Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8b75305c49c3e9fe3fb4665177af977cdfc9a582 https://github.com/galaxyproject/galaxy/commit/8b75305c49c3e9fe3fb4665177af9... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2016-12-21 (Wed, 21 Dec 2016)

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

Log Message: ----------- Merge pull request #3351 from jmchilton/galaxy_environment_fixes

[16.07] Do not allow Conda to replace Galaxy's Python environment for select tools.

Commit: 42a461353bc2dd07f60daf33a42e6d45ec7c86a8 https://github.com/galaxyproject/galaxy/commit/42a461353bc2dd07f60daf33a42e6... Author: John Chilton jmchilton@gmail.com Date: 2016-12-21 (Wed, 21 Dec 2016)

Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py

Log Message: ----------- Fix linting of 16.07 broken with security patches.

Commit: 69fe5ae83ae53cb84a2d0bdd9ea53389b8af5a3a https://github.com/galaxyproject/galaxy/commit/69fe5ae83ae53cb84a2d0bdd9ea53... Author: John Chilton jmchilton@gmail.com Date: 2016-12-21 (Wed, 21 Dec 2016)

Changed paths: M tox.ini

Log Message: ----------- Fix 16.07 linting of imports broken with release of flake8-import-order 0.11.

This is pinned to 0.11 in release_16.10 and unpinned in dev, when merging forward keep these "forward" branches the same (i.e. do not revert to flake8-import-order 0.10).

Commit: 3d155f0be0c91dbfe891394261c08922f75f3f17 https://github.com/galaxyproject/galaxy/commit/3d155f0be0c91dbfe891394261c08... Author: Dannon Baker dannon.baker@gmail.com Date: 2016-12-21 (Wed, 21 Dec 2016)

Changed paths: M config/plugins/tours/core.history.yaml

Log Message: ----------- Fix history list selector

Commit: b57a961f250968d6d62eff142b4ee6e046085fda https://github.com/galaxyproject/galaxy/commit/b57a961f250968d6d62eff142b4ee... Author: John Chilton jmchilton@gmail.com Date: 2016-12-21 (Wed, 21 Dec 2016)

Changed paths: M config/plugins/tours/core.history.yaml

Log Message: ----------- Merge changes fixing tour from dev commit 10720fa4f9e26b3feec1a90468f4ecc726a99c05

Cannot do a full cherry-pick because the test modified did not exist in 16.10.

Commit: b400a15c78faba3b873ecf1ce2237c36bc24f440 https://github.com/galaxyproject/galaxy/commit/b400a15c78faba3b873ecf1ce2237... Author: Martin Cech cech.marten@gmail.com Date: 2016-12-23 (Fri, 23 Dec 2016)

Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tox.ini

Log Message: ----------- Merge pull request #3352 from jmchilton/1607_lintfixes

[16.07] Attempt to fix TravisCI for release 16.07.

Commit: 4d84b3faa17872d1ebe22a1b8c622aa60a8a4324 https://github.com/galaxyproject/galaxy/commit/4d84b3faa17872d1ebe22a1b8c622... Author: Martin Cech cech.marten@gmail.com Date: 2016-12-23 (Fri, 23 Dec 2016)

Changed paths: M config/plugins/tours/core.history.yaml

Log Message: ----------- Merge pull request #3357 from jmchilton/backport_3185

[16.10] Backport #3185

Commit: c3687114d6f2f14df49af9a3fee6dbebe08aa7e5 https://github.com/galaxyproject/galaxy/commit/c3687114d6f2f14df49af9a3fee6d... Author: John Chilton jmchilton@gmail.com Date: 2017-01-05 (Thu, 05 Jan 2017)

Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py

Log Message: ----------- Set metadata on HDAs from dynamically discovered collections.

With test case that previously failed.

Fixes #3267.

Commit: 5b3debc510888bd44ae55700fad8e03f2cdc2bdc https://github.com/galaxyproject/galaxy/commit/5b3debc510888bd44ae55700fad8e... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-01-06 (Fri, 06 Jan 2017)

Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py

Log Message: ----------- Merge pull request #3386 from jmchilton/discovered_collection_metadata_1607

[16.07] Fix metadata on HDAs in dynamically discovered collections.

Commit: 4d73dfc2e03de4c7eaabfd2f6fadd2ca4eff62f8 https://github.com/galaxyproject/galaxy/commit/4d73dfc2e03de4c7eaabfd2f6fadd... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-01-06 (Fri, 06 Jan 2017)

Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py M tox.ini

Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.07' into release_16.10

Commit: 387c08b39b63b9e3abf738b67267b04baf949a67 https://github.com/galaxyproject/galaxy/commit/387c08b39b63b9e3abf738b67267b... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-01-06 (Fri, 06 Jan 2017)

Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py M tox.ini

Log Message: ----------- Merge branch 'release_16.10' into dev

Compare: https://github.com/galaxyproject/galaxy/compare/c9a876e659b3...387c08b39b63