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

[galaxyproject/galaxy] 6b2150: Restore WebHelpers functions used in visualization...
by GitHub 04 Feb '18

04 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6b2150b1feaca405d2e718bace5cb743b8a60376 https://github.com/galaxyproject/galaxy/commit/6b2150b1feaca405d2e718bace5c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M lib/galaxy/web/framework/helpers/__init__.py A lib/galaxy/web/framework/helpers/tags.py Log Message: ----------- Restore WebHelpers functions used in visualization makos Broken in commit fbd33a57e0033a1547c3bf6f9812dd574cdb36d2 . Reported by @guerler. Commit: f8d21f098af23db441ad4b81e1a25f2f8bd148b3 https://github.com/galaxyproject/galaxy/commit/f8d21f098af23db441ad4b81e1a2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-04 (Sun, 04 Feb 2018) Changed paths: M lib/galaxy/web/framework/helpers/__init__.py A lib/galaxy/web/framework/helpers/tags.py Log Message: ----------- Merge pull request #5451 from nsoranzo/webhelpers_removal_followup Restore WebHelpers functions used in visualization makos Compare: https://github.com/galaxyproject/galaxy/compare/0b60de76b93e...f8d21f098af2

1 0

[galaxyproject/galaxy] 2be7eb: Add py34-first_startup and py34-unit tox environme...
by GitHub 04 Feb '18

04 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2be7eb8cfa0640dbec5954de006bab3c10f700f2 https://github.com/galaxyproject/galaxy/commit/2be7eb8cfa0640dbec5954de006b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M .travis.yml M tox.ini Log Message: ----------- Add py34-first_startup and py34-unit tox environments Also: - rename `first_startup` to `py27-first_startup` - rename other tox environments to use hyphens only to delimit factors - use the more specific ``` setenv = GALAXY_VIRTUAL_ENV={envdir} ``` instead of passing `--no-create-venv` to run unit tests inside the tox virtualenv (xref. commit 744835bbfe8bb07041600326af2f2f5d203365f5). Previously, `.venv` would be used if present. Commit: 6346b9e30949cd72a57eb683abd9bbaf431dd732 https://github.com/galaxyproject/galaxy/commit/6346b9e30949cd72a57eb683abd9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M .ci/check_py3_compatibility.sh M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M .ci/flake8_wrapper_docstrings.sh M .gitignore Log Message: ----------- Ignore the future default Python3 virtualenv Commit: f2c6e083a15eab453ea7c94565464575b0356ae1 https://github.com/galaxyproject/galaxy/commit/f2c6e083a15eab453ea7c9456546… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- twill and pygithub3 are not Python3-compatible Commit: 0a44e77a89f6533c7ceaad99ffb9942517989ea4 https://github.com/galaxyproject/galaxy/commit/0a44e77a89f6533c7ceaad99ffb9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M lib/tool_shed/util/repository_util.py Log Message: ----------- Fix missing space Commit: 0b60de76b93edbfeae5560a3a531d27e31e027f6 https://github.com/galaxyproject/galaxy/commit/0b60de76b93edbfeae5560a3a531… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-04 (Sun, 04 Feb 2018) Changed paths: M .ci/check_py3_compatibility.sh M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M .ci/flake8_wrapper_docstrings.sh M .gitignore M .travis.yml M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/tool_shed/util/repository_util.py M tox.ini Log Message: ----------- Merge pull request #5453 from nsoranzo/python3 Preparations for testing under Python3 Compare: https://github.com/galaxyproject/galaxy/compare/245394acb694...0b60de76b93e

1 0

[galaxyproject/galaxy] 7bbc46: Fix setting job failure exception
by GitHub 03 Feb '18

03 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 7bbc46658a77d74a2447095b61b28e6e4ca32e06 https://github.com/galaxyproject/galaxy/commit/7bbc46658a77d74a2447095b61b2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Fix setting job failure exception This can happen when the job's tool is unavailble and outputs_to_working_directory is activated. Fixes https://github.com/galaxyproject/galaxy/issues/5424. Commit: b2e8d891b7ca7e24aaf86b6e559356e7d62f3373 https://github.com/galaxyproject/galaxy/commit/b2e8d891b7ca7e24aaf86b6e5593… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #5456 from mvdbeek/fail_job_fix_when_tool_unavailable Fix setting job failure exception Compare: https://github.com/galaxyproject/galaxy/compare/1bd8c4fd26b6...b2e8d891b7ca

1 0

[galaxyproject/galaxy] 935b8c: Add --skip_flakey_fails flag to CI script for API ...
by GitHub 03 Feb '18

