- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] c034a0: Fix FTP on Test and enable PBKDF2.
by GitHub 09 May '17

09 May '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c034a067b23940feee7d32f63abfed6e375077a0 https://github.com/galaxyproject/usegalaxy-playbook/commit/c034a067b23940fe… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-09 (Tue, 09 May 2017) Changed paths: M env/test/group_vars/ftpservers.yml M env/test/group_vars/galaxyservers/vars.yml M roles/galaxyprojectdotorg.proftpd/tasks/galaxy_auth.yml M roles/galaxyprojectdotorg.proftpd/templates/galaxy_auth.conf.j2 Log Message: ----------- Fix FTP on Test and enable PBKDF2.

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[galaxyproject/usegalaxy-playbook] dd1df6: Increase extract maf blocks to 16GB
by GitHub 09 May '17

09 May '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dd1df620bf43bfa0cb0c83258f93bd20eea621ba https://github.com/galaxyproject/usegalaxy-playbook/commit/dd1df620bf43bfa0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-09 (Tue, 09 May 2017) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Increase extract maf blocks to 16GB

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[galaxyproject/galaxy] 614d03: Add test case clarifying datasets do get "renamed"...
by GitHub 09 May '17

09 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 614d032f1254b5bf5032c4c3ddcecfeba6d1eea7 https://github.com/galaxyproject/galaxy/commit/614d032f1254b5bf5032c4c3ddce… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Add test case clarifying datasets do get "renamed" by rename PJA in collections. xref #1675 This is of limited utility since we don't really expose the name - and intentionally so. Related open bugs/enhancements that still need to be addressed are: - Applying rename to the collection (in addition to the elements) - #1680. - Download of collection elements with element identifier instead of the name: #2023 / #2140. Commit: 8acea3445019f0b69006fa48f4172bf08bdaa257 https://github.com/galaxyproject/galaxy/commit/8acea3445019f0b69006fa48f417… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-08 (Mon, 08 May 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Merge pull request #3983 from jmchilton/collection_rename Add test case clarifying datasets do get "renamed" by rename PJA in collections. Compare: https://github.com/galaxyproject/galaxy/compare/baa85bf78886...8acea3445019

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[galaxyproject/galaxy] 5ba5e8: One more fix for main_panel fix in #3992.
by GitHub 08 May '17

08 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5ba5e8a85fde38524a28cc907a894a8e9ada9c7e https://github.com/galaxyproject/galaxy/commit/5ba5e8a85fde38524a28cc907a89… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-08 (Mon, 08 May 2017) Changed paths: M test/selenium_tests/test_tool_form.py Log Message: ----------- One more fix for main_panel fix in #3992. See #4003 / d09ba53c8e4e51645ae2c37387493bfd2511196b for similar fix to other tests and more information. Commit: baa85bf788860171159593efdf1941a666324f5b https://github.com/galaxyproject/galaxy/commit/baa85bf788860171159593efdf19… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-08 (Mon, 08 May 2017) Changed paths: M test/selenium_tests/test_tool_form.py Log Message: ----------- Merge pull request #4042 from jmchilton/selenium_fixes_12 One more fix for main_panel fix in #3992. Compare: https://github.com/galaxyproject/galaxy/compare/80e2866bbcdd...baa85bf78886

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[galaxyproject/galaxy] a0c59d: Try activating conda environment again if previous...
by GitHub 08 May '17

08 May '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: a0c59d8f05c011f6c7b002599ed09c3fe091c340 https://github.com/galaxyproject/galaxy/commit/a0c59d8f05c011f6c7b002599ed0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Try activating conda environment again if previous activation failed Commit: c38c0276afb88ed5b1403ede53ae35247307890d https://github.com/galaxyproject/galaxy/commit/c38c0276afb88ed5b1403ede53ae… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-05-07 (Sun, 07 May 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Exit with error message when conda environemnt could not be activated (thx @nsoranzo). Commit: 9e6c1529929132414e240e306d2b244ef6853944 https://github.com/galaxyproject/galaxy/commit/9e6c1529929132414e240e306d2b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-08 (Mon, 08 May 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #4035 from mvdbeek/retry_conda_activation [17.05] Try activating conda environment again if previous activation failed Compare: https://github.com/galaxyproject/galaxy/compare/6ef7b9977a3e...9e6c15299291

