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

[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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[galaxyproject/usegalaxy-playbook] e10fcb: Update Main mutable configs
by GitHub 14 Sep '18

14 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e10fcb013f465822884f26bd8466302b56203082 https://github.com/galaxyproject/usegalaxy-playbook/commit/e10fcb013f465822… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Update Main mutable configs **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] b4b49d: Add self help to error reporting interface.
by GitHub 14 Sep '18

14 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: b4b49dc2028da2064fd34d7345b23b47150a1039 https://github.com/galaxyproject/galaxy/commit/b4b49dc2028da2064fd34d7345b2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js Log Message: ----------- Add self help to error reporting interface. Commit: 88bf3435775e94217bccfc46a5215311dea321aa https://github.com/galaxyproject/galaxy/commit/88bf3435775e94217bccfc46a521… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js Log Message: ----------- Import Backbone consistently across the app Commit: 84d66bea6008dc534aa6a2331e824005b204da19 https://github.com/galaxyproject/galaxy/commit/84d66bea6008dc534aa6a2331e82… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js Log Message: ----------- h2!=h3 Commit: 32223161c7ca735647d53ebfe4b90f1cd4051051 https://github.com/galaxyproject/galaxy/commit/32223161c7ca735647d53ebfe4b9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js Log Message: ----------- Merge pull request #6711 from dannon/error_help [18.09] Add self help to error reporting interface Compare: https://github.com/galaxyproject/galaxy/compare/9657cd6b32ed...32223161c7ca **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] f7c1d3: unquote the tool_version in the tools API
by GitHub 14 Sep '18

14 Sep '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: f7c1d31dbc6f23eb4fba37b82aeb2808fd69224f https://github.com/galaxyproject/galaxy/commit/f7c1d31dbc6f23eb4fba37b82aeb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- unquote the tool_version in the tools API if the tool version includes '+', which is a recommended way of versioning per https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_x… this would fail the comparison down the line in the toolbox.get_tool() method this commit also downgrades the unquote_plus to unquote for tool_id for similar reasons since it also contains the version Commit: 1b6d422afdd0c1f7291a0999bfc54284b90972d2 https://github.com/galaxyproject/galaxy/commit/1b6d422afdd0c1f7291a0999bfc5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- unquote similarly to previous commit but in the workflow controller Commit: f513594c31a3738420889b3f5e36d39796946587 https://github.com/galaxyproject/galaxy/commit/f513594c31a3738420889b3f5e36… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #6707 from martenson/unqoute_tool_version [18.05] unquote the tool_version in the tools API Compare: https://github.com/galaxyproject/galaxy/compare/1dacc35332cf...f513594c31a3 **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] 17d148: Use tool_version instead of version parameter
by GitHub 13 Sep '18

13 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 17d148eb8f40ed6f7046ad628e1bdcfbaa80f4bb https://github.com/galaxyproject/galaxy/commit/17d148eb8f40ed6f7046ad628e1b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py Log Message: ----------- Use tool_version instead of version parameter To be consistent with other routes that accept this parameter. Commit: 33cac64546a7ef7b04f65196b0ce919ad8f94d93 https://github.com/galaxyproject/galaxy/commit/33cac64546a7ef7b04f65196b0ce… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py Log Message: ----------- Merge pull request #6710 from mvdbeek/change_version_parameter_to_tool_version Use tool_version instead of version parameter Compare: https://github.com/galaxyproject/galaxy/compare/d1352c4b274a...33cac64546a7 **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] 943e67: Test that newest version will be returned if tool ...
by GitHub 13 Sep '18

13 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 943e67e4e59beea726912dc013a30903827f6277 https://github.com/galaxyproject/galaxy/commit/943e67e4e59beea726912dc013a3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py Log Message: ----------- Test that newest version will be returned if tool id or version don't match Commit: 5de1c2c980343d031b81bbc16fcde43ee4909c60 https://github.com/galaxyproject/galaxy/commit/5de1c2c980343d031b81bbc16fcd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Unit test that fails if we don't return the latest version upon version mismatch Commit: f8430b110dccfe53f347757d2284b4329218cec4 https://github.com/galaxyproject/galaxy/commit/f8430b110dccfe53f347757d2284… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Sort by tool version when picking a tool with an unavailable version Commit: 56ed50400f94a04e88c3a6a09721903d571dc969 https://github.com/galaxyproject/galaxy/commit/56ed50400f94a04e88c3a6a09721… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Sort rval so that newest tool appears last in rval Commit: d1352c4b274a91722e55dae634a332803b8fdc6e https://github.com/galaxyproject/galaxy/commit/d1352c4b274a91722e55dae634a3… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #6702 from mvdbeek/fix_latest_version Fix wrong version being returned if requested version doesn't exist Compare: https://github.com/galaxyproject/galaxy/compare/5286a1e757de...d1352c4b274a **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] ed28cd: Update galaxy to 1dacc35332cf956ed5631fe8c6fa8e231...
by GitHub 12 Sep '18

12 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ed28cdc622c6a9552dc0d6bc11320afe1640b8a4 https://github.com/galaxyproject/usegalaxy-playbook/commit/ed28cdc622c6a955… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update galaxy to 1dacc35332cf956ed5631fe8c6fa8e231dab663e via Ansible. **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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