- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 848196: Updating GIE build docs.
by GitHub 10 Oct '18

10 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 848196732db7a8b0a1ea6d5ebed9ebe39113085a https://github.com/galaxyproject/galaxy/commit/848196732db7a8b0a1ea6d5ebed9… Author: thobalose <lose.thoba(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M doc/source/dev/interactive_environments.rst Log Message: ----------- Updating GIE build docs. Commit: 292197386b4cdade98c4646cecb0507a88c2a0d2 https://github.com/galaxyproject/galaxy/commit/292197386b4cdade98c4646cecb0… Author: thobalose <lose.thoba(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M doc/source/admin/special_topics/interactive_environments.rst Log Message: ----------- Added NVM to manage multiple node versions. Commit: 3b3215138ff7773bad9446e4eb8357cd778990dd https://github.com/galaxyproject/galaxy/commit/3b3215138ff7773bad9446e4eb83… Author: thobalose <lose.thoba(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M doc/source/dev/interactive_environments.rst Log Message: ----------- Updated GIE build docs. Commit: 2cacb69d97553fc04c7cbcbe84b08f09c16c2ae6 https://github.com/galaxyproject/galaxy/commit/2cacb69d97553fc04c7cbcbe84b0… Author: thobalose <lose.thoba(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M doc/source/admin/special_topics/interactive_environments.rst Log Message: ----------- en-US spelling Commit: c9b0379230950546482c09a19eb2c8f246c2544b https://github.com/galaxyproject/galaxy/commit/c9b0379230950546482c09a19eb2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M doc/source/admin/special_topics/interactive_environments.rst M doc/source/dev/interactive_environments.rst Log Message: ----------- Merge pull request #6846 from thobalose/docs Updated GIE docs Compare: https://github.com/galaxyproject/galaxy/compare/caec18236d94...c9b037923095 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] d5cd53: Add request to authnz Strategy constructor signatu...
by GitHub 10 Oct '18

10 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d5cd53ab8e30934353e4409f32e7039ff9f9f993 https://github.com/galaxyproject/galaxy/commit/d5cd53ab8e30934353e4409f32e7… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Add request to authnz Strategy constructor signature. Commit: b420363436d3fcd94fdfe4b7f39f697999d3dd3c https://github.com/galaxyproject/galaxy/commit/b420363436d3fcd94fdfe4b7f39f… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Add session to authnz Strategy constructor signature. Commit: bc7017664cd625eae9803198ab1d6fbf12999fb1 https://github.com/galaxyproject/galaxy/commit/bc7017664cd625eae9803198ab1d… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Remove trans from authnz Strategy constructor signature. Commit: 376be2ec9d5d5e13e9d80d512dec20ad61843b89 https://github.com/galaxyproject/galaxy/commit/376be2ec9d5d5e13e9d80d512dec… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- In psa Strategy, check if request is given asserting for https redirect. Commit: d15263329ee98470b54c36106ad5f3a352e64af0 https://github.com/galaxyproject/galaxy/commit/d15263329ee98470b54c36106ad5… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Remove trans from _extend_cloudauthz_config. Commit: 74ce3c761129a7c48c1b11ce8ac83db50760d767 https://github.com/galaxyproject/galaxy/commit/74ce3c761129a7c48c1b11ce8ac8… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/managers/cloud.py Log Message: ----------- Remove trans from get_cloud_access_credentials. Commit: ea02d643fdd33aae89aad09c4ed4b59fd157adfb https://github.com/galaxyproject/galaxy/commit/ea02d643fdd33aae89aad09c4ed4… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Update get_cloud_access_credentials doc string. Commit: eb7653ee8130b6617a4c00bf24b9104b806d1522 https://github.com/galaxyproject/galaxy/commit/eb7653ee8130b6617a4c00bf24b9… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/managers/cloud.py Log Message: ----------- Remove `trans.session` dependency for getting cloudauthz tokens. Commit: 0cdf629d89aaa35d80709171e0e05cd64744fa9e https://github.com/galaxyproject/galaxy/commit/0cdf629d89aaa35d80709171e0e0… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/managers/cloud.py Log Message: ----------- Set request optional with default None in get_cloud_access_credentials. Commit: 07d3aa9f7913b5c8e2a6da4e561f8055befbd4b9 https://github.com/galaxyproject/galaxy/commit/07d3aa9f7913b5c8e2a6da4e561f… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Return path if request is none when building absolute auth backend URI. Commit: eda2f1a976e551626eeb2ecf5dfbe722929bfb15 https://github.com/galaxyproject/galaxy/commit/eda2f1a976e551626eeb2ecf5dfb… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Add a missing `z` from `authnz`. Commit: caec18236d94e63dd155d9551082c360aa69fd0d https://github.com/galaxyproject/galaxy/commit/caec18236d94e63dd155d9551082… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/managers/cloud.py Log Message: ----------- Merge pull request #6838 from VJalili/authnz_trans Replace trans with session and request in psa Storage Compare: https://github.com/galaxyproject/galaxy/compare/fb527556019f...caec18236d94 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 10dae9: Fixes for specifying test_data as a parameter to r...
by GitHub 10 Oct '18