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[galaxyproject/usegalaxy-playbook] 2c0645: Update Main to 17.05
by GitHub 08 May '17

08 May '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2c06456c007e38670d343967f1d601bb28923db6 https://github.com/galaxyproject/usegalaxy-playbook/commit/2c06456c007e3867… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-08 (Mon, 08 May 2017) Changed paths: M production/files/interactive_environments/plugins/.ansible_ie_role_current_version M production/files/interactive_environments/plugins/bam_iobio/config/bam_iobio.ini.sample M production/files/interactive_environments/plugins/bam_iobio/static/js/bam_iobio.js M production/files/interactive_environments/plugins/bam_iobio/templates/bam_iobio.mako M production/files/interactive_environments/plugins/common/templates/ie.mako A production/files/interactive_environments/plugins/ethercalc/config/allowed_images.yml.sample A production/files/interactive_environments/plugins/ethercalc/config/ethercalc.ini.sample A production/files/interactive_environments/plugins/ethercalc/config/ethercalc.xml A production/files/interactive_environments/plugins/ethercalc/static/js/ethercalc.js A production/files/interactive_environments/plugins/ethercalc/templates/ethercalc.mako M production/files/interactive_environments/plugins/jupyter/config/allowed_images.yml.sample M production/files/interactive_environments/plugins/jupyter/config/jupyter.ini.sample M production/files/interactive_environments/plugins/jupyter/config/jupyter.xml M production/files/interactive_environments/plugins/jupyter/static/js/jupyter.js M production/files/interactive_environments/plugins/jupyter/templates/jupyter.mako M production/files/interactive_environments/plugins/neo/config/neo.ini.sample M production/files/interactive_environments/plugins/neo/static/js/neo.js M production/files/interactive_environments/plugins/neo/templates/neo.mako M production/files/interactive_environments/plugins/phinch/config/phinch.ini.sample M production/files/interactive_environments/plugins/phinch/static/js/phinch.js M production/files/interactive_environments/plugins/phinch/templates/phinch.mako M production/files/interactive_environments/plugins/rstudio/config/allowed_images.yml.sample M production/files/interactive_environments/plugins/rstudio/config/rstudio.ini.sample M production/files/interactive_environments/plugins/rstudio/static/js/rstudio.js M production/files/interactive_environments/plugins/rstudio/templates/rstudio.mako M production/files/interactive_environments/proxy/.ansible_ie_role_current_version M production/files/interactive_environments/proxy/lib/mapper.js M production/files/interactive_environments/proxy/package.json M production/galaxy_version.yml M production/group_vars/all.yml Log Message: ----------- Update Main to 17.05

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[galaxyproject/usegalaxy-playbook] 61b4ab: Update Test
by GitHub 08 May '17

08 May '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 61b4ab56cf483a5398f3272d992e8106cdccd135 https://github.com/galaxyproject/usegalaxy-playbook/commit/61b4ab56cf483a53… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-08 (Mon, 08 May 2017) Changed paths: M env/test/files/galaxy/galaxy_version.yml M env/test/files/interactive_environments/plugins/.ansible_ie_role_current_version M env/test/files/interactive_environments/plugins/jupyter/config/allowed_images.yml.sample M env/test/files/interactive_environments/proxy/.ansible_ie_role_current_version M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Update Test

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[galaxyproject/galaxy] e8fdd8: two condor fixes, to make it fly
by GitHub 08 May '17

