Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 364f383ca8a3448e3cffa436acc0bf58d7895274 https://github.com/galaxyproject/galaxy/commit/364f383ca8a3448e3cffa436acc0b... Author: John Chilton <jmchilton@gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py A lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/__init__.py M lib/galaxy/tools/linters/citations.py M lib/galaxy/tools/linters/command.py A lib/galaxy/tools/linters/general.py M lib/galaxy/tools/linters/help.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/outputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py R lib/galaxy/tools/linters/top_level.py M lib/galaxy/tools/linters/xml_order.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/xml.py Log Message: ----------- Enhance library functions for tools. - Enhance lint and loaders to be able to handle tool parser objects instead of just raw XML. This will allow non-Galaxy-XML tool linting (e.g. CWL) and allow linters to use higher-level abstraction. - Rework CWL tool loading to allow more fine-grain loading. - Replace tol-level XML linter with a "general" linter that parses attributes using the ToolSource abstraction. - Small updates to linting for recent additions to tool framework. - More docstring usage and improved import order. - Fixes discovered through planemo for "finding" non-XML tools. Commit: e477504a8e371443da49f64139c27d037fa3b1d7 https://github.com/galaxyproject/galaxy/commit/e477504a8e371443da49f64139c27... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/help.py M lib/galaxy/tools/linters/xml_order.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parser/factory.py Log Message: ----------- Misc fixes to #2279 Commit: 49a4f352d148d126c3f428763288874d6d55cf37 https://github.com/galaxyproject/galaxy/commit/49a4f352d148d126c3f4287632888... Author: John Chilton <jmchilton@gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/help.py M lib/galaxy/tools/linters/xml_order.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parser/factory.py Log Message: ----------- Merge pull request #47 from dannon/lint_16.04 Misc fixes to #2279 Commit: 5ff1693dd4da53550401ae1b1f8b40338bd79706 https://github.com/galaxyproject/galaxy/commit/5ff1693dd4da53550401ae1b1f8b4... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py A lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/__init__.py M lib/galaxy/tools/linters/citations.py M lib/galaxy/tools/linters/command.py A lib/galaxy/tools/linters/general.py M lib/galaxy/tools/linters/help.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/outputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py R lib/galaxy/tools/linters/top_level.py M lib/galaxy/tools/linters/xml_order.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/xml.py Log Message: ----------- Merge pull request #2279 from jmchilton/lint_16.04 Enhance library functions for tools. Compare: https://github.com/galaxyproject/galaxy/compare/2df8edf6b149...5ff1693dd4da