10 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 10dae9461d36c0e9c7fa8483de6931096a8d79c7 https://github.com/galaxyproject/galaxy/commit/10dae9461d36c0e9c7fa8483de69… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M test/base/populators.py Log Message: ----------- Fixes for specifying test_data as a parameter to run_workflow. Commit: 1e2080242cd01a57eb24b71841d1cfd79626ba4e https://github.com/galaxyproject/galaxy/commit/1e2080242cd01a57eb24b71841d1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/workflow_fixtures.py Log Message: ----------- Toward newer style gxformat2 definitions. Commit: 8ba76c9704a999eb51aa466e312d5b6aa1953066 https://github.com/galaxyproject/galaxy/commit/8ba76c9704a999eb51aa466e312d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M test/api/test_workflows.py M test/base/workflow_fixtures.py Log Message: ----------- Switch to CWL-style format 2 workflow output definitions. Commit: fd251b16e8cf25d9c883745e8cbee1a178fd6e4e https://github.com/galaxyproject/galaxy/commit/fd251b16e8cf25d9c883745e8cbe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Rev gxformat2 dependencies to get latest features. Commit: 915c1a9b66a86485a42c4aab0ac1295924deda4e https://github.com/galaxyproject/galaxy/commit/915c1a9b66a86485a42c4aab0ac1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Remove unused variable in test_workflows. Commit: a8843ece349b0334353b9506169f82205f4928be https://github.com/galaxyproject/galaxy/commit/a8843ece349b0334353b9506169f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/workflow_fixtures.py Log Message: ----------- Allow CWL-style id map for workflow inputs Commit: fb527556019ffd406387d3eb97a87f717183c4e9 https://github.com/galaxyproject/galaxy/commit/fb527556019ffd406387d3eb97a8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/populators.py M test/base/workflow_fixtures.py Log Message: ----------- Merge pull request #6811 from jmchilton/gxformat2_060 Support for Enhancements to gxformat2 (part II) Compare: https://github.com/galaxyproject/galaxy/compare/afa7299705b9...fb527556019f **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 98a9c8: Allow testing tags in input collections.
by GitHub 10 Oct '18

10 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 98a9c86badd87a4db4a815490c06c717b67fced0 https://github.com/galaxyproject/galaxy/commit/98a9c86badd87a4db4a815490c06… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/tools/tag_collection_from_file.xml M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Allow testing tags in input collections. Commit: 9044e614f03b4d0daa3e67e32be15d7d3f1268f1 https://github.com/galaxyproject/galaxy/commit/9044e614f03b4d0daa3e67e32be1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-07 (Sun, 07 Oct 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Upgrade concurrently; this fixes a 'null' return from webpack run vi aconcurrently, which can fail the build in some situations. Commit: 58ea67eb457ce154e1d119e94c07a81a1e617ba4 https://github.com/galaxyproject/galaxy/commit/58ea67eb457ce154e1d119e94c07… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-07 (Sun, 07 Oct 2018) Changed paths: M lib/galaxy/tools/tag_collection_from_file.xml M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #6823 from jmchilton/tag_input_tests [18.09] Allow testing tags in input collections. Commit: b99fedefa81b3ca59c27eb64ea9a7e9865cd9db8 https://github.com/galaxyproject/galaxy/commit/b99fedefa81b3ca59c27eb64ea9a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Update to latest galaxy-lib Includes: - change channel priority ( https://github.com/galaxyproject/galaxy-lib/pull/132 ) - channel cleanup ( https://github.com/galaxyproject/galaxy-lib/pull/136 ) Commit: c83c5cb78475c96d8e49510619c76f737cca5c8e https://github.com/galaxyproject/galaxy/commit/c83c5cb78475c96d8e49510619c7… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst M lib/galaxy/dependencies/conda-file.sh M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Change conda channel priority: conda-forge > bioconda xref. https://github.com/bioconda/bioconda-utils/issues/330 Commit: 9b6833b5a04cea06d245086b7b74a24a524b0064 https://github.com/galaxyproject/galaxy/commit/9b6833b5a04cea06d245086b7b74… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst Log Message: ----------- make config-rebuild Commit: 5205ed7eebe4b9a2a25d0f19abd5fd732f42e302 https://github.com/galaxyproject/galaxy/commit/5205ed7eebe4b9a2a25d0f19abd5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Merge pull request #6828 from dannon/null_exit_bug_fix [18.09] Upgrade concurrently for 'null' return fix Commit: a43a60656a49ad0b53574dce61738764cf466287 https://github.com/galaxyproject/galaxy/commit/a43a60656a49ad0b53574dce6173… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M lib/galaxy/dependencies/conda-file.sh M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #6830 from nsoranzo/release_18.09_channel_priority_update [18.09] Update conda channel priority: conda-forge > bioconda Commit: afa7299705b92972979d63aa83e6e2f7080b5508 https://github.com/galaxyproject/galaxy/commit/afa7299705b92972979d63aa83e6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M client/package.json M client/yarn.lock M config/galaxy.yml.sample M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M lib/galaxy/dependencies/conda-file.sh M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/tag_collection_from_file.xml M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/dee3ce981c70...afa7299705b9 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] c0961e: Remove some model objects added in #5013 but unuse...
by GitHub 10 Oct '18

