Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: fad562876f886e3384fec1a9782685251d12e2c1
https://github.com/galaxyproject/galaxy/commit/fad562876f886e3384fec1a97826…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-10-10 (Mon, 10 Oct 2016)
Changed paths:
M lib/galaxy/datatypes/registry.py
Log Message:
-----------
Datatypes: include base classes in search by name
Fixes #2982
Adds the base class 'images.Image' to the list of classes
returnable by 'datatypes_registry.get_datatype_class_by_name'.
Normally that method searches the registry's list of datatypes and
those are instantiable classes only. The images.Image can be
considered an abstract base class and you'd never create a dataset
of that datatype.
The method is used for getting classes for 'isinstance' tests, however,
so including base classes like 'images.Image' allow testing for all
its image subclasses. This change makes that possible and allows the
method (and its consumers) to behave in a much more predictable and
useful manner.
Commit: 191bae9a2b9d06bb7d461633b0a43ce320a042c4
https://github.com/galaxyproject/galaxy/commit/191bae9a2b9d06bb7d461633b0a4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-10 (Mon, 10 Oct 2016)
Changed paths:
M lib/galaxy/datatypes/registry.py
Log Message:
-----------
Merge pull request #3028 from carlfeberhard/fix.tiff
Datatypes: include base classes in search by name
Compare: https://github.com/galaxyproject/galaxy/compare/75d1f8496acc...191bae9a2b9d
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 1e32c0926ca3fcee79f355577c5525c4bf73c8e4
https://github.com/galaxyproject/galaxy/commit/1e32c0926ca3fcee79f355577c55…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-10-10 (Mon, 10 Oct 2016)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M client/galaxy/style/source_material/circle.py
M doc/parse_gx_xsd.py
M test/api/helpers.py
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_dataset_collections.py
M test/api/test_history_contents.py
M test/api/test_page_revisions.py
M test/api/test_pages.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_users.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/workflows_format_2/__init__.py
M test/api/workflows_format_2/converter.py
M test/base/api.py
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/interactor.py
M test/base/test_logging.py
M test/base/twilltestcase.py
M test/functional/test_data_managers.py
M test/functional/test_library_templates.py
M test/functional/test_toolbox.py
M test/functional/workflow.py
M test/integration/test_resolvers.py
M test/manual/workflows_scaling.py
M test/shed_functional/base/test_db_util.py
M test/shed_functional/functional/test_0300_reset_all_metadata.py
M test/shed_functional/functional/test_1300_reset_all_metadata.py
M test/shed_functional/functional_tests.py
Log Message:
-----------
Fix import order and Python3 compatibility for most of test/
Commit: 75d1f8496acc060e8bd91cdaffd082fc9685ef1f
https://github.com/galaxyproject/galaxy/commit/75d1f8496acc060e8bd91cdaffd0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-10 (Mon, 10 Oct 2016)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M client/galaxy/style/source_material/circle.py
M doc/parse_gx_xsd.py
M test/api/helpers.py
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_dataset_collections.py
M test/api/test_history_contents.py
M test/api/test_page_revisions.py
M test/api/test_pages.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_users.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/workflows_format_2/__init__.py
M test/api/workflows_format_2/converter.py
M test/base/api.py
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/interactor.py
M test/base/test_logging.py
M test/base/twilltestcase.py
M test/functional/test_data_managers.py
M test/functional/test_library_templates.py
M test/functional/test_toolbox.py
M test/functional/workflow.py
M test/integration/test_resolvers.py
M test/manual/workflows_scaling.py
M test/shed_functional/base/test_db_util.py
M test/shed_functional/functional/test_0300_reset_all_metadata.py
M test/shed_functional/functional/test_1300_reset_all_metadata.py
M test/shed_functional/functional_tests.py
Log Message:
-----------
Merge pull request #3031 from nsoranzo/flake8-import-order
Fix import order and Python3 compatibility for most of test/
Compare: https://github.com/galaxyproject/galaxy/compare/7d642c063f18...75d1f8496acc
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 5a72449246be6f0f2fe3955bebf6f42ae89966bc
https://github.com/galaxyproject/galaxy/commit/5a72449246be6f0f2fe3955bebf6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-08 (Sat, 08 Oct 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/tools/deps/__init__.py
A lib/galaxy/tools/deps/conda_compat.py
M lib/galaxy/tools/deps/conda_util.py
A lib/galaxy/tools/deps/container_resolvers/__init__.py
A lib/galaxy/tools/deps/container_resolvers/explicit.py
A lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
A lib/galaxy/tools/deps/installable.py
A lib/galaxy/tools/deps/mulled/__init__.py
A lib/galaxy/tools/deps/mulled/_cli.py
A lib/galaxy/tools/deps/mulled/invfile.lua
A lib/galaxy/tools/deps/mulled/mulled_build.py
A lib/galaxy/tools/deps/mulled/mulled_build_channel.py
A lib/galaxy/tools/deps/mulled/mulled_build_files.py
A lib/galaxy/tools/deps/mulled/mulled_build_tool.py
A lib/galaxy/tools/deps/mulled/mulled_search.py
A lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
A test/functional/tools/mulled_example_multi_1.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Implement beta support for dynamically discovering mulled containers for dependencies.
