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

[galaxyproject/galaxy] 4dce06: Adjust code block to try to fix release doc format...
by GitHub 29 Oct '18

29 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 4dce069209c4da228629e7dddfbeda836098aedc https://github.com/galaxyproject/galaxy/commit/4dce069209c4da228629e7dddfbe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Adjust code block to try to fix release doc formatting -- I hate RST Commit: cea9521b1a0194c93c5e2bf7b7f02fa88bd2c0b9 https://github.com/galaxyproject/galaxy/commit/cea9521b1a0194c93c5e2bf7b7f0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge pull request #6938 from dannon/codeblock_formatting [18.09] Release announce codeblock formatting fix Compare: https://github.com/galaxyproject/galaxy/compare/d0a93ff62808...cea9521b1a01 **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.

1 0

[galaxyproject/galaxy] c59169: Fix typos in ``scripts/bootstrap_history.py``
by GitHub 29 Oct '18

29 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c5916912093ffaca57281db486c263108f263e88 https://github.com/galaxyproject/galaxy/commit/c5916912093ffaca57281db486c2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Fix typos in ``scripts/bootstrap_history.py`` Commit: a4abbb1d8a244e260412df8551f9f3d0f25f78c7 https://github.com/galaxyproject/galaxy/commit/a4abbb1d8a244e260412df8551f9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M lib/galaxy/datatypes/molecules.py Log Message: ----------- Fix flake8 errors introduced in #6816 Commit: 8e8ff78b459c68c4b54c0c722ed5619f9d117c62 https://github.com/galaxyproject/galaxy/commit/8e8ff78b459c68c4b54c0c722ed5… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M lib/galaxy/datatypes/molecules.py M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #6941 from nsoranzo/bootstrap_history_typos Fix typos in ``scripts/bootstrap_history.py`` Compare: https://github.com/galaxyproject/galaxy/compare/d41837cd9ccd...8e8ff78b459c **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.

1 0

[galaxyproject/galaxy] 09e6b1: Eliminate some mutable defaults in populators.py.
by GitHub 29 Oct '18

29 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 09e6b1dcde5eb30a76e7487eba9ee75475b29753 https://github.com/galaxyproject/galaxy/commit/09e6b1dcde5eb30a76e7487eba9e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M test/base/populators.py Log Message: ----------- Eliminate some mutable defaults in populators.py. Commit: d41837cd9ccde259941c8b643ebf1c38ebed871b https://github.com/galaxyproject/galaxy/commit/d41837cd9ccde259941c8b643ebf… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M test/base/populators.py Log Message: ----------- Merge pull request #6933 from jmchilton/mutable_default Eliminate some mutable defaults in populators.py. Compare: https://github.com/galaxyproject/galaxy/compare/e89773a20d5c...d41837cd9ccd **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.

1 0

[galaxyproject/galaxy] 4dce06: Adjust code block to try to fix release doc format...
by GitHub 29 Oct '18

29 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 4dce069209c4da228629e7dddfbeda836098aedc https://github.com/galaxyproject/galaxy/commit/4dce069209c4da228629e7dddfbe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Adjust code block to try to fix release doc formatting -- I hate RST Commit: cea9521b1a0194c93c5e2bf7b7f02fa88bd2c0b9 https://github.com/galaxyproject/galaxy/commit/cea9521b1a0194c93c5e2bf7b7f0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge pull request #6938 from dannon/codeblock_formatting [18.09] Release announce codeblock formatting fix Compare: https://github.com/galaxyproject/galaxy/compare/d0a93ff62808...cea9521b1a01 **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.

1 0

[galaxyproject/galaxy] f1a3a4: galaxy test needs to count data sets and collectio...
by GitHub 29 Oct '18

29 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f1a3a44b444d9914a97d26a0b0f5667efc211ac5 https://github.com/galaxyproject/galaxy/commit/f1a3a44b444d9914a97d26a0b0f5… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py Log Message: ----------- galaxy test needs to count data sets and collection outputs Commit: 1ec18484df22ec0d226415a6aa9379bb176fe329 https://github.com/galaxyproject/galaxy/commit/1ec18484df22ec0d226415a6aa93… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M test/functional/tools/output_filter.xml Log Message: ----------- added test Commit: e89773a20d5c3f18fd9b4766c1c7deb6485e88da https://github.com/galaxyproject/galaxy/commit/e89773a20d5c3f18fd9b4766c1c7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py M test/functional/tools/output_filter.xml Log Message: ----------- Merge pull request #6931 from bernt-matthias/topic/test-colouts tests need to count data sets and collections Compare: https://github.com/galaxyproject/galaxy/compare/adc62f6ba7d8...e89773a20d5c **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.