10 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c0961ec29619694bc86b4c146035c0e91329e19f https://github.com/galaxyproject/galaxy/commit/c0961ec29619694bc86b4c146035… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/execute.py Log Message: ----------- Remove some model objects added in #5013 but unused before the PR was merged. Also, fix the typo: WorkflowRequestInputStepParmeter -> WorkflowRequestInputStepParameter Both found by @nsoranzo in #6757. Commit: dee3ce981c70b88d60816906cce67345ba787578 https://github.com/galaxyproject/galaxy/commit/dee3ce981c70b88d60816906cce6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/execute.py Log Message: ----------- Merge pull request #6843 from natefoo/remove-unused-model-objects Remove some model objects added in #5013 but unused before the PR was merged, and fix a model object typo Compare: https://github.com/galaxyproject/galaxy/compare/9375ae9ff4ef...dee3ce981c70 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] c634a9: Fix unit test that uses fake trans.user_is_admin f...
by GitHub 10 Oct '18

10 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c634a9d3e6b8c5db2469931ce2e5d88f977938f9 https://github.com/galaxyproject/galaxy/commit/c634a9d3e6b8c5db2469931ce2e5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M test/unit/tools/test_toolbox_filters.py Log Message: ----------- Fix unit test that uses fake trans.user_is_admin for the change to a property made in aad1e3fd0ac3c44bba81d7c278beb06b2016117b. Commit: 9375ae9ff4eff58a0eec6ab3ce3ee247711c9a45 https://github.com/galaxyproject/galaxy/commit/9375ae9ff4eff58a0eec6ab3ce3e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M test/unit/tools/test_toolbox_filters.py Log Message: ----------- Merge pull request #6842 from natefoo/user-is-admin-property Fix unit test that uses fake trans.user_is_admin Compare: https://github.com/galaxyproject/galaxy/compare/f317be200eb1...9375ae9ff4ef **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 5d4755: Installed replace_column_by_key_value_file and add...
by GitHub 09 Oct '18

09 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5d47553625cb2dbde761fd60fb53f2a088173456 https://github.com/galaxyproject/usegalaxy-playbook/commit/5d47553625cb2dbd… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Installed replace_column_by_key_value_file and add_input_name_as_column. **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 6b3f67: Replace deprecated assertEquals() method
by GitHub 09 Oct '18