03 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 935b8c948cf4e47d1ea08fbe51332b7c6f15caa0 https://github.com/galaxyproject/galaxy/commit/935b8c948cf4e47d1ea08fbe5133… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M .ci/jenkins/api/run_tests.sh Log Message: ----------- Add --skip_flakey_fails flag to CI script for API tests xref. https://github.com/galaxyproject/galaxy/pull/5286#issuecomment-358404551 and following comments. Commit: 1bd8c4fd26b6dbb2824922cbc7f24ab9e8929bfe https://github.com/galaxyproject/galaxy/commit/1bd8c4fd26b6dbb2824922cbc7f2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M .ci/jenkins/api/run_tests.sh Log Message: ----------- Merge pull request #5455 from jmchilton/backport_flakey [18.01] Backport: Add --skip_flakey_fails flag to CI script for API tests Compare: https://github.com/galaxyproject/galaxy/compare/5aed347c3025...1bd8c4fd26b6

1 0

[galaxyproject/galaxy] 8e32e9: Implement more collection workflow post job action...
by GitHub 03 Feb '18

03 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 8e32e93d6d8e048cbc77cb94f7c97b5ae0cfc6d6 https://github.com/galaxyproject/galaxy/commit/8e32e93d6d8e048cbc77cb94f7c9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/base/workflows_format_2/converter.py Log Message: ----------- Implement more collection workflow post job actions. Implement hide, delete, add tag, and remove tag for output collections and mapped over collections. Fixes https://github.com/galaxyproject/galaxy/issues/1680. Commit: 5aed347c3025ad061c572c6a2bbdf53a7626d3cc https://github.com/galaxyproject/galaxy/commit/5aed347c3025ad061c572c6a2bbd… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/base/workflows_format_2/converter.py Log Message: ----------- Merge pull request #5418 from jmchilton/collection_pja [18.01] Implement more intuitive collection PJA Compare: https://github.com/galaxyproject/galaxy/compare/fbfbdd51bb3e...5aed347c3025

1 0

[galaxyproject/infrastructure-playbook] cbf3e0: Bug fixes for slurm partition balancing
by GitHub 03 Feb '18

03 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: cbf3e016a8ccf8d9f90b0f157ff517c105cf5d72 https://github.com/galaxyproject/infrastructure-playbook/commit/cbf3e016a8c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M taccenv/files/slurm/spartbalance Log Message: ----------- Bug fixes for slurm partition balancing

1 0

[galaxyproject/galaxy] 6d8edc: Admin doc corrections
by GitHub 02 Feb '18

02 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6d8edce33157e81112889ae7f241903747da3c92 https://github.com/galaxyproject/galaxy/commit/6d8edce33157e81112889ae7f241… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/admin/scaling.md Log Message: ----------- Admin doc corrections Commit: f24043e8a74e3cb2070b06652d9a72be46e6a278 https://github.com/galaxyproject/galaxy/commit/f24043e8a74e3cb2070b06652d9a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/admin/scaling.md Log Message: ----------- Merge pull request #5441 from natefoo/framework-dependencies-doc-update-18.01 [18.01] Admin doc corrections Commit: 7490fd452046b4a4578f6401501439773cbf2f28 https://github.com/galaxyproject/galaxy/commit/7490fd452046b4a4578f64015014… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py Log Message: ----------- More robust nametag discovery and propagation. - Nametags weren't being picked up on collection inputs - so for instance tools that take in a single collection and produce a dataset or file weren't propagating nametags (unless the collection contents had tags). To see this create two unnamed datasets without tags, create a pair from them, add a tag to the pair, and run the pair through the "paired_test" test tool. - Nametags weren't being propagated to the outputs of collection operations. Commit: 6f40f7098d507895c6c6608aff6a698289f2eeb6 https://github.com/galaxyproject/galaxy/commit/6f40f7098d507895c6c6608aff6a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Cleanup collection operation tagging implementation thanks to @mvdbeek comments. Commit: 6022fe7d7e90b0da0cad83589d5d630f6dd1d386 https://github.com/galaxyproject/galaxy/commit/6022fe7d7e90b0da0cad83589d5d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Handle optional inputs when collecting preserved tags. https://github.com/galaxyproject/galaxy/pull/5403/files#r165283450 Commit: 60561c20307cf0585e553d0fa5cd612716ab7975 https://github.com/galaxyproject/galaxy/commit/60561c20307cf0585e553d0fa5cd… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py Log Message: ----------- Merge pull request #5403 from jmchilton/collection_operation_tags [18.01] More robust nametag discovery and propagation. Commit: a392b5750aa776fbc8ba27736d78901ddf0db29d https://github.com/galaxyproject/galaxy/commit/a392b5750aa776fbc8ba27736d78… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- Ensure jobStateSummariesCollection exists; events can fire during deletion actions causing this event to fail Commit: 2b8df110d0fad7c874c35c3176bf18d65cbcdbe3 https://github.com/galaxyproject/galaxy/commit/2b8df110d0fad7c874c35c3176bf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Apply rename PJA to collection outputs including $ replacements. Update PJA collection test to test HDCA is renamed also. Commit: f6f9f9a8914845c995d665dc5396ac5e43187324 https://github.com/galaxyproject/galaxy/commit/f6f9f9a8914845c995d665dc5396… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Extend mapped collection output rename PJAs to include # replacements. Also make sure output collections in non-mapping scenarios are also properly renamed as well. Commit: 0529153ac090de0601f38af2fbf4f9a4fcccb615 https://github.com/galaxyproject/galaxy/commit/0529153ac090de0601f38af2fbf4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix bug in PJAs for collection mapping. Reported by @mvdbeek here (https://github.com/galaxyproject/galaxy/pull/5416#issuecomment-362194157) Commit: 6c013d0cb3eebffdb69c865a4cbe4019bd8ab95e https://github.com/galaxyproject/galaxy/commit/6c013d0cb3eebffdb69c865a4cbe… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- Merge pull request #5444 from dannon/multidelete_fix [18.01] Ensure jobStateSummariesCollection exists; Commit: fbfbdd51bb3e06754efc1ae9e0cec4c1c1db9ce4 https://github.com/galaxyproject/galaxy/commit/fbfbdd51bb3e06754efc1ae9e0ce… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #5416 from jmchilton/rename_collections_pja [18.01] Fix rename post job actions to be more intuitive when mapping over collections. Commit: 245394acb694020c0f9f78185749fbccf45ec587 https://github.com/galaxyproject/galaxy/commit/245394acb694020c0f9f78185749… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M doc/source/admin/framework_dependencies.rst M doc/source/admin/scaling.md M lib/galaxy/jobs/actions/post.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/988cab4db7ef...245394acb694

