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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 29 Jul '16

29 Jul '16

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

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[galaxyproject/galaxy] fcbaf8: Fix an error with getting the size of an object fr...
by GitHub 29 Jul '16

29 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fcbaf8d17a20b1a910c07d154b690c28689fcb63 https://github.com/galaxyproject/galaxy/commit/fcbaf8d17a20b1a910c07d154b69… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Fix an error with getting the size of an object from Azure. Attempted to future-proof it if the library is fixed. Commit: 05c537e38478ab0c4a674120860b5601f59bbf4a https://github.com/galaxyproject/galaxy/commit/05c537e38478ab0c4a674120860b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Merge pull request #2678 from dannon/azure_followup Fix an error with getting the size of an object from Azure. Attempte… Compare: https://github.com/galaxyproject/galaxy/compare/0066847e0ac1...05c537e38478

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[galaxyproject/galaxy] 4f1228: Limit creation of multitudes of default, empty his...
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4f1228213886bc9ba2443133ed75936c81e855e9 https://github.com/galaxyproject/galaxy/commit/4f1228213886bc9ba2443133ed75… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Limit creation of multitudes of default, empty histories. This was happening for every new session using remote auth Commit: 0066847e0ac19632c3091ac3148069de3bb3855f https://github.com/galaxyproject/galaxy/commit/0066847e0ac19632c3091ac31480… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #2684 from dannon/remote_auth_many_histories Limit creation of multitudes of default, empty histories. Compare: https://github.com/galaxyproject/galaxy/compare/5c2402f83741...0066847e0ac1

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[galaxyproject/galaxy] 5c79e2: Unpin flake8 in py27-lint-imports* test environmen...
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5c79e27436446f064674f29bbcd08760a419506f https://github.com/galaxyproject/galaxy/commit/5c79e27436446f064674f29bbcd0… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M tox.ini Log Message: ----------- Unpin flake8 in py27-lint-imports* test environments flake8-import-order 0.9 has been released Commit: ec6e6255c109b5c6a9096fcd281a02e6559dd585 https://github.com/galaxyproject/galaxy/commit/ec6e6255c109b5c6a9096fcd281a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M .ci/flake8_lint_include_list.txt Log Message: ----------- Extend the list to all files already passing Generated with: find . -path ./.venv -prune -o -path ./.tox -prune -o -path ./eggs -prune -o -path ./database -prune -o -name '*.py' -print0 | sort -z | xargs -0 -L 1 -I '{}' sh -c 'flake8 -qq {} && echo {}' | sed 's|^\./||' > .ci/flake8_lint_include_list.txt followed by some manual editing. Commit: 5c2402f837411972bb534918c4b72891a58a3816 https://github.com/galaxyproject/galaxy/commit/5c2402f837411972bb534918c4b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M .ci/flake8_lint_include_list.txt M tox.ini Log Message: ----------- Merge pull request #2682 from nsoranzo/flake8-import-order Extend the list of files tested with flake8-import-order to all files already passing Compare: https://github.com/galaxyproject/galaxy/compare/e8f2a74f21e0...5c2402f83741

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[galaxyproject/galaxy] 497817: Break tool parameter help words if necessary
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4978173e4ed6b76ef4520f6d395788d2c14cf888 https://github.com/galaxyproject/galaxy/commit/4978173e4ed6b76ef4520f6d3957… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Break tool parameter help words if necessary Commit: addc15179744ee01c2f11b198ae4c5f60f25b27d https://github.com/galaxyproject/galaxy/commit/addc15179744ee01c2f11b198ae4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Use word-wrap instead of word-break to apply break-word due to better browser support Commit: e8f2a74f21e034831c562b965e6c0189b719df7e https://github.com/galaxyproject/galaxy/commit/e8f2a74f21e034831c562b965e6c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Merge pull request #2681 from guerler/help_word_break Break tool parameter help words if necessary Compare: https://github.com/galaxyproject/galaxy/compare/c096be04bd53...e8f2a74f21e0