09 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6b3f6727709350b144e81513b9c22d8c648e203b https://github.com/galaxyproject/galaxy/commit/6b3f6727709350b144e81513b9c2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M test/api/test_api_batch.py M test/api/test_dataset_collections.py M test/api/test_histories.py M test/api/test_jobs.py M test/api/test_pages.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows_from_yaml.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_wrapper.py M test/unit/test_galaxy_mapping.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py M test/unit/workflows/test_extract_summary.py Log Message: ----------- Replace deprecated assertEquals() method Fix warnings during py34-unit tests like: ``` /home/travis/build/galaxyproject/galaxy/test/unit/workflows/test_extract_summary.py:46: DeprecationWarning: Please use assertEqual instead. self.assertEquals(job_dict[hda.job], [('out1', derived_hda_2)]) ``` See e.g. https://travis-ci.org/galaxyproject/galaxy/jobs/438829277 Commit: 2e6f96bcf661d54886d0d27e703650746380c681 https://github.com/galaxyproject/galaxy/commit/2e6f96bcf661d54886d0d27e7036… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove unneeded parentheses Commit: f317be200eb1c38c7938e9cc8b5e80f3c9e5dbaa https://github.com/galaxyproject/galaxy/commit/f317be200eb1c38c7938e9cc8b5e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M lib/galaxy/web/base/controller.py M test/api/test_api_batch.py M test/api/test_dataset_collections.py M test/api/test_histories.py M test/api/test_jobs.py M test/api/test_pages.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows_from_yaml.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_wrapper.py M test/unit/test_galaxy_mapping.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py M test/unit/workflows/test_extract_summary.py Log Message: ----------- Merge pull request #6841 from nsoranzo/assertEqual Replace deprecated assertEquals() method Compare: https://github.com/galaxyproject/galaxy/compare/c44b7cf8e8df...f317be200eb1 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] b99fed: Update to latest galaxy-lib
by GitHub 09 Oct '18

09 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: b99fedefa81b3ca59c27eb64ea9a7e9865cd9db8 https://github.com/galaxyproject/galaxy/commit/b99fedefa81b3ca59c27eb64ea9a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Update to latest galaxy-lib Includes: - change channel priority ( https://github.com/galaxyproject/galaxy-lib/pull/132 ) - channel cleanup ( https://github.com/galaxyproject/galaxy-lib/pull/136 ) Commit: c83c5cb78475c96d8e49510619c76f737cca5c8e https://github.com/galaxyproject/galaxy/commit/c83c5cb78475c96d8e49510619c7… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst M lib/galaxy/dependencies/conda-file.sh M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Change conda channel priority: conda-forge > bioconda xref. https://github.com/bioconda/bioconda-utils/issues/330 Commit: 9b6833b5a04cea06d245086b7b74a24a524b0064 https://github.com/galaxyproject/galaxy/commit/9b6833b5a04cea06d245086b7b74… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst Log Message: ----------- make config-rebuild Commit: a43a60656a49ad0b53574dce61738764cf466287 https://github.com/galaxyproject/galaxy/commit/a43a60656a49ad0b53574dce6173… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M lib/galaxy/dependencies/conda-file.sh M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #6830 from nsoranzo/release_18.09_channel_priority_update [18.09] Update conda channel priority: conda-forge > bioconda Compare: https://github.com/galaxyproject/galaxy/compare/5205ed7eebe4...a43a60656a49 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] aad1e3: Convert user_is_admin and user_can_do_run_as to pr...
by GitHub 09 Oct '18

09 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aad1e3fd0ac3c44bba81d7c278beb06b2016117b https://github.com/galaxyproject/galaxy/commit/aad1e3fd0ac3c44bba81d7c278be… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M lib/galaxy/actions/library.py M lib/galaxy/managers/base.py M lib/galaxy/managers/context.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/library_datasets.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/examples.py.sample M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/forms.py M lib/galaxy/webapps/galaxy/api/groups.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/roles.py M lib/galaxy/webapps/galaxy/api/search.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/groups.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M lib/tool_shed/managers/groups.py M lib/tool_shed/util/repository_util.py M templates/galaxy_client_app.mako M templates/ind_share_base.mako M templates/show_params.mako M templates/user/info.mako M templates/user/register.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/history/share.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/tool_shed/common/repository_actions_menu.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/role/role.mako M templates/webapps/tool_shed/user/username.mako Log Message: ----------- Convert user_is_admin and user_can_do_run_as to properties Commit: c44b7cf8e8df53612ca17d8aa2013b5e35695511 https://github.com/galaxyproject/galaxy/commit/c44b7cf8e8df53612ca17d8aa201… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M lib/galaxy/actions/library.py M lib/galaxy/managers/base.py M lib/galaxy/managers/context.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/library_datasets.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/examples.py.sample M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/forms.py M lib/galaxy/webapps/galaxy/api/groups.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/roles.py M lib/galaxy/webapps/galaxy/api/search.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/groups.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M lib/tool_shed/managers/groups.py M lib/tool_shed/util/repository_util.py M templates/galaxy_client_app.mako M templates/ind_share_base.mako M templates/show_params.mako M templates/user/info.mako M templates/user/register.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/history/share.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/tool_shed/common/repository_actions_menu.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/role/role.mako M templates/webapps/tool_shed/user/username.mako Log Message: ----------- Merge pull request #6835 from natefoo/user-is-admin-property Convert user_is_admin and user_can_do_run_as to properties Compare: https://github.com/galaxyproject/galaxy/compare/1f389ae3e773...c44b7cf8e8df **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 381d6a: Add two recently merged PRs.
by GitHub 08 Oct '18

