Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1de0ef437b32619a06b23411d26520e89793877b https://github.com/galaxyproject/galaxy/commit/1de0ef437b32619a06b23411d2652... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/dictifiable.py M lib/galaxy/util/handlers.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/galaxy_install/migrate/common.py M test/unit/jobs/test_mapper.py Log Message: ----------- Fix MRO issues Make Mixins new style classes Commit: d3895db861a003206dce0be833174493923dcc23 https://github.com/galaxyproject/galaxy/commit/d3895db861a003206dce0be833174... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Python3: dict_keys doesn't support indexing Commit: 15cd09d2c5e73e8721c9369bee518d68da3c8e44 https://github.com/galaxyproject/galaxy/commit/15cd09d2c5e73e8721c9369bee518... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Use newer psycopg2 library Commit: 31ec21d89fb91c00f368a46fe071d250a108c26f https://github.com/galaxyproject/galaxy/commit/31ec21d89fb91c00f368a46fe071d... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Switch to Cheetah3 Commit: 326f743d3a5582fe6f3c6c78a1f1d7cb6331c9b7 https://github.com/galaxyproject/galaxy/commit/326f743d3a5582fe6f3c6c78a1f1d... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Write integrated tool panel xml in one go Commit: fb9ebf980923858a1a4cbeb588d22a2b9820ff9a https://github.com/galaxyproject/galaxy/commit/fb9ebf980923858a1a4cbeb588d22... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Switch to Fabric3 for py2/3 support Commit: 00526c9928c3e1fdbdfe0f70d02549b632b82ef7 https://github.com/galaxyproject/galaxy/commit/00526c9928c3e1fdbdfe0f70d0254... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/configuration.py Log Message: ----------- Python3 fixes Commit: 973bfbafb980cfd15b545b2b0b4d873440bf1203 https://github.com/galaxyproject/galaxy/commit/973bfbafb980cfd15b545b2b0b4d8... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/web/security/__init__.py Log Message: ----------- Use Crypto's get_random_bytes instead of rolling our own Commit: fbd33a57e0033a1547c3bf6f9812dd574cdb36d2 https://github.com/galaxyproject/galaxy/commit/fbd33a57e0033a1547c3bf6f9812d... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/web/framework/helpers/__init__.py Log Message: ----------- Remove dependency on WebHelpers Workaround babel bug when locale is not set Commit: e87d1aa79d84a08721d76ae2b6cb234351b6356b https://github.com/galaxyproject/galaxy/commit/e87d1aa79d84a08721d76ae2b6cb2... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M .ci/jenkins/selenium-compose/run_tests.sh M config/galaxy.yml.sample M config/tool_shed.yml.sample M doc/Makefile M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml M scripts/common_startup.sh M test/manual/launch_and_run.sh Log Message: ----------- More Python3 print function fixes Commit: 6f6a671d36ff4f7ebe258c04aef6155384a4736e https://github.com/galaxyproject/galaxy/commit/6f6a671d36ff4f7ebe258c04aef61... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/security/__init__.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Make id encoding/decoding py3 compatible Commit: 0ce2d97c4dd65e5b2827c29dfa0aece4e6432666 https://github.com/galaxyproject/galaxy/commit/0ce2d97c4dd65e5b2827c29dfa0ae... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Create the virtualenv using the python that passed check_python This will make it easier to support Python3. Commit: 792a07148915ccc94d44f415db206e53addb12db https://github.com/galaxyproject/galaxy/commit/792a07148915ccc94d44f415db206... Author: John Chilton <jmchilton@gmail.com> Date: 2018-01-26 (Fri, 26 Jan 2018) Changed paths: M .ci/jenkins/selenium-compose/run_tests.sh M config/galaxy.yml.sample M config/tool_shed.yml.sample M doc/Makefile M doc/source/admin/galaxy_options.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/configuration.py M lib/galaxy/model/__init__.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/dictifiable.py M lib/galaxy/util/handlers.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/galaxy_install/migrate/common.py M scripts/common_startup.sh M test/manual/launch_and_run.sh M test/unit/jobs/test_mapper.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge pull request #5359 from mvdbeek/py3_fixes Various Python3 related fixes Compare: https://github.com/galaxyproject/galaxy/compare/046cb8f35956...792a07148915