08 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e8fdd88134ea34e680cb1b244f63e02bb0a31a37 https://github.com/galaxyproject/galaxy/commit/e8fdd88134ea34e680cb1b244f63… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- two condor fixes, to make it fly Commit: 0822d2220726446faf13d4be1a6f3643d746eea5 https://github.com/galaxyproject/galaxy/commit/0822d2220726446faf13d4be1a6f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-05-06 (Sat, 06 May 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Docker universe needs to wait Commit: 80e2866bbcdd46b1e5f7d84cfbd954590f3b3122 https://github.com/galaxyproject/galaxy/commit/80e2866bbcdd46b1e5f7d84cfbd9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-08 (Mon, 08 May 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge pull request #4038 from bgruening/release_17.05 [17.05] ht-condor fixe for running containers Compare: https://github.com/galaxyproject/galaxy/compare/b008ee445049...80e2866bbcdd

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[galaxyproject/galaxy] 57b8fd: Prevent graphite from dying loudly
by GitHub 05 May '17

05 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 57b8fdb391c44e548e312b5a031c1dfb72a03833 https://github.com/galaxyproject/galaxy/commit/57b8fdb391c44e548e312b5a031c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M lib/galaxy/web/framework/middleware/graphite.py Log Message: ----------- Prevent graphite from dying loudly Commit: b008ee44504916cfa696f7770f47b926feb2ab6b https://github.com/galaxyproject/galaxy/commit/b008ee44504916cfa696f7770f47… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M lib/galaxy/web/framework/middleware/graphite.py Log Message: ----------- Merge pull request #4036 from erasche/stats-death Prevent graphite from dying loudly Compare: https://github.com/galaxyproject/galaxy/compare/53eff63a3606...b008ee445049

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[galaxyproject/galaxy] d09ba5: Fix handling main_panel switching in various Selen...
by GitHub 05 May '17

05 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d09ba53c8e4e51645ae2c37387493bfd2511196b https://github.com/galaxyproject/galaxy/commit/d09ba53c8e4e51645ae2c3738749… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_login.py M test/selenium_tests/test_registration.py Log Message: ----------- Fix handling main_panel switching in various Selenium tests. PR #3992 fixed "with self.main_panel()" so that leaving the context actually restore the Selenium context back to the top level page. This surfaced a bunch of bugs related to assertions that were operating in the main panel without declaring it. This fixes those and makes the assertions a bit stronger - such as verifying error messages being asserted about are visible. Commit: 53eff63a3606fc31cc0a989ecd81fd8d6f8c624b https://github.com/galaxyproject/galaxy/commit/53eff63a3606fc31cc0a989ecd81… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_login.py M test/selenium_tests/test_registration.py Log Message: ----------- Merge pull request #4003 from jmchilton/selenium_fixes_11 Fix handling main_panel switching in various Selenium tests. Compare: https://github.com/galaxyproject/galaxy/compare/01d00a13b214...53eff63a3606

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[galaxyproject/usegalaxy-playbook] d32bb8: Updated slide show on landing page.
by GitHub 04 May '17

04 May '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d32bb89ae9efc13ae94a2ab9b4cba90d62f574eb https://github.com/galaxyproject/usegalaxy-playbook/commit/d32bb89ae9efc13a… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2017-05-04 (Thu, 04 May 2017) Changed paths: A files/galaxy/common/static/welcome_img/GCC2017EarlyReg.png A files/galaxy/common/static/welcome_img/ISMBECCB2017Tutorial.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Updated slide show on landing page.

