- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 03794c: Fix broken links on Job Configuration page
by GitHub 08 Nov '18

08 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 03794ce21aabe40bc942eed7ef3442ec9b0960b6 https://github.com/galaxyproject/galaxy/commit/03794ce21aabe40bc942eed7ef34… Author: Sergey Golitsynskiy <sgolitsynskiy(a)gmail.com> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M doc/source/admin/jobs.md Log Message: ----------- Fix broken links on Job Configuration page Commit: 46126cda099095c70079f3f297201f01e1350df1 https://github.com/galaxyproject/galaxy/commit/46126cda099095c70079f3f29720… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M doc/source/admin/jobs.md Log Message: ----------- Merge pull request #6992 from ic4f/dev Fix broken links on Job Configuration page (documentation) Compare: https://github.com/galaxyproject/galaxy/compare/7966ca5a95d5...46126cda0990 **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] ebb6e7: Don't mount external /tmp for tests.
by GitHub 08 Nov '18

08 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ebb6e78f0d86555be0b53d635f076cae3d945eb2 https://github.com/galaxyproject/galaxy/commit/ebb6e78f0d86555be0b53d635f07… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M .ci/jenkins/api/run_tests.sh M .ci/jenkins/framework/run_tests.sh M .ci/jenkins/integration/run_tests.sh M .ci/jenkins/main-tools/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .ci/jenkins/toolshed/run_tests.sh Log Message: ----------- Don't mount external /tmp for tests. Nate wants the file busy errors back ;). Commit: 7966ca5a95d57ee986621bd180e3ff8858e1624c https://github.com/galaxyproject/galaxy/commit/7966ca5a95d57ee986621bd180e3… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M .ci/jenkins/api/run_tests.sh M .ci/jenkins/framework/run_tests.sh M .ci/jenkins/integration/run_tests.sh M .ci/jenkins/main-tools/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .ci/jenkins/toolshed/run_tests.sh Log Message: ----------- Merge pull request #6990 from jmchilton/skip_mounting_external_tmp_in_ci_tests Don't mount external /tmp for tests. Compare: https://github.com/galaxyproject/galaxy/compare/f9a84b0ffe36...7966ca5a95d5 **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] 258ada: Added a metadata element to the biom1 datatype
by GitHub 08 Nov '18

08 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 258ada862ece5a06b8a86530cd9f22c355a80ac1 https://github.com/galaxyproject/galaxy/commit/258ada862ece5a06b8a86530cd9f… Author: Slugger70 <slugger70(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Added a metadata element to the biom1 datatype Commit: 789f7b2d8dd72833e2c295535ca58fb9f46806b5 https://github.com/galaxyproject/galaxy/commit/789f7b2d8dd72833e2c295535ca5… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- As per review Co-Authored-By: Slugger70 <slugger70(a)gmail.com> Commit: fc53123a94c2ba625c1e6075e0e3a284bddf2d29 https://github.com/galaxyproject/galaxy/commit/fc53123a94c2ba625c1e6075e0e3… Author: Slugger70 <slugger70(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Changes as per review Commit: 9d9bc9e27269d347e87846374492ce4a5290dad1 https://github.com/galaxyproject/galaxy/commit/9d9bc9e27269d347e87846374492… Author: Slugger70 <slugger70(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Log Message: ----------- Made changes as per review Commit: 0bc6e35ad60a1f3b4e5db5691cc26fb67728d2bc https://github.com/galaxyproject/galaxy/commit/0bc6e35ad60a1f3b4e5db5691cc2… Author: Slugger70 <slugger70(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Minor alteration for flake8 Commit: 6dd098f747c89ba3494b64bb5a64dc078bb3d5db https://github.com/galaxyproject/galaxy/commit/6dd098f747c89ba3494b64bb5a64… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Simplify code Commit: f9a84b0ffe36a79df7c83d7fcca23efa30f07d89 https://github.com/galaxyproject/galaxy/commit/f9a84b0ffe36a79df7c83d7fcca2… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #6972 from Slugger70/biom_datatype_changes Added a metadata element to the biom1 datatype Compare: https://github.com/galaxyproject/galaxy/compare/e4c00af38d38...f9a84b0ffe36 **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] 0ecb4e: List tags as attribute of TestCollection
by GitHub 08 Nov '18

