January 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] bf84ac: Attempt work around for race-y sort of condition i...
by GitHub 25 Jan '17

25 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf84aca059ea71c0755ee5c60a1a4214c4b0a5e5 https://github.com/galaxyproject/galaxy/commit/bf84aca059ea71c0755ee5c60a1a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M test/galaxy_selenium/sizzle.py Log Message: ----------- Attempt work around for race-y sort of condition in Selenium sizzle checkers. I believe this rare condition explains this failing test here - https://jenkins.galaxyproject.org/view/All/job/selenium/54/testReport/junit…. This test has never failed for me locally and this is the only time I've seen it fail on Jenkins as well. Commit: 27ec016cdf06ea57de73871396842affda3aeb2d https://github.com/galaxyproject/galaxy/commit/27ec016cdf06ea57de7387139684… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M test/galaxy_selenium/sizzle.py Log Message: ----------- Merge pull request #3451 from jmchilton/selenium_fixes_3 Attempt work around for race-y sort of condition in Selenium sizzle checkers. Compare: https://github.com/galaxyproject/galaxy/compare/e75242b95cb8...27ec016cdf06

1 0

[galaxyproject/galaxy] c7df03: Add an example group filter for displaying tool pa...
by GitHub 25 Jan '17

25 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c7df034bbc749904568cfdeb897675ec501116bd https://github.com/galaxyproject/galaxy/commit/c7df034bbc749904568cfdeb8976… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M lib/galaxy/tools/toolbox/filters/examples.py.sample Log Message: ----------- Add an example group filter for displaying tool panel sections Commit: e75242b95cb88f54ad9c21d945d3da34f970d169 https://github.com/galaxyproject/galaxy/commit/e75242b95cb88f54ad9c21d945d3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M lib/galaxy/tools/toolbox/filters/examples.py.sample Log Message: ----------- Merge pull request #3484 from gregvonkuster/group_tool_filter Add an example group filter for displaying tool panel sections Compare: https://github.com/galaxyproject/galaxy/compare/3eaad9a84ec6...e75242b95cb8

1 0

[galaxyproject/galaxy] 3cca45: Dependency resolver documentation revisions.
by GitHub 25 Jan '17

25 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3cca45b2bb570bb213d9a77764d606633aea7cfc https://github.com/galaxyproject/galaxy/commit/3cca45b2bb570bb213d9a77764d6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst Log Message: ----------- Dependency resolver documentation revisions. - Add documentation for cached dependency management as solution to LOCKERRORS. - Add documentation for overcoming problems with hard links. (Different approaches) - Add documentation on upgrading Conda as needed. - Correct and fill out documentation of defaults. - Fix some bugs in the Galaxy packages documentation. - Expand Galaxy package documentation to include a simpler example. - Update Conda configuration option documentation to reflect new defaults. - Update Conda configuration option documentation to discuss copy_dependencies. - Cross link Conda and dependency resolver documentation as it makes sense. - Add a link to the Bioconda channel order documentation for future reference. - Make things a bit more concise in places - start with the implicit tl;dr. Commit: 088e246006ff750e9a78849c4dbca6bfcccbf84f https://github.com/galaxyproject/galaxy/commit/088e246006ff750e9a78849c4dbc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- fix two typos Commit: f3810f842fa1bb4d960262d1d91ccd5207738f30 https://github.com/galaxyproject/galaxy/commit/f3810f842fa1bb4d960262d1d91c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M doc/source/admin/dependency_resolvers.rst Log Message: ----------- minor adjustments Commit: f40489e66ea479f56e96f9ba62b1040294a04ba5 https://github.com/galaxyproject/galaxy/commit/f40489e66ea479f56e96f9ba62b1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- 2 more typos spotted by @mvdbeek Commit: 133dc79d3eef9ebab5558d28b840acb80395a034 https://github.com/galaxyproject/galaxy/commit/133dc79d3eef9ebab5558d28b840… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M doc/source/admin/dependency_resolvers.rst Log Message: ----------- typo spotted by @mvdbeek Commit: 3eaad9a84ec6bda5f4dce190864b966b9d6287a5 https://github.com/galaxyproject/galaxy/commit/3eaad9a84ec6bda5f4dce190864b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst Log Message: ----------- Merge pull request #3483 from jmchilton/doc_revision_0 [17.01] Dependency resolver documentation revisions. Compare: https://github.com/galaxyproject/galaxy/compare/71876f6de7d9...3eaad9a84ec6

1 0

[galaxyproject/galaxy] 04eee6: Fix logs and unit tests for Conda placeholder bug ...
by GitHub 25 Jan '17

25 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 04eee6459a8e9f4566da61f819a937f4b04d1c40 https://github.com/galaxyproject/galaxy/commit/04eee6459a8e9f4566da61f819a9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M test/unit/tools/test_conda_resolution.py Log Message: ----------- Fix logs and unit tests for Conda placeholder bug resolution. Commit: 71876f6de7d9a92fc482b0ae0c2ed0ad4588b906 https://github.com/galaxyproject/galaxy/commit/71876f6de7d9a92fc482b0ae0c2e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M test/unit/tools/test_conda_resolution.py Log Message: ----------- Merge pull request #3482 from jmchilton/placeholder_fixes [17.01] Fix logs and unit tests for Conda placeholder bug resolution. Compare: https://github.com/galaxyproject/galaxy/compare/29c0c41666e4...71876f6de7d9

