Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: e06bf5a32052d6cf474cb5c3d195f632ffe8b9e4
https://github.com/galaxyproject/galaxy/commit/e06bf5a32052d6cf474cb5c3d195…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
Log Message:
-----------
Allow installation of different repositories with the same name in a single install transaction.
Commit: c6fbf987d2c4422eda793fa817f0ce83931d0119
https://github.com/galaxyproject/galaxy/commit/c6fbf987d2c4422eda793fa817f0…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
Log Message:
-----------
Whitespaces around operator.
Commit: 2c657b98e2945f48e1339f229e7de4de9f40fe4c
https://github.com/galaxyproject/galaxy/commit/2c657b98e2945f48e1339f229e7d…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
Log Message:
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Break out of loop once we know the repo is already in all_repo_info_dicts.
Commit: 9752fa76c54e927918560d474df4fbae6551d4ca
https://github.com/galaxyproject/galaxy/commit/9752fa76c54e927918560d474df4…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
Log Message:
-----------
Typo
Commit: cced5c3378937c14787884d91a613f56112ce7ff
https://github.com/galaxyproject/galaxy/commit/cced5c3378937c14787884d91a61…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
Log Message:
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Merge pull request #1366 from mvdbeek/fix_repository_install
Allow installation of different repositories with the same name in a …
Compare: https://github.com/galaxyproject/galaxy/compare/455372e6bf71...cced5c337893
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 61f64e828530c54bae6a090580a6e4278b32a699
https://github.com/galaxyproject/galaxy/commit/61f64e828530c54bae6a090580a6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-16 (Wed, 16 Dec 2015)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/parser/__init__.py
M lib/galaxy/tools/parser/output_actions.py
A lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/workflow/extract.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_evaluation.py
Log Message:
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Refactor tool output classes out of galaxy.tools and into parser module.
This makes the galaxy.tool.parser much more portable, it no longer has a dependency on anything in galaxy.tools or submodules except galaxy.tools.loader (which in turn has no dependencies on galaxy.tools or submodules).
Commit: 455372e6bf711d64947768f8b05418f8e6b49647
https://github.com/galaxyproject/galaxy/commit/455372e6bf711d64947768f8b054…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/parser/__init__.py
M lib/galaxy/tools/parser/output_actions.py
A lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/workflow/extract.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_evaluation.py
Log Message:
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Merge pull request #1353 from jmchilton/output_refactor
Refactor tool output classes out of galaxy.tools and into parser module.
Compare: https://github.com/galaxyproject/galaxy/compare/80a35c218416...455372e6bf71
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 50e531aa5971bee6f727ad0013b45c4a5d052fc9
https://github.com/galaxyproject/galaxy/commit/50e531aa5971bee6f727ad0013b4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-17 (Thu, 17 Dec 2015)
Changed paths:
R lib/galaxy/datatypes/checkers.py
M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
A lib/galaxy/util/checkers.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_util.py
M tools/data_source/upload.py
Log Message:
-----------
Refactor galaxy.datatypes.checkers into galaxy.util.checkers.
- Primary reason is because it is used all over the place in contexts that have nothing to do with Galaxy datatype classes or datatype registery or sniffing, most importantly by the code in the tool shed for determining if something is a tool or not.
- This code has no dependencies on the datatypes module or any hard dependencies on things not in the Python standard library.
Commit: 80a35c21841671907d326e4fb6cedb433389648d
https://github.com/galaxyproject/galaxy/commit/80a35c21841671907d326e4fb6ce…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
R lib/galaxy/datatypes/checkers.py
M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
A lib/galaxy/util/checkers.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_util.py
M tools/data_source/upload.py
Log Message:
-----------
Merge pull request #1363 from jmchilton/checkers_refactor
Refactor galaxy.datatypes.checkers into galaxy.util.checkers.
Compare: https://github.com/galaxyproject/galaxy/compare/e7f4ec9685f3...80a35c218416