July 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] af3f8c: Redefine svg datatype as subclass of GenericXml
by GitHub 29 Jul '16

29 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: af3f8cf8464a1c3d055ad9adb7122a4adc541dda https://github.com/galaxyproject/galaxy/commit/af3f8cf8464a1c3d055ad9adb712… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Redefine svg datatype as subclass of GenericXml SVG is XML-based and Python Pillow does not support it. Commit: 5b52b73fbb3a92a842cc6f9e36091c62ed7727f0 https://github.com/galaxyproject/galaxy/commit/5b52b73fbb3a92a842cc6f9e3609… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Datatype classes fixes: wrong file_ext, import order, Python3 - Specify some classes are abstracts - Use super() to call superclass methods - Various simplifications Commit: 3fd0e405fd6cb3333397ec19e627a4cf6ae36fe6 https://github.com/galaxyproject/galaxy/commit/3fd0e405fd6cb3333397ec19e627… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #2690 from nsoranzo/datatypes_fixes Misc datatypes fixes and enhancements Compare: https://github.com/galaxyproject/galaxy/compare/9aac1569f4b0...3fd0e405fd6c

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[galaxyproject/galaxy] 62fdbd: Fix the sanitization of None values in utils. Thi...
by GitHub 29 Jul '16

29 Jul '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 62fdbd526ae34357d3fbb44cedc46635c4df7cbb https://github.com/galaxyproject/galaxy/commit/62fdbd526ae34357d3fbb44cedc4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Fix the sanitization of None values in utils. This had previously not happened because Params had only been sanitizing strings coming in as part of the request, but if you're passing off (potentially manipulated, as in adding None default params) to a secondary request for a response, this can happen. Commit: ed7c357668df5bbb3381fae94353465594c7e184 https://github.com/galaxyproject/galaxy/commit/ed7c357668df5bbb3381fae94353… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #2693 from dannon/utils_fix_sanitization_of_none [16.07] Fix the sanitization of None values in utils. This had previously no… Compare: https://github.com/galaxyproject/galaxy/compare/62815aff39c2...ed7c357668df

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[galaxyproject/galaxy] 5c3822: A different form of upstream check that works on o...
by GitHub 29 Jul '16

29 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5c3822197195a932c4056b582c49b6b209a9f3d5 https://github.com/galaxyproject/galaxy/commit/5c3822197195a932c4056b582c49… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M Makefile Log Message: ----------- A different form of upstream check that works on osx (and hopefully still other locations). Commit: 820d545d3adae3a47384b831926992126f165b36 https://github.com/galaxyproject/galaxy/commit/820d545d3adae3a47384b8319269… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M Makefile Log Message: ----------- Roll the check into the rule so it gets reevaluated Commit: 6be8d6356d7f6b15ab3ddabf0efe286d398f1216 https://github.com/galaxyproject/galaxy/commit/6be8d6356d7f6b15ab3ddabf0efe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M Makefile Log Message: ----------- Remove unused def Commit: dc668a0bf3792af7052df9bffa07ab42d1b8b894 https://github.com/galaxyproject/galaxy/commit/dc668a0bf3792af7052df9bffa07… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M Makefile Log Message: ----------- Checkout dev again prior to version branch deletion. This prevents error: Cannot delete the branch 'blah' which you are currently on Commit: 9aac1569f4b082ba6eb3317ee1d287abfd724027 https://github.com/galaxyproject/galaxy/commit/9aac1569f4b082ba6eb3317ee1d2… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M Makefile Log Message: ----------- Merge pull request #2688 from dannon/makefile_updates Makefile updates for compatibility with OSX Compare: https://github.com/galaxyproject/galaxy/compare/e291012afd64...9aac1569f4b0

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[galaxyproject/galaxy] 1a0052: Merge pull request #2685 from dannon/version-16.07
by GitHub 29 Jul '16

29 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1a0052aa71ea2b78d3c1a5b8594c7109928bb454 https://github.com/galaxyproject/galaxy/commit/1a0052aa71ea2b78d3c1a5b8594c… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #2685 from dannon/version-16.07 Update version to 16.07.rc1 Commit: f06c895d618164af36cc419f4b1a717d6c595e89 https://github.com/galaxyproject/galaxy/commit/f06c895d618164af36cc419f4b1a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- Update INDETERMINATE_DEPENDENCY to NullDependency Fix unit test broken in https://github.com/galaxyproject/galaxy/pull/2554 Commit: 5e7f0c4b18eb26f3e7781206ba5e8ff17c854306 https://github.com/galaxyproject/galaxy/commit/5e7f0c4b18eb26f3e7781206ba5e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M run_tests.sh M scripts/nosetests.py Log Message: ----------- Fix unit tests exit status Broken in https://github.com/galaxyproject/galaxy/pull/2564 Also update scripts/nosetests.py Commit: 62815aff39c29a589f8bf3073cd0b19aa882a58d https://github.com/galaxyproject/galaxy/commit/62815aff39c29a589f8bf3073cd0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M run_tests.sh M scripts/nosetests.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #2691 from nsoranzo/release_16.07_fix_tests [16.07] Fix unit tests Commit: e291012afd6474f493c4984a14044a7a4667617a https://github.com/galaxyproject/galaxy/commit/e291012afd6474f493c4984a1404… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M run_tests.sh M scripts/nosetests.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c9a5d2913485...e291012afd64