1 0

[galaxyproject/galaxy] 30ac5d: Release scaffold tweaks.
by GitHub 29 Oct '18

29 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 30ac5d90d937a28dc61aef5d4a6b6cb05c1a05bf https://github.com/galaxyproject/galaxy/commit/30ac5d90d937a28dc61aef5d4a6b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Release scaffold tweaks. Commit: 66b05cbfc591a5de2d5d248c1f060a67ff369c44 https://github.com/galaxyproject/galaxy/commit/66b05cbfc591a5de2d5d248c1f06… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Minor clarification Commit: 5d51492a538dddb5eb5c45dc117f090104f70652 https://github.com/galaxyproject/galaxy/commit/5d51492a538dddb5eb5c45dc117f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Getgalaxy links Commit: 2fb4ea1e689e03a44712fd18942d86717e773e36 https://github.com/galaxyproject/galaxy/commit/2fb4ea1e689e03a44712fd18942d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #6935 from dannon/release-scaffold-tweaks Release issue scaffold tweaks. Compare: https://github.com/galaxyproject/galaxy/compare/6f6fffe9134e...2fb4ea1e689e **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.

1 0

[galaxyproject/galaxy] 79cff3: Add 18.09_announce to releases index.
by GitHub 29 Oct '18

29 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 79cff3ea6b34056a9a24a130dab6b25b98ae7ee4 https://github.com/galaxyproject/galaxy/commit/79cff3ea6b34056a9a24a130dab6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M doc/source/releases/index.rst Log Message: ----------- Add 18.09_announce to releases index. Commit: 165123863904daa1d7e96651b16f2c6dfa0629a2 https://github.com/galaxyproject/galaxy/commit/165123863904daa1d7e96651b16f… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M doc/source/releases/index.rst Log Message: ----------- Merge pull request #6930 from dannon/index-update [18.09] Add 18.09_announce to releases index. Commit: cf2645f9a658c5e122fea0309bf73a1f64590c39 https://github.com/galaxyproject/galaxy/commit/cf2645f9a658c5e122fea0309bf7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/workflow_util.py Log Message: ----------- Fix toolshed error in display_tool if tool is invalid Fixes the following exception: ``` AttributeError: 'NoneType' object has no attribute 'id' File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__ iterable = self.application(environ, start_response) File "/srv/toolshed/main/venv/local/lib/python2.7/site-packages/paste/translogger.py", line 69, in __call__ return self.application(environ, replacement_start_response) File "/srv/toolshed/main/venv/local/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "routes/middleware.py", line 141, in __call__ response = self.app(environ, start_response) File "/srv/toolshed/main/venv/local/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 143, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 222, in handle_request body = method(trans, **kwargs) File "galaxy/webapps/tool_shed/controllers/repository.py", line 888, in display_tool tool_state = tool_util.new_state(trans, tool, invalid=False) File "tool_shed/util/tool_util.py", line 211, in new_state log.debug('Failed to build tool state for tool "%s" using standard method, will try to fall back on custom method: %s', tool.id, e) ``` (from https://sentry.galaxyproject.org/sentry/toolshed/issues/279820/) Might also fix some other issues when redering workflow svg for workflows with invalid tools. Commit: e89f746a0713df76e1e86eb9507d3336aade9419 https://github.com/galaxyproject/galaxy/commit/e89f746a0713df76e1e86eb9507d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/workflow_util.py Log Message: ----------- Merge pull request #6932 from mvdbeek/fix_toolshed_bugs [18.09] Fix toolshed error in display_tool if tool is invalid Commit: 1fd1848a81532ecd0fb36800e7f1ae1609661141 https://github.com/galaxyproject/galaxy/commit/1fd1848a81532ecd0fb36800e7f1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Additional 18.09 bugfix Commit: d0a93ff62808e7e1727c7deb4a48853639bd7ece https://github.com/galaxyproject/galaxy/commit/d0a93ff62808e7e1727c7deb4a48… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Merge pull request #6934 from dannon/doc_update [18.09] Additional 18.09 doc update for toolshed bugfix. Commit: 6f6fffe9134e7becfd698340899a96c1cbd8a4fe https://github.com/galaxyproject/galaxy/commit/6f6fffe9134e7becfd698340899a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09.rst M doc/source/releases/index.rst M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/workflow_util.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/2d7e54831944...6f6fffe9134e **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.

