- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] b422fd: Swap main to 18.09 branch, update.
by GitHub 18 Sep '18

18 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b422fd722203473ca7a5ae672f78ef23f3146c99 https://github.com/galaxyproject/usegalaxy-playbook/commit/b422fd722203473c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml M env/main/group_vars/all.yml Log Message: ----------- Swap main to 18.09 branch, update. **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] d573fa: Update test
by GitHub 18 Sep '18

18 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d573fab922e246008ebfc8348522f742403e47c3 https://github.com/galaxyproject/usegalaxy-playbook/commit/d573fab922e24600… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update test **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] dfff5c: Add Loom datatype and remove rdata.seurat.
by GitHub 18 Sep '18

18 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dfff5c966342b38603514d8bfd3ed8e5b6e0bed9 https://github.com/galaxyproject/galaxy/commit/dfff5c966342b38603514d8bfd3e… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.loom Log Message: ----------- Add Loom datatype and remove rdata.seurat. Commit: f06da87189ccabd209f60509dd438bc690fc5523 https://github.com/galaxyproject/galaxy/commit/f06da87189ccabd209f60509dd43… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- remove comment Commit: 8462df83c9b3d5bdba93025f25dd182b7f22ea34 https://github.com/galaxyproject/galaxy/commit/8462df83c9b3d5bdba93025f25dd… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.loom Log Message: ----------- Merge pull request #6723 from blankenberg/18.09-loom [18.09] Add Loom datatype and remove rdata.seurat Commit: 5ace7d4015d5b5a21095ad1dc80344a90d13914d https://github.com/galaxyproject/galaxy/commit/5ace7d4015d5b5a21095ad1dc803… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.loom Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/ed147ee052a1...5ace7d4015d5 **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] dfff5c: Add Loom datatype and remove rdata.seurat.
by GitHub 18 Sep '18

18 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: dfff5c966342b38603514d8bfd3ed8e5b6e0bed9 https://github.com/galaxyproject/galaxy/commit/dfff5c966342b38603514d8bfd3e… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.loom Log Message: ----------- Add Loom datatype and remove rdata.seurat. Commit: f06da87189ccabd209f60509dd438bc690fc5523 https://github.com/galaxyproject/galaxy/commit/f06da87189ccabd209f60509dd43… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- remove comment Commit: 8462df83c9b3d5bdba93025f25dd182b7f22ea34 https://github.com/galaxyproject/galaxy/commit/8462df83c9b3d5bdba93025f25dd… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.loom Log Message: ----------- Merge pull request #6723 from blankenberg/18.09-loom [18.09] Add Loom datatype and remove rdata.seurat Compare: https://github.com/galaxyproject/galaxy/compare/aca30f0b158a...8462df83c9b3 **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] c8cb16: Merge pull request #6687 from dannon/version-18.09
by GitHub 18 Sep '18