1 0

[galaxyproject/galaxy] 7f232a: Fix path to Smat datatype
by GitHub 25 Jan '17

25 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7f232a25b5a9c91131b64d8c72744a9f34d30045 https://github.com/galaxyproject/galaxy/commit/7f232a25b5a9c91131b64d8c7274… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Fix path to Smat datatype Commit: a396b280dc6a26581bb3e5059e6aebcc4790b6cb https://github.com/galaxyproject/galaxy/commit/a396b280dc6a26581bb3e5059e6a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #3475 from nsoranzo/release_17.01_fix_smat_datatype [17.01] Fix path to Smat datatype Commit: 29c0c41666e4f0a27ef18587f8b93a03bd413c5f https://github.com/galaxyproject/galaxy/commit/29c0c41666e4f0a27ef18587f8b9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge branch 'release_17.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/6077456135d4...29c0c41666e4

1 0

[galaxyproject/galaxy] 7f232a: Fix path to Smat datatype
by GitHub 25 Jan '17

25 Jan '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 7f232a25b5a9c91131b64d8c72744a9f34d30045 https://github.com/galaxyproject/galaxy/commit/7f232a25b5a9c91131b64d8c7274… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Fix path to Smat datatype Commit: a396b280dc6a26581bb3e5059e6aebcc4790b6cb https://github.com/galaxyproject/galaxy/commit/a396b280dc6a26581bb3e5059e6a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #3475 from nsoranzo/release_17.01_fix_smat_datatype [17.01] Fix path to Smat datatype Compare: https://github.com/galaxyproject/galaxy/compare/191813ab80a2...a396b280dc6a

1 0

[galaxyproject/galaxy] f882cb: Pin flake8 and plugins in tox.ini
by GitHub 24 Jan '17

24 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f882cb9b2ef45fd3b1dfb36d7bf1edb64b540e01 https://github.com/galaxyproject/galaxy/commit/f882cb9b2ef45fd3b1dfb36d7bf1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M tox.ini Log Message: ----------- Pin flake8 and plugins in tox.ini For all tox environments used in .travis.yml except the ones allowed to fail. Commit: 191813ab80a237476012333a1cb96834ce933124 https://github.com/galaxyproject/galaxy/commit/191813ab80a237476012333a1cb9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M tox.ini Log Message: ----------- Merge pull request #3476 from nsoranzo/release_17.01_pin_flake8 [17.01] Pin flake8 and plugins in tox.ini Commit: 111d2aa2c667f064961f7fd62122fe1d1fa43c0c https://github.com/galaxyproject/galaxy/commit/111d2aa2c667f064961f7fd62122… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M tox.ini Log Message: ----------- Merge branch 'release_17.01' into dev Commit: 79c3b23346f099601950935c957ca920f89f5770 https://github.com/galaxyproject/galaxy/commit/79c3b23346f099601950935c957c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M tox.ini Log Message: ----------- Un-pin flake8 and plugins in tox.ini Commit: 6077456135d42150d281767e4a99da8813986a9e https://github.com/galaxyproject/galaxy/commit/6077456135d42150d281767e4a99… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M tox.ini Log Message: ----------- Merge pull request #3478 from nsoranzo/merge_17.01 Merge 17.01 and un-pin flake8 and plugins Compare: https://github.com/galaxyproject/galaxy/compare/3c4413d31d99...6077456135d4

1 0

[galaxyproject/usegalaxy-playbook] 61084c: update TTS
by GitHub 24 Jan '17

24 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 61084c54dfcb816fbc801ced5af700dba164fc92 https://github.com/galaxyproject/usegalaxy-playbook/commit/61084c54dfcb816f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M stage/group_vars/toolshedservers.yml Log Message: ----------- update TTS

1 0

[galaxyproject/usegalaxy-playbook] 0b2699: update Test
by GitHub 24 Jan '17

24 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0b2699ed513300a2738ec55d7ff8a67347894f44 https://github.com/galaxyproject/usegalaxy-playbook/commit/0b2699ed513300a2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M stage/galaxy_version.yml Log Message: ----------- update Test

1 0

[galaxyproject/galaxy] f882cb: Pin flake8 and plugins in tox.ini
by GitHub 24 Jan '17

24 Jan '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: f882cb9b2ef45fd3b1dfb36d7bf1edb64b540e01 https://github.com/galaxyproject/galaxy/commit/f882cb9b2ef45fd3b1dfb36d7bf1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M tox.ini Log Message: ----------- Pin flake8 and plugins in tox.ini For all tox environments used in .travis.yml except the ones allowed to fail. Commit: 191813ab80a237476012333a1cb96834ce933124 https://github.com/galaxyproject/galaxy/commit/191813ab80a237476012333a1cb9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M tox.ini Log Message: ----------- Merge pull request #3476 from nsoranzo/release_17.01_pin_flake8 [17.01] Pin flake8 and plugins in tox.ini Compare: https://github.com/galaxyproject/galaxy/compare/dc49b1c220bb...191813ab80a2

1 0