galaxy-commits January 2018

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[galaxyproject/galaxy] df597d: remove dead link
by GitHub 25 Jan '18

25 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: df597db60ef479a8499b7a3b34591527c5d86dd7 https://github.com/galaxyproject/galaxy/commit/df597db60ef479a8499b7a3b3459… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M run_tests.sh Log Message: ----------- remove dead link urls are not forever... Commit: 046cb8f35956c45e5c88786b1e9c081cd5584efe https://github.com/galaxyproject/galaxy/commit/046cb8f35956c45e5c88786b1e9c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #5392 from martenson/remove-spam remove dead link Compare: https://github.com/galaxyproject/galaxy/compare/2854643057dd...046cb8f35956

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[galaxyproject/galaxy] 04c16f: Add nodeenv to dev requirements
by GitHub 25 Jan '18

25 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 04c16f7e046945be3780b8431c492a9fac0d294a https://github.com/galaxyproject/galaxy/commit/04c16f7e046945be3780b8431c49… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-24 (Wed, 24 Jan 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- Add nodeenv to dev requirements Commit: 8e4eab6e6cc6686f7bfdf7b86e29d725183a7397 https://github.com/galaxyproject/galaxy/commit/8e4eab6e6cc6686f7bfdf7b86e29… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-24 (Wed, 24 Jan 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Install node and yarn in common_startup.sh using nodeenv and the venv's npm. Commit: 2854643057dd7d8517594299cf4c2d022c3fe78a https://github.com/galaxyproject/galaxy/commit/2854643057dd7d8517594299cf4c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M scripts/common_startup.sh Log Message: ----------- Merge pull request #5375 from natefoo/nodeenv Install node and yarn on startup if running a non-release branch Compare: https://github.com/galaxyproject/galaxy/compare/c31a0341714e...2854643057dd

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[galaxyproject/galaxy] 6a2e6b: Add --skip_flakey_fails flag to CI script for API ...
by GitHub 25 Jan '18

25 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6a2e6be733b8349842689c38fb11fbf734fc518b https://github.com/galaxyproject/galaxy/commit/6a2e6be733b8349842689c38fb11… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M .ci/jenkins/api/run_tests.sh Log Message: ----------- Add --skip_flakey_fails flag to CI script for API tests xref. https://github.com/galaxyproject/galaxy/pull/5286#issuecomment-358404551 and following comments. Commit: c31a0341714efa85a75df13da06ba34925673de5 https://github.com/galaxyproject/galaxy/commit/c31a0341714efa85a75df13da06b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M .ci/jenkins/api/run_tests.sh Log Message: ----------- Merge pull request #5388 from nsoranzo/skip_flakey_fails_for_api_tests Add --skip_flakey_fails flag to CI script for API tests Compare: https://github.com/galaxyproject/galaxy/compare/83bf0ccce71c...c31a0341714e

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[galaxyproject/galaxy] 392565: Update version to 18.01.rc1
by GitHub 25 Jan '18

25 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 392565489be3beed26944d07ce130ac96a3a0fc6 https://github.com/galaxyproject/galaxy/commit/392565489be3beed26944d07ce13… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 18.01.rc1 Commit: d32f0d2eb111dee6951e021b98b41c051f07e46f https://github.com/galaxyproject/galaxy/commit/d32f0d2eb111dee6951e021b98b4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 18.05.dev Commit: c1e78ae75c8849639f0db889a1f722e2473f12dd https://github.com/galaxyproject/galaxy/commit/c1e78ae75c8849639f0db889a1f7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-25 (Thu, 25 Jan 2018) Log Message: ----------- Merge branch 'version-18.01' into version-18.05.dev Commit: 83bf0ccce71c1244b362323efde0c89f2a4c8b60 https://github.com/galaxyproject/galaxy/commit/83bf0ccce71c1244b362323efde0… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #5386 from martenson/version-18.05.dev Version 18.05.dev Compare: https://github.com/galaxyproject/galaxy/compare/4e17ce81f4a3...83bf0ccce71c

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[galaxyproject/galaxy] 392565: Update version to 18.01.rc1
by GitHub 25 Jan '18

25 Jan '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 392565489be3beed26944d07ce130ac96a3a0fc6 https://github.com/galaxyproject/galaxy/commit/392565489be3beed26944d07ce13… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 18.01.rc1 Commit: 3b69c645dab86332c506bd0e510de77d6e7dc215 https://github.com/galaxyproject/galaxy/commit/3b69c645dab86332c506bd0e510d… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #5387 from martenson/version-18.01 [18.01] Update version to 18.01.rc1 Compare: https://github.com/galaxyproject/galaxy/compare/4e17ce81f4a3...3b69c645dab8

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[galaxyproject/galaxy]
by GitHub 25 Jan '18

25 Jan '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] 747309: Fix tool-shed-config-validate
by GitHub 25 Jan '18

25 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 747309b2786da3e18cdd962d977b2ee72afdb5dc https://github.com/galaxyproject/galaxy/commit/747309b2786da3e18cdd962d977b… Author: ValentinChCloud <chavaldranis(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- Fix tool-shed-config-validate Commit: 73418ab7875e7e5fb2669a13fc0d55a40b7180a3 https://github.com/galaxyproject/galaxy/commit/73418ab7875e7e5fb2669a13fc0d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- Merge pull request #5343 from ValentinChCloud/fixes [17.09] Fix tool-shed-config-validate Commit: 4e17ce81f4a36184c05accb483273380831fee4d https://github.com/galaxyproject/galaxy/commit/4e17ce81f4a36184c05accb48327… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/5defdc79192d...4e17ce81f4a3

