- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] f5301c: Dependencies fixes, follow up on #7070
by GitHub 06 Dec '18

06 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f5301c264592f5a6d3f7747b1f930f82384c9495 https://github.com/galaxyproject/galaxy/commit/f5301c264592f5a6d3f7747b1f93… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-05 (Wed, 05 Dec 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Dependencies fixes, follow up on #7070 Commit: 7eb436cebc39363330e9b0503c36b00cb763dbc5 https://github.com/galaxyproject/galaxy/commit/7eb436cebc39363330e9b0503c36… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-05 (Wed, 05 Dec 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh Log Message: ----------- Update all dependencies with `make update-dependencies` using pipenv 2018.11.26 . Also remove oscillating `python_version < '3.0'` environment marker for `azure-storage-nspkg` package. Commit: 4bf27f4642163be0c3b0b7399453833ba1013a8c https://github.com/galaxyproject/galaxy/commit/4bf27f4642163be0c3b0b7399453… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-12-06 (Thu, 06 Dec 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh Log Message: ----------- Merge pull request #7079 from nsoranzo/follow-up_on_7070 Follow-up on #7070 Compare: https://github.com/galaxyproject/galaxy/compare/c4dbf8615e98...4bf27f464216 **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] be4369: Avoid using make for autobuild; reducing necessary...
by GitHub 05 Dec '18

05 Dec '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: be43693ef05dfae85872412f198d87a31424f486 https://github.com/galaxyproject/galaxy/commit/be43693ef05dfae85872412f198d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-29 (Thu, 29 Nov 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Avoid using make for autobuild; reducing necessary dependencies out of the box. Commit: 77aec5a79dc18e224ca6246659f68a49864a46cf https://github.com/galaxyproject/galaxy/commit/77aec5a79dc18e224ca6246659f6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-29 (Thu, 29 Nov 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Standardize on spaces in common_startup.sh (tabs were mixed in here) Commit: fa408f485048ee8c7afeb96ac6c9da8dea4661f3 https://github.com/galaxyproject/galaxy/commit/fa408f485048ee8c7afeb96ac6c9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-29 (Thu, 29 Nov 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- exit with error code (and appropriate message) on either build failure Commit: 66fae561b29507a69f5c32690be4791f86f5cdd7 https://github.com/galaxyproject/galaxy/commit/66fae561b29507a69f5c32690be4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-12-02 (Sun, 02 Dec 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Don't use pushd/popd Commit: 57459954de189cb1fd9b6ab8654c8f4700241ea2 https://github.com/galaxyproject/galaxy/commit/57459954de189cb1fd9b6ab8654c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-05 (Wed, 05 Dec 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #7060 from dannon/no-make-for-autobuild [18.09] Eliminate dependency on make for automatic client build Compare: https://github.com/galaxyproject/galaxy/compare/46ad1992bdbf...57459954de18 **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] eeffb2: Implement colourful tags
by GitHub 05 Dec '18

05 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eeffb26423a2b6380087c01af5d3390c2fd9b0df https://github.com/galaxyproject/galaxy/commit/eeffb26423a2b6380087c01af5d3… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-item-li.js Log Message: ----------- Implement colourful tags Commit: e6c4292fd5a3182f01f16dfd445359f5dcb87e0c https://github.com/galaxyproject/galaxy/commit/e6c4292fd5a3182f01f16dfd4453… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js Log Message: ----------- Move to correct location Commit: 5865fe3513232fe893dd2a638a54218599be11a9 https://github.com/galaxyproject/galaxy/commit/5865fe3513232fe893dd2a638a54… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js Log Message: ----------- Add colorFg function Commit: 12576ef49477f51137cf0f223600a00c2c7b90e3 https://github.com/galaxyproject/galaxy/commit/12576ef49477f51137cf0f223600… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js Log Message: ----------- Replace with style function Commit: 0e7f2b3595a4235b1672205bd13b73153014f139 https://github.com/galaxyproject/galaxy/commit/0e7f2b3595a4235b1672205bd13b… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M client/galaxy/scripts/utils/utils.js Log Message: ----------- revert to grey border Commit: ad9787ef7050e3747b1b862ba857b1a2557174a0 https://github.com/galaxyproject/galaxy/commit/ad9787ef7050e3747b1b862ba857… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-12-05 (Wed, 05 Dec 2018) Changed paths: M client/galaxy/scripts/utils/utils.js Log Message: ----------- cleanup/docs Commit: c4dbf8615e98ae8778715e1169b537c8148af3b0 https://github.com/galaxyproject/galaxy/commit/c4dbf8615e98ae8778715e1169b5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-05 (Wed, 05 Dec 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js Log Message: ----------- Merge pull request #7072 from erasche/colour-tags Make tags more colourful Compare: https://github.com/galaxyproject/galaxy/compare/199cca9417d4...c4dbf8615e98 **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] 3931b8: improved parsing of sizes (bytes)
by GitHub 05 Dec '18