Contains all mulled fixes and enhancements through 16.10.7 including several bug fixes from @bgruening.
Commit: e389e1939160dfef7c364785a17869f5de30198b
https://github.com/galaxyproject/galaxy/commit/e389e1939160dfef7c364785a178…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-08 (Sat, 08 Oct 2016)
Changed paths:
M config/job_conf.xml.sample_advanced
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/runners/__init__.py
M test/unit/jobs/test_runner_local.py
Log Message:
-----------
Implement option to require containerization of jobs.
This is great for security in production. For my own greedy concerns, I'm adding it for development however. I don't want someone to be testing mulled containers and accidently run the job locally.
Commit: 654b5e9322f5c54332c8d8861bc8ed34c6e71a8e
https://github.com/galaxyproject/galaxy/commit/654b5e9322f5c54332c8d8861bc8…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
A doc/source/admin/mulled_containers.rst
Log Message:
-----------
Add initial documentation about the new mulled features.
Commit: 4b5114bed1c09c655654972b084274e74310ebe8
https://github.com/galaxyproject/galaxy/commit/4b5114bed1c09c655654972b0842…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-10 (Mon, 10 Oct 2016)
Changed paths:
A doc/source/admin/mulled_containers.rst
Log Message:
-----------
Merge pull request #50 from jmchilton/mulled_docs
Add initial documentation about the new mulled features.
Commit: f0b988da78f081bf6845ce2d280d153e221f3633
https://github.com/galaxyproject/galaxy/commit/f0b988da78f081bf6845ce2d280d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-10 (Mon, 10 Oct 2016)
Changed paths:
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/util.py
Log Message:
-----------
Bring in latest galaxy-lib fixes.
Commit: 20dcc4d693ae8fa7e846eb32e65292c3c4a38863
https://github.com/galaxyproject/galaxy/commit/20dcc4d693ae8fa7e846eb32e652…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-10 (Mon, 10 Oct 2016)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
remove duplicated option from config sample
Commit: bcabbd8707e0064e041e730e5abd1d8dfc0a692c
https://github.com/galaxyproject/galaxy/commit/bcabbd8707e0064e041e730e5abd…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-10 (Mon, 10 Oct 2016)
Changed paths:
M doc/source/admin/mulled_containers.rst
Log Message:
-----------
minor changes to mulled admin docs
Commit: 7db241faa6d505427108c5ddeae8dbc77c384613
https://github.com/galaxyproject/galaxy/commit/7db241faa6d505427108c5ddeae8…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-10 (Mon, 10 Oct 2016)
Changed paths:
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
A doc/source/admin/mulled_containers.rst
M lib/galaxy/config.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/tools/deps/__init__.py
A lib/galaxy/tools/deps/conda_compat.py
M lib/galaxy/tools/deps/conda_util.py
A lib/galaxy/tools/deps/container_resolvers/__init__.py
A lib/galaxy/tools/deps/container_resolvers/explicit.py
A lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
A lib/galaxy/tools/deps/installable.py
A lib/galaxy/tools/deps/mulled/__init__.py
A lib/galaxy/tools/deps/mulled/_cli.py
A lib/galaxy/tools/deps/mulled/invfile.lua
A lib/galaxy/tools/deps/mulled/mulled_build.py
A lib/galaxy/tools/deps/mulled/mulled_build_channel.py
A lib/galaxy/tools/deps/mulled/mulled_build_files.py
A lib/galaxy/tools/deps/mulled/mulled_build_tool.py
A lib/galaxy/tools/deps/mulled/mulled_search.py
A lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
A test/functional/tools/mulled_example_multi_1.xml
M test/functional/tools/samples_tool_conf.xml
M test/unit/jobs/test_runner_local.py
Log Message:
-----------
Merge pull request #2986 from jmchilton/mulled
Implement beta support for discovering mulled containers for dependencies.
Compare: https://github.com/galaxyproject/galaxy/compare/217854827ac7...7db241faa6d5
Branch: refs/heads/release_16.07
Home: https://github.com/galaxyproject/galaxy
Commit: 89278b0ec70b7a8f1cf42bda87335cf4f98f175b
https://github.com/galaxyproject/galaxy/commit/89278b0ec70b7a8f1cf42bda8733…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-07 (Fri, 07 Oct 2016)
Changed paths:
M config/galaxy.ini.sample
M doc/source/admin/dependency_resolvers.rst
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Fix for bioconda recipes depending on conda-forge.
Some bioconda recipes now depend on conda forge, this fix is needed for them to work properly.
Commit: ddacf38a11a9f752b3cfe13a8b63182ff1d02d06
https://github.com/galaxyproject/galaxy/commit/ddacf38a11a9f752b3cfe13a8b63…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-10-10 (Mon, 10 Oct 2016)
Changed paths:
M config/galaxy.ini.sample
M doc/source/admin/dependency_resolvers.rst
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Merge pull request #3023 from jmchilton/fix_abyss
[16.07] Fix for bioconda recipes depending on conda-forge.
Compare: https://github.com/galaxyproject/galaxy/compare/f32b6446a7a4...ddacf38a11a9