08 Oct '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: 381d6ad83183a822baebca44622e506d088f10b1 https://github.com/galaxyproject/galaxy/commit/381d6ad83183a822baebca44622e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add two recently merged PRs. **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] adcd73: Fix broken gxformat2 imports.
by GitHub 08 Oct '18

08 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: adcd7333325dc34b7edcb5540730b350ff3f4e33 https://github.com/galaxyproject/galaxy/commit/adcd7333325dc34b7edcb5540730… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M test/manual/workflows_scaling.py M test/selenium_tests/framework.py Log Message: ----------- Fix broken gxformat2 imports. Commit: 1f389ae3e77352920566f09c4f1be1a1e40ff862 https://github.com/galaxyproject/galaxy/commit/1f389ae3e77352920566f09c4f1b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M test/manual/workflows_scaling.py M test/selenium_tests/framework.py Log Message: ----------- Merge pull request #6834 from jmchilton/fix_gxformat2_imports Fix broken gxformat2 imports. Compare: https://github.com/galaxyproject/galaxy/compare/8ed5d8c9414f...1f389ae3e773 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] 1d6596: Automatically return roundup nodes to service upon...
by GitHub 08 Oct '18

08 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1d659600da46427c171cc9d02495e227484b124d https://github.com/galaxyproject/infrastructure-playbook/commit/1d659600da4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M env/tacc/templates/slurm/slurm.conf.j2 Log Message: ----------- Automatically return roundup nodes to service upon reboot **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/infrastructure-playbook] a5b5bf: Add some additional body filter spam rules
by GitHub 08 Oct '18

08 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: a5b5bfcb0227884187392f752e3c8a29612cc399 https://github.com/galaxyproject/infrastructure-playbook/commit/a5b5bfcb022… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M roles/postfix/templates/local.cf.j2 Log Message: ----------- Add some additional body filter spam rules **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 9044e6: Upgrade concurrently; this fixes a 'null' return f...
by GitHub 08 Oct '18

08 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 9044e614f03b4d0daa3e67e32be15d7d3f1268f1 https://github.com/galaxyproject/galaxy/commit/9044e614f03b4d0daa3e67e32be1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-07 (Sun, 07 Oct 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Upgrade concurrently; this fixes a 'null' return from webpack run vi aconcurrently, which can fail the build in some situations. Commit: 5205ed7eebe4b9a2a25d0f19abd5fd732f42e302 https://github.com/galaxyproject/galaxy/commit/5205ed7eebe4b9a2a25d0f19abd5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Merge pull request #6828 from dannon/null_exit_bug_fix [18.09] Upgrade concurrently for 'null' return fix Compare: https://github.com/galaxyproject/galaxy/compare/58ea67eb457c...5205ed7eebe4 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 98a9c8: Allow testing tags in input collections.
by GitHub 08 Oct '18

08 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 98a9c86badd87a4db4a815490c06c717b67fced0 https://github.com/galaxyproject/galaxy/commit/98a9c86badd87a4db4a815490c06… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/tools/tag_collection_from_file.xml M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Allow testing tags in input collections. Commit: 58ea67eb457ce154e1d119e94c07a81a1e617ba4 https://github.com/galaxyproject/galaxy/commit/58ea67eb457ce154e1d119e94c07… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-07 (Sun, 07 Oct 2018) Changed paths: M lib/galaxy/tools/tag_collection_from_file.xml M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #6823 from jmchilton/tag_input_tests [18.09] Allow testing tags in input collections. Compare: https://github.com/galaxyproject/galaxy/compare/8ea455303ab7...58ea67eb457c **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] c61617: Replace trans.sa_session with sa_session in PSACod...
by GitHub 07 Oct '18