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[galaxyproject/galaxy] f75e21: Fix spelling error in error message.
by GitHub 04 May '17

04 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f75e21898ae52cc91ed52db3ef01ee5770b9beb0 https://github.com/galaxyproject/galaxy/commit/f75e21898ae52cc91ed52db3ef01… Author: pvanheus <pvh(a)webbedfeet.co.za> Date: 2017-05-04 (Thu, 04 May 2017) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- Fix spelling error in error message. Commit: 01d00a13b21450e59cb366d0292e44525a7d1fbb https://github.com/galaxyproject/galaxy/commit/01d00a13b21450e59cb366d0292e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-04 (Thu, 04 May 2017) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- Merge pull request #4026 from pvanheus/patch-2 Fix spelling error in error message. Compare: https://github.com/galaxyproject/galaxy/compare/16d9a752e8e5...01d00a13b214

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[galaxyproject/galaxy] 609842: [17.05] Pin dependencies for linting Galaxy.
by GitHub 04 May '17

04 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 609842e558da5f60eef94809204b48204fc8158a https://github.com/galaxyproject/galaxy/commit/609842e558da5f60eef94809204b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M tox.ini Log Message: ----------- [17.05] Pin dependencies for linting Galaxy. Commit: aeed375c0286315c2b893d7b807d3522c5c21a36 https://github.com/galaxyproject/galaxy/commit/aeed375c0286315c2b893d7b807d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M tox.ini Log Message: ----------- Merge pull request #4012 from jmchilton/17.05_pin_release_linting [17.05] Pin dependencies for linting Galaxy. Commit: ce8f0dec0532266bff5d277f8acc50a4c6a9b2b5 https://github.com/galaxyproject/galaxy/commit/ce8f0dec0532266bff5d277f8acc… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #4009 from jmchilton/version-17.05 [17.05] Update version to 17.05.rc1 Commit: 460d1737beb5d6e3e966c33998a7d5d046ac3e87 https://github.com/galaxyproject/galaxy/commit/460d1737beb5d6e3e966c33998a7… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- typo Commit: 8dd5b153ed728591d3e44acb4271afc0210981f2 https://github.com/galaxyproject/galaxy/commit/8dd5b153ed728591d3e44acb4271… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py Log Message: ----------- Pass hdca and element_identifier to _serve_raw This is necessary for getting the new filenames introduced in #3985 if downloading tabular datatypes. Closes #4016. Commit: 99317c77557ed4daec4c36619ec90a45a51e35eb https://github.com/galaxyproject/galaxy/commit/99317c77557ed4daec4c36619ec9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #4017 from mvdbeek/fix_new_download_names_tabular Pass hdca and element_identifier to _serve_raw Commit: 6ef7b9977a3ed936c02b3e7fadfd105bbaea9595 https://github.com/galaxyproject/galaxy/commit/6ef7b9977a3ed936c02b3e7fadfd… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #4015 from erasche/remote-user-bug [17.05] Typo in remote user / user preferences exception Commit: 16d9a752e8e532fe503832698fed203626b872b5 https://github.com/galaxyproject/galaxy/commit/16d9a752e8e532fe503832698fed… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-05-04 (Thu, 04 May 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge branch 'release_17.05' into dev Revert changes to tox.ini Compare: https://github.com/galaxyproject/galaxy/compare/8d09854c1d7e...16d9a752e8e5

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[galaxyproject/galaxy] 788886: Adds supplemental group support for the Kubernetes...
by GitHub 04 May '17

