- galaxy-commits - lists.galaxyproject.org

[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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[galaxyproject/galaxy] 9b4d95: Remove deprecated `decode_param_names` parameter
by GitHub 17 Sep '18

17 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9b4d955853452856fffd5204c8242e077b1e15b1 https://github.com/galaxyproject/galaxy/commit/9b4d955853452856fffd5204c824… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-17 (Mon, 17 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: 7d71d986757b22f954c593084248f400086172d9 https://github.com/galaxyproject/galaxy/commit/7d71d986757b22f954c593084248… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-17 (Mon, 17 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: e950579bf25dcf564a2b7be3bba568af6a27055e https://github.com/galaxyproject/galaxy/commit/e950579bf25dcf564a2b7be3bba5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-17 (Mon, 17 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: 19bd8e0dffcafb09a65981b6cf00913fd09f3fd8 https://github.com/galaxyproject/galaxy/commit/19bd8e0dffcafb09a65981b6cf00… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M test/unit/tools/test_evaluation.py Log Message: ----------- Fix typos Commit: 721a4656d941a5462a4db046d192ef81cd1a23c1 https://github.com/galaxyproject/galaxy/commit/721a4656d941a5462a4db046d192… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-17 (Mon, 17 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: 0c931235af8e74dba10b4f748920219425cb2baa https://github.com/galaxyproject/galaxy/commit/0c931235af8e74dba10b4f748920… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M contrib/nagios/check_galaxy.py M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/streamball.py M scripts/api/library_upload_dir.py M scripts/apply_tags.py M scripts/check_galaxy.py M scripts/grt/export.py M scripts/microbes/util.py M test/base/api.py M test/base/populators.py M test/galaxy_selenium/has_driver.py M test/integration/test_job_environments.py M test/selenium_tests/framework.py M tools/filters/join.py M tools/filters/sff_extract.py M tools/phenotype_association/senatag.py M tools/stats/aggregate_scores_in_intervals.py Log Message: ----------- Change all remaining old-style classes to new style Commit: 4ebfad7526701c14b03ed3b381cc419316754f0e https://github.com/galaxyproject/galaxy/commit/4ebfad7526701c14b03ed3b381cc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M contrib/nagios/check_galaxy.py M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/streamball.py M lib/galaxy/util/xml_macros.py M lib/galaxy/web/framework/base.py M pytest.ini M scripts/api/library_upload_dir.py M scripts/apply_tags.py M scripts/check_galaxy.py M scripts/grt/export.py M scripts/loc_files/create_all_fasta_loc.py M scripts/microbes/util.py M test/base/api.py M test/base/populators.py M test/galaxy_selenium/has_driver.py M test/integration/test_job_environments.py M test/selenium_tests/framework.py M test/unit/tools/test_evaluation.py M tools/filters/join.py M tools/filters/sff_extract.py M tools/phenotype_association/senatag.py M tools/stats/aggregate_scores_in_intervals.py Log Message: ----------- Merge pull request #6722 from nsoranzo/fix_warnings Small mixed fixes Compare: https://github.com/galaxyproject/galaxy/compare/33cac64546a7...4ebfad752670 **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] df4fbe: Swap badge-default to badge-primary
by GitHub 17 Sep '18

17 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: df4fbe6b92457fa910f014bbd3a8dd84c25d3969 https://github.com/galaxyproject/galaxy/commit/df4fbe6b92457fa910f014bbd3a8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js Log Message: ----------- Swap badge-default to badge-primary Commit: b2193bddc2aea250a189171ae61ed992b0449c84 https://github.com/galaxyproject/galaxy/commit/b2193bddc2aea250a189171ae61e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/docs/bootstrap.md Log Message: ----------- Drop badge-default from docs, correctly refer to secondary. Commit: a9273218424c1687bedf112591f2bbf735d32aa8 https://github.com/galaxyproject/galaxy/commit/a9273218424c1687bedf112591f2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Client format. Commit: 0040c36d4561155af3f32262d186e186349d989d https://github.com/galaxyproject/galaxy/commit/0040c36d4561155af3f32262d186… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/docs/bootstrap.md M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #6726 from dannon/badge-default-fix [18.09] Badge default fix Compare: https://github.com/galaxyproject/galaxy/compare/32223161c7ca...0040c36d4561 **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] 976945: Update testtoolshed to 32223161c7ca735647d53ebfe4b...
by GitHub 17 Sep '18

17 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9769456df32ae829570ce5618143e0a18a7b493d https://github.com/galaxyproject/usegalaxy-playbook/commit/9769456df32ae829… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update testtoolshed to 32223161c7ca735647d53ebfe4b90f1cd4051051 **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] 7e2a77: Catch additional permutations of Slurm cgroup crea...
by GitHub 14 Sep '18

14 Sep '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 7e2a77e8af152a501f124a6d0f702a66502e0dd3 https://github.com/galaxyproject/galaxy/commit/7e2a77e8af152a501f124a6d0f70… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Catch additional permutations of Slurm cgroup creation warnings Commit: 3d508a01d3d58908b667e428f125df91d8c599c1 https://github.com/galaxyproject/galaxy/commit/3d508a01d3d58908b667e428f125… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Improvements from @nsoranzo Commit: 6993dbb6fcd112e077fbad66deae716a53247d07 https://github.com/galaxyproject/galaxy/commit/6993dbb6fcd112e077fbad66deae… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #6705 from natefoo/slurm-cgroup-enospc [18.05] Catch additional permutations of Slurm cgroup creation warnings Compare: https://github.com/galaxyproject/galaxy/compare/f513594c31a3...6993dbb6fcd1 **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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