18 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c8cb164ab8ad4fe5d7ea9768e3f7e58051200525 https://github.com/galaxyproject/galaxy/commit/c8cb164ab8ad4fe5d7ea9768e3f7… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #6687 from dannon/version-18.09 Update version to 18.09.rc1 Commit: 471162eadb4408318db534c6d24f7685bedb29eb https://github.com/galaxyproject/galaxy/commit/471162eadb4408318db534c6d24f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-11 (Tue, 11 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/extract_dataset.xml Log Message: ----------- [18.09] Fix new extract dataset to perserve collection element identifier. Commit: ba4e7d199b4bc080dcd741710d2241147bdbe745 https://github.com/galaxyproject/galaxy/commit/ba4e7d199b4bc080dcd741710d22… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Make gro and top datatypes tabular subclasses I think that was the intention in https://github.com/galaxyproject/galaxy/commit/56d55399ebe2ecd614a7ba5a1467… Commit: 80266129fe3d3d4b9657da0a3c5e8232bfa2a46b https://github.com/galaxyproject/galaxy/commit/80266129fe3d3d4b9657da0a3c5e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/extract_dataset.xml Log Message: ----------- Merge pull request #6692 from jmchilton/1809_fix_extract_name [18.09] Fix new extract dataset tool to preserve collection element identifier. Commit: 1f8c234c2be8baac9db94e17f4727e6c3c6c55ef https://github.com/galaxyproject/galaxy/commit/1f8c234c2be8baac9db94e17f472… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Make top datatype inherit from Text. Commit: 17157dd0633b4deb91a39bbc76288dd2968423f5 https://github.com/galaxyproject/galaxy/commit/17157dd0633b4deb91a39bbc7628… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #9 from blankenberg/gro2 Make top datatype inherit from Text. Commit: 9657cd6b32ed0768d2c73dd9d63c38432afb4b71 https://github.com/galaxyproject/galaxy/commit/9657cd6b32ed0768d2c73dd9d63c… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #6695 from mvdbeek/fix_gro_top_datatypes [18.09] Make gro and top datatypes tabular subclasses Commit: b4b49dc2028da2064fd34d7345b23b47150a1039 https://github.com/galaxyproject/galaxy/commit/b4b49dc2028da2064fd34d7345b2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js Log Message: ----------- Add self help to error reporting interface. Commit: 88bf3435775e94217bccfc46a5215311dea321aa https://github.com/galaxyproject/galaxy/commit/88bf3435775e94217bccfc46a521… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js Log Message: ----------- Import Backbone consistently across the app Commit: 84d66bea6008dc534aa6a2331e824005b204da19 https://github.com/galaxyproject/galaxy/commit/84d66bea6008dc534aa6a2331e82… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js Log Message: ----------- h2!=h3 Commit: 32223161c7ca735647d53ebfe4b90f1cd4051051 https://github.com/galaxyproject/galaxy/commit/32223161c7ca735647d53ebfe4b9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js Log Message: ----------- Merge pull request #6711 from dannon/error_help [18.09] Add self help to error reporting interface Commit: df4fbe6b92457fa910f014bbd3a8dd84c25d3969 https://github.com/galaxyproject/galaxy/commit/df4fbe6b92457fa910f014bbd3a8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js Log Message: ----------- Swap badge-default to badge-primary Commit: b2193bddc2aea250a189171ae61ed992b0449c84 https://github.com/galaxyproject/galaxy/commit/b2193bddc2aea250a189171ae61e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/docs/bootstrap.md Log Message: ----------- Drop badge-default from docs, correctly refer to secondary. Commit: a9273218424c1687bedf112591f2bbf735d32aa8 https://github.com/galaxyproject/galaxy/commit/a9273218424c1687bedf112591f2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Client format. Commit: 0040c36d4561155af3f32262d186e186349d989d https://github.com/galaxyproject/galaxy/commit/0040c36d4561155af3f32262d186… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/docs/bootstrap.md M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #6726 from dannon/badge-default-fix [18.09] Badge default fix Commit: 072d40f3e9a9050f034f440b76c8b84536bc0ead https://github.com/galaxyproject/galaxy/commit/072d40f3e9a9050f034f440b76c8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- remove html tags and newlines from the help text