04 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 788886e1cec7abe9b7e50de76a93117c4b64ca2e https://github.com/galaxyproject/galaxy/commit/788886e1cec7abe9b7e50de76a93… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Adds supplemental group support for the Kubernetes runner. Commit: aa2465db8684f807e5fdd6a8ae60079c37bf5723 https://github.com/galaxyproject/galaxy/commit/aa2465db8684f807e5fdd6a8ae60… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Improves handling of supplemental group. Commit: 528ea5c74831c3bc9e36e6a236956b784a3642ce https://github.com/galaxyproject/galaxy/commit/528ea5c74831c3bc9e36e6a23695… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Adds Kubernetes fsGroup id support. Commit: bc96a0c267410fa229126512bb016dc17581d242 https://github.com/galaxyproject/galaxy/commit/bc96a0c267410fa229126512bb01… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Adds support for job api version setting, and changes default to batch/v1 Commit: cc4a37d22b5e7cd3274ead8314f41a0ac419ebbc https://github.com/galaxyproject/galaxy/commit/cc4a37d22b5e7cd3274ead8314f4… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Adds pull policy support Commit: 9ffbcddb3918af2d55cd1383d6a8a148c4da179e https://github.com/galaxyproject/galaxy/commit/9ffbcddb3918af2d55cd1383d6a8… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Style improvements Commit: 8afcfa4ec926e589ea94dd2d84ada824ed2d7578 https://github.com/galaxyproject/galaxy/commit/8afcfa4ec926e589ea94dd2d84ad… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M .ci/jenkins/selenium/run_tests.sh M .travis.yml M CITATION M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.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/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/style/less/ui.less M config/galaxy.ini.sample M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako A doc/source/admin/special_topics/grafana.png M doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/performance_tracking.rst M lib/galaxy/config.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/managers/configuration.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py A lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/js/package.json M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py M lib/tool_shed/galaxy_install/tools/data_manager.py M run_tests.sh M static/maps/mvc/citation/citation-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/viz/phyloviz.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/citation/citation-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/viz/phyloviz.js M static/style/blue/base.css M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/user/index.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/tool_shed/base_panels.mako M test/api/test_jobs.py M test/api/test_workflows.py M test/galaxy_selenium/navigates_galaxy.py M test/qunit/tests/form_tests.js M test/qunit/tests/ui_tests.js M test/selenium_tests/framework.py M test/selenium_tests/test_workflow_run.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into feature/pr_fs_access_job_version Commit: 8fcf46d31c731eb5198305d1a8b5fd37d1d1c20b https://github.com/galaxyproject/galaxy/commit/8fcf46d31c731eb5198305d1a8b5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Touch up k8 options in job_conf sample. Optional options should be commented out - I guess only the two claim options need to have non-default values specified? Commit: 8a1cc7a7eb0627907b404e7ad69e5e4aaf279d69 https://github.com/galaxyproject/galaxy/commit/8a1cc7a7eb0627907b404e7ad69e… Author: Pablo Moreno <pcm32(a)users.noreply.github.com> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M .ci/jenkins/selenium/run_tests.sh M .travis.yml M CITATION M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.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/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/style/less/ui.less M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako A doc/source/admin/special_topics/grafana.png M doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/performance_tracking.rst M lib/galaxy/config.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/managers/configuration.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py A lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/js/package.json M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py M lib/tool_shed/galaxy_install/tools/data_manager.py M run_tests.sh M static/maps/mvc/citation/citation-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/viz/phyloviz.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/citation/citation-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/viz/phyloviz.js M static/style/blue/base.css M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/user/index.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/tool_shed/base_panels.mako M test/api/test_jobs.py M test/api/test_workflows.py M test/galaxy_selenium/navigates_galaxy.py M test/qunit/tests/form_tests.js M test/qunit/tests/ui_tests.js M test/selenium_tests/framework.py M test/selenium_tests/test_workflow_run.py M tox.ini Log Message: ----------- Merge pull request #8 from jmchilton/feature/pr_fs_access_job_version Touch up config options. Commit: b2871d15b7f0dab2291986173a7cd0825a26f6fe https://github.com/galaxyproject/galaxy/commit/b2871d15b7f0dab2291986173a7c… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Makes config path for k8s required in sample config file. Commit: 8d09854c1d7e7e33c777897f11d771cb933db35b https://github.com/galaxyproject/galaxy/commit/8d09854c1d7e7e33c777897f11d7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-04 (Thu, 04 May 2017) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge pull request #3972 from phnmnl/feature/pr_fs_access_job_version Kubernetes runner: Non-privileged filesystem access, updated k8s Job version Compare: https://github.com/galaxyproject/galaxy/compare/5077b7ce0e55...8d09854c1d7e

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[galaxyproject/galaxy] 6a9491: add dev requirement
by GitHub 04 May '17