08 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0ecb4e7c595f7fb6cd6e648c4d770e1e97530424 https://github.com/galaxyproject/galaxy/commit/0ecb4e7c595f7fb6cd6e648c4d77… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- List tags as attribute of TestCollection Commit: bff5d51245f76bfc0bbe5b71237b3709d9ff7079 https://github.com/galaxyproject/galaxy/commit/bff5d51245f76bfc0bbe5b71237b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Use comma-separated instead of comma separated Commit: 5e098857e5dee703741e070e24a40235fb5deff2 https://github.com/galaxyproject/galaxy/commit/5e098857e5dee703741e070e24a4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M doc/schema_template.md Log Message: ----------- Display test collection input in documentation Commit: 4760a0ac0f48b106f9a1cee348deeccc223eb64a https://github.com/galaxyproject/galaxy/commit/4760a0ac0f48b106f9a1cee348de… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Fix recursion issue in gff_filter_by_feature_count Commit: 5e1fb9a7a2935fc3a3e599b6111157c91fe7b345 https://github.com/galaxyproject/galaxy/commit/5e1fb9a7a2935fc3a3e599b61111… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M doc/schema_template.md M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #6983 from mvdbeek/schema_amamdment_tags_in_collection [18.09] List tags as attribute of TestCollection Commit: 45e475e19aa1988db2461c1d7fdf6135c02294d0 https://github.com/galaxyproject/galaxy/commit/45e475e19aa1988db2461c1d7fdf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Merge pull request #6986 from nsoranzo/release_18.05_backport_2d36e8955e020958334088d6ba5853c1027d8b75 [18.05] Backport commit 2d36e8955e020958334088d6ba5853c1027d8b75 Commit: f85afad9655b970f3af895a8dfafc0b8e301c705 https://github.com/galaxyproject/galaxy/commit/f85afad9655b970f3af895a8dfaf… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-08 (Thu, 08 Nov 2018) Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: e4c00af38d387ee860050916e6b2c28f57b2fd4e https://github.com/galaxyproject/galaxy/commit/e4c00af38d387ee860050916e6b2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M doc/schema_template.md M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/d28ce7686d12...e4c00af38d38 **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] 4760a0: Fix recursion issue in gff_filter_by_feature_count
by GitHub 08 Nov '18

08 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 4760a0ac0f48b106f9a1cee348deeccc223eb64a https://github.com/galaxyproject/galaxy/commit/4760a0ac0f48b106f9a1cee348de… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Fix recursion issue in gff_filter_by_feature_count Commit: 45e475e19aa1988db2461c1d7fdf6135c02294d0 https://github.com/galaxyproject/galaxy/commit/45e475e19aa1988db2461c1d7fdf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Merge pull request #6986 from nsoranzo/release_18.05_backport_2d36e8955e020958334088d6ba5853c1027d8b75 [18.05] Backport commit 2d36e8955e020958334088d6ba5853c1027d8b75 Commit: f85afad9655b970f3af895a8dfafc0b8e301c705 https://github.com/galaxyproject/galaxy/commit/f85afad9655b970f3af895a8dfaf… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-08 (Thu, 08 Nov 2018) Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Compare: https://github.com/galaxyproject/galaxy/compare/5e1fb9a7a293...f85afad9655b **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] ccb1e0: In enqueue, always set an object_store_id if one i...
by GitHub 08 Nov '18

08 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: ccb1e08000759184b2ebc4d26b8e88ebe9b4c9c4 https://github.com/galaxyproject/galaxy/commit/ccb1e08000759184b2ebc4d26b8e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- In enqueue, always set an object_store_id if one isn't set. Tool actions other than the regular tool action (such as the upload ones) might not set an object store id even in the legacy mode. Commit: dc9128213fbf4fd1d479fc94ace5b2416a5face5 https://github.com/galaxyproject/galaxy/commit/dc9128213fbf4fd1d479fc94ace5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Fix traceback when starting under Python3 with ``galaxy.ini`` Update `paste` requirement to 3.0.4 to include: https://github.com/cdent/paste/pull/14 to fix the following traceback: ``` Starting server in PID 6792. Traceback (most recent call last): File "./scripts/paster.py", line 27, in <module> serve.run() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 1055, in run invoke(command, command_name, options, args[1:]) File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 1061, in invoke exit_code = runner.run(args) File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 226, in run result = self.command() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 676, in command serve() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 653, in serve server(app) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 232, in server_wrapper **context.local_conf) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 90, in fix_call val = callable(*args, **kw) File "/opt/galaxy/.venv3/lib/python3.5/site-packages/paste/httpserver.py", line 1358, in server_runner for name, value in kwargs.items(): RuntimeError: dictionary changed size during iteration galaxy.app DEBUG 2018-11-05 13:38:00,059 Shutting down ``` Commit: 9029b95e69795992ecf67f3ffdfa6384b52e1f3a https://github.com/galaxyproject/galaxy/commit/9029b95e69795992ecf67f3ffdfa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #6969 from jmchilton/ensure_better [18.09] In enqueue, always set an object_store_id if one isn't set. Commit: 6487d52d513b6351bd3e3e44e74e79c8f949919a https://github.com/galaxyproject/galaxy/commit/6487d52d513b6351bd3e3e44e74e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #6978 from nsoranzo/release_18.09_paste [18.09] Fix traceback when starting under Python3 with ``galaxy.ini`` Commit: 0ecb4e7c595f7fb6cd6e648c4d770e1e97530424 https://github.com/galaxyproject/galaxy/commit/0ecb4e7c595f7fb6cd6e648c4d77… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- List tags as attribute of TestCollection Commit: bff5d51245f76bfc0bbe5b71237b3709d9ff7079 https://github.com/galaxyproject/galaxy/commit/bff5d51245f76bfc0bbe5b71237b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Use comma-separated instead of comma separated Commit: 5e098857e5dee703741e070e24a40235fb5deff2 https://github.com/galaxyproject/galaxy/commit/5e098857e5dee703741e070e24a4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M doc/schema_template.md Log Message: ----------- Display test collection input in documentation Commit: 5e1fb9a7a2935fc3a3e599b6111157c91fe7b345 https://github.com/galaxyproject/galaxy/commit/5e1fb9a7a2935fc3a3e599b61111… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M doc/schema_template.md M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #6983 from mvdbeek/schema_amamdment_tags_in_collection [18.09] List tags as attribute of TestCollection Commit: 51498fc994f10d7c7bb71948b265f3c93c6ca7bf https://github.com/galaxyproject/galaxy/commit/51498fc994f10d7c7bb71948b265… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M doc/schema_template.md M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge branch 'release_18.09' Compare: https://github.com/galaxyproject/galaxy/compare/fefa132cd741...51498fc994f1 **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/ansible-galaxy] ddda1d: Update deprecated syntax
by GitHub 08 Nov '18

