Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 66c94125ee258baf6578b439e9fb4b33f2bd5499 https://github.com/galaxyproject/galaxy/commit/66c94125ee258baf6578b439e9fb4... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-11 (Mon, 11 Jan 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/web/base/controller.py M test/api/test_workflows.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py Log Message: ----------- Copy workflow objects when importing them. If not anywhere workflow.stored_workflow is checked will be broken. Commit: 95d00b4174efd23b0ad9c350d3463bf9d696d8cc https://github.com/galaxyproject/galaxy/commit/95d00b4174efd23b0ad9c350d3463... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Fix MIMEText usage in galaxy.util Commit: e397ebba585ed578798645ee9352b891e3055372 https://github.com/galaxyproject/galaxy/commit/e397ebba585ed578798645ee9352b... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #1509 from dannon/release_16.01 Fix MIMEText usage in galaxy.util Commit: c143d659d4f7b598bc89a9d06b8040dff39a1b85 https://github.com/galaxyproject/galaxy/commit/c143d659d4f7b598bc89a9d06b804... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Revise tool caching to be less broken. Just switch the default for tool caching and only cache during initial loads of tool panels - as during a toolbox refresh. This should mean that all code from tool shed will ignore the cache and should fix #1515. Additionally, reloading the tool was broken since if would call the load tool code and then just trust the cache. This should fix tool reloading as well. Commit: 3d1ad5ad8dab30aa6c6372fbe85a0c3c7d198d61 https://github.com/galaxyproject/galaxy/commit/3d1ad5ad8dab30aa6c6372fbe85a0... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #1511 from martenson/log-user-exceptions-properly [16.01] catch Exception and properly log errors Commit: ae2ee4a4432b55a4b0fbdd218bc34f88f7ad1b2b https://github.com/galaxyproject/galaxy/commit/ae2ee4a4432b55a4b0fbdd218bc34... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #1517 from jmchilton/tool_cache_fixes [16.01] Tool cache fixes Commit: 817f36626d7e720b0dbb63d0071f2889146c1c41 https://github.com/galaxyproject/galaxy/commit/817f36626d7e720b0dbb63d0071f2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/web/base/controller.py M test/api/test_workflows.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py Log Message: ----------- Merge pull request #1474 from jmchilton/workflow_copy [16.01] Copy workflow objects when importing them. Commit: fc434d62e971df92bc51b296d119030ca85af303 https://github.com/galaxyproject/galaxy/commit/fc434d62e971df92bc51b296d1190... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Handle unvalidated values in depth Commit: 0e9302127f4478611170dee237d811e072100e99 https://github.com/galaxyproject/galaxy/commit/0e9302127f4478611170dee237d81... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2016-01-16 (Sat, 16 Jan 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- sourcing Conda will write to stderr, we need to redirect it to stdout Commit: a77403cc9e6ef2d90ba78822afca601eed09e6ec https://github.com/galaxyproject/galaxy/commit/a77403cc9e6ef2d90ba78822afca6... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #1527 from bgruening/release_16.01 Sourcing Conda will write to stderr Commit: 16e0bc08c8333c75c05a1a47de57eed8196bf9d9 https://github.com/galaxyproject/galaxy/commit/16e0bc08c8333c75c05a1a47de57e... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1526 from guerler/fix_unvalidated_001 [16.01] Handle unvalidated values in depth Commit: 151c90183bd0b0003048b706f91a835b8606a7ed https://github.com/galaxyproject/galaxy/commit/151c90183bd0b0003048b706f91a8... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-20 (Wed, 20 Jan 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/web/base/controller.py M test/api/test_workflows.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py Log Message: ----------- Merge remote-tracking branch 'jmchilton/release_16.01' into dev_merge_1 Commit: 747c981a25ded3689a9fa454fa1cd9d1f7990cca https://github.com/galaxyproject/galaxy/commit/747c981a25ded3689a9fa454fa1cd... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-20 (Wed, 20 Jan 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/web/base/controller.py M test/api/test_workflows.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py Log Message: ----------- Merge pull request #1547 from jmchilton/dev_merge_1 Merge release_16.01 into dev. Compare: https://github.com/galaxyproject/galaxy/compare/1b8f52807435...747c981a25de