1 0

[galaxyproject/galaxy] 2b8df1: Apply rename PJA to collection outputs including $...
by GitHub 02 Feb '18

02 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 2b8df110d0fad7c874c35c3176bf18d65cbcdbe3 https://github.com/galaxyproject/galaxy/commit/2b8df110d0fad7c874c35c3176bf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Apply rename PJA to collection outputs including $ replacements. Update PJA collection test to test HDCA is renamed also. Commit: f6f9f9a8914845c995d665dc5396ac5e43187324 https://github.com/galaxyproject/galaxy/commit/f6f9f9a8914845c995d665dc5396… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Extend mapped collection output rename PJAs to include # replacements. Also make sure output collections in non-mapping scenarios are also properly renamed as well. Commit: 0529153ac090de0601f38af2fbf4f9a4fcccb615 https://github.com/galaxyproject/galaxy/commit/0529153ac090de0601f38af2fbf4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix bug in PJAs for collection mapping. Reported by @mvdbeek here (https://github.com/galaxyproject/galaxy/pull/5416#issuecomment-362194157) Commit: fbfbdd51bb3e06754efc1ae9e0cec4c1c1db9ce4 https://github.com/galaxyproject/galaxy/commit/fbfbdd51bb3e06754efc1ae9e0ce… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #5416 from jmchilton/rename_collections_pja [18.01] Fix rename post job actions to be more intuitive when mapping over collections. Compare: https://github.com/galaxyproject/galaxy/compare/6c013d0cb3ee...fbfbdd51bb3e

1 0

[galaxyproject/galaxy] a392b5: Ensure jobStateSummariesCollection exists; events ...
by GitHub 02 Feb '18

02 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: a392b5750aa776fbc8ba27736d78901ddf0db29d https://github.com/galaxyproject/galaxy/commit/a392b5750aa776fbc8ba27736d78… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- Ensure jobStateSummariesCollection exists; events can fire during deletion actions causing this event to fail Commit: 6c013d0cb3eebffdb69c865a4cbe4019bd8ab95e https://github.com/galaxyproject/galaxy/commit/6c013d0cb3eebffdb69c865a4cbe… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- Merge pull request #5444 from dannon/multidelete_fix [18.01] Ensure jobStateSummariesCollection exists; Compare: https://github.com/galaxyproject/galaxy/compare/60561c20307c...6c013d0cb3ee

1 0

[galaxyproject/galaxy] bc50c1: Drop py26 XML parsing variant
by GitHub 02 Feb '18

