- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] d60699: Don't create jobs for inactive users
by GitHub 11 Oct '18

11 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d60699624139e09c1dd7d979eaaeecfeb77856ad https://github.com/galaxyproject/galaxy/commit/d60699624139e09c1dd7d979eaae… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/managers/context.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload.py Log Message: ----------- Don't create jobs for inactive users Commit: c4374f9a811762db7cc5dd999418ebe922d17a02 https://github.com/galaxyproject/galaxy/commit/c4374f9a811762db7cc5dd999418… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M lib/galaxy/tools/actions/upload.py Log Message: ----------- Fix tabs, wow Commit: c5700431c48cd0b2a2ebc2484a9e07d860c3aa9a https://github.com/galaxyproject/galaxy/commit/c5700431c48cd0b2a2ebc2484a9e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M lib/galaxy/managers/context.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload.py Log Message: ----------- check user activation with less duplication/imports Commit: 2bbabdae02bb08371429ddbda6737faea7ebc6b5 https://github.com/galaxyproject/galaxy/commit/2bbabdae02bb08371429ddbda673… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M test/unit/tools/test_actions.py Log Message: ----------- Fix unit tests for new job_is_active trans property and add a test for the feature. Commit: 8edeca024961a7f1856fc5586843137901fb6ff1 https://github.com/galaxyproject/galaxy/commit/8edeca024961a7f1856fc5586843… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M lib/galaxy/managers/context.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload.py Log Message: ----------- Merge pull request #9 from jmchilton/inactive-user-jobs check user activation with less duplication/imports Commit: 15944ce6e9d4bdf5818f3125efd63fc85c3161fe https://github.com/galaxyproject/galaxy/commit/15944ce6e9d4bdf5818f3125efd6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M test/unit/tools/test_actions.py Log Message: ----------- Fix unit tests broken by the addition of trans.check_user_activation() Commit: 483a23a5a4bdfe2e74190cb7182fafd05d992461 https://github.com/galaxyproject/galaxy/commit/483a23a5a4bdfe2e74190cb7182f… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/exceptions/error_codes.json Log Message: ----------- Fix sorting of error codes Commit: 85d4706662969e953dd04a5266dddb7b73d16920 https://github.com/galaxyproject/galaxy/commit/85d4706662969e953dd04a5266dd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/managers/context.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload.py M test/unit/tools/test_actions.py Log Message: ----------- Merge pull request #6837 from natefoo/inactive-user-jobs Don't create jobs for inactive users Compare: https://github.com/galaxyproject/galaxy/compare/12929f9acb0b...85d470666296 **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] a46984: Clarify code used in output <filter> tags
by GitHub 11 Oct '18

11 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a46984991ee976b80b06983e0548ec05724dce36 https://github.com/galaxyproject/galaxy/commit/a46984991ee976b80b06983e0548… Author: pvanheus <pvh(a)sanbi.ac.za> Date: 2018-10-07 (Sun, 07 Oct 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Clarify code used in output <filter> tags Add extra detail to the explanation of how the Python code to ``<filter>`` tags works in outputs. Commit: 3b4ffc2565d8cb776d96b6540afe9aeaeb5b6792 https://github.com/galaxyproject/galaxy/commit/3b4ffc2565d8cb776d96b6540afe… Author: pvanheus <pvh(a)sanbi.ac.za> Date: 2018-10-07 (Sun, 07 Oct 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Fix missing ] Commit: 12929f9acb0bed7373f1e600b90f4d3b917612f0 https://github.com/galaxyproject/galaxy/commit/12929f9acb0bed7373f1e600b90f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #6827 from pvanheus/patch-9 Clarify code used in output <filter> tags Compare: https://github.com/galaxyproject/galaxy/compare/f41128a946d1...12929f9acb0b **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] e22def: add new welcome page using BS4 cards
by GitHub 10 Oct '18

10 Oct '18

Branch: refs/heads/new-welcome Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e22defcd57210d9035b1388a7ab5c0afeced60de https://github.com/galaxyproject/usegalaxy-playbook/commit/e22defcd57210d90… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M env/common/templates/galaxy/static/welcome.html.j2 Log Message: ----------- add new welcome page using BS4 cards **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] 6b62a5: Should fix bug Jen saw with history panel being ma...
by GitHub 10 Oct '18

10 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 6b62a57047f8877ba36e0767aaee04879bbc20c0 https://github.com/galaxyproject/galaxy/commit/6b62a57047f8877ba36e0767aaee… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Should fix bug Jen saw with history panel being masked at bottom Commit: cd62461e8486bd4e44aee51907f7d515718ef3d8 https://github.com/galaxyproject/galaxy/commit/cd62461e8486bd4e44aee51907f7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6839 from dannon/unified-panel-style-tweaks [18.09] Unified panel style bottom padding fix Compare: https://github.com/galaxyproject/galaxy/compare/a43a60656a49...cd62461e8486 **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] 6c580b: Updated volume kwds.
by GitHub 10 Oct '18

10 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6c580b8c9d3b8ea509873683dba2a5d347017f03 https://github.com/galaxyproject/galaxy/commit/6c580b8c9d3b8ea509873683dba2… Author: thobalose <lose.thoba(a)gmail.com> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M config/plugins/interactive_environments/neo/templates/neo.mako Log Message: ----------- Updated volume kwds. Commit: f41128a946d14cc7e45fc7f97c7368652bbfd49c https://github.com/galaxyproject/galaxy/commit/f41128a946d14cc7e45fc7f97c73… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M config/plugins/interactive_environments/neo/templates/neo.mako Log Message: ----------- Merge pull request #6840 from thobalose/volume Updated volume kwds. Compare: https://github.com/galaxyproject/galaxy/compare/c9b037923095...f41128a946d1 **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] 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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