December 2018 - galaxy-commits - lists.galaxyproject.org

[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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[galaxyproject/usegalaxy-playbook] 1dc0e8: add helpsite config to Test and Main
by GitHub 03 Dec '18

03 Dec '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1dc0e8d68d9be0e49065d5d5c00c4e220e25dfb7 https://github.com/galaxyproject/usegalaxy-playbook/commit/1dc0e8d68d9be0e4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-03 (Mon, 03 Dec 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- add helpsite config to Test and 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] 670358: Fix link to requirements.txt
by GitHub 02 Dec '18

02 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6703584714507f129fee6e967df875bfa6027fc0 https://github.com/galaxyproject/galaxy/commit/6703584714507f129fee6e967df8… Author: Sergey Golitsynskiy <sgolitsynskiy(a)gmail.com> Date: 2018-11-30 (Fri, 30 Nov 2018) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- Fix link to requirements.txt Dependency files rearranged (commit 1b0ccf6, Nov. 1, 2017) Commit: c679b64272ccbff630fd68d9f201b95d54e75e00 https://github.com/galaxyproject/galaxy/commit/c679b64272ccbff630fd68d9f201… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-02 (Sun, 02 Dec 2018) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- Merge pull request #7065 from ic4f/dev Fix link to requirements.txt Compare: https://github.com/galaxyproject/galaxy/compare/030cf02fc800...c679b64272cc **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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