07 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c61617fed6ae59f237cb22fa0f6103508484fc3b https://github.com/galaxyproject/galaxy/commit/c61617fed6ae59f237cb22fa0f61… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Replace trans.sa_session with sa_session in PSACode. Commit: 12a3f7b54531f667885d1187538c9b06f244744b https://github.com/galaxyproject/galaxy/commit/12a3f7b54531f667885d1187538c… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Replace trans.sa_session with sa_session in PSAAssociation. Commit: 49bb3a66668f94bed1534b007237f0b1db3b71d9 https://github.com/galaxyproject/galaxy/commit/49bb3a66668f94bed1534b007237… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Replace trans.sa_session with sa_session in PSANonce. Commit: a4d03f0de07df762055210f0c3812cbe0c0bccaf https://github.com/galaxyproject/galaxy/commit/a4d03f0de07df762055210f0c381… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Replace trans.sa_session with sa_session in PSAPartial. Commit: 17eac4fe84465706f3b6b8290ae8872d6985afe7 https://github.com/galaxyproject/galaxy/commit/17eac4fe84465706f3b6b8290ae8… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Replace trans.sa_session with sa_session in UserAuthnzToken. Commit: ebb37f8ff02f246344d73db7c3751b531c4fd38f https://github.com/galaxyproject/galaxy/commit/ebb37f8ff02f246344d73db7c375… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Replace trans with app & sa_session in on_the_fly_config function. Commit: 69bd26e6046c0dd18eaae4cee433d34d26d87d80 https://github.com/galaxyproject/galaxy/commit/69bd26e6046c0dd18eaae4cee433… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Remove `app` from `on_the_fly_config` signature. Commit: 8ed5d8c9414f8b086852a2a347d79e530c231b0c https://github.com/galaxyproject/galaxy/commit/8ed5d8c9414f8b086852a2a347d7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-07 (Sun, 07 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #6826 from VJalili/authnz_trans Remove `trans` from OIDC-related types Compare: https://github.com/galaxyproject/galaxy/compare/7d9093d5ab30...8ed5d8c9414f **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 18b427: Import gxformat2 as an external dependency.
by GitHub 07 Oct '18

07 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 18b4274e651f85db2019faba0674613ef02921aa https://github.com/galaxyproject/galaxy/commit/18b4274e651f85db2019faba0674… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M test/base/populators.py R test/base/workflows_format_2/README.txt R test/base/workflows_format_2/__init__.py R test/base/workflows_format_2/converter.py R test/base/workflows_format_2/interface.py R test/base/workflows_format_2/main.py Log Message: ----------- Import gxformat2 as an external dependency. Commit: 319c29937e30075d0dab45bca87577fd86bc7492 https://github.com/galaxyproject/galaxy/commit/319c29937e30075d0dab45bca875… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py Log Message: ----------- gxformat2 - allow CWL style 'in' declarations for step connections. Makes gxformat2 look a lot closer to CWL workflows with Galaxy tools and state. Commit: c7fa2860d807229ebb29233d99c545534f3d7079 https://github.com/galaxyproject/galaxy/commit/c7fa2860d807229ebb29233d99c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py Log Message: ----------- Toward new format2 syntaxes in test workflows. Commit: d010077830ccdf2c28e978bc65c9871db646f880 https://github.com/galaxyproject/galaxy/commit/d010077830ccdf2c28e978bc65c9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/workflow/modules.py M test/api/test_workflows_from_yaml.py Log Message: ----------- Allow workflow import of workflows with connections that don't have matching empty tool state entries. There is a long conversation in the added doc string. Commit: 7d9093d5ab308301e2ec9e464ce8e7cfbeba77ea https://github.com/galaxyproject/galaxy/commit/7d9093d5ab308301e2ec9e464ce8… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-07 (Sun, 07 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/populators.py R test/base/workflows_format_2/README.txt R test/base/workflows_format_2/__init__.py R test/base/workflows_format_2/converter.py R test/base/workflows_format_2/interface.py R test/base/workflows_format_2/main.py Log Message: ----------- Merge pull request #6807 from jmchilton/gxformat2_030 Support for Enhancements to gxformat2. Compare: https://github.com/galaxyproject/galaxy/compare/10e984ce85c2...7d9093d5ab30 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 50019e: Refactor method for running format 2 workflows int...
by GitHub 06 Oct '18