08 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: ddda1d5a03e08a91f156da288a368b069398985b https://github.com/galaxyproject/ansible-galaxy/commit/ddda1d5a03e08a91f156… Author: Sergey Golitsynskiy <sgolitsynskiy(a)gmail.com> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M README.md Log Message: ----------- Update deprecated syntax Invoking "apt" only once while using a loop via squash_actions is deprecated. Use list of items as name value instead. Commit: 3853b8d5ee3a4a1830f7dd2f30208819afc996a2 https://github.com/galaxyproject/ansible-galaxy/commit/3853b8d5ee3a4a1830f7… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M README.md Log Message: ----------- Merge pull request #41 from ic4f/master Update deprecated syntax Compare: https://github.com/galaxyproject/ansible-galaxy/compare/1043f1c3931e...3853… **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] 0ecb4e: List tags as attribute of TestCollection
by GitHub 07 Nov '18

07 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 0ecb4e7c595f7fb6cd6e648c4d770e1e97530424 https://github.com/galaxyproject/galaxy/commit/0ecb4e7c595f7fb6cd6e648c4d77… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- List tags as attribute of TestCollection Commit: bff5d51245f76bfc0bbe5b71237b3709d9ff7079 https://github.com/galaxyproject/galaxy/commit/bff5d51245f76bfc0bbe5b71237b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Use comma-separated instead of comma separated Commit: 5e098857e5dee703741e070e24a40235fb5deff2 https://github.com/galaxyproject/galaxy/commit/5e098857e5dee703741e070e24a4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M doc/schema_template.md Log Message: ----------- Display test collection input in documentation Commit: 5e1fb9a7a2935fc3a3e599b6111157c91fe7b345 https://github.com/galaxyproject/galaxy/commit/5e1fb9a7a2935fc3a3e599b61111… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M doc/schema_template.md M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #6983 from mvdbeek/schema_amamdment_tags_in_collection [18.09] List tags as attribute of TestCollection Compare: https://github.com/galaxyproject/galaxy/compare/6487d52d513b...5e1fb9a7a293 **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] cd1a6b: Move disabled tool style from mako to scss
by GitHub 07 Nov '18