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[galaxyproject/galaxy] 4da1da: Fix for history multipanel view for when the 'curr...
by GitHub 25 Jan '18

25 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4da1dad39418703970a92bd4260b7892c18a79e3 https://github.com/galaxyproject/galaxy/commit/4da1dad39418703970a92bd4260b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js Log Message: ----------- Fix for history multipanel view for when the 'current' history is deleted and/or purged. Several bits of refactoring, import cleanup, and a start towards documenting globals in client files touched. Commit: 0dae63a578adaf1d3ef63248fe26cd1ba86aaf31 https://github.com/galaxyproject/galaxy/commit/0dae63a578adaf1d3ef63248fe26… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Fix a mutable default function arg noticed when digging through history API code. Commit: 541968bbd9237f0ca1679ae52cdf6ba98ed8752c https://github.com/galaxyproject/galaxy/commit/541968bbd9237f0ca1679ae52cdf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js Log Message: ----------- Swap to fat arrow functions, this reference in multipanel behavior handling. Commit: 5defdc79192d0305e935cc2fbf9760a3fc2e07fe https://github.com/galaxyproject/galaxy/commit/5defdc79192d0305e935cc2fbf97… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Merge pull request #5364 from dannon/history_multipanel_fixes History multipanel fixes Compare: https://github.com/galaxyproject/galaxy/compare/377291232fd2...5defdc79192d

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[galaxyproject/galaxy] 3e63b6: add Phylip datatype
by GitHub 25 Jan '18

25 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3e63b63720c7c5b2fc672f1bfa9b66bb38851f54 https://github.com/galaxyproject/galaxy/commit/3e63b63720c7c5b2fc672f1bfa9b… Author: khillion <hillion.kenzo(a)gmail.com> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/phylip.py Log Message: ----------- add Phylip datatype Commit: f1fabffabfb61585c1e07f59e77b0abca5af5065 https://github.com/galaxyproject/galaxy/commit/f1fabffabfb61585c1e07f59e77b… Author: khillion <hillion.kenzo(a)gmail.com> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/datatypes/phylip.py Log Message: ----------- fix missing import Commit: c11b1a349e618ee2b062ace385254818b8767660 https://github.com/galaxyproject/galaxy/commit/c11b1a349e618ee2b062ace38525… Author: khillion <hillion.kenzo(a)gmail.com> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: M lib/galaxy/datatypes/phylip.py Log Message: ----------- fix with flake8 recommandation Commit: e7f82f8fefd54ee54933c0d40f534385a7b349a9 https://github.com/galaxyproject/galaxy/commit/e7f82f8fefd54ee54933c0d40f53… Author: khillion <kenzo-hugo.hillion1(a)pasteur.fr> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/datatypes/phylip.py Log Message: ----------- drop __init__ Commit: b649886eb83701c6b2729e7b3e776cee85de387f https://github.com/galaxyproject/galaxy/commit/b649886eb83701c6b2729e7b3e77… Author: khillion <kenzo-hugo.hillion1(a)pasteur.fr> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/phylip.py Log Message: ----------- fix datatypes_conf sniffer and code gardening Commit: 35469c122d609fe3076c8ef99b2681341ac8cd45 https://github.com/galaxyproject/galaxy/commit/35469c122d609fe3076c8ef99b26… Author: khillion <kenzo-hugo.hillion1(a)pasteur.fr> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/datatypes/phylip.py A lib/galaxy/datatypes/test/test.phylip Log Message: ----------- add example phylip and docstring test Commit: 12917d933edb53075102680bf9dadbf10510463d https://github.com/galaxyproject/galaxy/commit/12917d933edb53075102680bf9da… Author: khillion <kenzo-hugo.hillion1(a)pasteur.fr> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/datatypes/phylip.py Log Message: ----------- fix flake8 Commit: 2a49cb6e57479d57ebffde2c29f62cba3ec7c903 https://github.com/galaxyproject/galaxy/commit/2a49cb6e57479d57ebffde2c29f6… Author: khillion <kenzo-hugo.hillion1(a)pasteur.fr> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/datatypes/phylip.py Log Message: ----------- code gardening Commit: 3029ac3932eec10eb2c0233361ef30dadaf26af6 https://github.com/galaxyproject/galaxy/commit/3029ac3932eec10eb2c0233361ef… Author: khillion <kenzo-hugo.hillion1(a)pasteur.fr> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/datatypes/phylip.py Log Message: ----------- fix travis Commit: 377291232fd291fc250d7f5016b11d8ad97d9988 https://github.com/galaxyproject/galaxy/commit/377291232fd291fc250d7f5016b1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/phylip.py A lib/galaxy/datatypes/test/test.phylip Log Message: ----------- Merge pull request #5301 from khillion/dev add Phylip datatype Compare: https://github.com/galaxyproject/galaxy/compare/446f6430be31...377291232fd2

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[galaxyproject/galaxy] f594eb: Remove additional checkbox workarounds.
by GitHub 25 Jan '18

25 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f594eb23466eff7c6428c590eba70c9365c3fff6 https://github.com/galaxyproject/galaxy/commit/f594eb23466eff7c6428c590eba7… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako Log Message: ----------- Remove additional checkbox workarounds. Commit: 446f6430be3111e3e8ccd820974f16394ea38276 https://github.com/galaxyproject/galaxy/commit/446f6430be3111e3e8ccd820974f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako Log Message: ----------- Merge pull request #5367 from davebx/checkbox_fix Remove additional checkbox workarounds. Compare: https://github.com/galaxyproject/galaxy/compare/b24217c25b3d...446f6430be31

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galaxy-commits January 2018