06 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 50019e503adf811a54b54011d64ef92b8a610b13 https://github.com/galaxyproject/galaxy/commit/50019e503adf811a54b54011d64e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M test/api/test_workflows.py M test/base/populators.py Log Message: ----------- Refactor method for running format 2 workflows into populators.py for reuse. Commit: 3e774713a902fb59b4164e4deac2688b9678f0ce https://github.com/galaxyproject/galaxy/commit/3e774713a902fb59b4164e4deac2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows_from_yaml.py M test/base/populators.py M test/base/workflows_format_2/main.py M test/functional/tools/disambiguate_cond.xml Log Message: ----------- Fill in needed state defaults when importing manually curated workflows. Commit: 10e984ce85c2d02d95cb96a11d1738fb1d6ab951 https://github.com/galaxyproject/galaxy/commit/10e984ce85c2d02d95cb96a11d17… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/populators.py M test/base/workflows_format_2/main.py M test/functional/tools/disambiguate_cond.xml Log Message: ----------- Merge pull request #6746 from jmchilton/workflow_state_touch_1 Fill in needed state defaults when importing manually crafted workflows. Compare: https://github.com/galaxyproject/galaxy/compare/56ca1cdef4d3...10e984ce85c2 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 0a6de6: Add more detail about container tags
by GitHub 05 Oct '18

05 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0a6de6b8d7581a2ca27bad3388b936c6b560ea93 https://github.com/galaxyproject/galaxy/commit/0a6de6b8d7581a2ca27bad3388b9… Author: pvanheus <pvh(a)sanbi.ac.za> Date: 2018-10-05 (Fri, 05 Oct 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Add more detail about container tags Explain that singularity container tags are now supported and add some detail about how to use them. Commit: 5601d893a3350a3efca0238d672f059d2404be5c https://github.com/galaxyproject/galaxy/commit/5601d893a3350a3efca0238d672f… Author: pvanheus <pvh(a)sanbi.ac.za> Date: 2018-10-05 (Fri, 05 Oct 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Fixes to workding as per nsoranzo Commit: 56ca1cdef4d373958426c5a0028542854edfb48a https://github.com/galaxyproject/galaxy/commit/56ca1cdef4d373958426c5a00285… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-05 (Fri, 05 Oct 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #6818 from pvanheus/patch-7 Add more detail about container tags Compare: https://github.com/galaxyproject/galaxy/compare/973c73ce722a...56ca1cdef4d3 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] a5d794: Add docs about running jobs in containers
by GitHub 05 Oct '18

05 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a5d794dc4d1ee48539aa36c82ec56ac40760e0fa https://github.com/galaxyproject/galaxy/commit/a5d794dc4d1ee48539aa36c82ec5… Author: pvanheus <pvh(a)sanbi.ac.za> Date: 2018-10-05 (Fri, 05 Oct 2018) Changed paths: M doc/source/admin/jobs.md Log Message: ----------- Add docs about running jobs in containers Explain how jobs can be run in containers (something currently documented in the `job_conf.xml.sample_advanced` file) Commit: 973c73ce722ae588d8aca9d5f71c6f6e938f10e4 https://github.com/galaxyproject/galaxy/commit/973c73ce722ae588d8aca9d5f71c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-05 (Fri, 05 Oct 2018) Changed paths: M doc/source/admin/jobs.md Log Message: ----------- Merge pull request #6820 from pvanheus/patch-8 Add docs about running jobs in containers Compare: https://github.com/galaxyproject/galaxy/compare/13d92c007001...973c73ce722a **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 5b8ae3: Update to latest galaxy-lib.
by GitHub 05 Oct '18

05 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5b8ae3e7314dbd96a13e8b32447fff6bdb358ae0 https://github.com/galaxyproject/galaxy/commit/5b8ae3e7314dbd96a13e8b32447f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/cwl/util.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/parser/cwl.py Log Message: ----------- Update to latest galaxy-lib. Commit: 13d92c007001b11a052f21b103c717a430861f66 https://github.com/galaxyproject/galaxy/commit/13d92c007001b11a052f21b103c7… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-05 (Fri, 05 Oct 2018) Changed paths: M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/cwl/util.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/parser/cwl.py Log Message: ----------- Merge pull request #6709 from jmchilton/galaxy-lib-update-20180913 Update to latest galaxy-lib. Compare: https://github.com/galaxyproject/galaxy/compare/997301cfe4c6...13d92c007001 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 4908b9: Fix types on "reserve_memory" / "reserve_cpu"
by GitHub 05 Oct '18