04 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6a949120832c414a4b891b33bc7b7bda86802e83 https://github.com/galaxyproject/galaxy/commit/6a949120832c414a4b891b33bc7b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M scripts/bootstrap_history.py Log Message: ----------- add dev requirement remove nitesh and carl from devteam Commit: 5077b7ce0e55646242d741311487ca8c0f0cdeb9 https://github.com/galaxyproject/galaxy/commit/5077b7ce0e55646242d741311487… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-04 (Thu, 04 May 2017) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #4008 from martenson/release-process-fix add dev requirement Compare: https://github.com/galaxyproject/galaxy/compare/d226390c1857...5077b7ce0e55

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[galaxyproject/galaxy] f78b57: Simplify RC creation in Makefile.
by GitHub 03 May '17

03 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f78b5709a55693313568c5bea5a08db3f083779b https://github.com/galaxyproject/galaxy/commit/f78b5709a55693313568c5bea5a0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M Makefile Log Message: ----------- Simplify RC creation in Makefile. These commands fail without any harm and then prevent the important echo statements from printing that follow them. Commit: d226390c185799d03ce9e42cc2939ad2a1ae4e6a https://github.com/galaxyproject/galaxy/commit/d226390c185799d03ce9e42cc293… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M Makefile Log Message: ----------- Merge pull request #4011 from jmchilton/simplify_makefile_create_rc Simplify RC creation in Makefile. Compare: https://github.com/galaxyproject/galaxy/compare/8bc0100165f4...d226390c1857

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[galaxyproject/galaxy] 460d17: typo
by GitHub 03 May '17

03 May '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 460d1737beb5d6e3e966c33998a7d5d046ac3e87 https://github.com/galaxyproject/galaxy/commit/460d1737beb5d6e3e966c33998a7… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- typo Commit: 6ef7b9977a3ed936c02b3e7fadfd105bbaea9595 https://github.com/galaxyproject/galaxy/commit/6ef7b9977a3ed936c02b3e7fadfd… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #4015 from erasche/remote-user-bug [17.05] Typo in remote user / user preferences exception Compare: https://github.com/galaxyproject/galaxy/compare/99317c77557e...6ef7b9977a3e

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[galaxyproject/galaxy] 8dd5b1: Pass hdca and element_identifier to _serve_raw
by GitHub 03 May '17

03 May '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 8dd5b153ed728591d3e44acb4271afc0210981f2 https://github.com/galaxyproject/galaxy/commit/8dd5b153ed728591d3e44acb4271… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py Log Message: ----------- Pass hdca and element_identifier to _serve_raw This is necessary for getting the new filenames introduced in #3985 if downloading tabular datatypes. Closes #4016. Commit: 99317c77557ed4daec4c36619ec90a45a51e35eb https://github.com/galaxyproject/galaxy/commit/99317c77557ed4daec4c36619ec9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #4017 from mvdbeek/fix_new_download_names_tabular Pass hdca and element_identifier to _serve_raw Compare: https://github.com/galaxyproject/galaxy/compare/ce8f0dec0532...99317c77557e

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[galaxyproject/infrastructure-playbook] c030d1: Update Jupyter image
by GitHub 03 May '17

03 May '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c030d1b91b13dec07fa74d11f5c74645a14fa5da https://github.com/galaxyproject/infrastructure-playbook/commit/c030d1b91b1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M jetstreamdockerenv/group_vars/imageinstances.yml Log Message: ----------- Update Jupyter image Commit: 1a034df83b5073b0aff779299dcec610cb3a0854 https://github.com/galaxyproject/infrastructure-playbook/commit/1a034df83b5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M roles/stats/defaults/main.yml M roles/stats/tasks/main.yml A roles/stats/templates/galaxy_slurp.py.j2 M taccenv/group_vars/statsservers.yml M taccenv/secret_group_vars/stats.yml Log Message: ----------- Slurp stats from Galaxy DB for Grafana Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/7002b8f547…