07 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cd1a6b2ef8f1169f39505bf67644100657b4a64c https://github.com/galaxyproject/galaxy/commit/cd1a6b2ef8f1169f39505bf67644… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Move disabled tool style from mako to scss Commit: 551ac053dd8a5d75f53681a314e4aeed161c629f https://github.com/galaxyproject/galaxy/commit/551ac053dd8a5d75f53681a314e4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Remove unused post job action form styles Commit: 3e3021d6f3cbfa4871e6c8836a6ac051f9c3041d https://github.com/galaxyproject/galaxy/commit/3e3021d6f3cbfa4871e6c8836a6a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Remove title and row styles from mako to scss Commit: 6247955ebb0b3755057a5b41c58175a6effaeec8 https://github.com/galaxyproject/galaxy/commit/6247955ebb0b3755057a5b41c581… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Move panel margins from mako to scss Commit: c7f65aee677fe5cc8c9322e99f5388e842191b39 https://github.com/galaxyproject/galaxy/commit/c7f65aee677fe5cc8c9322e99f53… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Remove custom body panel margins Commit: 1f82b33e704be5121c5c9b2eba4dfa59d8a586aa https://github.com/galaxyproject/galaxy/commit/1f82b33e704be5121c5c9b2eba4d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Move ruler style to scss Commit: 496e353e86aef3868c68756ec0184fe38942ef0c https://github.com/galaxyproject/galaxy/commit/496e353e86aef3868c68756ec018… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Move callout for hidden outputs to scss Commit: 5e0921cc9edd5ea0067b8da02bc119528eed2340 https://github.com/galaxyproject/galaxy/commit/5e0921cc9edd5ea0067b8da02bc1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Consolidate module step titles Commit: 4c2bc2222f5aadd102293cbd081b41511d15cd80 https://github.com/galaxyproject/galaxy/commit/4c2bc2222f5aadd102293cbd081b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Remove unused form-row-clear specification Commit: e9255599bd7de37ba57a6b72cad681e7c25a956a https://github.com/galaxyproject/galaxy/commit/e9255599bd7de37ba57a6b72cad6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Remove unused title row specification Commit: e0d891b2741f9e65c526d95bcb3c4474d8a8b9d0 https://github.com/galaxyproject/galaxy/commit/e0d891b2741f9e65c526d95bcb3c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Move error highlighting to scss Commit: c01f7d2b63cc120cea419eaf06f2ef99879d0b99 https://github.com/galaxyproject/galaxy/commit/c01f7d2b63cc120cea419eaf06f2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Move custom step margins to scss Commit: 6e41c8a404280e8bd13082b5ea6b7495da7002dd https://github.com/galaxyproject/galaxy/commit/6e41c8a404280e8bd13082b5ea6b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Fix callout style, currently global, attached to body Commit: ec97b380df757fb2c8282850a6b5178430d45ec5 https://github.com/galaxyproject/galaxy/commit/ec97b380df757fb2c8282850a6b5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Remove duplicate border highlighting for module forms Commit: 4417632cea7f90e21962a9f8f4d014644cf219f5 https://github.com/galaxyproject/galaxy/commit/4417632cea7f90e21962a9f8f4d0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Consolidate module representation specifications Commit: f19ac2d05270d06d7f1e5506471d53743506b733 https://github.com/galaxyproject/galaxy/commit/f19ac2d05270d06d7f1e5506471d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Remove unused panel button styles Commit: cfc4ed879997670c7963da095b85a06aea6f17ce https://github.com/galaxyproject/galaxy/commit/cfc4ed879997670c7963da095b85… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Move callout button specification to scss Commit: 3fc6191f9562da97bd993816a7d0104046dbc8d7 https://github.com/galaxyproject/galaxy/commit/3fc6191f9562da97bd993816a7d0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Remove unused canvas area styles Commit: f0df34eacadf5d6f23bc4791d612352de6fe102c https://github.com/galaxyproject/galaxy/commit/f0df34eacadf5d6f23bc4791d612… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #6967 from guerler/workflow_style_1 Refactor workflow editor styles and move from mako to css Compare: https://github.com/galaxyproject/galaxy/compare/be87d2402d09...f0df34eacadf **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] dc9128: Fix traceback when starting under Python3 with ``g...
by GitHub 07 Nov '18

07 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dc9128213fbf4fd1d479fc94ace5b2416a5face5 https://github.com/galaxyproject/galaxy/commit/dc9128213fbf4fd1d479fc94ace5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Fix traceback when starting under Python3 with ``galaxy.ini`` Update `paste` requirement to 3.0.4 to include: https://github.com/cdent/paste/pull/14 to fix the following traceback: ``` Starting server in PID 6792. Traceback (most recent call last): File "./scripts/paster.py", line 27, in <module> serve.run() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 1055, in run invoke(command, command_name, options, args[1:]) File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 1061, in invoke exit_code = runner.run(args) File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 226, in run result = self.command() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 676, in command serve() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 653, in serve server(app) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 232, in server_wrapper **context.local_conf) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 90, in fix_call val = callable(*args, **kw) File "/opt/galaxy/.venv3/lib/python3.5/site-packages/paste/httpserver.py", line 1358, in server_runner for name, value in kwargs.items(): RuntimeError: dictionary changed size during iteration galaxy.app DEBUG 2018-11-05 13:38:00,059 Shutting down ``` Commit: 6487d52d513b6351bd3e3e44e74e79c8f949919a https://github.com/galaxyproject/galaxy/commit/6487d52d513b6351bd3e3e44e74e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #6978 from nsoranzo/release_18.09_paste [18.09] Fix traceback when starting under Python3 with ``galaxy.ini`` Commit: be87d2402d09cee0f2e43677f7073f7333876c94 https://github.com/galaxyproject/galaxy/commit/be87d2402d09cee0f2e43677f707… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/09186c991ae8...be87d2402d09 **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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