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[galaxyproject/galaxy] f06c89: Update INDETERMINATE_DEPENDENCY to NullDependency
by GitHub 29 Jul '16

29 Jul '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: f06c895d618164af36cc419f4b1a717d6c595e89 https://github.com/galaxyproject/galaxy/commit/f06c895d618164af36cc419f4b1a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- Update INDETERMINATE_DEPENDENCY to NullDependency Fix unit test broken in https://github.com/galaxyproject/galaxy/pull/2554 Commit: 5e7f0c4b18eb26f3e7781206ba5e8ff17c854306 https://github.com/galaxyproject/galaxy/commit/5e7f0c4b18eb26f3e7781206ba5e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M run_tests.sh M scripts/nosetests.py Log Message: ----------- Fix unit tests exit status Broken in https://github.com/galaxyproject/galaxy/pull/2564 Also update scripts/nosetests.py Commit: 62815aff39c29a589f8bf3073cd0b19aa882a58d https://github.com/galaxyproject/galaxy/commit/62815aff39c29a589f8bf3073cd0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M run_tests.sh M scripts/nosetests.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #2691 from nsoranzo/release_16.07_fix_tests [16.07] Fix unit tests Compare: https://github.com/galaxyproject/galaxy/compare/1a0052aa71ea...62815aff39c2

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[galaxyproject/galaxy] 09aef7: mention need to update P4's conf when freezing
by GitHub 29 Jul '16

29 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 09aef7eda5b4a57051d65346130d979bbd6c894c https://github.com/galaxyproject/galaxy/commit/09aef7eda5b4a57051d65346130d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- mention need to update P4's conf when freezing Commit: c9a5d2913485d22845a5df7d0ab99e11041dbc58 https://github.com/galaxyproject/galaxy/commit/c9a5d2913485d22845a5df7d0ab9… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #2689 from martenson/add_p4_bootstrap mention need to update P4's conf when freezing Compare: https://github.com/galaxyproject/galaxy/compare/b2fbfcd6aca3...c9a5d2913485

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[galaxyproject/usegalaxy-playbook] 9cc02c: Add mo to admin users.
by GitHub 29 Jul '16

29 Jul '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9cc02ce8f1d6796984b4bddcf2c4d4d8ec70e4a4 https://github.com/galaxyproject/usegalaxy-playbook/commit/9cc02ce8f1d67969… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M production/secret_vars/galaxyservers.yml M stage/secret_vars/galaxyservers.yml Log Message: ----------- Add mo to admin users.

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[galaxyproject/galaxy] 19b363: Update version to 16.07.rc1
by GitHub 29 Jul '16

29 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 19b363cdcd0b23e9409f8beea387444b460768be https://github.com/galaxyproject/galaxy/commit/19b363cdcd0b23e9409f8beea387… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.07.rc1 Commit: 9789c116e65d9af974fdc997ec10890646b9197e https://github.com/galaxyproject/galaxy/commit/9789c116e65d9af974fdc997ec10… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.10.dev Commit: 7893f1a5713548d70d806da8f479827f0ee91e78 https://github.com/galaxyproject/galaxy/commit/7893f1a5713548d70d806da8f479… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Log Message: ----------- Merge branch 'version-16.07' into version-16.10.dev Commit: b2fbfcd6aca3a29440e7355101e579f4e649265b https://github.com/galaxyproject/galaxy/commit/b2fbfcd6aca3a29440e7355101e5… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #2686 from dannon/version-16.10.dev Version 16.10.dev Compare: https://github.com/galaxyproject/galaxy/compare/05c537e38478...b2fbfcd6aca3

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[galaxyproject/galaxy] 19b363: Update version to 16.07.rc1
by GitHub 29 Jul '16

29 Jul '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 19b363cdcd0b23e9409f8beea387444b460768be https://github.com/galaxyproject/galaxy/commit/19b363cdcd0b23e9409f8beea387… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.07.rc1 Commit: 1a0052aa71ea2b78d3c1a5b8594c7109928bb454 https://github.com/galaxyproject/galaxy/commit/1a0052aa71ea2b78d3c1a5b8594c… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #2685 from dannon/version-16.07 Update version to 16.07.rc1 Compare: https://github.com/galaxyproject/galaxy/compare/05c537e38478...1a0052aa71ea

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[galaxyproject/galaxy]
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy

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