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[galaxyproject/usegalaxy-playbook] ccd062: Add grafana for Main
by GitHub 03 May '17

03 May '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ccd062f81075a8399f2b0a1be627dc69bf2d0be6 https://github.com/galaxyproject/usegalaxy-playbook/commit/ccd062f81075a839… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M common/host_vars/galaxy-db-01.tacc.utexas.edu.yml M production/group_vars/galaxydbservers.yml M production/secret_vars/galaxydbservers.yml Log Message: ----------- Add grafana for Main

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[galaxyproject/usegalaxy-playbook] 49e404: Add grafana
by GitHub 03 May '17

03 May '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 49e404c4f6d83c9870f6c666fd9eaeb698920c59 https://github.com/galaxyproject/usegalaxy-playbook/commit/49e404c4f6d83c98… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M env/test/group_vars/dbservers/vault.yml Log Message: ----------- Add grafana

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[galaxyproject/galaxy] 8db51d: Update version to 17.05.rc1
by GitHub 02 May '17

02 May '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 8db51db70258463df762e6ed70f621f56d1a8d74 https://github.com/galaxyproject/galaxy/commit/8db51db70258463df762e6ed70f6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 17.05.rc1 Commit: ce8f0dec0532266bff5d277f8acc50a4c6a9b2b5 https://github.com/galaxyproject/galaxy/commit/ce8f0dec0532266bff5d277f8acc… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #4009 from jmchilton/version-17.05 [17.05] Update version to 17.05.rc1 Compare: https://github.com/galaxyproject/galaxy/compare/aeed375c0286...ce8f0dec0532

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[galaxyproject/galaxy] 8db51d: Update version to 17.05.rc1
by GitHub 02 May '17

02 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8db51db70258463df762e6ed70f621f56d1a8d74 https://github.com/galaxyproject/galaxy/commit/8db51db70258463df762e6ed70f6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 17.05.rc1 Commit: cc97e9f379ac8233bffdcf089468fc1e96f4942e https://github.com/galaxyproject/galaxy/commit/cc97e9f379ac8233bffdcf089468… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 17.09.dev Commit: 5079b925e37822f5b62003d03a1f29f4ae36e1ab https://github.com/galaxyproject/galaxy/commit/5079b925e37822f5b62003d03a1f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Log Message: ----------- Merge branch 'version-17.05' into version-17.09.dev Commit: 8bc0100165f4f39e76402303cf7d8fea73a6b200 https://github.com/galaxyproject/galaxy/commit/8bc0100165f4f39e76402303cf7d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #4010 from jmchilton/version-17.09.dev Version 17.09.dev Compare: https://github.com/galaxyproject/galaxy/compare/06d0e4fce57f...8bc0100165f4

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[galaxyproject/galaxy] 609842: [17.05] Pin dependencies for linting Galaxy.
by GitHub 02 May '17

02 May '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 609842e558da5f60eef94809204b48204fc8158a https://github.com/galaxyproject/galaxy/commit/609842e558da5f60eef94809204b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M tox.ini Log Message: ----------- [17.05] Pin dependencies for linting Galaxy. Commit: aeed375c0286315c2b893d7b807d3522c5c21a36 https://github.com/galaxyproject/galaxy/commit/aeed375c0286315c2b893d7b807d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M tox.ini Log Message: ----------- Merge pull request #4012 from jmchilton/17.05_pin_release_linting [17.05] Pin dependencies for linting Galaxy. Compare: https://github.com/galaxyproject/galaxy/compare/06d0e4fce57f...aeed375c0286

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[galaxyproject/usegalaxy-playbook] 9e45cf: Jupyter updates for Test
by GitHub 02 May '17

02 May '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9e45cf23ef9cbc87f398b5d7b302de0bd7c814b1 https://github.com/galaxyproject/usegalaxy-playbook/commit/9e45cf23ef9cbc87… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Jupyter updates for Test

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