this should improve the toolsearch for certain keywords and also make the search index smaller Commit: b7f16228575215c9be134d1bbc1cf9e37b700488 https://github.com/galaxyproject/galaxy/commit/b7f16228575215c9be134d1bbc1c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- replace the replacement for newline from empty string to space, that should avoid unwanted word merges Commit: 17d67e24c072c8953e482aff41e9b1faed78b4d3 https://github.com/galaxyproject/galaxy/commit/17d67e24c072c8953e482aff41e9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- use bleach isntead of custom regex thanks @nsoranzo Commit: 54d137edab3fb33beac87c23cd35fb19dd7f44fa https://github.com/galaxyproject/galaxy/commit/54d137edab3fb33beac87c23cd35… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Remove deprecated `decode_param_names` parameter It has been deprecated since WebOb 1.1 and ignored since WebOb 1.2 . Commit: 8ed19a3a09df9b66266f66bc53e504c781ae524d https://github.com/galaxyproject/galaxy/commit/8ed19a3a09df9b66266f66bc53e5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/verify/interactor.py Log Message: ----------- `async` is a reserved keyword in Python 3.7 - Remove unused `async` parameter of `stage_data_async()` method. - Rename `async` parameter of `quick_load()` method. Fix https://github.com/galaxyproject/galaxy/issues/6717 . xref. https://github.com/galaxyproject/galaxy/issues/1715 Commit: 8982212d396c1ab216c5c9ea0656e5231e05d745 https://github.com/galaxyproject/galaxy/commit/8982212d396c1ab216c5c9ea0656… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/util/xml_macros.py M scripts/loc_files/create_all_fasta_loc.py Log Message: ----------- Replace deprecated `xml.etree.ElementTree.Element.getiterator()` with `iter()` Commit: f0708488aa08393cfdf3ab3e0e45e37982d050d0 https://github.com/galaxyproject/galaxy/commit/f0708488aa08393cfdf3ab3e0e45… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M pytest.ini Log Message: ----------- pytest: disable test collection of classes starting with `Test` Fix warnings like: ``` /home/travis/build/galaxyproject/galaxy/lib/galaxy/tools/verify/test_data.py:29: PytestWarning: cannot collect test class 'TestDataResolver' because it has a __init__ constructor class TestDataResolver(object): ``` appearing e.g. in https://travis-ci.org/galaxyproject/galaxy/jobs/428114139 . See pytest documentation: https://docs.pytest.org/en/latest/reference.html#confval-python_classes Commit: 2874e87debcc1940e1f1143a7af4dacb38c95585 https://github.com/galaxyproject/galaxy/commit/2874e87debcc1940e1f1143a7af4… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- Merge pull request #6728 from martenson/fix-toolhelp-parsing [18.09] remove html tags and newlines from the help text Commit: 0974b130ef922e3177de27f6365ccd624bf194a7 https://github.com/galaxyproject/galaxy/commit/0974b130ef922e3177de27f6365c… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/util/xml_macros.py M lib/galaxy/web/framework/base.py M pytest.ini M scripts/loc_files/create_all_fasta_loc.py Log Message: ----------- Merge pull request #6730 from nsoranzo/release_18.09_backport_6722 [18.09] Partial backport of #6722 Commit: 376516610ef6ac28cef7a9558adab1a88d8c0c12 https://github.com/galaxyproject/galaxy/commit/376516610ef6ac28cef7a9558ada… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Bugfix - missing tests for data source sniffing. Ensure #6334 is fixed I think. Commit: aca30f0b158a9ab0647747b957f55ea6716a4d18 https://github.com/galaxyproject/galaxy/commit/aca30f0b158a9ab0647747b957f5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Merge pull request #6733 from jmchilton/1809_sniff_test [18.09] Fix missing tests for data source sniffing. Commit: ed147ee052a1628aa07e33b3849f1d4fb2778d2b https://github.com/galaxyproject/galaxy/commit/ed147ee052a1628aa07e33b3849f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M client/galaxy/docs/bootstrap.md M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/datatypes_conf.xml.sample M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/extract_dataset.xml M lib/galaxy/tools/search/__init__.py M test/api/test_tools.py Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/e049786c4c75...ed147ee052a1 **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] 376516: Bugfix - missing tests for data source sniffing.
by GitHub 18 Sep '18