05 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4908b98daaf45aa886a3b0a7badcf90acb949c19 https://github.com/galaxyproject/galaxy/commit/4908b98daaf45aa886a3b0a7badc… Author: pvanheus <pvh(a)sanbi.ac.za> Date: 2018-10-05 (Fri, 05 Oct 2018) Changed paths: M config/containers_conf.yml.sample Log Message: ----------- Fix types on "reserve_memory" / "reserve_cpu" resverve changed to reserve Commit: 997301cfe4c6ab1ec9596330c8267c73d465a3fc https://github.com/galaxyproject/galaxy/commit/997301cfe4c6ab1ec9596330c826… Author: Helena Rasche <erasche(a)users.noreply.github.com> Date: 2018-10-05 (Fri, 05 Oct 2018) Changed paths: M config/containers_conf.yml.sample Log Message: ----------- Merge pull request #6817 from pvanheus/patch-6 Fix typos on "reserve_memory" / "reserve_cpu" Compare: https://github.com/galaxyproject/galaxy/compare/18f351ae31ae...997301cfe4c6 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] b4e69c: Set a slurm reboot program so `scontrol reboot` wo...
by GitHub 04 Oct '18

04 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: b4e69cd3abb082a412404d48111093d07fdc1513 https://github.com/galaxyproject/infrastructure-playbook/commit/b4e69cd3abb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M env/tacc/templates/slurm/slurm.conf.j2 Log Message: ----------- Set a slurm reboot program so `scontrol reboot` works **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] 4fcfff: Remove duplicate athena key
by GitHub 04 Oct '18

04 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 4fcfff08ea457d3fc91f8e99628bce66feea5b71 https://github.com/galaxyproject/infrastructure-playbook/commit/4fcfff08ea4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M env/common/group_vars/sslservers/vault.yml Log Message: ----------- Remove duplicate athena key Commit: 6bf8ecf5223028bb96092dd2018896b8b147dab4 https://github.com/galaxyproject/infrastructure-playbook/commit/6bf8ecf5223… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: A roles/dj-wasabi.telegraf/.github/ISSUE_TEMPLATE/bug_report.md A roles/dj-wasabi.telegraf/.github/ISSUE_TEMPLATE/feature_request.md M roles/dj-wasabi.telegraf/.travis.yml M roles/dj-wasabi.telegraf/CHANGELOG.md A roles/dj-wasabi.telegraf/CODE_OF_CONDUCT.md A roles/dj-wasabi.telegraf/CONTRIBUTING.md A roles/dj-wasabi.telegraf/LICENSE A roles/dj-wasabi.telegraf/PULL_REQUEST_TEMPLATE.md M roles/dj-wasabi.telegraf/README.md M roles/dj-wasabi.telegraf/defaults/main.yml M roles/dj-wasabi.telegraf/meta/.galaxy_install_info M roles/dj-wasabi.telegraf/meta/main.yml M roles/dj-wasabi.telegraf/molecule/default/create.yml M roles/dj-wasabi.telegraf/molecule/default/molecule.yml M roles/dj-wasabi.telegraf/molecule/default/playbook.yml M roles/dj-wasabi.telegraf/molecule/default/yaml-lint.yml A roles/dj-wasabi.telegraf/requirements.txt M roles/dj-wasabi.telegraf/tasks/Debian.yml M roles/dj-wasabi.telegraf/tasks/RedHat.yml A roles/dj-wasabi.telegraf/tasks/configure.yml M roles/dj-wasabi.telegraf/tasks/main.yml M roles/dj-wasabi.telegraf/templates/etc-opt-telegraf-telegraf.conf.j2 M roles/dj-wasabi.telegraf/templates/telegraf-extra-plugin.conf.j2 M roles/dj-wasabi.telegraf/templates/telegraf.conf.j2 Log Message: ----------- Update dj-wasabi.telegraf Commit: d0d15fa672f7604a46f7190677b305dbc988c9e3 https://github.com/galaxyproject/infrastructure-playbook/commit/d0d15fa672f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: A env/tacc/group_vars/galaxydbservers.yml M env/tacc/group_vars/galaxyservers.yml A env/tacc/group_vars/maingalaxydbservers.yml A env/tacc/group_vars/testgalaxydbservers.yml M env/tacc/inventory A env/tacc/templates/stats/galaxy_db_slurp.sh.j2 M roles/stats/templates/galaxy_slurp.py.j2 Log Message: ----------- Use telegraf for collecting (some) of the SQL stats, thanks to a protip from @erasche Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/85852a755a… **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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