Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c2897c211b1d9a3743171e3e9b05c235b79c50f7 https://github.com/galaxyproject/galaxy/commit/c2897c211b1d9a3743171e3e9b05c... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-06-20 (Tue, 20 Jun 2017)
Changed paths: M lib/galaxy/config.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/toolbox/lineages/stock.py R lib/galaxy/tools/toolbox/lineages/tool_shed.py A lib/galaxy/util/tool_version.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/tools/tool_version_manager.py M test/unit/tools/test_toolbox.py
Log Message: ----------- Replace ShedToolLineage with enhanced StockLineage
This means we don't rely on the Tool Shed metadata anymore and instead deduce the tool lineage via the tool_id, which contains the version. Version comparison then happens via LooseVersions. This works for toolshed and non-toolshed tools, restoring proper grouping in the tool panel and version switches, even for tool shed tools whose lineage is broken.
Commit: 0017d167f100f84df95967a05b0551250828f7a4 https://github.com/galaxyproject/galaxy/commit/0017d167f100f84df95967a05b055... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-06-20 (Tue, 20 Jun 2017)
Changed paths: M test/unit/shed_unit/test_tool_panel_manager.py
Log Message: ----------- Use correct tool version for ToolPanelManager.test_add_twice test to pass
Commit: db5d0095a6a426efcd587eca6808f350a6e126cf https://github.com/galaxyproject/galaxy/commit/db5d0095a6a426efcd587eca6808f... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-06-20 (Tue, 20 Jun 2017)
Changed paths: M test/unit/tools/test_toolbox.py
Log Message: ----------- Fix grouping tests by setting up correct versions
Commit: aabb933fdf69719adcb6fb9e9ba82d795a3b9b74 https://github.com/galaxyproject/galaxy/commit/aabb933fdf69719adcb6fb9e9ba82... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-06-20 (Tue, 20 Jun 2017)
Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/lineages/stock.py M test/unit/tools/test_toolbox.py
Log Message: ----------- Keep StockLineage versions sorted
Commit: 77e016bbbd5de566484d1c74c4f5679354edf360 https://github.com/galaxyproject/galaxy/commit/77e016bbbd5de566484d1c74c4f56... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-06-20 (Tue, 20 Jun 2017)
Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py
Log Message: ----------- Remove unused next/previous version methods
Commit: 6864187725b0af03e2196d12722f78f71d84977e https://github.com/galaxyproject/galaxy/commit/6864187725b0af03e2196d12722f7... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-06-20 (Tue, 20 Jun 2017)
Changed paths: M lib/galaxy/tools/__init__.py M test/unit/tools_support.py
Log Message: ----------- ToolVersion to StockLineage, drop ToolVersionCache
remnant from unittests (thx @nsoranzo!).
Commit: 81e73969dce5102dec799e3ca8b2a3056969f6a3 https://github.com/galaxyproject/galaxy/commit/81e73969dce5102dec799e3ca8b2a... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-06-22 (Thu, 22 Jun 2017)
Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/stock.py M lib/galaxy/util/tool_version.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
Log Message: ----------- Remove duplication between ToolLineage and TVM
Getting tool versions and tool ids is now done through the tool lineage. Also assume that the lineage can always be found for a given loaded tool in the ToolVersionListGrid class. Thanks @nsoranzo for these suggestions!
Commit: 0830ea2e4172e3be51ae081f9578c2c582f12a7e https://github.com/galaxyproject/galaxy/commit/0830ea2e4172e3be51ae081f9578c... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-06-22 (Thu, 22 Jun 2017)
Changed paths: M lib/galaxy/util/tool_version.py
Log Message: ----------- Remove unused `get_version_from_guid` function
Commit: db5e41c186d4c4b452ee4b7e83a0b26474d72873 https://github.com/galaxyproject/galaxy/commit/db5e41c186d4c4b452ee4b7e83a0b... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-06-22 (Thu, 22 Jun 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message: ----------- Remove unused tool_id variable
Commit: 0257248152db3edb493bfd4420f105a19000ae89 https://github.com/galaxyproject/galaxy/commit/0257248152db3edb493bfd4420f10... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-06-22 (Thu, 22 Jun 2017)
Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/interface.py R lib/galaxy/tools/toolbox/lineages/stock.py
Log Message: ----------- Rename StockLineage to ToolLineage and merge stock.py contents into interface.py
Commit: 68981c16cc708514e879941f152be9a60f7ad290 https://github.com/galaxyproject/galaxy/commit/68981c16cc708514e879941f152be... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-06-22 (Thu, 22 Jun 2017)
Changed paths: M lib/galaxy/tools/__init__.py
Log Message: ----------- Remove unused lineage_ids from Tool class
Commit: e9658e8adb5d0bf0f8db42faa4d14cb50d4c90ce https://github.com/galaxyproject/galaxy/commit/e9658e8adb5d0bf0f8db42faa4d14... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-06-22 (Thu, 22 Jun 2017)
Changed paths: M lib/galaxy/tools/toolbox/lineages/factory.py
Log Message: ----------- Clarify when and why tool version is being registered
Commit: 41d739bdb4d1ac622fb7fd78f8b3dbc9acd978ad https://github.com/galaxyproject/galaxy/commit/41d739bdb4d1ac622fb7fd78f8b3d... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-06-23 (Fri, 23 Jun 2017)
Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
Log Message: ----------- Move tool.tool_version to tool.lineage
This change makes it obvious that a Lineage object will be returned.
Also removes two unused methods from ToolLineageVersion.
Commit: 84e0e7e01e732b28dedebdf8a3fbea8225fece9a https://github.com/galaxyproject/galaxy/commit/84e0e7e01e732b28dedebdf8a3fbe... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-06-24 (Sat, 24 Jun 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
Log Message: ----------- Access tool.lineage only if tool was loaded
Commit: a42abc03e0b018546137471f302e28a39f3f7b2b https://github.com/galaxyproject/galaxy/commit/a42abc03e0b018546137471f302e2... Author: John Chilton jmchilton@gmail.com Date: 2017-07-05 (Wed, 05 Jul 2017)
Changed paths: M lib/galaxy/config.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/interface.py R lib/galaxy/tools/toolbox/lineages/stock.py R lib/galaxy/tools/toolbox/lineages/tool_shed.py A lib/galaxy/util/tool_version.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/tools/tool_version_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py
Log Message: ----------- Merge pull request #4119 from mvdbeek/version_switch_fix
Merge ShedToolLineage and StockLineage to ToolLineage
Compare: https://github.com/galaxyproject/galaxy/compare/516f7bff63fe...a42abc03e0b0