Branch: refs/heads/release_17.01
Home: https://github.com/galaxyproject/galaxy
Commit: fe87cd889f2bdab122fccd0db99aa31af864d1db
https://github.com/galaxyproject/galaxy/commit/fe87cd889f2bdab122fccd0db99a…
Author: mvdbeek <m.vandenbeek(a)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/d3093013f95a4a0d324213f6ab44…
Author: mvdbeek <m.vandenbeek(a)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/44a90033dbe1c635e37952711e28…
Author: mvdbeek <m.vandenbeek(a)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/b92e9b509354a570424da4b1ff86…
Author: mvdbeek <m.vandenbeek(a)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/a30d6dfa2090096975ca614a85cd…
Author: mvdbeek <m.vandenbeek(a)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/14529b9dd56b45afe6d06babf88e…
Author: mvdbeek <m.vandenbeek(a)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/6ba0291eea85723514a7a983f009…
Author: John Chilton <jmchilton(a)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/ea7e1cc945cb529293a93b14612b…
Author: mvdbeek <m.vandenbeek(a)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/39c03fc6a0be3b56b1972411c281…
Author: Dannon Baker <dannon.baker(a)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
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 1a463f1688673196fd7d5fd02318484bfd0bb7a9
https://github.com/galaxyproject/galaxy/commit/1a463f1688673196fd7d5fd02318…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-01-30 (Mon, 30 Jan 2017)
Changed paths:
A config/build_sites.yml.sample
M config/datatypes_conf.xml.sample
M lib/galaxy/config.py
M lib/galaxy/datatypes/registry.py
M scripts/common_startup.sh
Log Message:
-----------
Pull build_sites out of datatypes conf.
So deployers may modify these paths and stil use the default datatypes config.
This should speed up set_metadata also since each of these config files won't be loaded as part of that.
Commit: bb318d36e6a2d760f93abee4a1801724244ec741
https://github.com/galaxyproject/galaxy/commit/bb318d36e6a2d760f93abee4a180…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-01-31 (Tue, 31 Jan 2017)
Changed paths:
A config/build_sites.yml.sample
M config/datatypes_conf.xml.sample
M lib/galaxy/config.py
M lib/galaxy/datatypes/registry.py
M scripts/common_startup.sh
Log Message:
-----------
Merge pull request #3503 from jmchilton/datatypes_build_sites
Improvements to build sites configuration
Compare: https://github.com/galaxyproject/galaxy/compare/80d3f735e2d0...bb318d36e6a2
Branch: refs/heads/release_17.01
Home: https://github.com/galaxyproject/galaxy
Commit: 5ad185590148390ec27750567273f59546eec219
https://github.com/galaxyproject/galaxy/commit/5ad185590148390ec27750567273…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-01-30 (Mon, 30 Jan 2017)
Changed paths:
M test/base/driver_util.py
Log Message:
-----------
Disable conda_auto_init by default for most tests.
Executing framework, API, and/or selenium tests was causing Conda to be installed. This isn't needed - the only tests that test Conda dependencies are unit tests and integration tests that explicitly configure this Conda installation.
Commit: a8e59b7b238d123d2407021bd7d62465fbb7d43d
https://github.com/galaxyproject/galaxy/commit/a8e59b7b238d123d2407021bd7d6…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-01-30 (Mon, 30 Jan 2017)
Changed paths:
M test/base/driver_util.py
Log Message:
-----------
Merge pull request #3517 from jmchilton/disable_testing_conda
[17.01] Disable conda_auto_init by default for most tests.
Compare: https://github.com/galaxyproject/galaxy/compare/8b08384be3bc...a8e59b7b238d