September 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 1d4643: Update toolshed to 0974b130ef922e3177de27f6365ccd6...
by GitHub 18 Sep '18

18 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1d46435f76e456cee6ea1cd352a6e6cd01e12f92 https://github.com/galaxyproject/usegalaxy-playbook/commit/1d46435f76e456ce… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M env/toolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update toolshed to 0974b130ef922e3177de27f6365ccd624bf194a7 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 402506: Update testtoolshed to 0974b130ef922e3177de27f6365...
by GitHub 18 Sep '18

18 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 40250611b8876512c25c52a84aa01e006ec8fd87 https://github.com/galaxyproject/usegalaxy-playbook/commit/40250611b8876512… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update testtoolshed to 0974b130ef922e3177de27f6365ccd624bf194a7 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 6233a4: Release notes templated; still needs manual curati...
by GitHub 18 Sep '18

18 Sep '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: 6233a408cc93152a379651db3cc143d368f78dda https://github.com/galaxyproject/galaxy/commit/6233a408cc93152a379651db3cc1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: A doc/source/releases/18.09.rst A doc/source/releases/18.09_announce.rst A doc/source/releases/19.01_announce.rst Log Message: ----------- Release notes templated; still needs manual curation **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 54d137: Remove deprecated `decode_param_names` parameter
by GitHub 18 Sep '18

18 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 54d137edab3fb33beac87c23cd35fb19dd7f44fa https://github.com/galaxyproject/galaxy/commit/54d137edab3fb33beac87c23cd35… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Remove deprecated `decode_param_names` parameter It has been deprecated since WebOb 1.1 and ignored since WebOb 1.2 . Commit: 8ed19a3a09df9b66266f66bc53e504c781ae524d https://github.com/galaxyproject/galaxy/commit/8ed19a3a09df9b66266f66bc53e5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/verify/interactor.py Log Message: ----------- `async` is a reserved keyword in Python 3.7 - Remove unused `async` parameter of `stage_data_async()` method. - Rename `async` parameter of `quick_load()` method. Fix https://github.com/galaxyproject/galaxy/issues/6717 . xref. https://github.com/galaxyproject/galaxy/issues/1715 Commit: 8982212d396c1ab216c5c9ea0656e5231e05d745 https://github.com/galaxyproject/galaxy/commit/8982212d396c1ab216c5c9ea0656… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/util/xml_macros.py M scripts/loc_files/create_all_fasta_loc.py Log Message: ----------- Replace deprecated `xml.etree.ElementTree.Element.getiterator()` with `iter()` Commit: f0708488aa08393cfdf3ab3e0e45e37982d050d0 https://github.com/galaxyproject/galaxy/commit/f0708488aa08393cfdf3ab3e0e45… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M pytest.ini Log Message: ----------- pytest: disable test collection of classes starting with `Test` Fix warnings like: ``` /home/travis/build/galaxyproject/galaxy/lib/galaxy/tools/verify/test_data.py:29: PytestWarning: cannot collect test class 'TestDataResolver' because it has a __init__ constructor class TestDataResolver(object): ``` appearing e.g. in https://travis-ci.org/galaxyproject/galaxy/jobs/428114139 . See pytest documentation: https://docs.pytest.org/en/latest/reference.html#confval-python_classes Commit: 0974b130ef922e3177de27f6365ccd624bf194a7 https://github.com/galaxyproject/galaxy/commit/0974b130ef922e3177de27f6365c… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/util/xml_macros.py M lib/galaxy/web/framework/base.py M pytest.ini M scripts/loc_files/create_all_fasta_loc.py Log Message: ----------- Merge pull request #6730 from nsoranzo/release_18.09_backport_6722 [18.09] Partial backport of #6722 Compare: https://github.com/galaxyproject/galaxy/compare/2874e87debcc...0974b130ef92 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 072d40: remove html tags and newlines from the help text
by GitHub 18 Sep '18

