Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bc50c14490e4f81144e5bc59f76e6abe2d93a8fa https://github.com/galaxyproject/galaxy/commit/bc50c14490e4f81144e5bc59f76e6... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/tool_shed/util/xml_util.py Log Message: ----------- Drop py26 XML parsing variant Commit: 49872e7612070df9aee607897fb4cf5cb9cb2242 https://github.com/galaxyproject/galaxy/commit/49872e7612070df9aee607897fb4c... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/util/logging/__init__.py M lib/galaxy/web/stack/message.py Log Message: ----------- Use six.create_bound_method() instead of types.MethodType() On Python2 the MethodType constructor requires the object's class to be passed. Commit: f43a3268b11841f65d3de195611bc6b0a940544c https://github.com/galaxyproject/galaxy/commit/f43a3268b11841f65d3de195611bc... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py M templates/webapps/galaxy/dataset/security_common.mako Log Message: ----------- Use builtin set Commit: 39104af3b42e6d253391a9b73f6912cf4423e783 https://github.com/galaxyproject/galaxy/commit/39104af3b42e6d253391a9b73f691... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Define file_types instead of types.FileType and pull up TarFile Commit: 046f3265dd50ec6ff53470a96a4dfdb0193d7c17 https://github.com/galaxyproject/galaxy/commit/046f3265dd50ec6ff53470a96a4df... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/model/custom_types.py Log Message: ----------- Fix loading custom JSONType Commit: 0be36ef4fce3b50bec37d199af2a404f3372ed65 https://github.com/galaxyproject/galaxy/commit/0be36ef4fce3b50bec37d199af2a4... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Use string.ascii_letters instead of string.letters for Py2/3 compat Update <sanitizer> documentation. Commit: 553d165087335528892232b17706b398bb3bf941 https://github.com/galaxyproject/galaxy/commit/553d165087335528892232b17706b... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M templates/galaxy_client_app.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/tool_shed/repository/tool_form.mako Log Message: ----------- Python3 exception syntax fixes in templates/ Commit: 52586fcca2ef6ef6926fcd25b6c6f1b9ed598a6e https://github.com/galaxyproject/galaxy/commit/52586fcca2ef6ef6926fcd25b6c6f... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/datatypes/phylip.py Log Message: ----------- Fix relative import to be Python3-compatible Commit: 386526d928be1de57268163db1814640baa13459 https://github.com/galaxyproject/galaxy/commit/386526d928be1de57268163db1814... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Replace distutils.version with packaging.version distutils under Python3 has this bug: https://bugs.python.org/issue14894 which causes this traceback: ``` Traceback (most recent call last): File "lib/galaxy/webapps/galaxy/buildapp.py", line 49, in app_factory app = galaxy.app.UniverseApplication(global_conf=global_conf, **kwargs) File "lib/galaxy/app.py", line 125, in __init__ self._configure_toolbox() File "lib/galaxy/config.py", line 930, in _configure_toolbox self.toolbox = tools.ToolBox(tool_configs, self.config.tool_path, self) File "lib/galaxy/tools/__init__.py", line 232, in __init__ app=app, File "lib/galaxy/tools/toolbox/base.py", line 1056, in __init__ super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app) File "lib/galaxy/tools/toolbox/base.py", line 84, in __init__ self._load_tool_panel() File "lib/galaxy/tools/toolbox/base.py", line 358, in _load_tool_panel self.__add_tool_to_tool_panel(section_val, section, section=True) File "lib/galaxy/tools/toolbox/base.py", line 278, in __add_tool_to_tool_panel related_tool = self._lineage_in_panel(panel_dict, tool=tool) File "lib/galaxy/tools/toolbox/base.py", line 961, in _lineage_in_panel lineage_tool_versions = reversed(tool_lineage.get_versions()) File "lib/galaxy/tools/toolbox/lineages/interface.py", line 77, in get_versions return [ToolLineageVersion(tool_id, tool_version) for tool_id, tool_version in zip(self.tool_ids, self.tool_versions)] File "lib/galaxy/tools/toolbox/lineages/interface.py", line 55, in tool_ids return ["%s/%s" % (tool_id, version) for version in self.tool_versions] File "lib/galaxy/tools/toolbox/lineages/interface.py", line 49, in tool_versions return sorted(self._tool_versions, key=LooseVersion) File "/usr/lib/python3.4/distutils/version.py", line 58, in __lt__ c = self._cmp(other) File "/usr/lib/python3.4/distutils/version.py", line 343, in _cmp if self.version < other.version: TypeError: unorderable types: str() < int() ``` when a tool version contains a letter in the "wrong" place (e.g. in the first position). Fix https://github.com/galaxyproject/galaxy/issues/5408 . Commit: 988cab4db7ef83714cf6f0c57f73f4255e3f075d https://github.com/galaxyproject/galaxy/commit/988cab4db7ef83714cf6f0c57f73f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/phylip.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/model/custom_types.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/logging/__init__.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/stack/message.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/tool_shed/util/xml_util.py M templates/galaxy_client_app.mako M templates/webapps/galaxy/dataset/security_common.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/tool_shed/repository/tool_form.mako Log Message: ----------- Merge pull request #5422 from nsoranzo/python3 Mixed Python3 fixes Compare: https://github.com/galaxyproject/galaxy/compare/5a31ac84ce12...988cab4db7ef