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

[galaxyproject/galaxy] af0b40: Bump sqlite3 dependency for web proxy
by GitHub 21 Feb '18

21 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: af0b40ea95c5244c58fbaa545b81ef4c4eff7cf0 https://github.com/galaxyproject/galaxy/commit/af0b40ea95c5244c58fbaa545b81… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/web/proxy/js/package.json Log Message: ----------- Bump sqlite3 dependency for web proxy Commit: 5d422898582446575dfe30d13805c9e13a3f8104 https://github.com/galaxyproject/galaxy/commit/5d422898582446575dfe30d13805… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/web/proxy/js/package.json Log Message: ----------- Minor updates to commander, http-proxy. eventemitter3 is several major versions behind, needs testing before upgrade. Commit: b5b41d6172bd7e2894efcc3b423b11a37fb92823 https://github.com/galaxyproject/galaxy/commit/b5b41d6172bd7e2894efcc3b423b… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/web/proxy/js/package.json Log Message: ----------- Merge pull request #5575 from dannon/web_proxy_fixes [18.01] Bump sqlite3 dependency for web proxy Compare: https://github.com/galaxyproject/galaxy/compare/7715838dbbbc...b5b41d6172bd

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[galaxyproject/galaxy] 1fca44: Python3: Update bx-python dependency to 0.8.1
by GitHub 21 Feb '18

21 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1fca449c7c6b383757e962bac70c851528b89ac4 https://github.com/galaxyproject/galaxy/commit/1fca449c7c6b383757e962bac70c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Python3: Update bx-python dependency to 0.8.1 Commit: c5adb2d2eb8736fb19282a530aa4669bf03f554e https://github.com/galaxyproject/galaxy/commit/c5adb2d2eb8736fb19282a530aa4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #5492 from nsoranzo/python3 Python3: Update bx-python dependency to 0.8.1 Compare: https://github.com/galaxyproject/galaxy/compare/3cf84ea3da0e...c5adb2d2eb87

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[galaxyproject/galaxy] 31e31e: added fasta.gz
by GitHub 20 Feb '18

20 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 31e31e692311ba2e9f11d3eabe5253628f8e39c9 https://github.com/galaxyproject/galaxy/commit/31e31e692311ba2e9f11d3eabe52… Author: nekrut <anton(a)nekrut.org> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/fastagz_to_fasta.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- added fasta.gz Commit: d79717b86e0b6ecf5e540eb939888066b88081de https://github.com/galaxyproject/galaxy/commit/d79717b86e0b6ecf5e540eb93988… Author: nekrut <anton(a)nekrut.org> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- fixed flake8 errors Commit: 8cec1fd592a354be9b055fbb8b7f3ce72df39990 https://github.com/galaxyproject/galaxy/commit/8cec1fd592a354be9b055fbb8b7f… Author: nekrut <anton(a)nekrut.org> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- removing stray whitespace Commit: d34524ff8adc694e41f0e582a57f705f2ed0dd7d https://github.com/galaxyproject/galaxy/commit/d34524ff8adc694e41f0e582a57f… Author: nekrut <anton(a)nekrut.org> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/fastagz_to_fasta.xml Log Message: ----------- fixed name of fastagz->fasta converter Commit: c4ce9695bbb577a0e9514c5cb71069156d33a943 https://github.com/galaxyproject/galaxy/commit/c4ce9695bbb577a0e9514c5cb710… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/fastagz_to_fasta.xml Log Message: ----------- fix copypasta Commit: 9feaf85585a30820dd71762431e1ed7d5b5c3b5e https://github.com/galaxyproject/galaxy/commit/9feaf85585a30820dd71762431e1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- fix more fasta copypasta Commit: 7715838dbbbcad980a47d1a96619b6e91fa7a623 https://github.com/galaxyproject/galaxy/commit/7715838dbbbcad980a47d1a96619… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/fastagz_to_fasta.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Merge pull request #5561 from martenson/backport-fastgz [18.01] add fasta.gz support Compare: https://github.com/galaxyproject/galaxy/compare/99f7de456ce9...7715838dbbbc

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[galaxyproject/galaxy] 17a5d2: In test framework only build client if running Sel...
by GitHub 20 Feb '18

20 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 17a5d20278f7306e69e77054f92d976020e048ee https://github.com/galaxyproject/galaxy/commit/17a5d20278f7306e69e77054f92d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M run_tests.sh Log Message: ----------- In test framework only build client if running Selenium tests. These shouldn't be required for any other test types I believe and it slows things down. Commit: 99f7de456ce953f36e6122270209083fe443654b https://github.com/galaxyproject/galaxy/commit/99f7de456ce953f36e6122270209… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #5566 from jmchilton/optimize_tests_0 [18.01] In test framework only build client if running Selenium tests. Compare: https://github.com/galaxyproject/galaxy/compare/01776c617b69...99f7de456ce9

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[galaxyproject/usegalaxy-playbook] fd3eec: Remove banner from main
by GitHub 20 Feb '18

20 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fd3eec003de41470d194bd44947a29a9102c7257 https://github.com/galaxyproject/usegalaxy-playbook/commit/fd3eec003de41470… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Remove banner from main

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[galaxyproject/usegalaxy-playbook] 1d6875: Update Main Pulsars
by GitHub 20 Feb '18

20 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1d68758035274c4fb1ede87f1a36357d4b8a0a36 https://github.com/galaxyproject/usegalaxy-playbook/commit/1d68758035274c4f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M env/main/group_vars/pulsarservers/vars.yml Log Message: ----------- Update Main Pulsars

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[galaxyproject/usegalaxy-playbook] ee3ef3: Add conda mulling to changelog
by GitHub 20 Feb '18

20 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ee3ef3bca22a6cb8884c5c58f5ccb864f2cc81be https://github.com/galaxyproject/usegalaxy-playbook/commit/ee3ef3bca22a6cb8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M CHANGELOG.md Log Message: ----------- Add conda mulling to changelog

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[galaxyproject/usegalaxy-playbook] ba472f: Upgrade Test Pulsar
by GitHub 20 Feb '18

20 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ba472f62d7fb2217fd2523a471857b52ccb06198 https://github.com/galaxyproject/usegalaxy-playbook/commit/ba472f62d7fb2217… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M env/test/group_vars/pulsarservers/vars.yml Log Message: ----------- Upgrade Test Pulsar

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[galaxyproject/usegalaxy-playbook] 21bd0b: Someone updated ncbi tools, also reordered plant t...
by GitHub 20 Feb '18

20 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 21bd0b534321d1773eead7010516615e1d0a7337 https://github.com/galaxyproject/usegalaxy-playbook/commit/21bd0b534321d177… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Someone updated ncbi tools, also reordered plant tribes tools in the tool panel.

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[galaxyproject/galaxy] 2ca339: fix broken admin 'create new user' when registrati...
by GitHub 20 Feb '18

20 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 2ca339d2b7cfdde817097837033e317a19b4a801 https://github.com/galaxyproject/galaxy/commit/2ca339d2b7cfdde817097837033e… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M lib/galaxy/auth/__init__.py Log Message: ----------- fix broken admin 'create new user' when registration =='challenge' Commit: 01776c617b691c467e423c7a5f60c17be9b71503 https://github.com/galaxyproject/galaxy/commit/01776c617b691c467e423c7a5f60… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M lib/galaxy/auth/__init__.py Log Message: ----------- Merge pull request #5569 from scholtalbers/fix/broken_create_new_user_challenge [18.01] fix broken admin 'create new user' when registration =='challenge' Compare: https://github.com/galaxyproject/galaxy/compare/6a3ce34c09bd...01776c617b69

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