02 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bc50c14490e4f81144e5bc59f76e6abe2d93a8fa https://github.com/galaxyproject/galaxy/commit/bc50c14490e4f81144e5bc59f76e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/tool_shed/util/xml_util.py Log Message: ----------- Drop py26 XML parsing variant Commit: 49872e7612070df9aee607897fb4cf5cb9cb2242 https://github.com/galaxyproject/galaxy/commit/49872e7612070df9aee607897fb4… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/util/logging/__init__.py M lib/galaxy/web/stack/message.py Log Message: ----------- Use six.create_bound_method() instead of types.MethodType() On Python2 the MethodType constructor requires the object's class to be passed. Commit: f43a3268b11841f65d3de195611bc6b0a940544c https://github.com/galaxyproject/galaxy/commit/f43a3268b11841f65d3de195611b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py M templates/webapps/galaxy/dataset/security_common.mako Log Message: ----------- Use builtin set Commit: 39104af3b42e6d253391a9b73f6912cf4423e783 https://github.com/galaxyproject/galaxy/commit/39104af3b42e6d253391a9b73f69… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Define file_types instead of types.FileType and pull up TarFile Commit: 046f3265dd50ec6ff53470a96a4dfdb0193d7c17 https://github.com/galaxyproject/galaxy/commit/046f3265dd50ec6ff53470a96a4d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/model/custom_types.py Log Message: ----------- Fix loading custom JSONType Commit: 0be36ef4fce3b50bec37d199af2a404f3372ed65 https://github.com/galaxyproject/galaxy/commit/0be36ef4fce3b50bec37d199af2a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Use string.ascii_letters instead of string.letters for Py2/3 compat Update <sanitizer> documentation. Commit: 553d165087335528892232b17706b398bb3bf941 https://github.com/galaxyproject/galaxy/commit/553d165087335528892232b17706… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M templates/galaxy_client_app.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/tool_shed/repository/tool_form.mako Log Message: ----------- Python3 exception syntax fixes in templates/ Commit: 52586fcca2ef6ef6926fcd25b6c6f1b9ed598a6e https://github.com/galaxyproject/galaxy/commit/52586fcca2ef6ef6926fcd25b6c6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/datatypes/phylip.py Log Message: ----------- Fix relative import to be Python3-compatible Commit: 386526d928be1de57268163db1814640baa13459 https://github.com/galaxyproject/galaxy/commit/386526d928be1de57268163db181… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Replace distutils.version with packaging.version distutils under Python3 has this bug: https://bugs.python.org/issue14894 which causes this traceback: ``` Traceback (most recent call last): File "lib/galaxy/webapps/galaxy/buildapp.py", line 49, in app_factory app = galaxy.app.UniverseApplication(global_conf=global_conf, **kwargs) File "lib/galaxy/app.py", line 125, in __init__ self._configure_toolbox() File "lib/galaxy/config.py", line 930, in _configure_toolbox self.toolbox = tools.ToolBox(tool_configs, self.config.tool_path, self) File "lib/galaxy/tools/__init__.py", line 232, in __init__ app=app, File "lib/galaxy/tools/toolbox/base.py", line 1056, in __init__ super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app) File "lib/galaxy/tools/toolbox/base.py", line 84, in __init__ self._load_tool_panel() File "lib/galaxy/tools/toolbox/base.py", line 358, in _load_tool_panel self.__add_tool_to_tool_panel(section_val, section, section=True) File "lib/galaxy/tools/toolbox/base.py", line 278, in __add_tool_to_tool_panel related_tool = self._lineage_in_panel(panel_dict, tool=tool) File "lib/galaxy/tools/toolbox/base.py", line 961, in _lineage_in_panel lineage_tool_versions = reversed(tool_lineage.get_versions()) File "lib/galaxy/tools/toolbox/lineages/interface.py", line 77, in get_versions return [ToolLineageVersion(tool_id, tool_version) for tool_id, tool_version in zip(self.tool_ids, self.tool_versions)] File "lib/galaxy/tools/toolbox/lineages/interface.py", line 55, in tool_ids return ["%s/%s" % (tool_id, version) for version in self.tool_versions] File "lib/galaxy/tools/toolbox/lineages/interface.py", line 49, in tool_versions return sorted(self._tool_versions, key=LooseVersion) File "/usr/lib/python3.4/distutils/version.py", line 58, in __lt__ c = self._cmp(other) File "/usr/lib/python3.4/distutils/version.py", line 343, in _cmp if self.version < other.version: TypeError: unorderable types: str() < int() ``` when a tool version contains a letter in the "wrong" place (e.g. in the first position). Fix https://github.com/galaxyproject/galaxy/issues/5408 . Commit: 988cab4db7ef83714cf6f0c57f73f4255e3f075d https://github.com/galaxyproject/galaxy/commit/988cab4db7ef83714cf6f0c57f73… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/phylip.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/model/custom_types.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/logging/__init__.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/stack/message.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/tool_shed/util/xml_util.py M templates/galaxy_client_app.mako M templates/webapps/galaxy/dataset/security_common.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/tool_shed/repository/tool_form.mako Log Message: ----------- Merge pull request #5422 from nsoranzo/python3 Mixed Python3 fixes Compare: https://github.com/galaxyproject/galaxy/compare/5a31ac84ce12...988cab4db7ef

1 0