October 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] fad562: Datatypes: include base classes in search by name
by GitHub 10 Oct '16

10 Oct '16

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

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[galaxyproject/galaxy] 1e32c0: Fix import order and Python3 compatibility for mos...
by GitHub 10 Oct '16

10 Oct '16

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

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[galaxyproject/galaxy] 1a2d75: add muled docs to admin index
by GitHub 10 Oct '16

10 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1a2d75fade1077359b2a9b1072feab793022b7f4 https://github.com/galaxyproject/galaxy/commit/1a2d75fade1077359b2a9b1072fe… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M doc/source/admin/index.rst Log Message: ----------- add muled docs to admin index Commit: 7d642c063f18b18b438a4840705f09652f3b586d https://github.com/galaxyproject/galaxy/commit/7d642c063f18b18b438a4840705f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M doc/source/admin/index.rst Log Message: ----------- Merge pull request #3032 from martenson/link-mulled-docs add muled docs to admin index Compare: https://github.com/galaxyproject/galaxy/compare/7db241faa6d5...7d642c063f18

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[galaxyproject/galaxy] 5a7244: Implement beta support for dynamically discovering...
by GitHub 10 Oct '16

10 Oct '16

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

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[galaxyproject/galaxy] 89278b: Fix for bioconda recipes depending on conda-forge.
by GitHub 10 Oct '16

10 Oct '16

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

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[galaxyproject/galaxy] ad0d0b: Missing double quotation
by GitHub 10 Oct '16

10 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ad0d0bc7cec7c281052610b9453db42cfce8dcea https://github.com/galaxyproject/galaxy/commit/ad0d0bc7cec7c281052610b9453d… Author: ramezrawas <ramezrawas(a)gmail.com> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Missing double quotation line 3664: name="output_vcf> Commit: 217854827ac7dfc88c5388cd2ecb24fffd86c060 https://github.com/galaxyproject/galaxy/commit/217854827ac7dfc88c5388cd2ecb… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #3027 from ramezrawas/patch-1 Missing double quotation Compare: https://github.com/galaxyproject/galaxy/compare/056a7e0d1e7a...217854827ac7

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[galaxyproject/galaxy] c39f8c: Fix for XSD
by GitHub 07 Oct '16

07 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c39f8c92ea47c73e2cef8295e4816f06a6e72f44 https://github.com/galaxyproject/galaxy/commit/c39f8c92ea47c73e2cef8295e481… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Fix for XSD Commit: 056a7e0d1e7a6e3bb78f22903df6b941b44fad69 https://github.com/galaxyproject/galaxy/commit/056a7e0d1e7a6e3bb78f22903df6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #3020 from bgruening/xsd_fix Fix for XSD Compare: https://github.com/galaxyproject/galaxy/compare/a08b849f6db5...056a7e0d1e7a

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[galaxyproject/galaxy] 5e8da4: Fix bare exception.
by GitHub 07 Oct '16

07 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5e8da4ec82848407a4f1127da57eed5006b6ea39 https://github.com/galaxyproject/galaxy/commit/5e8da4ec82848407a4f1127da57e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix bare exception. https://docs.python.org/2/howto/doanddont.html#except Commit: e310453fd0bde9c0c565c6f68b2fcd09942ac49a https://github.com/galaxyproject/galaxy/commit/e310453fd0bde9c0c565c6f68b2f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/color_param.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Improved docs and testing for color params. Commit: a08b849f6db5041dc56173051bc45aaa8c469ae4 https://github.com/galaxyproject/galaxy/commit/a08b849f6db5041dc56173051bc4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/color_param.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3016 from jmchilton/color_followup Improved docs and testing for color params. Compare: https://github.com/galaxyproject/galaxy/compare/3345dd4a92b9...a08b849f6db5

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[galaxyproject/galaxy] d6639b: encourage wittiness in release notes
by GitHub 07 Oct '16

07 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d6639bee403a8cc79df647a21b79e905c3b6474d https://github.com/galaxyproject/galaxy/commit/d6639bee403a8cc79df647a21b79… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- encourage wittiness in release notes Commit: 3345dd4a92b9224a6a4e864326b60c8e92f29ad0 https://github.com/galaxyproject/galaxy/commit/3345dd4a92b9224a6a4e864326b6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #2865 from martenson/forced-wittiness encourage wittiness in release notes Compare: https://github.com/galaxyproject/galaxy/compare/f72b46198ef7...3345dd4a92b9

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[galaxyproject/galaxy] 1a6127: Revert "Update job_conf.xml.sample_advanced"
by GitHub 07 Oct '16

07 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1a61275153c38f849fd096b890973dd41543021c https://github.com/galaxyproject/galaxy/commit/1a61275153c38f849fd096b89097… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Revert "Update job_conf.xml.sample_advanced" This reverts commit a6d3c54522a11d6dc467e737a65b90c47ce5c960. Commit: 1fe5ae1a5eafc44c108e94878d4c966822d6325a https://github.com/galaxyproject/galaxy/commit/1fe5ae1a5eafc44c108e94878d4c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: A lib/galaxy/jobs/runners/godocker.py Log Message: ----------- Revert "Delete godocker.py" This reverts commit 57b2171a79c8993d57256fdbe557fe597fbc9612. Commit: 01209211f7d03c3349ac1b569f6345f89fdbc3b9 https://github.com/galaxyproject/galaxy/commit/01209211f7d03c3349ac1b569f63… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/jobs/runners/godocker.py Log Message: ----------- Rework some GoDocker logging to be more useful. Commit: 837507060c26a96b2011ac14e5c607b4b6d8b16c https://github.com/galaxyproject/galaxy/commit/837507060c26a96b2011ac14e5c6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/jobs/runners/godocker.py Log Message: ----------- Set spell Commit: b865952bab1a659e70e65aaf63740d776fbb3249 https://github.com/galaxyproject/galaxy/commit/b865952bab1a659e70e65aaf6374… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Add reference to Go-Docker repository and a little blurb. Commit: 4664a64c15d9989a5fd0589e0551d7a681db8f9e https://github.com/galaxyproject/galaxy/commit/4664a64c15d9989a5fd0589e0551… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M lib/galaxy/jobs/runners/godocker.py Log Message: ----------- Remove ssl warning disable -- these are good to have/see when using unverified SSL connections. Commit: f72b46198ef7f03533b7d400195828d0976027c4 https://github.com/galaxyproject/galaxy/commit/f72b46198ef7f03533b7d4001958… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M config/job_conf.xml.sample_advanced A lib/galaxy/jobs/runners/godocker.py Log Message: ----------- Merge pull request #2791 from dannon/godocker Godocker job runner Compare: https://github.com/galaxyproject/galaxy/compare/9e299e934680...f72b46198ef7

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