffabaf7b83538151070bd8a21 https://github.com/galaxyproject/galaxy/commit/981f904c3f8a501ffabaf7b835381... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/util/__init__.py Log Message: ----------- Attempt to fix transiently failing test due to object store makedirs call. Failing test - https://jenkins.galaxyproject.org/job/docker-api/2421/testReport/junit/api.t.... If you look at the actual source code for os.makedirs - it does inconsistently handle errno.EEXIST - this is probably a better approach than raw os.makedirs for most cases. xref #1617 Commit: 81535c5778b70001bfeb3da5690eba6426ea4638 https://github.com/galaxyproject/galaxy/commit/81535c5778b70001bfeb3da5690eb... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #1500 from blankenberg/peek-fix [16.01] Fix line wrapping for peek of tabular files. Commit: 4ae49fbfec952a2087a9cf3f9b9940f86fd05220 https://github.com/galaxyproject/galaxy/commit/4ae49fbfec952a2087a9cf3f9b994... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css Log Message: ----------- Fix module/step border style in workflow canvas Commit: 44336b289bd5ba7d9911bf1c1fcc0a604fda7358 https://github.com/galaxyproject/galaxy/commit/44336b289bd5ba7d9911bf1c1fcc0... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css Log Message: ----------- Merge pull request #1620 from guerler/fix_module_border_000 [16.01] Fix module/step border style in workflow canvas Commit: ade18b3cd23c54c347d38585736d32da5fccc4dd https://github.com/galaxyproject/galaxy/commit/ade18b3cd23c54c347d38585736d3... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #1623 from jmchilton/makedirs [16.01] Attempt to fix transiently failing test due to objectstore makedirs … Commit: 30ccebfb0c8ef0809bbd3f1d2d64be5ac23bb3a2 https://github.com/galaxyproject/galaxy/commit/30ccebfb0c8ef0809bbd3f1d2d64b... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- remove forgotten util.params that fails when POSTing a payload{} dict (because it cannot sanitize dict in dict) Commit: 61818948a163602b3c135937d053fe42c46bb4d2 https://github.com/galaxyproject/galaxy/commit/61818948a163602b3c135937d053f... Author: guerler <aysam.guerler@gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M static/maps/mvc/form/form-section.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-section.js Log Message: ----------- Fix default option for repeats Commit: ee4f58ce7d6a81477e5e4fc3e544e5da909f1198 https://github.com/galaxyproject/galaxy/commit/ee4f58ce7d6a81477e5e4fc3e544e... Author: John Chilton <jmchilton@gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M static/maps/mvc/form/form-section.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-section.js Log Message: ----------- Merge pull request #1635 from guerler/fix_repeat_default_001 [16.01] Fix default option for repeats Commit: 9170865dfbe0f8588ec47449e683236e5ba92a39 https://github.com/galaxyproject/galaxy/commit/9170865dfbe0f8588ec47449e6832... Author: John Chilton <jmchilton@gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Merge pull request #1634 from martenson/remove-utilparams [16.01] libraries: remove forgotten util.params that fails when POSTing a payload {} Commit: afc5f2a45399c474d86f1530a62afe280a0eb3be https://github.com/galaxyproject/galaxy/commit/afc5f2a45399c474d86f1530a62af... Author: John Chilton <jmchilton@gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Fix: Use dependency resolvers if any config exists. This way resolvers like the Module resolver work even if tool_dependency_dir is not set. Commit: 50ea4694af82ac33eaac1ddc9ca8aee1e71e1f00 https://github.com/galaxyproject/galaxy/commit/50ea4694af82ac33eaac1ddc9ca8a... Author: Mark Einon <mark.einon@gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M scripts/binary_compatibility.py Log Message: ----------- Change python print() format to be backward compatible with older versions In python versions prior to 3.1, the print("{}", .format(x)) form throws an error, use the more compatible print("{0}", .format(x)) form instead. Commit: 85eccba79151a545af1e7aa07f24cece9c5398bd https://github.com/galaxyproject/galaxy/commit/85eccba79151a545af1e7aa07f24c... Author: John Chilton <jmchilton@gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M templates/user/info.mako M templates/user/username.mako Log Message: ----------- Public name is mandatory not optional, update help text. Commit: e4e48941a6174a148cde06ef2218ef6480568716 https://github.com/galaxyproject/galaxy/commit/e4e48941a6174a148cde06ef2218e... Author: John Chilton <jmchilton@gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M scripts/binary_compatibility.py Log Message: ----------- Merge pull request #1651 from jmchilton/backport_print_fix [16.01] Backport print fix. Commit: 916ddb575f40c445a47cf91a58aad00bf9360ae8 https://github.com/galaxyproject/galaxy/commit/916ddb575f40c445a47cf91a58aad... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #1648 from jmchilton/dependencies_conf [16.01] Fix use_tool_dependencies for non-default dependency_resolver_conf files. Commit: 6635e91170b310beafe629bc2956607234c41cb0 https://github.com/galaxyproject/galaxy/commit/6635e91170b310beafe629bc29566... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Bump gx pip version to fix OSX platform issues. Commit: 05e68addbe846a8f39cd1192285f936df166bf35 https://github.com/galaxyproject/galaxy/commit/05e68addbe846a8f39cd1192285f9... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #1652 from dannon/pip_bump [16.01] Bump gx pip version to fix OSX platform issues. Commit: 39aff8457201fc383d49cc8e90798795b7923189 https://github.com/galaxyproject/galaxy/commit/39aff8457201fc383d49cc8e90798... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M templates/user/info.mako M templates/user/username.mako Log Message: ----------- Merge pull request #1655 from jmchilton/public-name-fixes [16.01] Public name is mandatory not optional, update help text. Commit: a8be2222ebb448ebac5996a2a9a042d0d618344f https://github.com/galaxyproject/galaxy/commit/a8be2222ebb448ebac5996a2a9a04... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/style/less/base.less M lib/galaxy/config.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M scripts/common_startup.sh M static/maps/mvc/form/form-section.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-section.js M static/style/blue/base.css M templates/user/info.mako M templates/user/username.mako Log Message: ----------- Merge branch 'release_16.01' into dev Conflicts: static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/style/blue/base.css Commit: 1d6208f9ae317b1d10aed49cdcd2c9f653c9c8b8 https://github.com/galaxyproject/galaxy/commit/1d6208f9ae317b1d10aed49cdcd2c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/style/less/base.less M lib/galaxy/config.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M scripts/common_startup.sh M static/maps/mvc/form/form-section.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-section.js M static/style/blue/base.css M templates/user/info.mako M templates/user/username.mako Log Message: ----------- Merge pull request #1656 from nsoranzo/merge_16.01_into_dev Merge 16.01 into dev. Compare: https://github.com/galaxyproject/galaxy/compare/a5c4e0402547...1d6208f9ae31