1 0

[galaxyproject/galaxy] cf2645: Fix toolshed error in display_tool if tool is inva...
by GitHub 29 Oct '18

29 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: cf2645f9a658c5e122fea0309bf73a1f64590c39 https://github.com/galaxyproject/galaxy/commit/cf2645f9a658c5e122fea0309bf7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/workflow_util.py Log Message: ----------- Fix toolshed error in display_tool if tool is invalid Fixes the following exception: ``` AttributeError: 'NoneType' object has no attribute 'id' File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__ iterable = self.application(environ, start_response) File "/srv/toolshed/main/venv/local/lib/python2.7/site-packages/paste/translogger.py", line 69, in __call__ return self.application(environ, replacement_start_response) File "/srv/toolshed/main/venv/local/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "routes/middleware.py", line 141, in __call__ response = self.app(environ, start_response) File "/srv/toolshed/main/venv/local/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 143, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 222, in handle_request body = method(trans, **kwargs) File "galaxy/webapps/tool_shed/controllers/repository.py", line 888, in display_tool tool_state = tool_util.new_state(trans, tool, invalid=False) File "tool_shed/util/tool_util.py", line 211, in new_state log.debug('Failed to build tool state for tool "%s" using standard method, will try to fall back on custom method: %s', tool.id, e) ``` (from https://sentry.galaxyproject.org/sentry/toolshed/issues/279820/) Might also fix some other issues when redering workflow svg for workflows with invalid tools. Commit: e89f746a0713df76e1e86eb9507d3336aade9419 https://github.com/galaxyproject/galaxy/commit/e89f746a0713df76e1e86eb9507d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/workflow_util.py Log Message: ----------- Merge pull request #6932 from mvdbeek/fix_toolshed_bugs [18.09] Fix toolshed error in display_tool if tool is invalid Commit: 1fd1848a81532ecd0fb36800e7f1ae1609661141 https://github.com/galaxyproject/galaxy/commit/1fd1848a81532ecd0fb36800e7f1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Additional 18.09 bugfix Commit: d0a93ff62808e7e1727c7deb4a48853639bd7ece https://github.com/galaxyproject/galaxy/commit/d0a93ff62808e7e1727c7deb4a48… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Merge pull request #6934 from dannon/doc_update [18.09] Additional 18.09 doc update for toolshed bugfix. Compare: https://github.com/galaxyproject/galaxy/compare/165123863904...d0a93ff62808 **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.

1 0

[galaxyproject/galaxy]
by GitHub 29 Oct '18

29 Oct '18

Branch: refs/tags/v18.09 Home: https://github.com/galaxyproject/galaxy **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.

1 0

[galaxyproject/galaxy] 1fd184: Additional 18.09 bugfix
by GitHub 29 Oct '18

29 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 1fd1848a81532ecd0fb36800e7f1ae1609661141 https://github.com/galaxyproject/galaxy/commit/1fd1848a81532ecd0fb36800e7f1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Additional 18.09 bugfix Commit: d0a93ff62808e7e1727c7deb4a48853639bd7ece https://github.com/galaxyproject/galaxy/commit/d0a93ff62808e7e1727c7deb4a48… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Merge pull request #6934 from dannon/doc_update [18.09] Additional 18.09 doc update for toolshed bugfix. Compare: https://github.com/galaxyproject/galaxy/compare/e89f746a0713...d0a93ff62808 **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.

1 0