18 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 072d40f3e9a9050f034f440b76c8b84536bc0ead https://github.com/galaxyproject/galaxy/commit/072d40f3e9a9050f034f440b76c8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- remove html tags and newlines from the help text this should improve the toolsearch for certain keywords and also make the search index smaller Commit: b7f16228575215c9be134d1bbc1cf9e37b700488 https://github.com/galaxyproject/galaxy/commit/b7f16228575215c9be134d1bbc1c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- replace the replacement for newline from empty string to space, that should avoid unwanted word merges Commit: 17d67e24c072c8953e482aff41e9b1faed78b4d3 https://github.com/galaxyproject/galaxy/commit/17d67e24c072c8953e482aff41e9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- use bleach isntead of custom regex thanks @nsoranzo Commit: 2874e87debcc1940e1f1143a7af4dacb38c95585 https://github.com/galaxyproject/galaxy/commit/2874e87debcc1940e1f1143a7af4… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- Merge pull request #6728 from martenson/fix-toolhelp-parsing [18.09] remove html tags and newlines from the help text Compare: https://github.com/galaxyproject/galaxy/compare/0040c36d4561...2874e87debcc **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 3c0963: Update id_secret
by GitHub 17 Sep '18

17 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3c0963f0c742b21e391ff7bcc4365f82a3e9180f https://github.com/galaxyproject/usegalaxy-playbook/commit/3c0963f0c742b21e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M env/main/group_vars/galaxyservers/vault.yml Log Message: ----------- Update id_secret **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 398cf6: Update Galaxy to version 19.01.dev commit e049786c...
by GitHub 17 Sep '18

17 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 398cf62fef15ddf558c0e7b3c54f624217337d7e https://github.com/galaxyproject/usegalaxy-playbook/commit/398cf62fef15ddf5… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Galaxy to version 19.01.dev commit e049786c4c7540870042c096d5f70d796d448f92 via Ansible Commit: c03534c9f853be2d2432281e2de803bbe33d3232 https://github.com/galaxyproject/usegalaxy-playbook/commit/c03534c9f853be2d… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Log Message: ----------- Merge earlier update Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/847e8e2e8a8c...… **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 847e8e: Update Test
by GitHub 17 Sep '18

17 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 847e8e2e8a8c9b5f79a0eb71a2523c977e937dcc https://github.com/galaxyproject/usegalaxy-playbook/commit/847e8e2e8a8c9b5f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] e04978: Merge pull request #6703 from davebx/updates_api
by GitHub 17 Sep '18

17 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e049786c4c7540870042c096d5f70d796d448f92 https://github.com/galaxyproject/galaxy/commit/e049786c4c7540870042c096d5f7… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #6703 from davebx/updates_api [18.05] Add missing route for API endpoint. **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 04a75b: Change default prompt option for Google OIDC IdP.
by GitHub 17 Sep '18

17 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 04a75bd33bb0c9f251169d44a36d4ce905f4c454 https://github.com/galaxyproject/galaxy/commit/04a75bd33bb0c9f251169d44a36d… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M config/oidc_backends_config.xml.sample Log Message: ----------- Change default prompt option for Google OIDC IdP. Commit: 56fb283d9b366d9d1224e0402409d31e011057db https://github.com/galaxyproject/galaxy/commit/56fb283d9b366d9d1224e0402409… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M config/oidc_backends_config.xml.sample Log Message: ----------- Add a comment on why user does not see a consent screen with Google. Commit: 5a784890de81c9a0408ddea6623ed51a0ff761aa https://github.com/galaxyproject/galaxy/commit/5a784890de81c9a0408ddea6623e… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M config/oidc_backends_config.xml.sample Log Message: ----------- Update a comment in the default config of OIDC backends. Commit: e080babaadf81e2675f4d263c8a47bd55a15762e https://github.com/galaxyproject/galaxy/commit/e080babaadf81e2675f4d263c8a4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M config/oidc_backends_config.xml.sample Log Message: ----------- Merge pull request #6727 from VJalili/oidc_consent Updates to OIDC backends default config Compare: https://github.com/galaxyproject/galaxy/compare/4ebfad752670...e080babaadf8 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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