Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: fe87cd889f2bdab122fccd0db99aa31af864d1db https://github.com/galaxyproject/galaxy/commit/fe87cd889f2bdab122fccd0db99aa... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-01-27 (Fri, 27 Jan 2017)

Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py

Log Message: ----------- Allow mapping requirements with version None to a specific version (so that all-in-one dependency resolution is applied)

but do not match a specific requirement (i.e samtools 0.1.19) when mapping ``` - from: name: samtools version: None to: name: samtools version: 1.3.1 ``` This will only map samtools requirements that do not specify a version. If you want to override a specifically requested version, you need to include that version, i.e ``` - from: name: samtools version: None to: name: samtools version: 1.3.1 - from: name: samtools version: 0.1.19 to: name: samtools version: 1.2 ```

Commit: d3093013f95a4a0d324213f6ab4461f6d196d1fd https://github.com/galaxyproject/galaxy/commit/d3093013f95a4a0d324213f6ab446... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-01-27 (Fri, 27 Jan 2017)

Changed paths: M config/local_conda_mapping.yml.sample

Log Message: ----------- Extend default mapping

Commit: 44a90033dbe1c635e37952711e28de1016ee1090 https://github.com/galaxyproject/galaxy/commit/44a90033dbe1c635e37952711e28d... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-01-27 (Fri, 27 Jan 2017)

Changed paths: M config/local_conda_mapping.yml.sample

Log Message: ----------- Use Null instead of None

to get the non-string None value. str(from_raw.get(version)) will turn it into 'None' anyway.

Commit: b92e9b509354a570424da4b1ff86a5f75bba585a https://github.com/galaxyproject/galaxy/commit/b92e9b509354a570424da4b1ff86a... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-01-27 (Fri, 27 Jan 2017)

Changed paths: M test/unit/tools/test_tool_deps.py

Log Message: ----------- Add unit tests that asserts new dependency mapping rules

Commit: a30d6dfa2090096975ca614a85cde53ae9c948bb https://github.com/galaxyproject/galaxy/commit/a30d6dfa2090096975ca614a85cde... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-01-29 (Sun, 29 Jan 2017)

Changed paths: M config/local_conda_mapping.yml.sample

Log Message: ----------- Drop openbabel mapping from 2.32 to 2.4.1 (thx @bgruening)

Commit: 14529b9dd56b45afe6d06babf88eb6a164c517e5 https://github.com/galaxyproject/galaxy/commit/14529b9dd56b45afe6d06babf88eb... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-01-29 (Sun, 29 Jan 2017)

Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py

Log Message: ----------- Collapse list of tool requirements after mapping

With this change, the merged environment name for requirements that have been specified using multiple names (e.g. sickle (for TS) and sickle-trim (conda/docker)) will be sickle-trim if mapping sickle to sickle-trim (instead of mulled-v1-<hash>).

Commit: 6ba0291eea85723514a7a983f009e4033f660ea0 https://github.com/galaxyproject/galaxy/commit/6ba0291eea85723514a7a983f009e... Author: John Chilton jmchilton@gmail.com Date: 2017-01-30 (Mon, 30 Jan 2017)

Changed paths: M config/local_conda_mapping.yml.sample M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml M test/unit/tools/test_tool_deps.py

Log Message: ----------- Modify representation of mapping to None. (#4)

I feel that mapping from

``` - from: blast+ to: blast ```

should be the same as

``` - from: name: blast+ version: Null to: blast ```

since it should just be syntatic sugar. And I think that second version reads like it should by default apply to all versions.

I feel therefore it is probably better to explicitly require stating that a mapping only applies to unversioned requirements. This commit does that by introducing the syntax:

``` - from: name: blast+ unversioned: true to: name: blast version: 1.3.4 ```

It feels better to have strongly typed entities like this than to introduce magic constants such as:

``` - from: name: blast+ version: __unversioned__ to: name: blast version: 1.3.4 ```

which is another route this could have gone I guess.

Commit: ea7e1cc945cb529293a93b14612bb03f5096902a https://github.com/galaxyproject/galaxy/commit/ea7e1cc945cb529293a93b14612bb... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-01-30 (Mon, 30 Jan 2017)

Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py

Log Message: ----------- Use ToolRequirements (uses OrderedSet internally)

to collapse redundant requirements instead of set to maintain the order of specified requirements.

Commit: 39c03fc6a0be3b56b1972411c281b06391ac65c1 https://github.com/galaxyproject/galaxy/commit/39c03fc6a0be3b56b1972411c281b... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-01-31 (Tue, 31 Jan 2017)

Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml M test/unit/tools/test_tool_deps.py

Log Message: ----------- Merge pull request #3509 from mvdbeek/allow_mapping_from_none

[17.01] Add `unversioned` keyword to limit mappings to requirements without version

Compare: https://github.com/galaxyproject/galaxy/compare/82ec7828af24...39c03fc6a0be