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[galaxyproject/galaxy] 4a8310: Generate metadata in separate conda environment
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4a831033ed820e3f1220d9d326f8bd8079c390f9 https://github.com/galaxyproject/galaxy/commit/4a831033ed820e3f1220d9d326f8… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Generate metadata in separate conda environment Galaxy supports generating metadata in a separate command (enable beta_tool_command_isolation). This command has its own dependency resolution, that may interfere with thedependency resolution of the actual tool, if the same environment is being used. With this PR we create a new environment when resolving metadata dependencies with conda, that will be active only for metadata generation. Commit: 28da4b6371b23c69d15e7fc59473d4bde5639fde https://github.com/galaxyproject/galaxy/commit/28da4b6371b23c69d15e7fc59473… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Fix whitespace and comma use Commit: f8cf81d73693e5f075b6c9e612244221bbd6e5bb https://github.com/galaxyproject/galaxy/commit/f8cf81d73693e5f075b6c9e61224… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M .ci/flake8_blacklist.txt Log Message: ----------- Ignore .tox directory. Used to be ignored by default w/ flake8 apparently, but not anymore. Commit: f0024d64e15815dcb6c2ac027ed5fb2977651e64 https://github.com/galaxyproject/galaxy/commit/f0024d64e15815dcb6c2ac027ed5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/web/framework/helpers/__init__.py M test/base/driver_util.py Log Message: ----------- Apply @nsoranzo's fix for noqa changes (must end the line, comment comes before it) Commit: 8f978b8957f0cbc7e5d78ca3f3bce9e87e6e8f76 https://github.com/galaxyproject/galaxy/commit/8f978b8957f0cbc7e5d78ca3f3bc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/web/framework/helpers/__init__.py M test/base/driver_util.py Log Message: ----------- Merge pull request #2662 from jmchilton/backport_2253 [16.04] Backport #2253 as requested by Eagle Eyes Commit: 5d8d932425c879177c40a008a5a2ef3e45020b73 https://github.com/galaxyproject/galaxy/commit/5d8d932425c879177c40a008a5a2… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- Add hg38 to main for ucsc_build_sites.txt.sample (cherry picked from commit 04b7d11f053e66b14232440e6ff534a62ff26666) Commit: e4ca3bf80fcab185e8ea3502926563707b047236 https://github.com/galaxyproject/galaxy/commit/e4ca3bf80fcab185e8ea35029265… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- Merge pull request #2673 from blankenberg/ucsc-hg38-display-16.04 [16.04] Add hg38 to main for ucsc_build_sites.txt.sample Commit: c096be04bd53c8184a4c5880c99abe02649e7570 https://github.com/galaxyproject/galaxy/commit/c096be04bd53c8184a4c5880c99a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/fdbaf437c9ba...c096be04bd53

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[galaxyproject/galaxy] 5d8d93: Add hg38 to main for ucsc_build_sites.txt.sample
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 5d8d932425c879177c40a008a5a2ef3e45020b73 https://github.com/galaxyproject/galaxy/commit/5d8d932425c879177c40a008a5a2… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- Add hg38 to main for ucsc_build_sites.txt.sample (cherry picked from commit 04b7d11f053e66b14232440e6ff534a62ff26666) Commit: e4ca3bf80fcab185e8ea3502926563707b047236 https://github.com/galaxyproject/galaxy/commit/e4ca3bf80fcab185e8ea35029265… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- Merge pull request #2673 from blankenberg/ucsc-hg38-display-16.04 [16.04] Add hg38 to main for ucsc_build_sites.txt.sample Compare: https://github.com/galaxyproject/galaxy/compare/8f978b8957f0...e4ca3bf80fca

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[galaxyproject/galaxy] 8dbc35: Collections should be populated regardless of the ...
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8dbc35784e209c640f0c010077452f5c32be463c https://github.com/galaxyproject/galaxy/commit/8dbc35784e209c640f0c01007745… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Collections should be populated regardless of the availability of other values Commit: 25fd142667a716775f7230e5e38aadeb3365b9e9 https://github.com/galaxyproject/galaxy/commit/25fd142667a716775f7230e5e38a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Initialize empty other_values dictionary when populating collections Commit: fdbaf437c9bac1c9179347b3bc54093bcdc52ceb https://github.com/galaxyproject/galaxy/commit/fdbaf437c9bac1c9179347b3bc54… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2672 from guerler/fix_populating_collections Properly populate collections regardless of context values Compare: https://github.com/galaxyproject/galaxy/compare/fed3665fcfa9...fdbaf437c9ba

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