18 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 376516610ef6ac28cef7a9558adab1a88d8c0c12 https://github.com/galaxyproject/galaxy/commit/376516610ef6ac28cef7a9558ada… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Bugfix - missing tests for data source sniffing. Ensure #6334 is fixed I think. Commit: aca30f0b158a9ab0647747b957f55ea6716a4d18 https://github.com/galaxyproject/galaxy/commit/aca30f0b158a9ab0647747b957f5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Merge pull request #6733 from jmchilton/1809_sniff_test [18.09] Fix missing tests for data source sniffing. Compare: https://github.com/galaxyproject/galaxy/compare/0974b130ef92...aca30f0b158a **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] 1d4643: Update toolshed to 0974b130ef922e3177de27f6365ccd6...
by GitHub 18 Sep '18

18 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1d46435f76e456cee6ea1cd352a6e6cd01e12f92 https://github.com/galaxyproject/usegalaxy-playbook/commit/1d46435f76e456ce… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M env/toolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update toolshed to 0974b130ef922e3177de27f6365ccd624bf194a7 **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] 402506: Update testtoolshed to 0974b130ef922e3177de27f6365...
by GitHub 18 Sep '18

18 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 40250611b8876512c25c52a84aa01e006ec8fd87 https://github.com/galaxyproject/usegalaxy-playbook/commit/40250611b8876512… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update testtoolshed to 0974b130ef922e3177de27f6365ccd624bf194a7 **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] 6233a4: Release notes templated; still needs manual curati...
by GitHub 18 Sep '18

18 Sep '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: 6233a408cc93152a379651db3cc143d368f78dda https://github.com/galaxyproject/galaxy/commit/6233a408cc93152a379651db3cc1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: A doc/source/releases/18.09.rst A doc/source/releases/18.09_announce.rst A doc/source/releases/19.01_announce.rst Log Message: ----------- Release notes templated; still needs manual curation **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] 54d137: Remove deprecated `decode_param_names` parameter
by GitHub 18 Sep '18

18 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 54d137edab3fb33beac87c23cd35fb19dd7f44fa https://github.com/galaxyproject/galaxy/commit/54d137edab3fb33beac87c23cd35… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Remove deprecated `decode_param_names` parameter It has been deprecated since WebOb 1.1 and ignored since WebOb 1.2 . Commit: 8ed19a3a09df9b66266f66bc53e504c781ae524d https://github.com/galaxyproject/galaxy/commit/8ed19a3a09df9b66266f66bc53e5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/verify/interactor.py Log Message: ----------- `async` is a reserved keyword in Python 3.7 - Remove unused `async` parameter of `stage_data_async()` method. - Rename `async` parameter of `quick_load()` method. Fix https://github.com/galaxyproject/galaxy/issues/6717 . xref. https://github.com/galaxyproject/galaxy/issues/1715 Commit: 8982212d396c1ab216c5c9ea0656e5231e05d745 https://github.com/galaxyproject/galaxy/commit/8982212d396c1ab216c5c9ea0656… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/util/xml_macros.py M scripts/loc_files/create_all_fasta_loc.py Log Message: ----------- Replace deprecated `xml.etree.ElementTree.Element.getiterator()` with `iter()` Commit: f0708488aa08393cfdf3ab3e0e45e37982d050d0 https://github.com/galaxyproject/galaxy/commit/f0708488aa08393cfdf3ab3e0e45… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M pytest.ini Log Message: ----------- pytest: disable test collection of classes starting with `Test` Fix warnings like: ``` /home/travis/build/galaxyproject/galaxy/lib/galaxy/tools/verify/test_data.py:29: PytestWarning: cannot collect test class 'TestDataResolver' because it has a __init__ constructor class TestDataResolver(object): ``` appearing e.g. in https://travis-ci.org/galaxyproject/galaxy/jobs/428114139 . See pytest documentation: https://docs.pytest.org/en/latest/reference.html#confval-python_classes Commit: 0974b130ef922e3177de27f6365ccd624bf194a7 https://github.com/galaxyproject/galaxy/commit/0974b130ef922e3177de27f6365c… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/util/xml_macros.py M lib/galaxy/web/framework/base.py M pytest.ini M scripts/loc_files/create_all_fasta_loc.py Log Message: ----------- Merge pull request #6730 from nsoranzo/release_18.09_backport_6722 [18.09] Partial backport of #6722 Compare: https://github.com/galaxyproject/galaxy/compare/2874e87debcc...0974b130ef92 **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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