Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9b4d955853452856fffd5204c8242e077b1e15b1 https://github.com/galaxyproject/galaxy/commit/9b4d955853452856fffd5204c8242... Author: Nicola Soranzo <nicola.soranzo@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/7d71d986757b22f954c593084248f... Author: Nicola Soranzo <nicola.soranzo@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/e950579bf25dcf564a2b7be3bba56... Author: Nicola Soranzo <nicola.soranzo@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/19bd8e0dffcafb09a65981b6cf009... Author: Nicola Soranzo <nicola.soranzo@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/721a4656d941a5462a4db046d192e... Author: Nicola Soranzo <nicola.soranzo@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/0c931235af8e74dba10b4f7489202... Author: Nicola Soranzo <nicola.soranzo@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/4ebfad7526701c14b03ed3b381cc4... Author: John Chilton <jmchilton@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.