05 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3931b8ec355df64e780f640d39ac0928d7c8afde https://github.com/galaxyproject/galaxy/commit/3931b8ec355df64e780f640d39ac… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- improved parsing of sizes (bytes) before floats like without byte extension were not recognized (eg 1.0) Commit: 27cc49d3f785c643b4dcdbf0da09d1bf63ee44f9 https://github.com/galaxyproject/galaxy/commit/27cc49d3f785c643b4dcdbf0da09… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- size_to_bytes: use only regex, remove assert, add exceptions Commit: c90d71dd44794f8499813804290d08d3fdae6a6f https://github.com/galaxyproject/galaxy/commit/c90d71dd44794f8499813804290d… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Raise ValueError, fix spacing Commit: df51c468898e6bbc236e5a30a2758de4d06c9642 https://github.com/galaxyproject/galaxy/commit/df51c468898e6bbc236e5a30a275… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add missing empty line Commit: 26a6b1c83381d1c75131f330d8b8f4c23680f1dd https://github.com/galaxyproject/galaxy/commit/26a6b1c83381d1c75131f330d8b8… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Stricter regexp Commit: 199cca9417d484b8c4998f66beb4892de69accf3 https://github.com/galaxyproject/galaxy/commit/199cca9417d484b8c4998f66beb4… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-12-05 (Wed, 05 Dec 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #7067 from bernt-matthias/topic/size-parse Improved parsing of sizes (bytes) Compare: https://github.com/galaxyproject/galaxy/compare/ee8880657865...199cca9417d4 **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] c13eca: remove biostar config from Main
by GitHub 04 Dec '18

04 Dec '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c13eca7a954958839de6c7ae96eea3705a031801 https://github.com/galaxyproject/usegalaxy-playbook/commit/c13eca7a95495883… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- remove biostar config from Main **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] cf25f7: Fix nesting of repeats and error when repeat is pr...
by GitHub 04 Dec '18

04 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cf25f7dcec6f7f7b13aac93a18ced291d5e74444 https://github.com/galaxyproject/galaxy/commit/cf25f7dcec6f7f7b13aac93a18ce… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M lib/galaxy/tools/parameters/meta.py Log Message: ----------- Fix nesting of repeats and error when repeat is provided literally. This fixex #7048, where in addition to repeat values ('repeat_0|param: some_value') there are also values for the repeat param itself ('repeat': []). Commit: 3a93fd4f2321bf141b2ccf34ea80c42ee517b33d https://github.com/galaxyproject/galaxy/commit/3a93fd4f2321bf141b2ccf34ea80… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M test/unit/tools/test_parameter_parsing.py Log Message: ----------- Add test for proper nesting in process_keys and a unit test for https://github.com/galaxyproject/galaxy/issues/7048 Commit: 46ad1992bdbf478495b14780e96e251d00ceb700 https://github.com/galaxyproject/galaxy/commit/46ad1992bdbf478495b14780e96e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M lib/galaxy/tools/parameters/meta.py M test/unit/tools/test_parameter_parsing.py Log Message: ----------- Merge pull request #7071 from mvdbeek/fix_process_key [18.09] Fix process key Commit: ee88806578655fff9d32e72e90468e0ca87c877b https://github.com/galaxyproject/galaxy/commit/ee88806578655fff9d32e72e9046… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M lib/galaxy/tools/parameters/meta.py M test/unit/tools/test_parameter_parsing.py Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/aaa8d1a61cb5...ee8880657865 **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] cf25f7: Fix nesting of repeats and error when repeat is pr...
by GitHub 04 Dec '18

04 Dec '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: cf25f7dcec6f7f7b13aac93a18ced291d5e74444 https://github.com/galaxyproject/galaxy/commit/cf25f7dcec6f7f7b13aac93a18ce… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M lib/galaxy/tools/parameters/meta.py Log Message: ----------- Fix nesting of repeats and error when repeat is provided literally. This fixex #7048, where in addition to repeat values ('repeat_0|param: some_value') there are also values for the repeat param itself ('repeat': []). Commit: 3a93fd4f2321bf141b2ccf34ea80c42ee517b33d https://github.com/galaxyproject/galaxy/commit/3a93fd4f2321bf141b2ccf34ea80… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M test/unit/tools/test_parameter_parsing.py Log Message: ----------- Add test for proper nesting in process_keys and a unit test for https://github.com/galaxyproject/galaxy/issues/7048 Commit: 46ad1992bdbf478495b14780e96e251d00ceb700 https://github.com/galaxyproject/galaxy/commit/46ad1992bdbf478495b14780e96e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M lib/galaxy/tools/parameters/meta.py M test/unit/tools/test_parameter_parsing.py Log Message: ----------- Merge pull request #7071 from mvdbeek/fix_process_key [18.09] Fix process key Compare: https://github.com/galaxyproject/galaxy/compare/51afe15f86c0...46ad1992bdbf **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] 118cd1: downgrade bdbag, 1.5.0 requires python:>=2.7.9 whi...
by GitHub 04 Dec '18

04 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 118cd15186fc3d8d4784f8847355542ee07a8a5a https://github.com/galaxyproject/galaxy/commit/118cd15186fc3d8d4784f8847355… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-03 (Mon, 03 Dec 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- downgrade bdbag, 1.5.0 requires python:>=2.7.9 which centos7 does not have Commit: aaa8d1a61cb567b49b2171e27bc623b59c0227fe https://github.com/galaxyproject/galaxy/commit/aaa8d1a61cb567b49b2171e27bc6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #7070 from martenson/downgrade-bdbag downgrade bdbag, 1.5.0 requires python:>=2.7.9 Compare: https://github.com/galaxyproject/galaxy/compare/c679b64272cc...aaa8d1a61cb5 **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] 582597: Update Main
by GitHub 03 Dec '18

03 Dec '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 582597f68c785d034fe8139e4031226c610b8631 https://github.com/galaxyproject/usegalaxy-playbook/commit/582597f68c785d03… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-03 (Mon, 03 Dec 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main **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] 1e771e: update test
by GitHub 03 Dec '18

03 Dec '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1e771e3bdd521764ab9d89b43ef1c6019f7d0082 https://github.com/galaxyproject/usegalaxy-playbook/commit/1e771e3bdd521764… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-03 (Mon, 03 Dec 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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